Starting phenix.real_space_refine on Mon Mar 11 15:44:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3a_32275/03_2024/7w3a_32275_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3a_32275/03_2024/7w3a_32275.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3a_32275/03_2024/7w3a_32275.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3a_32275/03_2024/7w3a_32275.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3a_32275/03_2024/7w3a_32275_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3a_32275/03_2024/7w3a_32275_updated.pdb" } resolution = 3.5 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 16 5.49 5 S 641 5.16 5 C 70087 2.51 5 N 19033 2.21 5 O 21111 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.24s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 110889 Number of models: 1 Model: "" Number of chains: 56 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: 11 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: "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: "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: "v" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 170 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'TRANS': 33} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'UNK:plan-1': 34} Unresolved non-hydrogen planarities: 34 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: "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: "V" Number of atoms: 3612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3612 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 15, 'TRANS': 428} Chain: "W" Number of atoms: 3635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3635 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 437} Chain: "X" Number of atoms: 3009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3009 Classifications: {'peptide': 380} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 369} Chain: "Y" Number of atoms: 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: "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: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 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: 41.57, per 1000 atoms: 0.37 Number of scatterers: 110889 At special positions: 0 Unit cell: (332.225, 219.2, 221.94, 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 16 15.00 O 21111 8.00 N 19033 7.00 C 70087 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=2.04 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: 31.00 Conformation dependent library (CDL) restraints added in 15.1 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: 26406 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: 521 helices and 93 sheets defined 54.3% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 53.73 Creating SS restraints... Processing helix chain 'A' and resid 28 through 36 removed outlier: 3.813A pdb=" N LEU A 32 " --> pdb=" O GLY A 28 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR A 36 " --> pdb=" O LEU A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 62 removed outlier: 4.696A pdb=" N ARG A 43 " --> pdb=" O SER A 39 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N GLN A 44 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN A 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL A 48 " --> pdb=" O GLN A 44 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ASP A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ASP A 51 " --> pdb=" O GLN A 47 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ILE A 52 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N GLN A 53 " --> pdb=" O GLU A 49 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N LYS A 58 " --> pdb=" O GLN A 54 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ILE A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASN A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N GLU A 61 " --> pdb=" O LYS A 57 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 82 removed outlier: 3.726A pdb=" N TRP A 78 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASP A 79 " --> pdb=" O PRO A 75 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LEU A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 92 removed outlier: 4.207A pdb=" N LEU A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) Proline residue: A 92 - end of helix Processing helix chain 'A' and resid 173 through 178 removed outlier: 4.009A pdb=" N VAL A 177 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLY A 178 " --> pdb=" O TYR A 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 173 through 178' Processing helix chain 'A' and resid 180 through 197 removed outlier: 3.617A pdb=" N VAL A 190 " --> pdb=" O LYS A 186 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N THR A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Proline residue: A 194 - end of helix Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.503A pdb=" N VAL A 202 " --> pdb=" O PRO A 198 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN A 203 " --> pdb=" O GLU A 199 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU A 204 " --> pdb=" O ARG A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 233 removed outlier: 3.522A pdb=" N CYS A 225 " --> pdb=" O GLY A 221 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA A 226 " --> pdb=" O LYS A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 246 removed outlier: 4.136A pdb=" N LEU A 245 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N VAL A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 241 through 246' Processing helix chain 'A' and resid 251 through 268 removed outlier: 3.786A pdb=" N ARG A 255 " --> pdb=" O GLY A 251 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET A 256 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL A 257 " --> pdb=" O GLY A 253 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS A 267 " --> pdb=" O MET A 263 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LYS A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 281 removed outlier: 4.561A pdb=" N ILE A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 308 removed outlier: 4.783A pdb=" N VAL A 295 " --> pdb=" O GLY A 291 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLY A 308 " --> pdb=" O ASN A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 328 removed outlier: 3.780A pdb=" N LEU A 327 " --> pdb=" O ARG A 323 " (cutoff:3.500A) removed outlier: 4.219A 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 349 through 363 removed outlier: 3.978A pdb=" N HIS A 353 " --> pdb=" O GLU A 349 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N SER A 361 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N MET A 362 " --> pdb=" O HIS A 358 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N SER A 363 " --> pdb=" O ALA A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 378 removed outlier: 4.942A pdb=" N LEU A 373 " --> pdb=" O ARG A 369 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG A 375 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N CYS A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 381 through 400 removed outlier: 3.693A pdb=" N ALA A 396 " --> pdb=" O ALA A 392 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG A 400 " --> pdb=" O ALA A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 422 Processing helix chain 'A' and resid 130 through 135 removed outlier: 3.574A pdb=" N ASP A 133 " --> pdb=" O ALA A 130 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ILE A 134 " --> pdb=" O PRO A 131 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N GLU A 135 " --> pdb=" O THR A 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 130 through 135' Processing helix chain 'B' and resid 58 through 81 removed outlier: 3.797A pdb=" N LEU B 62 " --> pdb=" O CYS B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 5.554A pdb=" N SER B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N GLY B 104 " --> pdb=" O ASP B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 145 removed outlier: 4.306A pdb=" N LEU B 144 " --> pdb=" O ASP B 140 " (cutoff:3.500A) removed outlier: 5.762A 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 168 through 176 removed outlier: 4.450A pdb=" N THR B 172 " --> pdb=" O ASP B 168 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL B 173 " --> pdb=" O PRO B 169 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N MET B 174 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N VAL B 176 " --> pdb=" O THR B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 188 removed outlier: 4.546A pdb=" N ILE B 187 " --> pdb=" O THR B 183 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N GLY B 188 " --> pdb=" O TYR B 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 183 through 188' Processing helix chain 'B' and resid 190 through 206 removed outlier: 6.000A pdb=" N ILE B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLN B 195 " --> pdb=" O ASP B 191 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU B 196 " --> pdb=" O ASN B 192 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU B 199 " --> pdb=" O GLN B 195 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 4.263A 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: 5.406A pdb=" N GLU B 212 " --> pdb=" O PRO B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 244 removed outlier: 3.659A pdb=" N ALA B 236 " --> pdb=" O LYS B 232 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR B 243 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N SER B 244 " --> pdb=" O ALA B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 256 removed outlier: 4.444A pdb=" N LEU B 255 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE B 256 " --> pdb=" O GLY B 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 251 through 256' Processing helix chain 'B' and resid 261 through 278 removed outlier: 3.600A pdb=" N ALA B 278 " --> pdb=" O ALA B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 292 removed outlier: 3.608A pdb=" N ILE B 290 " --> pdb=" O GLU B 286 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N THR B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 318 removed outlier: 3.603A pdb=" N ILE B 305 " --> pdb=" O GLY B 301 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ASP B 317 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY B 318 " --> pdb=" O ASN B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.651A pdb=" N ILE B 342 " --> pdb=" O ASP B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 370 removed outlier: 4.476A pdb=" N LYS B 362 " --> pdb=" O GLU B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 407 Processing helix chain 'B' and resid 415 through 434 removed outlier: 3.554A pdb=" N GLY B 433 " --> pdb=" O LYS B 429 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR B 434 " --> pdb=" O LYS B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 39 Processing helix chain 'C' and resid 11 through 65 removed outlier: 6.889A pdb=" N GLY C 19 " --> pdb=" O LYS C 15 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU C 20 " --> pdb=" O ALA C 16 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N TYR C 23 " --> pdb=" O GLY C 19 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N GLU C 29 " --> pdb=" O LEU C 25 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU C 30 " --> pdb=" O SER C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 109 removed outlier: 5.238A pdb=" N THR C 109 " --> pdb=" O ILE C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 139 removed outlier: 5.328A pdb=" N MET C 139 " --> pdb=" O VAL C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 170 Proline residue: C 168 - end of helix Processing helix chain 'C' and resid 171 through 179 removed outlier: 4.043A pdb=" N PHE C 175 " --> pdb=" O HIS C 171 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY C 179 " --> pdb=" O PHE C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 207 Processing helix chain 'C' and resid 215 through 220 removed outlier: 4.069A pdb=" N LEU C 219 " --> pdb=" O SER C 215 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N VAL C 220 " --> pdb=" O GLY C 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 215 through 220' Processing helix chain 'C' and resid 225 through 242 removed outlier: 4.125A pdb=" N ALA C 242 " --> pdb=" O ALA C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 282 Processing helix chain 'C' and resid 321 through 334 removed outlier: 3.733A pdb=" N ARG C 334 " --> pdb=" O LYS C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 352 removed outlier: 4.031A pdb=" N ILE C 347 " --> pdb=" O ASN C 343 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N MET C 351 " --> pdb=" O ILE C 347 " (cutoff:3.500A) Proline residue: C 352 - end of helix Processing helix chain 'C' and resid 355 through 374 removed outlier: 6.654A pdb=" N VAL C 359 " --> pdb=" O SER C 355 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS C 360 " --> pdb=" O GLY C 356 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU C 373 " --> pdb=" O TYR C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 389 Processing helix chain 'C' and resid 400 through 406 removed outlier: 4.946A pdb=" N LEU C 404 " --> pdb=" O SER C 400 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N TRP C 405 " --> pdb=" O ILE C 401 " (cutoff:3.500A) removed outlier: 3.665A 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 39 through 83 removed outlier: 3.776A pdb=" N ARG D 43 " --> pdb=" O ASP D 39 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N LYS D 45 " --> pdb=" O TYR D 41 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N LYS D 46 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS D 70 " --> pdb=" O LYS D 66 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLN D 83 " --> pdb=" O VAL D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 125 removed outlier: 4.256A pdb=" N LEU D 124 " --> pdb=" O ASP D 120 " (cutoff:3.500A) removed outlier: 5.574A 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 170 through 187 Proline residue: D 184 - end of helix Processing helix chain 'D' and resid 188 through 195 removed outlier: 3.607A pdb=" N ILE D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 223 removed outlier: 3.768A pdb=" N THR D 223 " --> pdb=" O VAL D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 257 Processing helix chain 'D' and resid 266 through 271 removed outlier: 4.848A pdb=" N ILE D 270 " --> pdb=" O GLU D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 299 removed outlier: 4.533A pdb=" N VAL D 285 " --> pdb=" O ALA D 281 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLY D 298 " --> pdb=" O ASN D 294 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE D 299 " --> pdb=" O GLN D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 323 Processing helix chain 'D' and resid 337 through 353 removed outlier: 4.789A pdb=" N LYS D 351 " --> pdb=" O THR D 347 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N MET D 352 " --> pdb=" O ILE D 348 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ASN D 353 " --> pdb=" O THR D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 365 removed outlier: 4.098A pdb=" N TYR D 363 " --> pdb=" O ASP D 359 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL D 364 " --> pdb=" O LEU D 360 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ALA D 365 " --> pdb=" O GLU D 361 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 359 through 365' Processing helix chain 'D' and resid 371 through 390 removed outlier: 4.217A pdb=" N ILE D 375 " --> pdb=" O SER D 371 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ASN D 376 " --> pdb=" O GLY D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 406 removed outlier: 3.787A pdb=" N PHE D 399 " --> pdb=" O LEU D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 149 removed outlier: 4.891A pdb=" N ASP D 148 " --> pdb=" O PRO D 145 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N SER D 149 " --> pdb=" O GLU D 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 52 removed outlier: 4.790A pdb=" N GLN E 10 " --> pdb=" O ASP E 6 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N TYR E 12 " --> pdb=" O ALA E 8 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ARG E 13 " --> pdb=" O LEU E 9 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLN E 51 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N SER E 52 " --> pdb=" O LYS E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 93 removed outlier: 3.909A pdb=" N LEU E 92 " --> pdb=" O ASP E 88 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N LYS E 93 " --> pdb=" O LYS E 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 88 through 93' Processing helix chain 'E' and resid 116 through 125 removed outlier: 4.242A pdb=" N TYR E 120 " --> pdb=" O ASP E 116 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N MET E 122 " --> pdb=" O LEU E 118 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU E 125 " --> pdb=" O ASN E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 155 removed outlier: 5.514A 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 180 through 192 removed outlier: 3.719A pdb=" N GLN E 190 " --> pdb=" O ALA E 186 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU E 191 " --> pdb=" O VAL E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 204 removed outlier: 6.545A pdb=" N ILE E 203 " --> pdb=" O VAL E 199 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N VAL E 204 " --> pdb=" O SER E 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 199 through 204' Processing helix chain 'E' and resid 209 through 226 removed outlier: 6.471A pdb=" N ARG E 213 " --> pdb=" O GLY E 209 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU E 214 " --> pdb=" O GLU E 210 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE E 215 " --> pdb=" O SER E 211 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS E 225 " --> pdb=" O TYR E 221 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N GLN E 226 " --> pdb=" O ALA E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 240 removed outlier: 4.496A pdb=" N ILE E 238 " --> pdb=" O GLU E 234 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY E 240 " --> pdb=" O ASP E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 265 Processing helix chain 'E' and resid 286 through 291 removed outlier: 3.520A pdb=" N LEU E 290 " --> pdb=" O ASP E 286 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG E 291 " --> pdb=" O PRO E 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 286 through 291' Processing helix chain 'E' and resid 305 through 318 removed outlier: 4.013A pdb=" N GLY E 318 " --> pdb=" O LYS E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 336 removed outlier: 3.541A pdb=" N ILE E 331 " --> pdb=" O ASP E 327 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ASP E 336 " --> pdb=" O VAL E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 358 removed outlier: 4.941A pdb=" N ALA E 357 " --> pdb=" O PHE E 353 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ASP E 358 " --> pdb=" O ALA E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 379 removed outlier: 4.180A pdb=" N LYS E 379 " --> pdb=" O ALA E 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 35 removed outlier: 4.118A pdb=" N VAL F 33 " --> pdb=" O ILE F 29 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LEU F 34 " --> pdb=" O GLY F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 85 removed outlier: 3.692A pdb=" N LEU F 47 " --> pdb=" O GLN F 43 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP F 49 " --> pdb=" O THR F 45 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N SER F 50 " --> pdb=" O ARG F 46 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU F 51 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS F 53 " --> pdb=" O ASP F 49 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N SER F 57 " --> pdb=" O LYS F 53 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLU F 58 " --> pdb=" O ILE F 54 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL F 59 " --> pdb=" O MET F 55 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU F 60 " --> pdb=" O LYS F 56 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASP F 71 " --> pdb=" O GLN F 67 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS F 72 " --> pdb=" O ALA F 68 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS F 74 " --> pdb=" O LYS F 70 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N THR F 85 " --> pdb=" O LYS F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 146 removed outlier: 3.676A pdb=" N LEU F 145 " --> pdb=" O ASP F 141 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N LYS F 146 " --> pdb=" O ALA F 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 141 through 146' Processing helix chain 'F' and resid 169 through 176 removed outlier: 3.943A pdb=" N GLU F 176 " --> pdb=" O VAL F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 189 removed outlier: 4.221A pdb=" N ILE F 188 " --> pdb=" O GLN F 184 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N GLY F 189 " --> pdb=" O TYR F 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 184 through 189' Processing helix chain 'F' and resid 191 through 208 removed outlier: 4.767A pdb=" N LEU F 204 " --> pdb=" O GLU F 200 " (cutoff:3.500A) Proline residue: F 205 - end of helix Processing helix chain 'F' and resid 209 through 216 removed outlier: 4.432A pdb=" N LEU F 215 " --> pdb=" O LYS F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 232 through 244 removed outlier: 4.715A pdb=" N LEU F 236 " --> pdb=" O GLY F 232 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA F 237 " --> pdb=" O LYS F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 258 removed outlier: 4.485A pdb=" N LEU F 256 " --> pdb=" O ALA F 252 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL F 257 " --> pdb=" O GLY F 253 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N GLN F 258 " --> pdb=" O PRO F 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 252 through 258' Processing helix chain 'F' and resid 262 through 279 removed outlier: 6.404A pdb=" N LYS F 266 " --> pdb=" O GLY F 262 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU F 267 " --> pdb=" O ASP F 263 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG F 269 " --> pdb=" O ALA F 265 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ASP F 270 " --> pdb=" O LYS F 266 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS F 278 " --> pdb=" O LEU F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 292 removed outlier: 4.516A pdb=" N ILE F 291 " --> pdb=" O GLU F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 318 removed outlier: 6.562A pdb=" N GLU F 305 " --> pdb=" O ALA F 301 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL F 306 " --> pdb=" O GLY F 302 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ARG F 308 " --> pdb=" O ARG F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 344 removed outlier: 3.898A pdb=" N LEU F 343 " --> pdb=" O ASP F 339 " (cutoff:3.500A) removed outlier: 5.079A 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: 6.058A pdb=" N ARG F 362 " --> pdb=" O ASN F 358 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ALA F 363 " --> pdb=" O GLU F 359 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG F 371 " --> pdb=" O GLN F 367 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N LYS F 372 " --> pdb=" O ILE F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 388 Processing helix chain 'F' and resid 392 through 411 Processing helix chain 'F' and resid 416 through 429 removed outlier: 4.061A pdb=" N ALA F 429 " --> pdb=" O LEU F 425 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 35 removed outlier: 3.727A pdb=" N GLU G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ASN G 33 " --> pdb=" O PHE G 29 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLN G 34 " --> pdb=" O LYS G 30 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N GLY G 35 " --> pdb=" O ALA G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 67 removed outlier: 4.109A pdb=" N VAL G 66 " --> pdb=" O ASP G 62 " (cutoff:3.500A) removed outlier: 4.822A 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: 3.802A pdb=" N VAL G 124 " --> pdb=" O ASP G 120 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N TYR G 125 " --> pdb=" O ILE G 121 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N THR G 126 " --> pdb=" O SER G 122 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLN G 127 " --> pdb=" O GLN G 123 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N ALA G 129 " --> pdb=" O TYR G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 186 removed outlier: 3.980A pdb=" N LYS G 185 " --> pdb=" O LYS G 181 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LYS G 186 " --> pdb=" O LYS G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 207 removed outlier: 4.178A pdb=" N LEU G 206 " --> pdb=" O LEU G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 231 through 245 Processing helix chain 'G' and resid 7 through 12 removed outlier: 6.030A pdb=" N ASP G 10 " --> pdb=" O ALA G 7 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARG G 11 " --> pdb=" O GLY G 8 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N HIS G 12 " --> pdb=" O PHE G 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 7 through 12' Processing helix chain 'H' and resid 3 through 8 removed outlier: 3.521A pdb=" N SER H 7 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N PHE H 8 " --> pdb=" O ARG H 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 3 through 8' Processing helix chain 'H' and resid 19 through 32 removed outlier: 4.279A pdb=" N GLU H 23 " --> pdb=" O LEU H 19 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA H 30 " --> pdb=" O LEU H 26 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N GLY H 31 " --> pdb=" O ALA H 27 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N GLY H 32 " --> pdb=" O ALA H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 102 removed outlier: 4.190A pdb=" N TYR H 83 " --> pdb=" O MET H 79 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG H 84 " --> pdb=" O GLY H 80 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL H 85 " --> pdb=" O PRO H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 124 removed outlier: 3.750A pdb=" N GLU H 120 " --> pdb=" O SER H 116 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TYR H 121 " --> pdb=" O VAL H 117 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N THR H 122 " --> pdb=" O MET H 118 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLN H 123 " --> pdb=" O GLN H 119 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N SER H 124 " --> pdb=" O GLU H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 178 removed outlier: 3.670A pdb=" N GLY H 170 " --> pdb=" O ASN H 166 " (cutoff:3.500A) 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: 3.971A pdb=" N GLY h 32 " --> pdb=" O ALA h 28 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ALA h 33 " --> pdb=" O VAL h 29 " (cutoff:3.500A) Processing helix chain 'h' and resid 79 through 102 removed outlier: 3.832A pdb=" N TYR h 83 " --> pdb=" O MET h 79 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG h 84 " --> pdb=" O GLY h 80 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL h 85 " --> pdb=" O PRO h 81 " (cutoff:3.500A) Processing helix chain 'h' and resid 106 through 124 Processing helix chain 'h' and resid 166 through 178 removed outlier: 3.907A pdb=" N GLY h 170 " --> pdb=" O ASN h 166 " (cutoff:3.500A) Processing helix chain 'h' and resid 183 through 199 removed outlier: 4.087A 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: 3.770A pdb=" N GLU I 22 " --> pdb=" O LEU I 18 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE I 28 " --> pdb=" O ALA I 24 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLY I 29 " --> pdb=" O MET I 25 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N HIS I 30 " --> pdb=" O GLU I 26 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ALA I 31 " --> pdb=" O ALA I 27 " (cutoff:3.500A) removed outlier: 5.434A 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: 3.805A pdb=" N TYR I 121 " --> pdb=" O ILE I 117 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR I 122 " --> pdb=" O LYS I 118 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN I 123 " --> pdb=" O GLN I 119 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N PHE I 124 " --> pdb=" O ALA I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 179 removed outlier: 3.608A pdb=" N ALA I 171 " --> pdb=" O ASN I 167 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLN I 177 " --> pdb=" O SER I 173 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP I 178 " --> pdb=" O MET I 174 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR I 179 " --> pdb=" O LEU I 175 " (cutoff:3.500A) Processing helix chain 'I' and resid 185 through 202 removed outlier: 3.817A pdb=" N MET I 201 " --> pdb=" O LEU I 197 " (cutoff:3.500A) removed outlier: 5.463A 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: 5.385A pdb=" N GLU I 212 " --> pdb=" O ALA I 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 207 through 212' Processing helix chain 'I' and resid 229 through 251 removed outlier: 3.709A pdb=" N ARG I 249 " --> pdb=" O ALA I 245 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLU I 250 " --> pdb=" O LYS I 246 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LYS I 251 " --> pdb=" O ALA I 247 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 29 removed outlier: 4.277A pdb=" N GLU J 20 " --> pdb=" O LEU J 16 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA J 25 " --> pdb=" O TYR J 21 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL J 26 " --> pdb=" O ALA J 22 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LYS J 27 " --> pdb=" O GLN J 23 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LYS J 28 " --> pdb=" O GLU J 24 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLY J 29 " --> pdb=" O ALA J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 removed outlier: 4.884A pdb=" N VAL J 59 " --> pdb=" O ASP J 55 " (cutoff:3.500A) removed outlier: 5.070A 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: 3.651A pdb=" N TYR J 118 " --> pdb=" O LEU J 114 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR J 119 " --> pdb=" O LYS J 115 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN J 120 " --> pdb=" O GLN J 116 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER J 121 " --> pdb=" O ARG J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 164 through 176 Processing helix chain 'J' and resid 177 through 183 removed outlier: 4.030A pdb=" N ILE J 181 " --> pdb=" O THR J 177 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU J 182 " --> pdb=" O ASP J 178 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N THR J 183 " --> pdb=" O GLU J 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 177 through 183' Processing helix chain 'J' and resid 184 through 200 removed outlier: 4.038A pdb=" N VAL J 198 " --> pdb=" O ALA J 194 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N GLN J 200 " --> pdb=" O LEU J 196 " (cutoff:3.500A) Processing helix chain 'J' and resid 221 through 240 Processing helix chain 'j' and resid 16 through 30 removed outlier: 3.632A pdb=" N LYS j 28 " --> pdb=" O GLU j 24 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY j 29 " --> pdb=" O ALA j 25 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N SER j 30 " --> pdb=" O VAL j 26 " (cutoff:3.500A) Processing helix chain 'j' and resid 55 through 60 removed outlier: 4.565A pdb=" N VAL j 59 " --> pdb=" O ASP j 55 " (cutoff:3.500A) removed outlier: 4.629A 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: 3.561A pdb=" N TYR j 118 " --> pdb=" O LEU j 114 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR j 119 " --> pdb=" O LYS j 115 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN j 120 " --> pdb=" O GLN j 116 " (cutoff:3.500A) Processing helix chain 'j' and resid 164 through 176 removed outlier: 4.101A pdb=" N LYS j 174 " --> pdb=" O GLU j 170 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN j 175 " --> pdb=" O PHE j 171 " (cutoff:3.500A) Processing helix chain 'j' and resid 177 through 184 removed outlier: 4.280A pdb=" N ILE j 181 " --> pdb=" O THR j 177 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLU j 182 " --> pdb=" O ASP j 178 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N THR j 183 " --> pdb=" O GLU j 179 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N ASP j 184 " --> pdb=" O ALA j 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 177 through 184' Processing helix chain 'j' and resid 185 through 199 removed outlier: 4.017A pdb=" N GLU j 197 " --> pdb=" O LYS j 193 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N VAL j 198 " --> pdb=" O ALA j 194 " (cutoff:3.500A) Processing helix chain 'j' and resid 201 through 206 removed outlier: 7.144A pdb=" N ASN j 205 " --> pdb=" O SER j 201 " (cutoff:3.500A) removed outlier: 5.776A 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 removed outlier: 3.528A pdb=" N GLU j 240 " --> pdb=" O LYS j 236 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 10 removed outlier: 4.392A pdb=" N ASP K 9 " --> pdb=" O ARG K 5 " (cutoff:3.500A) removed outlier: 4.977A 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: 3.734A pdb=" N GLU K 25 " --> pdb=" O LEU K 21 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE K 31 " --> pdb=" O ALA K 27 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LYS K 32 " --> pdb=" O ILE K 28 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU K 33 " --> pdb=" O GLU K 29 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N GLY K 34 " --> pdb=" O ALA K 30 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N SER K 35 " --> pdb=" O ILE K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 65 removed outlier: 4.380A pdb=" N ILE K 64 " --> pdb=" O GLU K 60 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N GLU K 65 " --> pdb=" O PRO K 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 60 through 65' Processing helix chain 'K' and resid 81 through 103 removed outlier: 3.524A pdb=" N ALA K 85 " --> pdb=" O LEU K 81 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS K 86 " --> pdb=" O ILE K 82 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR K 87 " --> pdb=" O ALA K 83 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 122 removed outlier: 4.104A pdb=" N LEU K 121 " --> pdb=" O SER K 117 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N GLN K 122 " --> pdb=" O ASN K 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 173 through 185 removed outlier: 3.694A 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: 4.351A pdb=" N ILE K 215 " --> pdb=" O ASN K 211 " (cutoff:3.500A) removed outlier: 6.483A 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: 4.413A pdb=" N ASP K 240 " --> pdb=" O GLU K 236 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ILE K 241 " --> pdb=" O VAL K 237 " (cutoff:3.500A) Processing helix chain 'K' and resid 125 through 130 removed outlier: 4.425A pdb=" N ALA K 128 " --> pdb=" O GLU K 125 " (cutoff:3.500A) removed outlier: 3.793A 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 33 removed outlier: 3.740A pdb=" N MET L 26 " --> pdb=" O ILE L 22 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLU L 27 " --> pdb=" O GLU L 23 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA L 28 " --> pdb=" O TYR L 24 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL L 29 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS L 30 " --> pdb=" O MET L 26 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY L 32 " --> pdb=" O ALA L 28 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N SER L 33 " --> pdb=" O VAL L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 99 Processing helix chain 'L' and resid 104 through 122 removed outlier: 3.907A pdb=" N ILE L 118 " --> pdb=" O SER L 114 " (cutoff:3.500A) Proline residue: L 119 - end of helix removed outlier: 3.502A pdb=" N ARG L 122 " --> pdb=" O ILE L 118 " (cutoff:3.500A) Processing helix chain 'L' and resid 164 through 180 removed outlier: 4.819A pdb=" N ALA L 168 " --> pdb=" O ARG L 164 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N SER L 177 " --> pdb=" O GLU L 173 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLU L 178 " --> pdb=" O ARG L 174 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE L 179 " --> pdb=" O HIS L 175 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N MET L 180 " --> pdb=" O MET L 176 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 199 removed outlier: 3.926A pdb=" N THR L 198 " --> pdb=" O ALA L 194 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LEU L 199 " --> pdb=" O LEU L 195 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 211 removed outlier: 4.134A pdb=" N VAL L 210 " --> pdb=" O THR L 206 " (cutoff:3.500A) removed outlier: 6.586A 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 235 removed outlier: 4.132A pdb=" N SER L 230 " --> pdb=" O ASP L 226 " (cutoff:3.500A) Proline residue: L 231 - end of helix removed outlier: 4.787A pdb=" N GLY L 235 " --> pdb=" O PRO L 231 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 9 removed outlier: 4.141A pdb=" N TYR L 6 " --> pdb=" O ARG L 3 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASN L 8 " --> pdb=" O GLN L 5 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ASP L 9 " --> pdb=" O TYR L 6 " (cutoff:3.500A) Processing helix chain 'M' and resid 20 through 33 removed outlier: 3.739A pdb=" N GLU M 24 " --> pdb=" O VAL M 20 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA M 29 " --> pdb=" O TYR M 25 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL M 30 " --> pdb=" O ALA M 26 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU M 31 " --> pdb=" O MET M 27 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASN M 32 " --> pdb=" O LYS M 28 " (cutoff:3.500A) removed outlier: 4.420A 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: 3.946A pdb=" N TYR M 122 " --> pdb=" O TYR M 118 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N THR M 123 " --> pdb=" O VAL M 119 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU M 124 " --> pdb=" O HIS M 120 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TYR M 125 " --> pdb=" O ALA M 121 " (cutoff:3.500A) Processing helix chain 'M' and resid 168 through 179 removed outlier: 4.006A pdb=" N LYS M 178 " --> pdb=" O THR M 174 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU M 179 " --> pdb=" O GLU M 175 " (cutoff:3.500A) Processing helix chain 'M' and resid 180 through 185 removed outlier: 4.066A pdb=" N MET M 184 " --> pdb=" O GLN M 180 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N THR M 185 " --> pdb=" O MET M 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 180 through 185' Processing helix chain 'M' and resid 186 through 202 removed outlier: 4.554A pdb=" N LYS M 191 " --> pdb=" O ARG M 187 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLU M 192 " --> pdb=" O ASP M 188 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ASP M 202 " --> pdb=" O TYR M 198 " (cutoff:3.500A) Processing helix chain 'M' and resid 228 through 244 removed outlier: 4.217A 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: 3.526A pdb=" N ALA N 79 " --> pdb=" O LEU N 75 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR N 90 " --> pdb=" O MET N 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 131 through 143 removed outlier: 4.779A pdb=" N ILE N 135 " --> pdb=" O GLY N 131 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR N 136 " --> pdb=" O SER N 132 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLY N 137 " --> pdb=" O SER N 133 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N TYR N 138 " --> pdb=" O TYR N 134 " (cutoff:3.500A) Processing helix chain 'N' and resid 148 through 167 removed outlier: 3.765A pdb=" N ARG N 166 " --> pdb=" O LEU N 162 " (cutoff:3.500A) Processing helix chain 'O' and resid 48 through 71 Processing helix chain 'O' and resid 75 through 91 removed outlier: 3.673A pdb=" N ALA O 79 " --> pdb=" O ARG O 75 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG O 89 " --> pdb=" O GLN O 85 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N TYR O 90 " --> pdb=" O MET O 86 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN O 91 " --> pdb=" O LEU O 87 " (cutoff:3.500A) Processing helix chain 'O' and resid 130 through 142 removed outlier: 3.973A pdb=" N ALA O 134 " --> pdb=" O GLY O 130 " (cutoff:3.500A) Processing helix chain 'O' and resid 147 through 166 removed outlier: 3.681A pdb=" N ASN O 165 " --> pdb=" O ALA O 161 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP O 166 " --> pdb=" O GLY O 162 " (cutoff:3.500A) Processing helix chain 'o' and resid 48 through 71 Processing helix chain 'o' and resid 75 through 91 removed outlier: 3.579A pdb=" N ALA o 79 " --> pdb=" O ARG o 75 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR o 90 " --> pdb=" O MET o 86 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN o 91 " --> pdb=" O LEU o 87 " (cutoff:3.500A) Processing helix chain 'o' and resid 130 through 142 removed outlier: 3.796A pdb=" N ALA o 134 " --> pdb=" O GLY o 130 " (cutoff:3.500A) Processing helix chain 'o' and resid 147 through 166 removed outlier: 3.523A pdb=" N ASP o 166 " --> pdb=" O GLY o 162 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 8 removed outlier: 3.576A pdb=" N TYR P 6 " --> pdb=" O SER P 2 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ASN P 7 " --> pdb=" O ILE P 3 " (cutoff:3.500A) removed outlier: 3.900A 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 removed outlier: 3.644A pdb=" N LEU P 73 " --> pdb=" O PHE P 69 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 99 removed outlier: 4.237A pdb=" N LYS P 98 " --> pdb=" O LEU P 94 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ARG P 99 " --> pdb=" O LEU P 95 " (cutoff:3.500A) Processing helix chain 'P' and resid 142 through 154 removed outlier: 4.254A pdb=" N SER P 152 " --> pdb=" O GLY P 148 " (cutoff:3.500A) Processing helix chain 'P' and resid 159 through 179 removed outlier: 3.643A pdb=" N GLU P 165 " --> pdb=" O ASP P 161 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ARG P 177 " --> pdb=" O ASN P 173 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP P 178 " --> pdb=" O ALA P 174 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ALA P 179 " --> pdb=" O VAL P 175 " (cutoff:3.500A) Processing helix chain 'p' and resid 2 through 8 removed outlier: 4.924A pdb=" N ASN p 7 " --> pdb=" O ILE p 3 " (cutoff:3.500A) removed outlier: 3.877A 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: 4.219A pdb=" N LYS p 98 " --> pdb=" O LEU p 94 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ARG p 99 " --> pdb=" O LEU p 95 " (cutoff:3.500A) Processing helix chain 'p' and resid 142 through 154 removed outlier: 3.582A pdb=" N MET p 146 " --> pdb=" O CYS p 142 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N SER p 152 " --> pdb=" O GLY p 148 " (cutoff:3.500A) Processing helix chain 'p' and resid 159 through 179 removed outlier: 4.141A pdb=" N ARG p 177 " --> pdb=" O ASN p 173 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP p 178 " --> pdb=" O ALA p 174 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ALA p 179 " --> pdb=" O VAL p 175 " (cutoff:3.500A) Processing helix chain 'Q' and resid 50 through 72 removed outlier: 7.142A pdb=" N VAL Q 54 " --> pdb=" O ALA Q 50 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN Q 55 " --> pdb=" O GLY Q 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 93 removed outlier: 3.905A pdb=" N CYS Q 91 " --> pdb=" O ASN Q 87 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU Q 92 " --> pdb=" O LEU Q 88 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ARG Q 93 " --> pdb=" O ALA Q 89 " (cutoff:3.500A) Processing helix chain 'Q' and resid 134 through 147 removed outlier: 4.743A pdb=" N LEU Q 138 " --> pdb=" O TYR Q 134 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR Q 139 " --> pdb=" O GLY Q 135 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N SER Q 141 " --> pdb=" O PHE Q 137 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ILE Q 142 " --> pdb=" O LEU Q 138 " (cutoff:3.500A) Processing helix chain 'Q' and resid 152 through 170 removed outlier: 4.152A pdb=" N VAL Q 157 " --> pdb=" O ARG Q 153 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU Q 158 " --> pdb=" O GLU Q 154 " (cutoff:3.500A) Processing helix chain 'q' and resid 50 through 72 removed outlier: 7.016A pdb=" N VAL q 54 " --> pdb=" O ALA q 50 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN q 55 " --> pdb=" O GLY q 51 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLU q 58 " --> pdb=" O VAL q 54 " (cutoff:3.500A) Processing helix chain 'q' and resid 76 through 93 removed outlier: 3.936A pdb=" N CYS q 91 " --> pdb=" O ASN q 87 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU q 92 " --> pdb=" O LEU q 88 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ARG q 93 " --> pdb=" O ALA q 89 " (cutoff:3.500A) Processing helix chain 'q' and resid 134 through 147 removed outlier: 4.398A pdb=" N LEU q 138 " --> pdb=" O TYR q 134 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N SER q 141 " --> pdb=" O PHE q 137 " (cutoff:3.500A) removed outlier: 4.879A 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: 3.944A pdb=" N GLN R 89 " --> pdb=" O ASN R 85 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N TYR R 90 " --> pdb=" O MET R 86 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS R 91 " --> pdb=" O VAL R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 143 removed outlier: 4.050A pdb=" N GLY R 137 " --> pdb=" O VAL R 133 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL R 138 " --> pdb=" O TYR R 134 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG R 141 " --> pdb=" O GLY R 137 " (cutoff:3.500A) removed outlier: 3.650A 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: 3.548A 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: 3.853A pdb=" N GLN r 89 " --> pdb=" O ASN r 85 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N TYR r 90 " --> pdb=" O MET r 86 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LYS r 91 " --> pdb=" O VAL r 87 " (cutoff:3.500A) Processing helix chain 'r' and resid 131 through 143 removed outlier: 4.289A pdb=" N ARG r 141 " --> pdb=" O GLY r 137 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY r 142 " --> pdb=" O VAL r 138 " (cutoff:3.500A) Processing helix chain 'r' and resid 148 through 167 removed outlier: 3.791A pdb=" N TYR r 153 " --> pdb=" O VAL r 149 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASP r 154 " --> pdb=" O GLU r 150 " (cutoff:3.500A) Processing helix chain 'r' and resid 191 through 201 removed outlier: 3.543A pdb=" N GLY r 201 " --> pdb=" O GLU r 197 " (cutoff:3.500A) Processing helix chain 'S' and resid 57 through 80 Processing helix chain 'S' and resid 84 through 100 removed outlier: 3.894A pdb=" N ARG S 99 " --> pdb=" O ILE S 95 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ARG S 100 " --> pdb=" O LEU S 96 " (cutoff:3.500A) Processing helix chain 'S' and resid 141 through 153 Proline residue: S 147 - end of helix Processing helix chain 'S' and resid 167 through 186 removed outlier: 3.814A pdb=" N GLU S 184 " --> pdb=" O ILE S 180 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG S 185 " --> pdb=" O SER S 181 " (cutoff:3.500A) Processing helix chain 's' and resid 57 through 80 Processing helix chain 's' and resid 84 through 100 removed outlier: 3.869A pdb=" N ARG s 99 " --> pdb=" O ILE s 95 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ARG s 100 " --> pdb=" O LEU s 96 " (cutoff:3.500A) Processing helix chain 's' and resid 141 through 153 Proline residue: s 147 - end of helix Processing helix chain 's' and resid 167 through 186 removed outlier: 4.314A pdb=" N GLU s 184 " --> pdb=" O ILE s 180 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ARG s 185 " --> pdb=" O SER s 181 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP s 186 " --> pdb=" O ALA s 182 " (cutoff:3.500A) Processing helix chain 'T' and resid 56 through 78 removed outlier: 3.551A pdb=" N PHE T 60 " --> pdb=" O ASP T 56 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU T 77 " --> pdb=" O ASP T 73 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLY T 78 " --> pdb=" O GLU T 74 " (cutoff:3.500A) Processing helix chain 'T' and resid 84 through 103 removed outlier: 3.532A pdb=" N MET T 103 " --> pdb=" O ARG T 99 " (cutoff:3.500A) Processing helix chain 'T' and resid 140 through 158 removed outlier: 4.770A pdb=" N TYR T 144 " --> pdb=" O GLY T 140 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLN T 147 " --> pdb=" O ALA T 143 " (cutoff:3.500A) Proline residue: T 148 - end of helix removed outlier: 3.790A pdb=" N LYS T 156 " --> pdb=" O GLU T 152 " (cutoff:3.500A) Proline residue: T 158 - end of helix Processing helix chain 'T' and resid 161 through 180 Processing helix chain 'T' and resid 209 through 215 removed outlier: 4.924A pdb=" N HIS T 213 " --> pdb=" O TRP T 209 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N MET T 214 " --> pdb=" O ASP T 210 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ILE T 215 " --> pdb=" O ILE T 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 209 through 215' Processing helix chain 't' and resid 56 through 78 removed outlier: 3.590A pdb=" N PHE t 60 " --> pdb=" O ASP t 56 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEU t 77 " --> pdb=" O ASP t 73 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY t 78 " --> pdb=" O GLU t 74 " (cutoff:3.500A) Processing helix chain 't' and resid 84 through 103 removed outlier: 4.023A pdb=" N MET t 103 " --> pdb=" O ARG t 99 " (cutoff:3.500A) Processing helix chain 't' and resid 140 through 158 removed outlier: 4.111A pdb=" N TYR t 144 " --> pdb=" O GLY t 140 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLN t 147 " --> pdb=" O ALA t 143 " (cutoff:3.500A) Proline residue: t 148 - end of helix Proline residue: t 158 - end of helix Processing helix chain 't' and resid 161 through 180 Processing helix chain 't' and resid 209 through 215 removed outlier: 4.916A pdb=" N HIS t 213 " --> pdb=" O TRP t 209 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N MET t 214 " --> pdb=" O ASP t 210 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ILE t 215 " --> pdb=" O ILE t 211 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 209 through 215' Processing helix chain 'g' and resid 22 through 35 removed outlier: 3.938A pdb=" N ALA g 28 " --> pdb=" O GLN g 24 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE g 29 " --> pdb=" O VAL g 25 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS g 30 " --> pdb=" O GLU g 26 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN g 33 " --> pdb=" O PHE g 29 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN g 34 " --> pdb=" O LYS g 30 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N GLY g 35 " --> pdb=" O ALA g 31 " (cutoff:3.500A) Processing helix chain 'g' and resid 62 through 67 removed outlier: 4.202A pdb=" N VAL g 66 " --> pdb=" O ASP g 62 " (cutoff:3.500A) removed outlier: 5.268A 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: 3.916A pdb=" N TYR g 125 " --> pdb=" O ILE g 121 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR g 126 " --> pdb=" O SER g 122 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN g 127 " --> pdb=" O GLN g 123 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN g 128 " --> pdb=" O VAL g 124 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ALA g 129 " --> pdb=" O TYR g 125 " (cutoff:3.500A) Processing helix chain 'g' and resid 171 through 186 removed outlier: 3.943A pdb=" N LYS g 184 " --> pdb=" O GLU g 180 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LYS g 185 " --> pdb=" O LYS g 181 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS g 186 " --> pdb=" O LYS g 182 " (cutoff:3.500A) Processing helix chain 'g' and resid 190 through 207 removed outlier: 3.664A pdb=" N LEU g 202 " --> pdb=" O ALA g 198 " (cutoff:3.500A) Processing helix chain 'g' and resid 231 through 245 removed outlier: 3.505A pdb=" N ILE g 235 " --> pdb=" O THR g 231 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU g 244 " --> pdb=" O VAL g 240 " (cutoff:3.500A) Processing helix chain 'i' and resid 2 through 7 removed outlier: 3.895A pdb=" N ASP i 6 " --> pdb=" O SER i 2 " (cutoff:3.500A) removed outlier: 5.848A 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: 3.870A pdb=" N HIS i 30 " --> pdb=" O GLU i 26 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA i 31 " --> pdb=" O ALA i 27 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N GLY i 32 " --> pdb=" O ILE i 28 " (cutoff:3.500A) Processing helix chain 'i' and resid 79 through 102 removed outlier: 3.644A pdb=" N ALA i 83 " --> pdb=" O ILE i 79 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASN i 84 " --> pdb=" O THR i 80 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL i 85 " --> pdb=" O SER i 81 " (cutoff:3.500A) Processing helix chain 'i' and resid 106 through 124 removed outlier: 3.622A pdb=" N LEU i 110 " --> pdb=" O PRO i 106 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TYR i 121 " --> pdb=" O ILE i 117 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR i 122 " --> pdb=" O LYS i 118 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE i 124 " --> pdb=" O ALA i 120 " (cutoff:3.500A) Processing helix chain 'i' and resid 167 through 179 removed outlier: 3.598A pdb=" N ALA i 171 " --> pdb=" O ASN i 167 " (cutoff:3.500A) Processing helix chain 'i' and resid 185 through 202 removed outlier: 4.812A pdb=" N ASP i 202 " --> pdb=" O ASN i 198 " (cutoff:3.500A) Processing helix chain 'i' and resid 229 through 251 removed outlier: 4.041A pdb=" N GLU i 250 " --> pdb=" O LYS i 246 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LYS i 251 " --> pdb=" O ALA i 247 " (cutoff:3.500A) Processing helix chain 'k' and resid 21 through 34 removed outlier: 3.650A pdb=" N GLU k 25 " --> pdb=" O LEU k 21 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS k 32 " --> pdb=" O ILE k 28 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LEU k 33 " --> pdb=" O GLU k 29 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLY k 34 " --> pdb=" O ALA k 30 " (cutoff:3.500A) Processing helix chain 'k' and resid 81 through 103 removed outlier: 3.728A pdb=" N ALA k 85 " --> pdb=" O LEU k 81 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LYS k 86 " --> pdb=" O ILE k 82 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N THR k 87 " --> pdb=" O ALA k 83 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU k 88 " --> pdb=" O ASP k 84 " (cutoff:3.500A) Processing helix chain 'k' and resid 108 through 121 removed outlier: 4.041A pdb=" N LEU k 119 " --> pdb=" O ALA k 115 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ALA k 120 " --> pdb=" O VAL k 116 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N LEU k 121 " --> pdb=" O SER k 117 " (cutoff:3.500A) Processing helix chain 'k' and resid 173 through 185 removed outlier: 3.638A pdb=" N ALA k 177 " --> pdb=" O ALA k 173 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N SER k 179 " --> pdb=" O GLU k 175 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLU k 183 " --> pdb=" O SER k 179 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR k 185 " --> pdb=" O LEU k 181 " (cutoff:3.500A) Processing helix chain 'k' and resid 190 through 207 removed outlier: 5.604A pdb=" N GLU k 207 " --> pdb=" O LYS k 203 " (cutoff:3.500A) Processing helix chain 'k' and resid 211 through 216 removed outlier: 4.239A pdb=" N ILE k 215 " --> pdb=" O ASN k 211 " (cutoff:3.500A) removed outlier: 6.619A 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: 4.796A pdb=" N ASP k 240 " --> pdb=" O GLU k 236 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ILE k 241 " --> pdb=" O VAL k 237 " (cutoff:3.500A) Processing helix chain 'l' and resid 19 through 32 removed outlier: 3.563A pdb=" N GLU l 23 " --> pdb=" O ILE l 19 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS l 30 " --> pdb=" O MET l 26 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLN l 31 " --> pdb=" O GLU l 27 " (cutoff:3.500A) removed outlier: 4.761A 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: 4.221A pdb=" N ILE l 118 " --> pdb=" O SER l 114 " (cutoff:3.500A) Proline residue: l 119 - end of helix Processing helix chain 'l' and resid 164 through 180 removed outlier: 4.585A pdb=" N ALA l 168 " --> pdb=" O ARG l 164 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N SER l 177 " --> pdb=" O GLU l 173 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLU l 178 " --> pdb=" O ARG l 174 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N PHE l 179 " --> pdb=" O HIS l 175 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N MET l 180 " --> pdb=" O MET l 176 " (cutoff:3.500A) Processing helix chain 'l' and resid 183 through 200 removed outlier: 3.966A pdb=" N THR l 198 " --> pdb=" O ALA l 194 " (cutoff:3.500A) removed outlier: 3.959A 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: 3.890A pdb=" N SER l 230 " --> pdb=" O ASP l 226 " (cutoff:3.500A) Proline residue: l 231 - end of helix removed outlier: 4.174A pdb=" N GLU l 234 " --> pdb=" O SER l 230 " (cutoff:3.500A) Processing helix chain 'm' and resid 20 through 33 removed outlier: 3.728A pdb=" N GLU m 24 " --> pdb=" O VAL m 20 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASN m 32 " --> pdb=" O LYS m 28 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N SER m 33 " --> pdb=" O ALA m 29 " (cutoff:3.500A) Processing helix chain 'm' and resid 80 through 102 removed outlier: 3.550A pdb=" N ALA m 84 " --> pdb=" O LEU m 80 " (cutoff:3.500A) Processing helix chain 'm' and resid 107 through 124 removed outlier: 3.928A pdb=" N TYR m 122 " --> pdb=" O TYR m 118 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N THR m 123 " --> pdb=" O VAL m 119 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU m 124 " --> pdb=" O HIS m 120 " (cutoff:3.500A) Processing helix chain 'm' and resid 168 through 179 removed outlier: 3.891A pdb=" N LYS m 178 " --> pdb=" O THR m 174 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEU m 179 " --> pdb=" O GLU m 175 " (cutoff:3.500A) Processing helix chain 'm' and resid 180 through 185 removed outlier: 4.013A pdb=" N MET m 184 " --> pdb=" O GLN m 180 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N THR m 185 " --> pdb=" O MET m 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 180 through 185' Processing helix chain 'm' and resid 186 through 201 removed outlier: 3.841A pdb=" N VAL m 190 " --> pdb=" O CYS m 186 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N LYS m 191 " --> pdb=" O ARG m 187 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU m 192 " --> pdb=" O ASP m 188 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS m 201 " --> pdb=" O ILE m 197 " (cutoff:3.500A) Processing helix chain 'm' and resid 202 through 207 removed outlier: 4.147A pdb=" N ASP m 206 " --> pdb=" O ASP m 202 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LYS m 207 " --> pdb=" O GLU m 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 202 through 207' Processing helix chain 'm' and resid 228 through 244 removed outlier: 4.074A pdb=" N LYS m 244 " --> pdb=" O LYS m 240 " (cutoff:3.500A) Processing helix chain 'm' and resid 5 through 10 removed outlier: 5.790A pdb=" N ASP m 8 " --> pdb=" O THR m 5 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LEU m 9 " --> pdb=" O GLY m 6 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N SER m 10 " --> pdb=" O TYR m 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 5 through 10' Processing helix chain 'n' and resid 48 through 71 Processing helix chain 'n' and resid 75 through 91 removed outlier: 3.678A pdb=" N TYR n 90 " --> pdb=" O MET n 86 " (cutoff:3.500A) Processing helix chain 'n' and resid 131 through 143 removed outlier: 4.118A pdb=" N ILE n 135 " --> pdb=" O GLY n 131 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N GLY n 137 " --> pdb=" O SER n 133 " (cutoff:3.500A) removed outlier: 5.311A 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: 4.133A pdb=" N PHE x 29 " --> pdb=" O PRO x 25 " (cutoff:3.500A) Processing helix chain 'x' and resid 93 through 102 Processing helix chain 'x' and resid 113 through 126 removed outlier: 3.550A pdb=" N ASN x 117 " --> pdb=" O THR x 113 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL x 126 " --> pdb=" O CYS x 122 " (cutoff:3.500A) Processing helix chain 'x' and resid 127 through 136 Processing helix chain 'x' and resid 144 through 166 removed outlier: 4.494A pdb=" N ALA x 149 " --> pdb=" O GLU x 145 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLN x 150 " --> pdb=" O MET x 146 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N TYR x 151 " --> pdb=" O ALA x 147 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ILE x 152 " --> pdb=" O SER x 148 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS x 165 " --> pdb=" O ASP x 161 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR x 166 " --> pdb=" O SER x 162 " (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 Processing helix chain 'x' and resid 220 through 226 removed outlier: 4.306A pdb=" N LYS x 224 " --> pdb=" O ASP x 220 " (cutoff:3.500A) Processing helix chain 'x' and resid 241 through 247 removed outlier: 4.196A pdb=" N GLN x 245 " --> pdb=" O SER x 241 " (cutoff:3.500A) Processing helix chain 'x' and resid 285 through 295 removed outlier: 3.526A pdb=" N GLY x 289 " --> pdb=" O TYR x 285 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLN x 295 " --> pdb=" O LYS x 291 " (cutoff:3.500A) Processing helix chain 'x' and resid 360 through 385 removed outlier: 3.846A pdb=" N GLU x 365 " --> pdb=" O PRO x 361 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LYS x 366 " --> pdb=" O GLU x 362 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE x 370 " --> pdb=" O LYS x 366 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LYS x 373 " --> pdb=" O SER x 369 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE x 374 " --> pdb=" O PHE x 370 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU x 377 " --> pdb=" O LYS x 373 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLN x 384 " --> pdb=" O LYS x 380 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLN x 385 " --> pdb=" O LYS x 381 " (cutoff:3.500A) Processing helix chain 'x' and resid 459 through 467 removed outlier: 3.855A pdb=" N ILE x 463 " --> pdb=" O THR x 459 " (cutoff:3.500A) removed outlier: 4.243A 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 37 through 42 removed outlier: 3.733A pdb=" N GLN y 41 " --> pdb=" O PRO y 37 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N ARG y 42 " --> pdb=" O PRO y 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 37 through 42' Processing helix chain 'y' and resid 55 through 60 removed outlier: 4.017A pdb=" N TYR y 59 " --> pdb=" O THR y 55 " (cutoff:3.500A) removed outlier: 3.522A 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 'U' and resid 7 through 12 removed outlier: 4.180A pdb=" N LEU U 11 " --> pdb=" O GLY U 7 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N LEU U 12 " --> pdb=" O ILE U 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 7 through 12' Processing helix chain 'U' and resid 18 through 24 removed outlier: 6.278A pdb=" N PHE U 22 " --> pdb=" O GLN U 18 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ALA U 23 " --> pdb=" O LEU U 19 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU U 24 " --> pdb=" O LYS U 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 18 through 24' Processing helix chain 'U' and resid 26 through 35 removed outlier: 4.138A pdb=" N VAL U 30 " --> pdb=" O LYS U 26 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL U 31 " --> pdb=" O LEU U 27 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ASN U 32 " --> pdb=" O ASN U 28 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ASP U 33 " --> pdb=" O ALA U 29 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TRP U 35 " --> pdb=" O VAL U 31 " (cutoff:3.500A) Processing helix chain 'U' and resid 36 through 42 removed outlier: 4.430A pdb=" N SER U 41 " --> pdb=" O GLU U 37 " (cutoff:3.500A) Processing helix chain 'U' and resid 43 through 52 removed outlier: 5.095A 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 87 through 92 removed outlier: 5.636A pdb=" N ASN U 91 " --> pdb=" O LEU U 87 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASP U 92 " --> pdb=" O PHE U 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 87 through 92' Processing helix chain 'U' and resid 94 through 119 removed outlier: 3.833A pdb=" N ALA U 102 " --> pdb=" O GLU U 98 " (cutoff:3.500A) removed outlier: 3.898A 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: 3.893A pdb=" N HIS U 145 " --> pdb=" O CYS U 141 " (cutoff:3.500A) Processing helix chain 'U' and resid 147 through 158 removed outlier: 4.092A pdb=" N GLY U 152 " --> pdb=" O LYS U 148 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG U 158 " --> pdb=" O ALA U 154 " (cutoff:3.500A) Processing helix chain 'U' and resid 159 through 169 removed outlier: 4.029A pdb=" N PHE U 163 " --> pdb=" O ARG U 159 " (cutoff:3.500A) Processing helix chain 'U' and resid 174 through 187 removed outlier: 4.580A pdb=" N ALA U 178 " --> pdb=" O PRO U 174 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET U 185 " --> pdb=" O LEU U 181 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER U 186 " --> pdb=" O LYS U 182 " (cutoff:3.500A) Processing helix chain 'U' and resid 190 through 208 removed outlier: 3.541A pdb=" N ARG U 194 " --> pdb=" O ASN U 190 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N LYS U 196 " --> pdb=" O GLN U 192 " (cutoff:3.500A) Processing helix chain 'U' and resid 212 through 224 removed outlier: 5.630A pdb=" N VAL U 216 " --> pdb=" O ASP U 212 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS U 217 " --> pdb=" O PHE U 213 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN U 218 " --> pdb=" O ILE U 214 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N CYS U 219 " --> pdb=" O ASN U 215 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU U 220 " --> pdb=" O VAL U 216 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ILE U 221 " --> pdb=" O CYS U 217 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE U 222 " --> pdb=" O GLN U 218 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU U 223 " --> pdb=" O CYS U 219 " (cutoff:3.500A) Processing helix chain 'U' and resid 225 through 240 Processing helix chain 'U' and resid 241 through 256 removed outlier: 3.783A pdb=" N GLN U 247 " --> pdb=" O LEU U 243 " (cutoff:3.500A) Processing helix chain 'U' and resid 257 through 270 removed outlier: 3.681A pdb=" N LEU U 261 " --> pdb=" O SER U 257 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N SER U 262 " --> pdb=" O GLN U 258 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER U 263 " --> pdb=" O GLN U 259 " (cutoff:3.500A) Processing helix chain 'U' and resid 320 through 331 removed outlier: 4.167A pdb=" N LYS U 324 " --> pdb=" O ASP U 320 " (cutoff:3.500A) Processing helix chain 'U' and resid 332 through 346 removed outlier: 3.526A pdb=" N ASN U 346 " --> pdb=" O LEU U 342 " (cutoff:3.500A) Processing helix chain 'U' and resid 349 through 360 removed outlier: 4.515A pdb=" N LEU U 353 " --> pdb=" O ASP U 349 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA U 359 " --> pdb=" O ASN U 355 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL U 360 " --> pdb=" O THR U 356 " (cutoff:3.500A) Processing helix chain 'U' and resid 364 through 378 removed outlier: 5.525A pdb=" N ALA U 368 " --> pdb=" O VAL U 364 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE U 371 " --> pdb=" O THR U 367 " (cutoff:3.500A) Processing helix chain 'U' and resid 383 through 388 removed outlier: 4.834A pdb=" N ARG U 387 " --> pdb=" O ASP U 383 " (cutoff:3.500A) Processing helix chain 'U' and resid 390 through 397 removed outlier: 3.927A pdb=" N ALA U 394 " --> pdb=" O LEU U 390 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ARG U 395 " --> pdb=" O GLU U 391 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ALA U 396 " --> pdb=" O TRP U 392 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N THR U 397 " --> pdb=" O LEU U 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 390 through 397' Processing helix chain 'U' and resid 398 through 413 removed outlier: 6.277A pdb=" N PHE U 402 " --> pdb=" O ASN U 398 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N THR U 405 " --> pdb=" O LYS U 401 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA U 406 " --> pdb=" O PHE U 402 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS U 413 " --> pdb=" O GLY U 409 " (cutoff:3.500A) Processing helix chain 'U' and resid 419 through 427 removed outlier: 4.229A pdb=" N MET U 423 " --> pdb=" O ALA U 419 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N TYR U 426 " --> pdb=" O LEU U 422 " (cutoff:3.500A) Processing helix chain 'U' and resid 435 through 451 removed outlier: 3.592A pdb=" N GLU U 439 " --> pdb=" O SER U 435 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N HIS U 450 " --> pdb=" O LEU U 446 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA U 451 " --> pdb=" O GLY U 447 " (cutoff:3.500A) Processing helix chain 'U' and resid 455 through 468 removed outlier: 4.154A pdb=" N ASP U 459 " --> pdb=" O GLY U 455 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN U 467 " --> pdb=" O ASN U 463 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA U 468 " --> pdb=" O GLN U 464 " (cutoff:3.500A) Processing helix chain 'U' and resid 472 through 486 removed outlier: 3.823A pdb=" N GLY U 476 " --> pdb=" O ILE U 472 " (cutoff:3.500A) Processing helix chain 'U' and resid 490 through 504 removed outlier: 3.529A pdb=" N TYR U 494 " --> pdb=" O ARG U 490 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLN U 503 " --> pdb=" O THR U 499 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N ASP U 504 " --> pdb=" O ASN U 500 " (cutoff:3.500A) Processing helix chain 'U' and resid 505 through 521 removed outlier: 3.502A pdb=" N GLY U 509 " --> pdb=" O ASP U 505 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLU U 510 " --> pdb=" O ALA U 506 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ALA U 511 " --> pdb=" O VAL U 507 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET U 520 " --> pdb=" O LEU U 516 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU U 521 " --> pdb=" O GLY U 517 " (cutoff:3.500A) Processing helix chain 'U' and resid 525 through 539 removed outlier: 4.175A pdb=" N GLN U 537 " --> pdb=" O VAL U 533 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLU U 538 " --> pdb=" O GLY U 534 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR U 539 " --> pdb=" O TYR U 535 " (cutoff:3.500A) Processing helix chain 'U' and resid 541 through 556 removed outlier: 4.882A pdb=" N LEU U 545 " --> pdb=" O HIS U 541 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N MET U 556 " --> pdb=" O ILE U 552 " (cutoff:3.500A) Processing helix chain 'U' and resid 559 through 573 removed outlier: 6.066A pdb=" N ALA U 563 " --> pdb=" O ARG U 559 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASP U 564 " --> pdb=" O MET U 560 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ALA U 565 " --> pdb=" O GLU U 561 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LEU U 566 " --> pdb=" O GLU U 562 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG U 572 " --> pdb=" O GLU U 568 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASP U 573 " --> pdb=" O SER U 569 " (cutoff:3.500A) Processing helix chain 'U' and resid 575 through 591 removed outlier: 3.888A pdb=" N TYR U 590 " --> pdb=" O VAL U 586 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N CYS U 591 " --> pdb=" O ALA U 587 " (cutoff:3.500A) Processing helix chain 'U' and resid 595 through 609 removed outlier: 3.716A pdb=" N ASP U 609 " --> pdb=" O VAL U 605 " (cutoff:3.500A) Processing helix chain 'U' and resid 611 through 627 removed outlier: 3.524A pdb=" N ARG U 615 " --> pdb=" O ASN U 611 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU U 622 " --> pdb=" O ALA U 618 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N GLY U 623 " --> pdb=" O VAL U 619 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N PHE U 624 " --> pdb=" O GLU U 620 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE U 625 " --> pdb=" O SER U 621 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE U 627 " --> pdb=" O GLY U 623 " (cutoff:3.500A) Processing helix chain 'U' and resid 629 through 643 removed outlier: 4.315A pdb=" N CYS U 633 " --> pdb=" O THR U 629 " (cutoff:3.500A) Proline residue: U 634 - end of helix removed outlier: 3.813A pdb=" N SER U 638 " --> pdb=" O PRO U 634 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N LEU U 639 " --> pdb=" O SER U 635 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU U 640 " --> pdb=" O VAL U 636 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER U 641 " --> pdb=" O VAL U 637 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLU U 642 " --> pdb=" O SER U 638 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER U 643 " --> pdb=" O LEU U 639 " (cutoff:3.500A) Processing helix chain 'U' and resid 645 through 660 removed outlier: 3.932A pdb=" N ARG U 649 " --> pdb=" O ASN U 645 " (cutoff:3.500A) Processing helix chain 'U' and resid 665 through 676 removed outlier: 6.188A pdb=" N ILE U 669 " --> pdb=" O ASN U 665 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASN U 670 " --> pdb=" O LYS U 666 " (cutoff:3.500A) Proline residue: U 674 - end of helix Processing helix chain 'U' and resid 680 through 696 removed outlier: 3.954A pdb=" N ILE U 696 " --> pdb=" O ALA U 692 " (cutoff:3.500A) Processing helix chain 'U' and resid 699 through 704 removed outlier: 3.508A pdb=" N CYS U 703 " --> pdb=" O THR U 699 " (cutoff:3.500A) Proline residue: U 704 - end of helix No H-bonds generated for 'chain 'U' and resid 699 through 704' Processing helix chain 'U' and resid 705 through 719 Processing helix chain 'U' and resid 723 through 739 removed outlier: 4.248A pdb=" N ASP U 738 " --> pdb=" O GLN U 734 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA U 739 " --> pdb=" O GLY U 735 " (cutoff:3.500A) Processing helix chain 'U' and resid 756 through 764 removed outlier: 4.759A pdb=" N LEU U 764 " --> pdb=" O VAL U 760 " (cutoff:3.500A) Processing helix chain 'U' and resid 777 through 784 removed outlier: 4.813A pdb=" N LEU U 781 " --> pdb=" O HIS U 777 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA U 782 " --> pdb=" O PHE U 778 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N THR U 784 " --> pdb=" O SER U 780 " (cutoff:3.500A) Processing helix chain 'U' and resid 835 through 852 removed outlier: 4.188A pdb=" N LYS U 841 " --> pdb=" O ALA U 837 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N LYS U 849 " --> pdb=" O GLU U 845 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N GLU U 850 " --> pdb=" O LYS U 846 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU U 851 " --> pdb=" O GLU U 847 " (cutoff:3.500A) Processing helix chain 'U' and resid 885 through 890 removed outlier: 3.617A pdb=" N LEU U 889 " --> pdb=" O MET U 885 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LYS U 890 " --> pdb=" O PRO U 886 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 885 through 890' Processing helix chain 'V' and resid 54 through 89 Processing helix chain 'V' and resid 90 through 108 removed outlier: 4.601A pdb=" N VAL V 94 " --> pdb=" O GLU V 90 " (cutoff:3.500A) Proline residue: V 102 - end of helix removed outlier: 4.098A pdb=" N ARG V 106 " --> pdb=" O PRO V 102 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ARG V 107 " --> pdb=" O SER V 103 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LEU V 108 " --> pdb=" O THR V 104 " (cutoff:3.500A) Processing helix chain 'V' and resid 109 through 121 Processing helix chain 'V' and resid 125 through 136 removed outlier: 3.656A pdb=" N ASP V 129 " --> pdb=" O ASN V 125 " (cutoff:3.500A) Proline residue: V 133 - end of helix removed outlier: 4.923A pdb=" N GLU V 136 " --> pdb=" O LEU V 132 " (cutoff:3.500A) Processing helix chain 'V' and resid 152 through 158 Proline residue: V 158 - end of helix Processing helix chain 'V' and resid 160 through 179 Processing helix chain 'V' and resid 180 through 199 removed outlier: 3.616A pdb=" N ALA V 184 " --> pdb=" O ARG V 180 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN V 198 " --> pdb=" O LYS V 194 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ASN V 199 " --> pdb=" O ILE V 195 " (cutoff:3.500A) Processing helix chain 'V' and resid 200 through 222 removed outlier: 4.291A pdb=" N ASP V 204 " --> pdb=" O ARG V 200 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LEU V 205 " --> pdb=" O ARG V 201 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N VAL V 206 " --> pdb=" O ALA V 202 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS V 209 " --> pdb=" O LEU V 205 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE V 220 " --> pdb=" O ARG V 216 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU V 221 " --> pdb=" O VAL V 217 " (cutoff:3.500A) Processing helix chain 'V' and resid 225 through 242 removed outlier: 4.575A pdb=" N SER V 229 " --> pdb=" O ASP V 225 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N PHE V 230 " --> pdb=" O VAL V 226 " (cutoff:3.500A) Processing helix chain 'V' and resid 243 through 262 removed outlier: 3.802A pdb=" N TYR V 261 " --> pdb=" O ASN V 257 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER V 262 " --> pdb=" O TYR V 258 " (cutoff:3.500A) Processing helix chain 'V' and resid 263 through 274 removed outlier: 3.880A pdb=" N LYS V 273 " --> pdb=" O LYS V 269 " (cutoff:3.500A) Processing helix chain 'V' and resid 281 through 300 removed outlier: 3.653A pdb=" N LEU V 300 " --> pdb=" O LYS V 296 " (cutoff:3.500A) Processing helix chain 'V' and resid 301 through 317 removed outlier: 3.543A pdb=" N ALA V 305 " --> pdb=" O GLU V 301 " (cutoff:3.500A) Proline residue: V 317 - end of helix Processing helix chain 'V' and resid 321 through 340 Processing helix chain 'V' and resid 344 through 350 removed outlier: 4.596A pdb=" N PHE V 348 " --> pdb=" O ASP V 344 " (cutoff:3.500A) removed outlier: 3.725A 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: 3.669A pdb=" N PHE V 375 " --> pdb=" O ASN V 371 " (cutoff:3.500A) Processing helix chain 'V' and resid 384 through 390 removed outlier: 3.529A pdb=" N GLY V 390 " --> pdb=" O PHE V 386 " (cutoff:3.500A) Processing helix chain 'V' and resid 391 through 414 removed outlier: 3.568A pdb=" N ILE V 395 " --> pdb=" O THR V 391 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N HIS V 400 " --> pdb=" O ILE V 396 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N ILE V 403 " --> pdb=" O ARG V 399 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LYS V 404 " --> pdb=" O HIS V 400 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N THR V 405 " --> pdb=" O ASN V 401 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY V 406 " --> pdb=" O VAL V 402 " (cutoff:3.500A) Processing helix chain 'V' and resid 418 through 427 removed outlier: 4.141A pdb=" N ALA V 423 " --> pdb=" O LEU V 419 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLN V 424 " --> pdb=" O ALA V 420 " (cutoff:3.500A) Processing helix chain 'V' and resid 430 through 445 removed outlier: 3.751A pdb=" N ALA V 434 " --> pdb=" O SER V 430 " (cutoff:3.500A) Processing helix chain 'V' and resid 465 through 494 removed outlier: 4.867A pdb=" N THR V 469 " --> pdb=" O ASP V 465 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ARG V 470 " --> pdb=" O ILE V 466 " (cutoff:3.500A) Proline residue: V 472 - end of helix removed outlier: 5.033A pdb=" N GLN V 478 " --> pdb=" O LEU V 474 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ARG V 479 " --> pdb=" O ALA V 475 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ILE V 480 " --> pdb=" O PHE V 476 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N SER V 481 " --> pdb=" O HIS V 477 " (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 39 through 58 removed outlier: 3.734A pdb=" N VAL W 43 " --> pdb=" O ARG W 39 " (cutoff:3.500A) Processing helix chain 'W' and resid 59 through 78 Processing helix chain 'W' and resid 79 through 93 removed outlier: 4.537A pdb=" N GLU W 85 " --> pdb=" O ASP W 81 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS W 92 " --> pdb=" O MET W 88 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG W 93 " --> pdb=" O LEU W 89 " (cutoff:3.500A) Processing helix chain 'W' and resid 97 through 113 removed outlier: 3.535A pdb=" N VAL W 101 " --> pdb=" O LEU W 97 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLU W 113 " --> pdb=" O CYS W 109 " (cutoff:3.500A) Processing helix chain 'W' and resid 117 through 133 removed outlier: 4.937A pdb=" N LYS W 121 " --> pdb=" O ASP W 117 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU W 133 " --> pdb=" O ARG W 129 " (cutoff:3.500A) Processing helix chain 'W' and resid 141 through 154 removed outlier: 3.622A pdb=" N LEU W 145 " --> pdb=" O GLU W 141 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA W 150 " --> pdb=" O THR W 146 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS W 153 " --> pdb=" O LEU W 149 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU W 154 " --> pdb=" O ALA W 150 " (cutoff:3.500A) Processing helix chain 'W' and resid 158 through 167 removed outlier: 3.777A pdb=" N ALA W 162 " --> pdb=" O ASP W 158 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLN W 167 " --> pdb=" O ALA W 163 " (cutoff:3.500A) Processing helix chain 'W' and resid 169 through 177 removed outlier: 5.008A pdb=" N THR W 173 " --> pdb=" O LEU W 169 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR W 174 " --> pdb=" O GLN W 170 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLY W 175 " --> pdb=" O VAL W 171 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER W 176 " --> pdb=" O GLU W 172 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET W 177 " --> pdb=" O THR W 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 169 through 177' Processing helix chain 'W' and resid 180 through 197 removed outlier: 4.267A pdb=" N GLU W 184 " --> pdb=" O LYS W 180 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU W 188 " --> pdb=" O GLU W 184 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLN W 189 " --> pdb=" O PHE W 185 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N MET W 190 " --> pdb=" O ILE W 186 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ARG W 191 " --> pdb=" O LEU W 187 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU W 192 " --> pdb=" O GLU W 188 " (cutoff:3.500A) Processing helix chain 'W' and resid 199 through 211 removed outlier: 4.138A pdb=" N ILE W 204 " --> pdb=" O ILE W 200 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N THR W 211 " --> pdb=" O LYS W 207 " (cutoff:3.500A) Processing helix chain 'W' and resid 222 through 238 removed outlier: 4.618A pdb=" N ASN W 228 " --> pdb=" O LEU W 224 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N LEU W 229 " --> pdb=" O LYS W 225 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N MET W 230 " --> pdb=" O TYR W 226 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE W 231 " --> pdb=" O TYR W 227 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLN W 232 " --> pdb=" O ASN W 228 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLU W 237 " --> pdb=" O LEU W 233 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLY W 238 " --> pdb=" O ASP W 234 " (cutoff:3.500A) Processing helix chain 'W' and resid 239 through 258 removed outlier: 5.456A pdb=" N ILE W 243 " --> pdb=" O SER W 239 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ASP W 252 " --> pdb=" O ARG W 248 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N THR W 253 " --> pdb=" O ALA W 249 " (cutoff:3.500A) Proline residue: W 254 - end of helix Processing helix chain 'W' and resid 259 through 278 removed outlier: 4.148A pdb=" N TYR W 273 " --> pdb=" O SER W 269 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL W 274 " --> pdb=" O VAL W 270 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ILE W 275 " --> pdb=" O VAL W 271 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LEU W 276 " --> pdb=" O LEU W 272 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA W 277 " --> pdb=" O TYR W 273 " (cutoff:3.500A) Proline residue: W 278 - end of helix Processing helix chain 'W' and resid 280 through 292 removed outlier: 4.956A pdb=" N GLY W 292 " --> pdb=" O HIS W 288 " (cutoff:3.500A) Processing helix chain 'W' and resid 295 through 300 removed outlier: 4.806A 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: 3.936A pdb=" N LEU W 308 " --> pdb=" O ASP W 304 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE W 309 " --> pdb=" O LEU W 305 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N THR W 310 " --> pdb=" O LEU W 306 " (cutoff:3.500A) Processing helix chain 'W' and resid 316 through 324 removed outlier: 4.150A pdb=" N GLU W 322 " --> pdb=" O SER W 318 " (cutoff:3.500A) Processing helix chain 'W' and resid 325 through 330 removed outlier: 4.273A pdb=" N ARG W 329 " --> pdb=" O GLY W 325 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS W 330 " --> pdb=" O MET W 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 325 through 330' Processing helix chain 'W' and resid 334 through 341 Processing helix chain 'W' and resid 344 through 370 removed outlier: 4.457A pdb=" N GLU W 348 " --> pdb=" O THR W 344 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS W 368 " --> pdb=" O ARG W 364 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N TYR W 369 " --> pdb=" O ILE W 365 " (cutoff:3.500A) Processing helix chain 'W' and resid 374 through 382 Processing helix chain 'W' and resid 385 through 400 removed outlier: 4.105A pdb=" N ASN W 399 " --> pdb=" O ASN W 395 " (cutoff:3.500A) Processing helix chain 'W' and resid 420 through 456 removed outlier: 3.504A pdb=" N LEU W 424 " --> pdb=" O ASP W 420 " (cutoff:3.500A) Processing helix chain 'X' and resid 44 through 61 removed outlier: 4.199A pdb=" N GLN X 48 " --> pdb=" O GLN X 44 " (cutoff:3.500A) Processing helix chain 'X' and resid 62 through 81 removed outlier: 4.654A pdb=" N LEU X 66 " --> pdb=" O GLN X 62 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ARG X 74 " --> pdb=" O LEU X 70 " (cutoff:3.500A) Proline residue: X 75 - end of helix removed outlier: 3.931A pdb=" N ILE X 80 " --> pdb=" O PHE X 76 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N SER X 81 " --> pdb=" O LEU X 77 " (cutoff:3.500A) Processing helix chain 'X' and resid 82 through 100 removed outlier: 4.027A pdb=" N MET X 99 " --> pdb=" O LEU X 95 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLU X 100 " --> pdb=" O PHE X 96 " (cutoff:3.500A) Processing helix chain 'X' and resid 102 through 121 removed outlier: 3.864A pdb=" N GLU X 106 " --> pdb=" O ALA X 102 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N VAL X 107 " --> pdb=" O THR X 103 " (cutoff:3.500A) removed outlier: 5.509A 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: 4.638A pdb=" N LEU X 147 " --> pdb=" O TYR X 143 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LYS X 159 " --> pdb=" O ARG X 155 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET X 160 " --> pdb=" O GLU X 156 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASP X 161 " --> pdb=" O LEU X 157 " (cutoff:3.500A) Processing helix chain 'X' and resid 162 through 181 removed outlier: 5.099A pdb=" N LEU X 166 " --> pdb=" O ASP X 162 " (cutoff:3.500A) Processing helix chain 'X' and resid 182 through 199 removed outlier: 5.327A pdb=" N ALA X 199 " --> pdb=" O THR X 195 " (cutoff:3.500A) Processing helix chain 'X' and resid 204 through 222 removed outlier: 5.513A pdb=" N ALA X 208 " --> pdb=" O PRO X 204 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU X 222 " --> pdb=" O HIS X 218 " (cutoff:3.500A) Processing helix chain 'X' and resid 224 through 240 removed outlier: 4.614A pdb=" N ALA X 228 " --> pdb=" O ASP X 224 " (cutoff:3.500A) Processing helix chain 'X' and resid 243 through 262 removed outlier: 3.933A pdb=" N ASN X 262 " --> pdb=" O LYS X 258 " (cutoff:3.500A) Processing helix chain 'X' and resid 265 through 273 removed outlier: 4.271A pdb=" N ALA X 269 " --> pdb=" O GLU X 265 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY X 273 " --> pdb=" O ALA X 269 " (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: 4.223A pdb=" N TYR X 309 " --> pdb=" O ALA X 305 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ARG X 310 " --> pdb=" O LEU X 306 " (cutoff:3.500A) Processing helix chain 'X' and resid 312 through 317 removed outlier: 5.225A pdb=" N ASP X 316 " --> pdb=" O GLU X 312 " (cutoff:3.500A) Proline residue: X 317 - end of helix No H-bonds generated for 'chain 'X' and resid 312 through 317' Processing helix chain 'X' and resid 318 through 340 removed outlier: 3.504A pdb=" N ILE X 339 " --> pdb=" O LEU X 335 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N GLU X 340 " --> pdb=" O ILE X 336 " (cutoff:3.500A) Processing helix chain 'X' and resid 346 through 355 removed outlier: 3.534A pdb=" N ILE X 350 " --> pdb=" O GLN X 346 " (cutoff:3.500A) Processing helix chain 'X' and resid 357 through 372 removed outlier: 4.516A pdb=" N VAL X 361 " --> pdb=" O SER X 357 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP X 371 " --> pdb=" O GLN X 367 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LYS X 372 " --> pdb=" O MET X 368 " (cutoff:3.500A) Processing helix chain 'X' and resid 394 through 408 removed outlier: 3.542A pdb=" N GLU X 398 " --> pdb=" O ASP X 394 " (cutoff:3.500A) Processing helix chain 'X' and resid 414 through 420 removed outlier: 4.941A pdb=" N LYS X 420 " --> pdb=" O ASN X 416 " (cutoff:3.500A) Processing helix chain 'Y' and resid 16 through 28 Processing helix chain 'Y' and resid 29 through 34 removed outlier: 4.040A pdb=" N GLY Y 33 " --> pdb=" O PRO Y 29 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ASP Y 34 " --> pdb=" O GLU Y 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 29 through 34' Processing helix chain 'Y' and resid 35 through 48 removed outlier: 3.879A pdb=" N MET Y 42 " --> pdb=" O ARG Y 38 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA Y 43 " --> pdb=" O ASP Y 39 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ARG Y 46 " --> pdb=" O MET Y 42 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ASP Y 47 " --> pdb=" O ALA Y 43 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASN Y 48 " --> pdb=" O ALA Y 44 " (cutoff:3.500A) Processing helix chain 'Y' and resid 50 through 60 removed outlier: 3.819A pdb=" N TYR Y 54 " --> pdb=" O MET Y 50 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N GLU Y 55 " --> pdb=" O ALA Y 51 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ALA Y 56 " --> pdb=" O PRO Y 52 " (cutoff:3.500A) Processing helix chain 'Y' and resid 65 through 92 removed outlier: 5.838A pdb=" N LEU Y 69 " --> pdb=" O ILE Y 65 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N MET Y 73 " --> pdb=" O LEU Y 69 " (cutoff:3.500A) Processing helix chain 'Y' and resid 98 through 114 removed outlier: 4.185A pdb=" N ARG Y 113 " --> pdb=" O GLU Y 109 " (cutoff:3.500A) Processing helix chain 'Y' and resid 116 through 131 removed outlier: 3.844A 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 175 through 191 removed outlier: 4.390A pdb=" N ARG Y 179 " --> pdb=" O ASP Y 175 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LYS Y 181 " --> pdb=" O ARG Y 177 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N VAL Y 182 " --> pdb=" O ASN Y 178 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN Y 184 " --> pdb=" O LEU Y 180 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N TYR Y 187 " --> pdb=" O TYR Y 183 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL Y 189 " --> pdb=" O GLY Y 185 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE Y 191 " --> pdb=" O TYR Y 187 " (cutoff:3.500A) Processing helix chain 'Y' and resid 194 through 202 removed outlier: 5.007A pdb=" N ALA Y 198 " --> pdb=" O PHE Y 194 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU Y 202 " --> pdb=" O ALA Y 198 " (cutoff:3.500A) Processing helix chain 'Y' and resid 215 through 231 removed outlier: 3.669A pdb=" N ILE Y 229 " --> pdb=" O TYR Y 225 " (cutoff:3.500A) Processing helix chain 'Y' and resid 235 through 240 removed outlier: 3.602A pdb=" N LYS Y 239 " --> pdb=" O ASP Y 235 " (cutoff:3.500A) Processing helix chain 'Y' and resid 243 through 254 removed outlier: 3.880A pdb=" N SER Y 252 " --> pdb=" O GLU Y 248 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU Y 253 " --> pdb=" O VAL Y 249 " (cutoff:3.500A) Proline residue: Y 254 - end of helix Processing helix chain 'Y' and resid 255 through 266 Processing helix chain 'Y' and resid 268 through 286 removed outlier: 3.926A pdb=" N GLN Y 273 " --> pdb=" O SER Y 269 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LYS Y 284 " --> pdb=" O GLN Y 280 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ASP Y 285 " --> pdb=" O GLU Y 281 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N TRP Y 286 " --> pdb=" O MET Y 282 " (cutoff:3.500A) Processing helix chain 'Y' and resid 295 through 310 removed outlier: 5.308A pdb=" N SER Y 310 " --> pdb=" O GLN Y 306 " (cutoff:3.500A) Processing helix chain 'Y' and resid 315 through 323 removed outlier: 3.594A pdb=" N MET Y 319 " --> pdb=" O THR Y 315 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU Y 321 " --> pdb=" O GLY Y 317 " (cutoff:3.500A) Processing helix chain 'Y' and resid 326 through 341 removed outlier: 3.641A pdb=" N GLY Y 341 " --> pdb=" O PHE Y 337 " (cutoff:3.500A) Processing helix chain 'Y' and resid 360 through 388 removed outlier: 4.820A pdb=" N ASN Y 388 " --> pdb=" O SER Y 384 " (cutoff:3.500A) Processing helix chain 'Z' and resid 12 through 30 removed outlier: 4.255A pdb=" N LEU Z 16 " --> pdb=" O HIS Z 12 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LEU Z 17 " --> pdb=" O PRO Z 13 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS Z 28 " --> pdb=" O ASN Z 24 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N VAL Z 29 " --> pdb=" O ARG Z 25 " (cutoff:3.500A) Processing helix chain 'Z' and resid 71 through 86 Processing helix chain 'Z' and resid 102 through 116 removed outlier: 4.621A pdb=" N ILE Z 106 " --> pdb=" O HIS Z 102 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ALA Z 107 " --> pdb=" O LYS Z 103 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ARG Z 114 " --> pdb=" O GLU Z 110 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N TYR Z 115 " --> pdb=" O LEU Z 111 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N CYS Z 116 " --> pdb=" O MET Z 112 " (cutoff:3.500A) Processing helix chain 'Z' and resid 167 through 177 removed outlier: 4.449A pdb=" N GLY Z 171 " --> pdb=" O ALA Z 167 " (cutoff:3.500A) Processing helix chain 'Z' and resid 185 through 218 removed outlier: 3.664A pdb=" N THR Z 217 " --> pdb=" O GLU Z 213 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLY Z 218 " --> pdb=" O LYS Z 214 " (cutoff:3.500A) Processing helix chain 'Z' and resid 226 through 237 removed outlier: 4.013A pdb=" N LEU Z 230 " --> pdb=" O ILE Z 226 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N GLN Z 231 " --> pdb=" O ILE Z 227 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL Z 233 " --> pdb=" O GLN Z 229 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N PHE Z 234 " --> pdb=" O LEU Z 230 " (cutoff:3.500A) Processing helix chain 'Z' and resid 243 through 249 removed outlier: 4.093A pdb=" N LYS Z 247 " --> pdb=" O GLN Z 243 " (cutoff:3.500A) Processing helix chain 'Z' and resid 252 through 290 removed outlier: 4.316A pdb=" N TYR Z 261 " --> pdb=" O MET Z 257 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N SER Z 264 " --> pdb=" O VAL Z 260 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ILE Z 266 " --> pdb=" O LEU Z 262 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG Z 267 " --> pdb=" O ALA Z 263 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY Z 290 " --> pdb=" O GLU Z 286 " (cutoff:3.500A) Processing helix chain 'Z' and resid 142 through 147 removed outlier: 6.781A pdb=" N HIS Z 145 " --> pdb=" O GLU Z 142 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ASP Z 146 " --> pdb=" O GLU Z 143 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASP Z 147 " --> pdb=" O VAL Z 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 142 through 147' Processing helix chain 'a' and resid 4 through 14 removed outlier: 4.177A pdb=" N ASN a 13 " --> pdb=" O GLN a 9 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N SER a 14 " --> pdb=" O GLN a 10 " (cutoff:3.500A) Processing helix chain 'a' and resid 19 through 30 removed outlier: 4.139A pdb=" N ARG a 24 " --> pdb=" O ALA a 20 " (cutoff:3.500A) Processing helix chain 'a' and resid 33 through 47 removed outlier: 4.602A pdb=" N LEU a 37 " --> pdb=" O LEU a 33 " (cutoff:3.500A) Processing helix chain 'a' and resid 53 through 68 removed outlier: 4.305A pdb=" N LEU a 59 " --> pdb=" O GLY a 55 " (cutoff:3.500A) Processing helix chain 'a' and resid 72 through 88 removed outlier: 4.550A pdb=" N HIS a 82 " --> pdb=" O GLU a 78 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL a 83 " --> pdb=" O ILE a 79 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR a 88 " --> pdb=" O VAL a 84 " (cutoff:3.500A) Processing helix chain 'a' and resid 90 through 105 removed outlier: 3.830A pdb=" N THR a 95 " --> pdb=" O ASN a 91 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL a 104 " --> pdb=" O THR a 100 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N LYS a 105 " --> pdb=" O ARG a 101 " (cutoff:3.500A) Processing helix chain 'a' and resid 108 through 126 removed outlier: 4.421A pdb=" N ILE a 112 " --> pdb=" O ASP a 108 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE a 125 " --> pdb=" O LEU a 121 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLY a 126 " --> pdb=" O LYS a 122 " (cutoff:3.500A) Processing helix chain 'a' and resid 130 through 142 removed outlier: 4.217A pdb=" N VAL a 138 " --> pdb=" O THR a 134 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU a 139 " --> pdb=" O ILE a 135 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU a 140 " --> pdb=" O GLU a 136 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N MET a 141 " --> pdb=" O ASP a 137 " (cutoff:3.500A) Processing helix chain 'a' and resid 149 through 164 removed outlier: 4.661A pdb=" N ARG a 154 " --> pdb=" O SER a 150 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLN a 164 " --> pdb=" O SER a 160 " (cutoff:3.500A) Processing helix chain 'a' and resid 169 through 184 removed outlier: 3.535A pdb=" N VAL a 183 " --> pdb=" O PHE a 179 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ASP a 184 " --> pdb=" O LEU a 180 " (cutoff:3.500A) Processing helix chain 'a' and resid 189 through 207 removed outlier: 3.645A pdb=" N GLN a 193 " --> pdb=" O PRO a 189 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N GLU a 195 " --> pdb=" O SER a 191 " (cutoff:3.500A) Processing helix chain 'a' and resid 214 through 219 removed outlier: 6.932A pdb=" N MET a 218 " --> pdb=" O GLY a 214 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N HIS a 219 " --> pdb=" O GLU a 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 214 through 219' Processing helix chain 'a' and resid 230 through 243 removed outlier: 4.302A pdb=" N ILE a 234 " --> pdb=" O ARG a 230 " (cutoff:3.500A) Processing helix chain 'a' and resid 246 through 258 removed outlier: 3.566A pdb=" N THR a 250 " --> pdb=" O GLU a 246 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TRP a 255 " --> pdb=" O LEU a 251 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLN a 258 " --> pdb=" O ALA a 254 " (cutoff:3.500A) Processing helix chain 'a' and resid 259 through 265 removed outlier: 6.334A pdb=" N ALA a 263 " --> pdb=" O PRO a 259 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N ASN a 264 " --> pdb=" O ASP a 260 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU a 265 " --> pdb=" O LEU a 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 259 through 265' Processing helix chain 'a' and resid 266 through 285 removed outlier: 4.138A pdb=" N LEU a 277 " --> pdb=" O GLN a 273 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N MET a 278 " --> pdb=" O LEU a 274 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLU a 279 " --> pdb=" O LEU a 275 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N MET a 280 " --> pdb=" O CYS a 276 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N THR a 281 " --> pdb=" O LEU a 277 " (cutoff:3.500A) Proline residue: a 285 - end of helix Processing helix chain 'a' and resid 292 through 301 Processing helix chain 'a' and resid 304 through 318 removed outlier: 4.535A pdb=" N GLU a 308 " --> pdb=" O VAL a 304 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LEU a 309 " --> pdb=" O ASN a 305 " (cutoff:3.500A) Processing helix chain 'a' and resid 344 through 376 removed outlier: 4.457A pdb=" N GLY a 348 " --> pdb=" O GLN a 344 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ASP a 359 " --> pdb=" O PHE a 355 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL a 360 " --> pdb=" O TRP a 356 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS a 361 " --> pdb=" O CYS a 357 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER a 362 " --> pdb=" O THR a 358 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET a 363 " --> pdb=" O ASP a 359 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ASP a 373 " --> pdb=" O HIS a 369 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ILE a 374 " --> pdb=" O GLN a 370 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N THR a 376 " --> pdb=" O HIS a 372 " (cutoff:3.500A) Processing helix chain 'a' and resid 220 through 227 removed outlier: 3.834A pdb=" N LEU a 225 " --> pdb=" O PRO a 220 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ARG a 226 " --> pdb=" O VAL a 221 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASN a 227 " --> pdb=" O LEU a 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 220 through 227' Processing helix chain 'b' and resid 24 through 45 removed outlier: 3.822A pdb=" N ASN b 44 " --> pdb=" O LYS b 40 " (cutoff:3.500A) Proline residue: b 45 - end of helix Processing helix chain 'b' and resid 67 through 76 removed outlier: 5.678A pdb=" N ILE b 71 " --> pdb=" O ASP b 67 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N HIS b 76 " --> pdb=" O LEU b 72 " (cutoff:3.500A) Processing helix chain 'b' and resid 85 through 100 removed outlier: 5.129A pdb=" N GLY b 89 " --> pdb=" O THR b 85 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE b 90 " --> pdb=" O PHE b 86 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ARG b 91 " --> pdb=" O CYS b 87 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N HIS b 99 " --> pdb=" O LEU b 95 " (cutoff:3.500A) removed outlier: 4.698A 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 186 removed outlier: 3.751A pdb=" N LEU b 183 " --> pdb=" O LEU b 179 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE b 184 " --> pdb=" O ALA b 180 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N SER b 186 " --> pdb=" O ALA b 182 " (cutoff:3.500A) Processing helix chain 'b' and resid 13 through 18 removed outlier: 3.670A pdb=" N ASN b 18 " --> pdb=" O TYR b 15 " (cutoff:3.500A) Processing helix chain 'c' and resid 34 through 49 removed outlier: 3.694A pdb=" N GLY c 48 " --> pdb=" O HIS c 44 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VAL c 49 " --> pdb=" O GLY c 45 " (cutoff:3.500A) Processing helix chain 'c' and resid 88 through 103 removed outlier: 3.873A pdb=" N GLN c 101 " --> pdb=" O ASP c 97 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR c 102 " --> pdb=" O MET c 98 " (cutoff:3.500A) removed outlier: 4.694A 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: 3.523A pdb=" N SER c 150 " --> pdb=" O ASP c 146 " (cutoff:3.500A) removed outlier: 4.889A 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 164 through 171 removed outlier: 4.151A pdb=" N MET c 168 " --> pdb=" O ASN c 164 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL c 169 " --> pdb=" O ALA c 165 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLY c 171 " --> pdb=" O MET c 167 " (cutoff:3.500A) Processing helix chain 'c' and resid 179 through 185 removed outlier: 4.566A pdb=" N HIS c 183 " --> pdb=" O SER c 179 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ASN c 185 " --> pdb=" O LEU c 181 " (cutoff:3.500A) Processing helix chain 'c' and resid 188 through 195 removed outlier: 3.559A pdb=" N LEU c 192 " --> pdb=" O SER c 188 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N HIS c 194 " --> pdb=" O GLN c 190 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLY c 195 " --> pdb=" O ALA c 191 " (cutoff:3.500A) Processing helix chain 'c' and resid 211 through 230 removed outlier: 5.969A pdb=" N LYS c 215 " --> pdb=" O GLU c 211 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N MET c 216 " --> pdb=" O LEU c 212 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS c 222 " --> pdb=" O LEU c 218 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS c 223 " --> pdb=" O ASN c 219 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N SER c 224 " --> pdb=" O LEU c 220 " (cutoff:3.500A) removed outlier: 10.138A pdb=" N TRP c 225 " --> pdb=" O HIS c 221 " (cutoff:3.500A) removed outlier: 9.868A pdb=" N MET c 226 " --> pdb=" O LYS c 222 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLU c 227 " --> pdb=" O LYS c 223 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLY c 228 " --> pdb=" O SER c 224 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU c 229 " --> pdb=" O TRP c 225 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR c 230 " --> pdb=" O MET c 226 " (cutoff:3.500A) Processing helix chain 'c' and resid 236 through 262 removed outlier: 3.966A pdb=" N GLU c 262 " --> pdb=" O ALA c 258 " (cutoff:3.500A) Processing helix chain 'c' and resid 266 through 275 removed outlier: 3.934A pdb=" N LEU c 270 " --> pdb=" O THR c 266 " (cutoff:3.500A) Processing helix chain 'c' and resid 284 through 310 removed outlier: 4.122A pdb=" N VAL c 288 " --> pdb=" O LEU c 284 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU c 291 " --> pdb=" O HIS c 287 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N MET c 292 " --> pdb=" O VAL c 288 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N THR c 293 " --> pdb=" O ASP c 289 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N SER c 294 " --> pdb=" O VAL c 290 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ASN c 295 " --> pdb=" O LEU c 291 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE c 296 " --> pdb=" O MET c 292 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N LYS c 310 " --> pdb=" O THR c 306 " (cutoff:3.500A) Processing helix chain 'd' and resid 15 through 34 removed outlier: 5.492A pdb=" N CYS d 19 " --> pdb=" O ASN d 15 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLY d 20 " --> pdb=" O LEU d 16 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU d 30 " --> pdb=" O LEU d 26 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU d 31 " --> pdb=" O LYS d 27 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N LEU d 33 " --> pdb=" O VAL d 29 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ASN d 34 " --> pdb=" O LEU d 30 " (cutoff:3.500A) Processing helix chain 'd' and resid 41 through 66 Processing helix chain 'd' and resid 67 through 84 Processing helix chain 'd' and resid 94 through 110 Processing helix chain 'd' and resid 111 through 122 removed outlier: 4.453A pdb=" N ARG d 121 " --> pdb=" O THR d 117 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LEU d 122 " --> pdb=" O GLU d 118 " (cutoff:3.500A) Processing helix chain 'd' and resid 130 through 146 Proline residue: d 136 - end of helix removed outlier: 3.933A pdb=" N GLU d 145 " --> pdb=" O GLN d 141 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLY d 146 " --> pdb=" O TYR d 142 " (cutoff:3.500A) Processing helix chain 'd' and resid 147 through 158 removed outlier: 4.970A pdb=" N VAL d 151 " --> pdb=" O SER d 147 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY d 156 " --> pdb=" O PHE d 152 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ASN d 157 " --> pdb=" O LEU d 153 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ILE d 158 " --> pdb=" O ALA d 154 " (cutoff:3.500A) Processing helix chain 'd' and resid 163 through 184 removed outlier: 4.697A pdb=" N ILE d 169 " --> pdb=" O PHE d 165 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LYS d 184 " --> pdb=" O GLY d 180 " (cutoff:3.500A) Processing helix chain 'd' and resid 190 through 196 removed outlier: 3.981A pdb=" N ALA d 194 " --> pdb=" O LEU d 190 " (cutoff:3.500A) Processing helix chain 'd' and resid 205 through 212 Processing helix chain 'd' and resid 238 through 255 removed outlier: 4.569A pdb=" N MET d 255 " --> pdb=" O ARG d 251 " (cutoff:3.500A) Processing helix chain 'f' and resid 10 through 23 removed outlier: 4.611A pdb=" N GLN f 14 " --> pdb=" O PRO f 10 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N SER f 16 " --> pdb=" O GLN f 12 " (cutoff:3.500A) Proline residue: f 17 - end of helix Proline residue: f 21 - end of helix Processing helix chain 'f' and resid 27 through 46 removed outlier: 4.242A pdb=" N GLU f 32 " --> pdb=" O PRO f 28 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ARG f 33 " --> pdb=" O SER f 29 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS f 39 " --> pdb=" O ASP f 35 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP f 40 " --> pdb=" O ALA f 36 " (cutoff:3.500A) Processing helix chain 'f' and resid 54 through 72 removed outlier: 4.702A pdb=" N MET f 58 " --> pdb=" O ASP f 54 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU f 59 " --> pdb=" O GLU f 55 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL f 60 " --> pdb=" O LEU f 56 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU f 61 " --> pdb=" O GLU f 57 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N LEU f 63 " --> pdb=" O LEU f 59 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N GLY f 64 " --> pdb=" O VAL f 60 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LYS f 66 " --> pdb=" O ARG f 62 " (cutoff:3.500A) Processing helix chain 'f' and resid 79 through 94 removed outlier: 3.907A pdb=" N ARG f 83 " --> pdb=" O ARG f 79 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N SER f 84 " --> pdb=" O ARG f 80 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER f 85 " --> pdb=" O GLN f 81 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER f 88 " --> pdb=" O SER f 84 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N MET f 89 " --> pdb=" O SER f 85 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR f 90 " --> pdb=" O THR f 86 " (cutoff:3.500A) Proline residue: f 93 - end of helix Processing helix chain 'f' and resid 99 through 104 removed outlier: 6.736A pdb=" N TYR f 103 " --> pdb=" O LEU f 99 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLY f 104 " --> pdb=" O ARG f 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 99 through 104' Processing helix chain 'f' and resid 117 through 123 removed outlier: 4.571A pdb=" N PHE f 121 " --> pdb=" O GLU f 117 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA f 122 " --> pdb=" O ASN f 118 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA f 123 " --> pdb=" O LYS f 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 117 through 123' Processing helix chain 'f' and resid 130 through 146 removed outlier: 3.682A pdb=" N GLU f 138 " --> pdb=" O SER f 134 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR f 142 " --> pdb=" O GLU f 138 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG f 143 " --> pdb=" O CYS f 139 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL f 145 " --> pdb=" O LYS f 141 " (cutoff:3.500A) Processing helix chain 'f' and resid 153 through 175 removed outlier: 4.008A pdb=" N GLU f 157 " --> pdb=" O SER f 153 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N GLU f 169 " --> pdb=" O GLU f 165 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N GLN f 171 " --> pdb=" O ALA f 167 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N GLU f 172 " --> pdb=" O LYS f 168 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ASP f 174 " --> pdb=" O TRP f 170 " (cutoff:3.500A) Processing helix chain 'f' and resid 176 through 191 removed outlier: 3.954A pdb=" N GLN f 180 " --> pdb=" O ALA f 176 " (cutoff:3.500A) Proline residue: f 183 - end of helix removed outlier: 3.977A pdb=" N VAL f 188 " --> pdb=" O LEU f 184 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LYS f 189 " --> pdb=" O LEU f 185 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N GLU f 190 " --> pdb=" O THR f 186 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE f 191 " --> pdb=" O LEU f 187 " (cutoff:3.500A) Processing helix chain 'f' and resid 193 through 206 removed outlier: 4.024A pdb=" N ALA f 197 " --> pdb=" O PRO f 193 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA f 200 " --> pdb=" O MET f 196 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLU f 201 " --> pdb=" O ALA f 197 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA f 204 " --> pdb=" O ALA f 200 " (cutoff:3.500A) Processing helix chain 'f' and resid 209 through 223 removed outlier: 4.215A pdb=" N GLN f 213 " --> pdb=" O MET f 209 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N MET f 216 " --> pdb=" O GLU f 212 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N LEU f 217 " --> pdb=" O GLN f 213 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLU f 218 " --> pdb=" O VAL f 214 " (cutoff:3.500A) Processing helix chain 'f' and resid 230 through 248 removed outlier: 4.037A pdb=" N CYS f 236 " --> pdb=" O TYR f 232 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ASN f 238 " --> pdb=" O THR f 234 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL f 240 " --> pdb=" O CYS f 236 " (cutoff:3.500A) Proline residue: f 241 - end of helix removed outlier: 4.560A pdb=" N GLU f 244 " --> pdb=" O VAL f 240 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ALA f 247 " --> pdb=" O PRO f 243 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU f 248 " --> pdb=" O GLU f 244 " (cutoff:3.500A) Processing helix chain 'f' and resid 253 through 264 removed outlier: 4.039A pdb=" N ARG f 257 " --> pdb=" O LEU f 253 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS f 258 " --> pdb=" O GLY f 254 " (cutoff:3.500A) removed outlier: 4.525A 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 278 through 285 removed outlier: 7.071A pdb=" N PHE f 282 " --> pdb=" O VAL f 278 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N THR f 283 " --> pdb=" O GLU f 279 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N SER f 284 " --> pdb=" O ASP f 280 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N CYS f 285 " --> pdb=" O ILE f 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 278 through 285' Processing helix chain 'f' and resid 286 through 293 removed outlier: 4.130A pdb=" N GLN f 291 " --> pdb=" O ASP f 287 " (cutoff:3.500A) Processing helix chain 'f' and resid 299 through 307 removed outlier: 4.600A pdb=" N VAL f 303 " --> pdb=" O GLY f 299 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N PHE f 304 " --> pdb=" O ARG f 300 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N GLU f 306 " --> pdb=" O GLY f 302 " (cutoff:3.500A) Processing helix chain 'f' and resid 314 through 321 removed outlier: 4.964A pdb=" N THR f 318 " --> pdb=" O TYR f 314 " (cutoff:3.500A) Processing helix chain 'f' and resid 323 through 336 Processing helix chain 'f' and resid 347 through 354 removed outlier: 3.832A pdb=" N GLU f 354 " --> pdb=" O LYS f 350 " (cutoff:3.500A) Processing helix chain 'f' and resid 367 through 382 removed outlier: 4.197A pdb=" N ASN f 371 " --> pdb=" O SER f 367 " (cutoff:3.500A) Processing helix chain 'f' and resid 395 through 402 removed outlier: 4.762A pdb=" N ASN f 402 " --> pdb=" O TRP f 398 " (cutoff:3.500A) Processing helix chain 'f' and resid 403 through 419 removed outlier: 4.293A pdb=" N LEU f 408 " --> pdb=" O ASP f 404 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU f 418 " --> pdb=" O LEU f 414 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU f 419 " --> pdb=" O GLY f 415 " (cutoff:3.500A) Processing helix chain 'f' and resid 422 through 435 removed outlier: 3.539A pdb=" N LEU f 426 " --> pdb=" O VAL f 422 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N THR f 427 " --> pdb=" O ASP f 423 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLN f 428 " --> pdb=" O GLY f 424 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE f 429 " --> pdb=" O GLY f 425 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LYS f 431 " --> pdb=" O THR f 427 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N TYR f 432 " --> pdb=" O GLN f 428 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N SER f 435 " --> pdb=" O LYS f 431 " (cutoff:3.500A) Processing helix chain 'f' and resid 437 through 453 removed outlier: 4.384A pdb=" N ASN f 452 " --> pdb=" O CYS f 448 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N SER f 453 " --> pdb=" O GLY f 449 " (cutoff:3.500A) Processing helix chain 'f' and resid 460 through 471 removed outlier: 4.528A pdb=" N ALA f 464 " --> pdb=" O ASP f 460 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU f 465 " --> pdb=" O PRO f 461 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N SER f 467 " --> pdb=" O LEU f 463 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ASP f 468 " --> pdb=" O ALA f 464 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N TYR f 469 " --> pdb=" O LEU f 465 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL f 470 " --> pdb=" O LEU f 466 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N LEU f 471 " --> pdb=" O SER f 467 " (cutoff:3.500A) Processing helix chain 'f' and resid 474 through 490 removed outlier: 4.560A pdb=" N ARG f 478 " --> pdb=" O SER f 474 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY f 484 " --> pdb=" O GLY f 480 " (cutoff:3.500A) Processing helix chain 'f' and resid 494 through 507 removed outlier: 3.680A 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: 3.739A pdb=" N ALA f 526 " --> pdb=" O CYS f 522 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL f 527 " --> pdb=" O GLY f 523 " (cutoff:3.500A) Processing helix chain 'f' and resid 530 through 542 removed outlier: 3.916A pdb=" N VAL f 534 " --> pdb=" O CYS f 530 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR f 535 " --> pdb=" O ASN f 531 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER f 536 " --> pdb=" O GLY f 532 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU f 539 " --> pdb=" O THR f 535 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN f 540 " --> pdb=" O SER f 536 " (cutoff:3.500A) Processing helix chain 'f' and resid 545 through 552 removed outlier: 3.860A pdb=" N GLU f 549 " --> pdb=" O LYS f 545 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LEU f 550 " --> pdb=" O SER f 546 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LYS f 551 " --> pdb=" O GLU f 547 " (cutoff:3.500A) Processing helix chain 'f' and resid 555 through 567 Proline residue: f 559 - end of helix removed outlier: 3.692A pdb=" N LEU f 562 " --> pdb=" O LEU f 558 " (cutoff:3.500A) Processing helix chain 'f' and resid 570 through 582 removed outlier: 3.565A pdb=" N GLU f 574 " --> pdb=" O GLY f 570 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE f 576 " --> pdb=" O ALA f 572 " (cutoff:3.500A) Processing helix chain 'f' and resid 590 through 600 removed outlier: 3.680A pdb=" N LEU f 594 " --> pdb=" O PHE f 590 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N TYR f 600 " --> pdb=" O ASP f 596 " (cutoff:3.500A) Processing helix chain 'f' and resid 616 through 621 removed outlier: 5.529A pdb=" N PHE f 620 " --> pdb=" O CYS f 616 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ASP f 621 " --> pdb=" O SER f 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 616 through 621' Processing helix chain 'f' and resid 627 through 635 removed outlier: 5.838A pdb=" N LYS f 631 " --> pdb=" O GLU f 627 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LYS f 632 " --> pdb=" O ASP f 628 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLU f 633 " --> pdb=" O LYS f 629 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS f 634 " --> pdb=" O ASP f 630 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LYS f 635 " --> pdb=" O LYS f 631 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 627 through 635' Processing helix chain 'f' and resid 642 through 647 removed outlier: 7.166A pdb=" N MET f 646 " --> pdb=" O ALA f 642 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY f 647 " --> pdb=" O PRO f 643 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 642 through 647' Processing helix chain 'f' and resid 648 through 658 removed outlier: 4.318A pdb=" N ALA f 653 " --> pdb=" O HIS f 649 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY f 656 " --> pdb=" O VAL f 652 " (cutoff:3.500A) Processing helix chain 'f' and resid 671 through 680 removed outlier: 4.832A pdb=" N PHE f 675 " --> pdb=" O ALA f 671 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU f 679 " --> pdb=" O PHE f 675 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ARG f 680 " --> pdb=" O GLY f 676 " (cutoff:3.500A) Processing helix chain 'f' and resid 686 through 698 removed outlier: 5.368A pdb=" N VAL f 690 " --> pdb=" O LEU f 686 " (cutoff:3.500A) Proline residue: f 691 - end of helix removed outlier: 3.661A pdb=" N LEU f 694 " --> pdb=" O VAL f 690 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N LEU f 696 " --> pdb=" O LEU f 692 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ILE f 697 " --> pdb=" O ALA f 693 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N SER f 698 " --> pdb=" O LEU f 694 " (cutoff:3.500A) Processing helix chain 'f' and resid 701 through 717 removed outlier: 3.711A pdb=" N ASN f 705 " --> pdb=" O ASN f 701 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP f 716 " --> pdb=" O LYS f 712 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ALA f 717 " --> pdb=" O PHE f 713 " (cutoff:3.500A) Processing helix chain 'f' and resid 725 through 734 removed outlier: 4.854A pdb=" N MET f 729 " --> pdb=" O SER f 725 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLY f 730 " --> pdb=" O ILE f 726 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N GLY f 733 " --> pdb=" O MET f 729 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N SER f 734 " --> pdb=" O GLY f 730 " (cutoff:3.500A) Processing helix chain 'f' and resid 742 through 748 removed outlier: 4.154A pdb=" N ARG f 746 " --> pdb=" O ALA f 742 " (cutoff:3.500A) Processing helix chain 'f' and resid 771 through 779 removed outlier: 4.330A pdb=" N THR f 775 " --> pdb=" O LEU f 771 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N LEU f 776 " --> pdb=" O GLY f 772 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N THR f 777 " --> pdb=" O LYS f 773 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU f 778 " --> pdb=" O GLY f 774 " (cutoff:3.500A) Processing helix chain 'f' and resid 781 through 787 removed outlier: 4.528A pdb=" N ARG f 785 " --> pdb=" O TYR f 781 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LEU f 787 " --> pdb=" O SER f 783 " (cutoff:3.500A) Processing helix chain 'f' and resid 797 through 803 removed outlier: 4.579A pdb=" N VAL f 801 " --> pdb=" O LEU f 797 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE f 803 " --> pdb=" O VAL f 799 " (cutoff:3.500A) Processing helix chain 'f' and resid 266 through 271 removed outlier: 3.841A pdb=" N MET f 271 " --> pdb=" O LEU f 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 266 through 271' Processing helix chain 'f' and resid 664 through 669 Processing helix chain 'f' and resid 788 through 793 removed outlier: 6.191A pdb=" N VAL f 793 " --> pdb=" O MET f 788 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 788 through 793' Processing helix chain 'e' and resid 51 through 64 removed outlier: 5.098A pdb=" N GLN e 55 " --> pdb=" O ASP e 51 " (cutoff:3.500A) Processing helix chain 'e' and resid 42 through 47 removed outlier: 3.535A pdb=" N ASP e 45 " --> pdb=" O ASN e 42 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP e 46 " --> pdb=" O TRP e 43 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN e 47 " --> pdb=" O ASP e 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 42 through 47' Processing sheet with id= 1, first strand: chain 'A' and resid 120 through 124 removed outlier: 7.012A pdb=" N ILE A 112 " --> pdb=" O ILE A 102 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N MET A 138 " --> pdb=" O ILE A 101 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 236 through 240 removed outlier: 3.570A pdb=" N CYS A 236 " --> pdb=" O ALA A 269 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS A 270 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS A 316 " --> pdb=" O CYS A 270 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA A 320 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU A 214 " --> pdb=" O MET A 319 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY A 216 " --> pdb=" O THR A 321 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ARG A 339 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 213 " --> pdb=" O ARG A 339 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE A 215 " --> pdb=" O ILE A 341 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'B' and resid 129 through 134 removed outlier: 4.418A pdb=" N SER B 129 " --> pdb=" O THR B 125 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR B 125 " --> pdb=" O SER B 129 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE B 122 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N CYS B 148 " --> pdb=" O LEU B 112 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'B' and resid 246 through 250 removed outlier: 4.166A pdb=" N THR B 246 " --> pdb=" O PRO B 279 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER B 280 " --> pdb=" O ASP B 324 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N LYS B 220 " --> pdb=" O VAL B 325 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY B 226 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ARG B 349 " --> pdb=" O GLY B 221 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE B 223 " --> pdb=" O ARG B 349 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'C' and resid 71 through 77 removed outlier: 3.918A pdb=" N CYS C 112 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ARG C 113 " --> pdb=" O LEU C 127 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'C' and resid 84 through 88 Processing sheet with id= 7, first strand: chain 'C' and resid 210 through 214 removed outlier: 3.725A pdb=" N THR C 210 " --> pdb=" O PRO C 243 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS C 290 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET C 248 " --> pdb=" O ILE C 292 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ALA C 294 " --> pdb=" O MET C 248 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLY C 190 " --> pdb=" O THR C 295 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG C 313 " --> pdb=" O GLY C 185 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'D' and resid 108 through 113 removed outlier: 4.020A pdb=" N SER D 109 " --> pdb=" O SER D 105 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ILE D 102 " --> pdb=" O LEU D 93 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR D 106 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N ILE D 89 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'D' and resid 226 through 231 removed outlier: 3.661A pdb=" N ALA D 226 " --> pdb=" O PRO D 259 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY D 206 " --> pdb=" O THR D 311 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG D 329 " --> pdb=" O GLY D 201 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'E' and resid 61 through 64 removed outlier: 6.407A pdb=" N LYS E 68 " --> pdb=" O LEU E 64 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'E' and resid 97 through 100 removed outlier: 4.103A pdb=" N ARG E 97 " --> pdb=" O LEU E 111 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ARG E 109 " --> pdb=" O ALA E 99 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'E' and resid 194 through 198 removed outlier: 5.480A pdb=" N ASN E 194 " --> pdb=" O PRO E 227 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N CYS E 228 " --> pdb=" O ARG E 272 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA E 278 " --> pdb=" O MET E 232 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY E 174 " --> pdb=" O THR E 279 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG E 297 " --> pdb=" O GLY E 169 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'F' and resid 95 through 99 removed outlier: 3.646A pdb=" N GLU F 95 " --> pdb=" O VAL F 123 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLY F 119 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL F 123 " --> pdb=" O ILE F 94 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ASP F 149 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LEU F 150 " --> pdb=" O LEU F 164 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'F' and resid 246 through 251 removed outlier: 4.099A pdb=" N GLY F 227 " --> pdb=" O THR F 332 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'F' and resid 121 through 126 removed outlier: 3.517A pdb=" N ALA F 122 " --> pdb=" O LEU F 134 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLN F 130 " --> pdb=" O THR F 126 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'G' and resid 68 through 72 removed outlier: 6.477A pdb=" N HIS G 68 " --> pdb=" O MET G 80 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE G 76 " --> pdb=" O ILE G 72 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY G 77 " --> pdb=" O ILE G 141 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE G 139 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR G 81 " --> pdb=" O CYS G 137 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N MET G 138 " --> pdb=" O CYS G 154 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'G' and resid 165 through 169 removed outlier: 5.778A pdb=" N THR G 38 " --> pdb=" O GLN G 53 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN G 53 " --> pdb=" O THR G 38 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N GLU G 214 " --> pdb=" O LYS G 54 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N VAL G 217 " --> pdb=" O LEU G 230 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'H' and resid 65 through 68 removed outlier: 6.612A pdb=" N ILE H 72 " --> pdb=" O ILE H 68 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N HIS H 71 " --> pdb=" O TRP H 139 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N CYS H 137 " --> pdb=" O GLY H 73 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER H 133 " --> pdb=" O SER H 77 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N LEU H 146 " --> pdb=" O TRP H 158 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA H 154 " --> pdb=" O ASP H 150 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'H' and resid 160 through 164 removed outlier: 5.581A pdb=" N ASN H 207 " --> pdb=" O LYS H 50 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N VAL H 210 " --> pdb=" O LEU H 221 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'h' and resid 65 through 68 removed outlier: 6.483A pdb=" N ILE h 72 " --> pdb=" O ILE h 68 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER h 133 " --> pdb=" O SER h 77 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N LEU h 146 " --> pdb=" O TRP h 158 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'h' and resid 160 through 164 removed outlier: 3.636A pdb=" N GLU h 49 " --> pdb=" O PRO h 34 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ASN h 207 " --> pdb=" O LYS h 50 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N VAL h 210 " --> pdb=" O LEU h 221 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'I' and resid 65 through 68 removed outlier: 6.591A pdb=" N MET I 72 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEU I 147 " --> pdb=" O TRP I 159 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'I' and resid 161 through 165 removed outlier: 4.742A pdb=" N THR I 33 " --> pdb=" O GLU I 48 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N ILE I 213 " --> pdb=" O LEU I 228 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'J' and resid 62 through 65 removed outlier: 6.714A pdb=" N VAL J 69 " --> pdb=" O LEU J 65 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU J 144 " --> pdb=" O TRP J 156 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'J' and resid 158 through 162 removed outlier: 5.078A pdb=" N THR J 31 " --> pdb=" O GLU J 46 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ASN J 205 " --> pdb=" O LYS J 47 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'j' and resid 68 through 75 removed outlier: 6.265A pdb=" N ASN j 68 " --> pdb=" O PHE j 136 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU j 144 " --> pdb=" O TRP j 156 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'j' and resid 158 through 162 removed outlier: 5.345A pdb=" N THR j 31 " --> pdb=" O GLU j 46 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LEU j 208 " --> pdb=" O LEU j 220 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'K' and resid 66 through 70 removed outlier: 6.332A pdb=" N LYS K 66 " --> pdb=" O MET K 78 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE K 74 " --> pdb=" O ILE K 70 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'K' and resid 167 through 171 removed outlier: 4.991A pdb=" N THR K 36 " --> pdb=" O GLU K 51 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N LEU K 217 " --> pdb=" O PHE K 229 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'L' and resid 63 through 66 removed outlier: 6.497A pdb=" N ILE L 70 " --> pdb=" O VAL L 66 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N HIS L 69 " --> pdb=" O TYR L 137 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE L 144 " --> pdb=" O CYS L 156 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASN L 152 " --> pdb=" O CYS L 148 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'L' and resid 158 through 162 removed outlier: 3.753A pdb=" N ILE L 212 " --> pdb=" O TYR L 224 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'M' and resid 66 through 69 removed outlier: 3.515A pdb=" N VAL M 69 " --> pdb=" O VAL M 73 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL M 73 " --> pdb=" O VAL M 69 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE M 135 " --> pdb=" O ILE M 151 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER M 141 " --> pdb=" O GLY M 145 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU M 148 " --> pdb=" O TYR M 160 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'M' and resid 162 through 166 removed outlier: 4.698A pdb=" N THR M 35 " --> pdb=" O GLU M 50 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'N' and resid 34 through 37 removed outlier: 6.479A pdb=" N ILE N 41 " --> pdb=" O ILE N 37 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ARG N 40 " --> pdb=" O TRP N 103 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VAL N 111 " --> pdb=" O GLN N 123 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'N' and resid 125 through 129 removed outlier: 6.416A pdb=" N THR N 2 " --> pdb=" O ASP N 17 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N VAL N 173 " --> pdb=" O SER N 18 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY N 183 " --> pdb=" O ALA N 180 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'O' and resid 34 through 37 removed outlier: 6.315A pdb=" N ILE O 41 " --> pdb=" O ILE O 37 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ASN O 40 " --> pdb=" O VAL O 103 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'O' and resid 124 through 128 removed outlier: 6.190A pdb=" N THR O 2 " --> pdb=" O ASP O 17 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N THR O 18 " --> pdb=" O ASN O 172 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N ASN O 172 " --> pdb=" O THR O 18 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS O 182 " --> pdb=" O SER O 179 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'o' and resid 34 through 37 removed outlier: 6.460A pdb=" N ILE o 41 " --> pdb=" O ILE o 37 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N ASN o 40 " --> pdb=" O VAL o 103 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'o' and resid 124 through 128 removed outlier: 6.121A pdb=" N THR o 2 " --> pdb=" O ASP o 17 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR o 18 " --> pdb=" O ASN o 172 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ASN o 172 " --> pdb=" O THR o 18 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS o 182 " --> pdb=" O SER o 179 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'P' and resid 42 through 45 removed outlier: 6.047A pdb=" N LEU P 49 " --> pdb=" O MET P 45 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ARG P 48 " --> pdb=" O LEU P 112 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA P 54 " --> pdb=" O GLU P 106 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'P' and resid 136 through 140 removed outlier: 6.074A pdb=" N ALA P 10 " --> pdb=" O ASP P 25 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLY P 184 " --> pdb=" O ARG P 26 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N VAL P 185 " --> pdb=" O LEU P 200 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'p' and resid 42 through 45 removed outlier: 5.304A pdb=" N LEU p 49 " --> pdb=" O MET p 45 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ARG p 48 " --> pdb=" O LEU p 112 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ALA p 54 " --> pdb=" O GLU p 106 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'p' and resid 136 through 140 removed outlier: 6.124A pdb=" N ALA p 10 " --> pdb=" O ASP p 25 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N GLY p 184 " --> pdb=" O ARG p 26 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N VAL p 185 " --> pdb=" O LEU p 200 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'Q' and resid 35 through 38 removed outlier: 6.542A pdb=" N ILE Q 42 " --> pdb=" O MET Q 38 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N LYS Q 41 " --> pdb=" O TYR Q 107 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'Q' and resid 129 through 133 removed outlier: 3.966A pdb=" N LEU Q 4 " --> pdb=" O HIS Q 132 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TYR Q 3 " --> pdb=" O ASP Q 18 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP Q 18 " --> pdb=" O TYR Q 3 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N VAL Q 180 " --> pdb=" O LEU Q 191 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'q' and resid 35 through 38 removed outlier: 6.342A pdb=" N ILE q 42 " --> pdb=" O MET q 38 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LYS q 41 " --> pdb=" O TYR q 107 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA q 105 " --> pdb=" O LEU q 43 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'q' and resid 129 through 133 removed outlier: 3.540A pdb=" N LEU q 4 " --> pdb=" O HIS q 132 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TYR q 3 " --> pdb=" O ASP q 18 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL q 180 " --> pdb=" O LEU q 191 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'R' and resid 34 through 37 removed outlier: 3.757A pdb=" N ILE R 37 " --> pdb=" O LEU R 41 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LEU R 41 " --> pdb=" O ILE R 37 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'R' and resid 99 through 104 Processing sheet with id= 50, first strand: chain 'R' and resid 125 through 129 removed outlier: 6.351A pdb=" N THR R 2 " --> pdb=" O ASP R 17 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ALA R 173 " --> pdb=" O SER R 18 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N LEU R 176 " --> pdb=" O VAL R 187 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY R 183 " --> pdb=" O ARG R 180 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'r' and resid 34 through 37 removed outlier: 3.537A pdb=" N ILE r 37 " --> pdb=" O LEU r 41 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU r 41 " --> pdb=" O ILE r 37 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'r' and resid 99 through 104 Processing sheet with id= 53, first strand: chain 'r' and resid 125 through 129 removed outlier: 6.515A pdb=" N THR r 2 " --> pdb=" O ASP r 17 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL r 12 " --> pdb=" O VAL r 179 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ALA r 173 " --> pdb=" O SER r 18 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N LEU r 176 " --> pdb=" O VAL r 187 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY r 183 " --> pdb=" O ARG r 180 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'S' and resid 43 through 46 removed outlier: 6.694A pdb=" N THR S 50 " --> pdb=" O LEU S 46 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N LYS S 49 " --> pdb=" O LEU S 113 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'S' and resid 135 through 139 removed outlier: 6.007A pdb=" N THR S 11 " --> pdb=" O ASP S 26 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP S 26 " --> pdb=" O THR S 11 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N THR S 27 " --> pdb=" O ALA S 192 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ALA S 192 " --> pdb=" O THR S 27 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 's' and resid 43 through 46 removed outlier: 6.635A pdb=" N THR s 50 " --> pdb=" O LEU s 46 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LYS s 49 " --> pdb=" O LEU s 113 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 's' and resid 135 through 139 removed outlier: 5.602A pdb=" N THR s 11 " --> pdb=" O ASP s 26 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N THR s 27 " --> pdb=" O ALA s 192 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ALA s 192 " --> pdb=" O THR s 27 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'T' and resid 42 through 45 removed outlier: 6.678A pdb=" N THR T 49 " --> pdb=" O VAL T 45 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N SER T 48 " --> pdb=" O TYR T 115 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'T' and resid 136 through 139 removed outlier: 4.407A pdb=" N VAL T 11 " --> pdb=" O THR T 139 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL T 6 " --> pdb=" O SER T 29 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N SER T 29 " --> pdb=" O VAL T 6 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLY T 8 " --> pdb=" O LEU T 27 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N LEU T 27 " --> pdb=" O GLY T 8 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N SER T 10 " --> pdb=" O ASP T 25 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ASP T 25 " --> pdb=" O SER T 10 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL T 20 " --> pdb=" O VAL T 192 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ARG T 186 " --> pdb=" O MET T 26 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 't' and resid 42 through 45 removed outlier: 6.750A pdb=" N THR t 49 " --> pdb=" O VAL t 45 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N SER t 48 " --> pdb=" O TYR t 115 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 't' and resid 136 through 139 removed outlier: 4.361A pdb=" N VAL t 11 " --> pdb=" O THR t 139 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL t 6 " --> pdb=" O SER t 29 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N SER t 29 " --> pdb=" O VAL t 6 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N GLY t 8 " --> pdb=" O LEU t 27 " (cutoff:3.500A) removed outlier: 8.714A pdb=" N LEU t 27 " --> pdb=" O GLY t 8 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N SER t 10 " --> pdb=" O ASP t 25 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASP t 25 " --> pdb=" O SER t 10 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ARG t 186 " --> pdb=" O MET t 26 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ILE t 189 " --> pdb=" O GLU t 200 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY t 196 " --> pdb=" O THR t 193 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'g' and resid 68 through 72 removed outlier: 6.554A pdb=" N HIS g 68 " --> pdb=" O MET g 80 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE g 76 " --> pdb=" O ILE g 72 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY g 77 " --> pdb=" O ILE g 141 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N MET g 138 " --> pdb=" O CYS g 154 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'g' and resid 165 through 169 removed outlier: 6.233A pdb=" N THR g 38 " --> pdb=" O GLN g 53 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N GLU g 214 " --> pdb=" O LYS g 54 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'i' and resid 65 through 68 removed outlier: 3.563A pdb=" N LEU i 68 " --> pdb=" O MET i 72 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N MET i 72 " --> pdb=" O LEU i 68 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LEU i 134 " --> pdb=" O SER i 150 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LEU i 147 " --> pdb=" O TRP i 159 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP i 151 " --> pdb=" O ASN i 155 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ASN i 155 " --> pdb=" O ASP i 151 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'i' and resid 161 through 165 removed outlier: 4.924A pdb=" N THR i 33 " --> pdb=" O GLU i 48 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA i 214 " --> pdb=" O LEU i 45 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LYS i 210 " --> pdb=" O ARG i 49 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ILE i 213 " --> pdb=" O LEU i 228 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'k' and resid 67 through 70 removed outlier: 6.428A pdb=" N ILE k 74 " --> pdb=" O ILE k 70 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N HIS k 73 " --> pdb=" O VAL k 146 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N THR k 161 " --> pdb=" O ASP k 157 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'k' and resid 166 through 171 removed outlier: 6.250A pdb=" N ASP k 166 " --> pdb=" O GLN k 41 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N THR k 36 " --> pdb=" O GLU k 51 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY k 45 " --> pdb=" O THR k 42 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N LEU k 217 " --> pdb=" O PHE k 229 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'l' and resid 63 through 66 removed outlier: 6.523A pdb=" N ILE l 70 " --> pdb=" O VAL l 66 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N HIS l 69 " --> pdb=" O TYR l 137 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ILE l 144 " --> pdb=" O CYS l 156 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASN l 152 " --> pdb=" O CYS l 148 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'l' and resid 158 through 162 removed outlier: 5.066A pdb=" N ALA l 34 " --> pdb=" O LEU l 49 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ASN l 209 " --> pdb=" O LYS l 50 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'm' and resid 65 through 69 removed outlier: 6.674A pdb=" N ARG m 65 " --> pdb=" O VAL m 77 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL m 69 " --> pdb=" O VAL m 73 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL m 73 " --> pdb=" O VAL m 69 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY m 138 " --> pdb=" O GLY m 74 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU m 148 " --> pdb=" O TYR m 160 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'm' and resid 161 through 166 removed outlier: 6.862A pdb=" N TRP m 161 " --> pdb=" O ARG m 40 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N THR m 35 " --> pdb=" O GLU m 50 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU m 50 " --> pdb=" O THR m 35 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'n' and resid 34 through 37 removed outlier: 6.610A pdb=" N ILE n 41 " --> pdb=" O ILE n 37 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ARG n 40 " --> pdb=" O TRP n 103 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N VAL n 111 " --> pdb=" O GLN n 123 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'n' and resid 125 through 129 removed outlier: 6.631A pdb=" N THR n 2 " --> pdb=" O ASP n 17 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N VAL n 173 " --> pdb=" O SER n 18 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY n 183 " --> pdb=" O ALA n 180 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'x' and resid 3 through 7 Processing sheet with id= 75, first strand: chain 'x' and resid 44 through 47 removed outlier: 3.746A pdb=" N LYS x 45 " --> pdb=" O MET x 72 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET x 72 " --> pdb=" O LYS x 45 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'x' and resid 265 through 273 removed outlier: 3.552A pdb=" N LYS x 316 " --> pdb=" O GLU x 252 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER x 314 " --> pdb=" O THR x 254 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'x' and resid 274 through 278 Processing sheet with id= 78, first strand: chain 'x' and resid 331 through 335 removed outlier: 3.526A pdb=" N VAL x 339 " --> pdb=" O LYS x 334 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'x' and resid 454 through 458 removed outlier: 3.791A pdb=" N SER x 456 " --> pdb=" O LYS x 449 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLU x 446 " --> pdb=" O ARG x 442 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU x 424 " --> pdb=" O TYR x 476 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'x' and resid 248 through 251 removed outlier: 6.988A pdb=" N GLY x 248 " --> pdb=" O PRO x 321 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU x 250 " --> pdb=" O ARG x 319 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'y' and resid 11 through 16 removed outlier: 4.674A pdb=" N LYS y 11 " --> pdb=" O THR y 7 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER y 65 " --> pdb=" O GLN y 2 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'U' and resid 802 through 805 No H-bonds generated for sheet with id= 82 Processing sheet with id= 83, first strand: chain 'W' and resid 404 through 408 removed outlier: 3.517A pdb=" N ASP W 407 " --> pdb=" O ILE W 412 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE W 412 " --> pdb=" O ASP W 407 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'X' and resid 375 through 380 removed outlier: 5.218A pdb=" N HIS X 375 " --> pdb=" O PHE X 388 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'Y' and resid 345 through 349 removed outlier: 3.517A pdb=" N ILE Y 353 " --> pdb=" O ASP Y 348 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'Z' and resid 47 through 50 removed outlier: 3.581A pdb=" N VAL Z 9 " --> pdb=" O THR Z 159 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU Z 121 " --> pdb=" O TYR Z 138 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N SER Z 140 " --> pdb=" O SER Z 119 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N SER Z 119 " --> pdb=" O SER Z 140 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL Z 120 " --> pdb=" O VAL Z 92 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE Z 124 " --> pdb=" O HIS Z 96 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR Z 95 " --> pdb=" O GLY Z 37 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY Z 37 " --> pdb=" O TYR Z 95 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR Z 97 " --> pdb=" O VAL Z 35 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N VAL Z 35 " --> pdb=" O THR Z 97 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN Z 52 " --> pdb=" O LEU Z 40 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'a' and resid 319 through 326 removed outlier: 6.340A pdb=" N LEU a 319 " --> pdb=" O VAL a 336 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N THR a 334 " --> pdb=" O LYS a 321 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG a 330 " --> pdb=" O ASP a 325 " (cutoff:3.500A) Processing sheet with id= 88, first strand: chain 'b' and resid 47 through 53 removed outlier: 3.820A pdb=" N ASN b 48 " --> pdb=" O GLU b 4 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG b 108 " --> pdb=" O SER b 5 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASN b 137 " --> pdb=" O MET b 107 " (cutoff:3.500A) Processing sheet with id= 89, first strand: chain 'c' and resid 65 through 69 removed outlier: 4.813A pdb=" N THR c 204 " --> pdb=" O GLU c 29 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE c 33 " --> pdb=" O ASN c 206 " (cutoff:3.500A) Processing sheet with id= 90, first strand: chain 'c' and resid 71 through 74 Processing sheet with id= 91, first strand: chain 'c' and resid 141 through 145 Processing sheet with id= 92, first strand: chain 'f' and resid 757 through 760 removed outlier: 7.958A pdb=" N ASN f 757 " --> pdb=" O ILE f 809 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE f 809 " --> pdb=" O ASN f 757 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N GLU f 878 " --> pdb=" O ILE f 810 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER f 814 " --> pdb=" O ALA f 880 " (cutoff:3.500A) Processing sheet with id= 93, first strand: chain 'f' and resid 825 through 829 removed outlier: 3.797A pdb=" N GLN f 826 " --> pdb=" O THR f 863 " (cutoff:3.500A) 5539 hydrogen bonds defined for protein. 16509 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: 47.12 Time building geometry restraints manager: 34.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 36600 1.34 - 1.46: 23122 1.46 - 1.58: 51994 1.58 - 1.70: 13 1.70 - 1.83: 1073 Bond restraints: 112802 Sorted by residual: bond pdb=" N GLU Y 8 " pdb=" CA GLU Y 8 " ideal model delta sigma weight residual 1.457 1.496 -0.038 1.29e-02 6.01e+03 8.83e+00 bond pdb=" C ARG X 74 " pdb=" N PRO X 75 " ideal model delta sigma weight residual 1.336 1.369 -0.033 1.20e-02 6.94e+03 7.54e+00 bond pdb=" C VAL f 192 " pdb=" N PRO f 193 " ideal model delta sigma weight residual 1.334 1.395 -0.062 2.34e-02 1.83e+03 6.92e+00 bond pdb=" C SER b 186 " pdb=" N PRO b 187 " ideal model delta sigma weight residual 1.339 1.423 -0.084 3.40e-02 8.65e+02 6.08e+00 bond pdb=" N PHE Y 208 " pdb=" CA PHE Y 208 " ideal model delta sigma weight residual 1.457 1.489 -0.031 1.29e-02 6.01e+03 5.82e+00 ... (remaining 112797 not shown) Histogram of bond angle deviations from ideal: 96.51 - 105.15: 1912 105.15 - 113.79: 63937 113.79 - 122.43: 71418 122.43 - 131.07: 14710 131.07 - 139.71: 413 Bond angle restraints: 152390 Sorted by residual: angle pdb=" C ASN g 224 " pdb=" N PRO g 225 " pdb=" CA PRO g 225 " ideal model delta sigma weight residual 120.83 112.86 7.97 1.02e+00 9.61e-01 6.10e+01 angle pdb=" C GLN W 96 " pdb=" CA GLN W 96 " pdb=" CB GLN W 96 " ideal model delta sigma weight residual 116.63 109.42 7.21 1.16e+00 7.43e-01 3.86e+01 angle pdb=" C LEU f 99 " pdb=" N ARG f 100 " pdb=" CA ARG f 100 " ideal model delta sigma weight residual 121.80 135.64 -13.84 2.44e+00 1.68e-01 3.22e+01 angle pdb=" N VAL U 763 " pdb=" CA VAL U 763 " pdb=" C VAL U 763 " ideal model delta sigma weight residual 111.91 107.04 4.87 8.90e-01 1.26e+00 2.99e+01 angle pdb=" C ARG W 94 " pdb=" N SER W 95 " pdb=" CA SER W 95 " ideal model delta sigma weight residual 121.54 131.78 -10.24 1.91e+00 2.74e-01 2.87e+01 ... (remaining 152385 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.56: 67067 32.56 - 65.13: 1756 65.13 - 97.69: 153 97.69 - 130.25: 4 130.25 - 162.82: 1 Dihedral angle restraints: 68981 sinusoidal: 27960 harmonic: 41021 Sorted by residual: dihedral pdb=" C5' ADP B 501 " pdb=" O5' ADP B 501 " pdb=" PA ADP B 501 " pdb=" O2A ADP B 501 " ideal model delta sinusoidal sigma weight residual -60.00 102.82 -162.82 1 2.00e+01 2.50e-03 4.69e+01 dihedral pdb=" O2A ADP B 501 " pdb=" O3A ADP B 501 " pdb=" PA ADP B 501 " pdb=" PB ADP B 501 " ideal model delta sinusoidal sigma weight residual -60.00 66.52 -126.52 1 2.00e+01 2.50e-03 3.83e+01 dihedral pdb=" CB CYS A 236 " pdb=" SG CYS A 236 " pdb=" SG CYS A 270 " pdb=" CB CYS A 270 " ideal model delta sinusoidal sigma weight residual -86.00 -34.09 -51.91 1 1.00e+01 1.00e-02 3.68e+01 ... (remaining 68978 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 15262 0.078 - 0.156: 1894 0.156 - 0.234: 84 0.234 - 0.312: 7 0.312 - 0.391: 2 Chirality restraints: 17249 Sorted by residual: chirality pdb=" CB THR U 629 " pdb=" CA THR U 629 " pdb=" OG1 THR U 629 " pdb=" CG2 THR U 629 " both_signs ideal model delta sigma weight residual False 2.55 2.16 0.39 2.00e-01 2.50e+01 3.81e+00 chirality pdb=" CB VAL J 98 " pdb=" CA VAL J 98 " pdb=" CG1 VAL J 98 " pdb=" CG2 VAL J 98 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CG LEU c 36 " pdb=" CB LEU c 36 " pdb=" CD1 LEU c 36 " pdb=" CD2 LEU c 36 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.24e+00 ... (remaining 17246 not shown) Planarity restraints: 19646 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP m 215 " 0.027 2.00e-02 2.50e+03 2.14e-02 1.14e+01 pdb=" CG TRP m 215 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP m 215 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP m 215 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP m 215 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP m 215 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP m 215 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP m 215 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP m 215 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP m 215 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN r 38 " -0.046 5.00e-02 4.00e+02 6.99e-02 7.82e+00 pdb=" N PRO r 39 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO r 39 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO r 39 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU U 16 " -0.046 5.00e-02 4.00e+02 6.87e-02 7.54e+00 pdb=" N PRO U 17 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO U 17 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO U 17 " -0.038 5.00e-02 4.00e+02 ... (remaining 19643 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 260 2.42 - 3.04: 62716 3.04 - 3.66: 169862 3.66 - 4.28: 241076 4.28 - 4.90: 403227 Nonbonded interactions: 877141 Sorted by model distance: nonbonded pdb=" OD2 ASP c 126 " pdb="ZN ZN c 401 " model vdw 1.801 2.230 nonbonded pdb=" OG SER a 159 " pdb=" OD2 ASP a 175 " model vdw 2.230 2.440 nonbonded pdb=" OG1 THR g 190 " pdb=" OE1 GLN g 193 " model vdw 2.233 2.440 nonbonded pdb=" O THR g 190 " pdb=" OG1 THR g 194 " model vdw 2.237 2.440 nonbonded pdb=" O PHE D 345 " pdb=" OG1 THR D 349 " model vdw 2.243 2.440 ... (remaining 877136 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: 13.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 51.160 Check model and map are aligned: 1.230 Set scattering table: 0.790 Process input model: 279.750 Find NCS groups from input model: 6.840 Set up NCS constraints: 0.520 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:2.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 356.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 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 0.088 112802 Z= 0.245 Angle : 0.809 13.835 152390 Z= 0.419 Chirality : 0.049 0.391 17249 Planarity : 0.005 0.071 19646 Dihedral : 14.642 162.818 42569 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.72 % Favored : 93.18 % Rotamer: Outliers : 0.38 % Allowed : 0.64 % Favored : 98.97 % 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: -1.11 (0.07), residues: 13990 helix: -0.09 (0.06), residues: 6132 sheet: 0.37 (0.12), residues: 2087 loop : -1.84 (0.08), residues: 5771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP m 215 HIS 0.029 0.001 HIS V 477 PHE 0.037 0.002 PHE D 275 TYR 0.034 0.001 TYR X 177 ARG 0.012 0.000 ARG B 59 *********************** 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 537 residues out of total 12043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 491 time to evaluate : 10.055 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: A 62 LEU cc_start: 0.4037 (OUTLIER) cc_final: 0.3104 (mt) REVERT: A 65 ILE cc_start: 0.5801 (OUTLIER) cc_final: 0.5485 (pt) REVERT: A 420 TYR cc_start: 0.6480 (m-80) cc_final: 0.6111 (m-80) REVERT: B 372 MET cc_start: 0.8204 (pmm) cc_final: 0.7969 (pmm) REVERT: C 230 MET cc_start: 0.8712 (ttm) cc_final: 0.8379 (tpp) REVERT: C 248 MET cc_start: 0.8821 (mtm) cc_final: 0.8601 (mtp) REVERT: K 133 MET cc_start: 0.8131 (tpp) cc_final: 0.7783 (tpt) REVERT: l 26 MET cc_start: 0.6277 (mmt) cc_final: 0.5506 (mtp) REVERT: n 95 MET cc_start: 0.5211 (tpt) cc_final: 0.4973 (tpt) REVERT: n 116 MET cc_start: 0.7447 (mtt) cc_final: 0.7110 (mtm) REVERT: x 1 MET cc_start: 0.3831 (mmt) cc_final: 0.3458 (tpt) REVERT: x 67 MET cc_start: 0.1344 (mpp) cc_final: 0.0950 (mtt) REVERT: x 181 MET cc_start: 0.8251 (ptp) cc_final: 0.7997 (ptm) REVERT: x 488 MET cc_start: 0.6827 (ppp) cc_final: 0.6620 (mmt) REVERT: U 333 MET cc_start: 0.8337 (pmm) cc_final: 0.7802 (pmm) REVERT: U 376 MET cc_start: 0.8329 (mmm) cc_final: 0.8023 (mmm) REVERT: U 486 MET cc_start: 0.8019 (tmm) cc_final: 0.7526 (tmm) REVERT: W 60 MET cc_start: 0.8817 (ttm) cc_final: 0.8539 (tpp) REVERT: W 436 MET cc_start: 0.8705 (ptp) cc_final: 0.8202 (ptp) REVERT: Z 144 VAL cc_start: 0.6892 (OUTLIER) cc_final: 0.6682 (p) REVERT: Z 149 THR cc_start: 0.7741 (OUTLIER) cc_final: 0.7531 (p) REVERT: a 333 MET cc_start: 0.6173 (pmm) cc_final: 0.5937 (ptp) REVERT: b 107 MET cc_start: 0.5935 (tpp) cc_final: 0.5630 (tpp) REVERT: c 54 MET cc_start: 0.9017 (ppp) cc_final: 0.8574 (ppp) REVERT: c 226 MET cc_start: 0.7359 (mmp) cc_final: 0.7008 (mmt) REVERT: f 297 MET cc_start: 0.0956 (ppp) cc_final: 0.0607 (ppp) REVERT: f 543 MET cc_start: 0.6802 (tmm) cc_final: 0.6048 (mpp) REVERT: f 744 MET cc_start: 0.8889 (tmm) cc_final: 0.8653 (tpp) outliers start: 46 outliers final: 7 residues processed: 534 average time/residue: 0.8800 time to fit residues: 839.7050 Evaluate side-chains 469 residues out of total 12043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 458 time to evaluate : 10.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain Y residue 209 THR Chi-restraints excluded: chain Z residue 143 GLU Chi-restraints excluded: chain Z residue 144 VAL Chi-restraints excluded: chain Z residue 149 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1393 random chunks: chunk 1176 optimal weight: 20.0000 chunk 1055 optimal weight: 20.0000 chunk 585 optimal weight: 10.0000 chunk 360 optimal weight: 9.9990 chunk 712 optimal weight: 20.0000 chunk 564 optimal weight: 8.9990 chunk 1091 optimal weight: 6.9990 chunk 422 optimal weight: 20.0000 chunk 663 optimal weight: 10.0000 chunk 812 optimal weight: 20.0000 chunk 1265 optimal weight: 5.9990 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 GLN D 83 GLN ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 ASN ** E 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 84 ASN I 146 GLN ** J 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 143 ASN S 108 ASN g 128 ASN g 224 ASN h 169 ASN ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 66 HIS q 24 ASN ** x 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 218 GLN U 362 ASN ** U 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 707 ASN W 380 GLN ** W 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 77 ASN ** Z 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 231 GLN a 344 GLN b 158 ASN c 128 ASN d 46 GLN d 110 ASN ** f 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 293 GLN f 325 GLN f 757 ASN ** f 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 112802 Z= 0.302 Angle : 0.626 14.208 152390 Z= 0.327 Chirality : 0.043 0.169 17249 Planarity : 0.004 0.055 19646 Dihedral : 6.495 165.559 15552 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.62 % Favored : 93.30 % Rotamer: Outliers : 0.44 % Allowed : 6.94 % Favored : 92.62 % 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: -0.29 (0.07), residues: 13990 helix: 0.99 (0.07), residues: 6230 sheet: 0.28 (0.11), residues: 2077 loop : -1.74 (0.08), residues: 5683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP m 215 HIS 0.014 0.001 HIS V 477 PHE 0.030 0.001 PHE Y 208 TYR 0.020 0.001 TYR d 249 ARG 0.004 0.000 ARG B 268 *********************** 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 512 residues out of total 12043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 459 time to evaluate : 10.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LYS cc_start: 0.7457 (ptmt) cc_final: 0.7071 (tptt) REVERT: A 62 LEU cc_start: 0.3783 (OUTLIER) cc_final: 0.3007 (mt) REVERT: B 74 MET cc_start: 0.1862 (OUTLIER) cc_final: 0.1352 (ptp) REVERT: B 214 MET cc_start: 0.8822 (mmm) cc_final: 0.8546 (mmm) REVERT: C 230 MET cc_start: 0.8702 (ttm) cc_final: 0.8432 (tpp) REVERT: D 296 MET cc_start: 0.9013 (ppp) cc_final: 0.8615 (ppp) REVERT: j 211 MET cc_start: 0.7331 (ttt) cc_final: 0.6993 (ttm) REVERT: l 26 MET cc_start: 0.6561 (mmt) cc_final: 0.5850 (mtp) REVERT: q 69 MET cc_start: 0.8386 (tpp) cc_final: 0.8162 (tpp) REVERT: t 103 MET cc_start: 0.8634 (mmm) cc_final: 0.8369 (mmm) REVERT: x 1 MET cc_start: 0.3923 (mmt) cc_final: 0.3587 (tpt) REVERT: x 67 MET cc_start: 0.1009 (mpp) cc_final: 0.0542 (mtt) REVERT: x 181 MET cc_start: 0.8191 (ptp) cc_final: 0.7968 (ptm) REVERT: U 486 MET cc_start: 0.8172 (tmm) cc_final: 0.7840 (tmm) REVERT: V 175 MET cc_start: 0.9183 (tpp) cc_final: 0.8830 (tpp) REVERT: W 16 MET cc_start: 0.8183 (tpp) cc_final: 0.6077 (mmm) REVERT: X 254 MET cc_start: 0.8490 (mtm) cc_final: 0.8200 (ptp) REVERT: b 107 MET cc_start: 0.5738 (tpp) cc_final: 0.5357 (tpp) REVERT: c 54 MET cc_start: 0.8920 (ppp) cc_final: 0.8439 (ppp) REVERT: f 271 MET cc_start: 0.5823 (mpp) cc_final: 0.4782 (mmt) REVERT: f 297 MET cc_start: 0.0719 (ppp) cc_final: -0.0378 (ppp) REVERT: f 505 MET cc_start: 0.4527 (tmm) cc_final: 0.4155 (ttp) REVERT: f 543 MET cc_start: 0.6706 (tmm) cc_final: 0.5828 (mpp) REVERT: f 744 MET cc_start: 0.8960 (tmm) cc_final: 0.8686 (tpp) outliers start: 53 outliers final: 28 residues processed: 481 average time/residue: 0.8929 time to fit residues: 770.8509 Evaluate side-chains 485 residues out of total 12043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 455 time to evaluate : 9.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain B residue 74 MET Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain I residue 201 MET Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain P residue 12 MET Chi-restraints excluded: chain Q residue 28 MET Chi-restraints excluded: chain T residue 127 MET Chi-restraints excluded: chain h residue 181 ASP Chi-restraints excluded: chain l residue 180 MET Chi-restraints excluded: chain l residue 217 LYS Chi-restraints excluded: chain t residue 127 MET Chi-restraints excluded: chain x residue 355 MET Chi-restraints excluded: chain X residue 342 PHE Chi-restraints excluded: chain Y residue 209 THR Chi-restraints excluded: chain Y residue 299 MET Chi-restraints excluded: chain Z residue 145 HIS Chi-restraints excluded: chain a residue 248 PHE Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain f residue 47 GLU Chi-restraints excluded: chain f residue 321 MET Chi-restraints excluded: chain f residue 340 MET Chi-restraints excluded: chain f residue 370 MET Chi-restraints excluded: chain f residue 512 MET Chi-restraints excluded: chain e residue 65 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1393 random chunks: chunk 703 optimal weight: 7.9990 chunk 392 optimal weight: 9.9990 chunk 1052 optimal weight: 8.9990 chunk 861 optimal weight: 8.9990 chunk 348 optimal weight: 10.0000 chunk 1267 optimal weight: 9.9990 chunk 1369 optimal weight: 9.9990 chunk 1128 optimal weight: 4.9990 chunk 1256 optimal weight: 30.0000 chunk 432 optimal weight: 9.9990 chunk 1016 optimal weight: 5.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 GLN ** D 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 146 GLN ** J 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 734 GLN ** W 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 231 GLN b 94 HIS ** f 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 715 HIS ** f 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 112802 Z= 0.260 Angle : 0.579 12.634 152390 Z= 0.301 Chirality : 0.042 0.168 17249 Planarity : 0.004 0.053 19646 Dihedral : 6.312 165.200 15542 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.64 % Favored : 93.28 % Rotamer: Outliers : 0.75 % Allowed : 11.16 % Favored : 88.09 % 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: 1.31 (0.07), residues: 6240 sheet: 0.26 (0.11), residues: 2085 loop : -1.68 (0.08), residues: 5665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP m 215 HIS 0.011 0.001 HIS V 477 PHE 0.022 0.001 PHE f 713 TYR 0.021 0.001 TYR d 249 ARG 0.005 0.000 ARG d 175 *********************** 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 546 residues out of total 12043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 456 time to evaluate : 9.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LYS cc_start: 0.7458 (ptmt) cc_final: 0.7097 (tptt) REVERT: A 62 LEU cc_start: 0.3958 (OUTLIER) cc_final: 0.3150 (mt) REVERT: A 420 TYR cc_start: 0.6566 (m-80) cc_final: 0.6297 (m-80) REVERT: C 230 MET cc_start: 0.8733 (ttm) cc_final: 0.8430 (tpp) REVERT: C 298 ILE cc_start: 0.9140 (OUTLIER) cc_final: 0.8718 (tp) REVERT: D 296 MET cc_start: 0.9050 (ppp) cc_final: 0.8801 (ppp) REVERT: g 138 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.7983 (tpp) REVERT: j 211 MET cc_start: 0.7337 (ttt) cc_final: 0.6975 (ttm) REVERT: k 59 MET cc_start: 0.7560 (tpp) cc_final: 0.6875 (tmm) REVERT: l 26 MET cc_start: 0.6449 (mmt) cc_final: 0.5595 (mtp) REVERT: t 103 MET cc_start: 0.8678 (mmm) cc_final: 0.8422 (mmm) REVERT: x 1 MET cc_start: 0.4040 (mmt) cc_final: 0.3669 (tpt) REVERT: x 101 MET cc_start: 0.7210 (ptp) cc_final: 0.6632 (ptp) REVERT: x 181 MET cc_start: 0.8176 (ptp) cc_final: 0.7927 (ptm) REVERT: x 488 MET cc_start: 0.6375 (ppp) cc_final: 0.5561 (mmt) REVERT: U 333 MET cc_start: 0.8554 (pmm) cc_final: 0.7675 (pmm) REVERT: U 486 MET cc_start: 0.8153 (tmm) cc_final: 0.7853 (tmm) REVERT: U 879 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7871 (t0) REVERT: V 175 MET cc_start: 0.9134 (tpp) cc_final: 0.8807 (tpp) REVERT: Y 73 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8183 (mpp) REVERT: Z 250 TYR cc_start: 0.5303 (OUTLIER) cc_final: 0.4256 (m-80) REVERT: a 127 ASP cc_start: 0.6695 (OUTLIER) cc_final: 0.6385 (p0) REVERT: b 107 MET cc_start: 0.5721 (tpp) cc_final: 0.5303 (tpp) REVERT: c 54 MET cc_start: 0.8963 (ppp) cc_final: 0.8405 (ppp) REVERT: f 216 MET cc_start: 0.6794 (mmm) cc_final: 0.6509 (mmp) REVERT: f 505 MET cc_start: 0.4546 (tmm) cc_final: 0.4244 (ttp) REVERT: f 744 MET cc_start: 0.8992 (tmm) cc_final: 0.8759 (tpp) outliers start: 90 outliers final: 40 residues processed: 514 average time/residue: 0.8911 time to fit residues: 821.4661 Evaluate side-chains 500 residues out of total 12043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 453 time to evaluate : 9.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain P residue 12 MET Chi-restraints excluded: chain Q residue 28 MET Chi-restraints excluded: chain R residue 93 MET Chi-restraints excluded: chain g residue 138 MET Chi-restraints excluded: chain h residue 181 ASP Chi-restraints excluded: chain l residue 159 MET Chi-restraints excluded: chain l residue 180 MET Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 180 VAL Chi-restraints excluded: chain r residue 187 VAL Chi-restraints excluded: chain t residue 127 MET Chi-restraints excluded: chain x residue 355 MET Chi-restraints excluded: chain U residue 879 ASP Chi-restraints excluded: chain U residue 884 VAL Chi-restraints excluded: chain V residue 112 VAL Chi-restraints excluded: chain W residue 106 GLN Chi-restraints excluded: chain W residue 213 PHE Chi-restraints excluded: chain W residue 366 MET Chi-restraints excluded: chain X residue 342 PHE Chi-restraints excluded: chain Y residue 73 MET Chi-restraints excluded: chain Y residue 209 THR Chi-restraints excluded: chain Y residue 299 MET Chi-restraints excluded: chain Z residue 250 TYR Chi-restraints excluded: chain a residue 127 ASP Chi-restraints excluded: chain a residue 248 PHE Chi-restraints excluded: chain a residue 312 MET Chi-restraints excluded: chain c residue 169 VAL Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain f residue 47 GLU Chi-restraints excluded: chain f residue 321 MET Chi-restraints excluded: chain f residue 340 MET Chi-restraints excluded: chain f residue 655 LEU Chi-restraints excluded: chain e residue 65 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1393 random chunks: chunk 1252 optimal weight: 10.0000 chunk 952 optimal weight: 20.0000 chunk 657 optimal weight: 6.9990 chunk 140 optimal weight: 9.9990 chunk 604 optimal weight: 20.0000 chunk 850 optimal weight: 4.9990 chunk 1271 optimal weight: 7.9990 chunk 1346 optimal weight: 0.1980 chunk 664 optimal weight: 20.0000 chunk 1205 optimal weight: 7.9990 chunk 362 optimal weight: 5.9990 overall best weight: 5.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 ASN ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 GLN ** E 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 205 ASN J 215 GLN ** m 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 707 ASN ** W 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 112802 Z= 0.201 Angle : 0.549 14.070 152390 Z= 0.283 Chirality : 0.041 0.184 17249 Planarity : 0.004 0.054 19646 Dihedral : 6.154 166.073 15541 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.65 % Favored : 93.27 % Rotamer: Outliers : 1.18 % Allowed : 13.08 % Favored : 85.74 % 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: 0.13 (0.07), residues: 13990 helix: 1.48 (0.07), residues: 6242 sheet: 0.28 (0.11), residues: 2083 loop : -1.64 (0.08), residues: 5665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP f 154 HIS 0.008 0.001 HIS V 477 PHE 0.023 0.001 PHE f 713 TYR 0.021 0.001 TYR Y 259 ARG 0.008 0.000 ARG F 362 *********************** 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 593 residues out of total 12043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 452 time to evaluate : 10.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LYS cc_start: 0.7409 (ptmt) cc_final: 0.7035 (tptt) REVERT: A 62 LEU cc_start: 0.3935 (OUTLIER) cc_final: 0.3032 (mt) REVERT: A 420 TYR cc_start: 0.6524 (m-80) cc_final: 0.6215 (m-80) REVERT: C 138 MET cc_start: 0.6209 (mmm) cc_final: 0.5622 (mmm) REVERT: C 230 MET cc_start: 0.8718 (ttm) cc_final: 0.8428 (tpp) REVERT: C 298 ILE cc_start: 0.9125 (OUTLIER) cc_final: 0.8713 (tp) REVERT: C 399 MET cc_start: 0.8065 (pmm) cc_final: 0.7644 (pmm) REVERT: D 296 MET cc_start: 0.9086 (ppp) cc_final: 0.8745 (tmm) REVERT: g 138 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.7905 (tpp) REVERT: j 71 MET cc_start: 0.8811 (ppp) cc_final: 0.8587 (ptm) REVERT: j 211 MET cc_start: 0.7290 (ttt) cc_final: 0.6948 (ttm) REVERT: l 26 MET cc_start: 0.6468 (mmt) cc_final: 0.5830 (mtp) REVERT: t 103 MET cc_start: 0.8666 (mmm) cc_final: 0.8412 (mmm) REVERT: x 1 MET cc_start: 0.4052 (mmt) cc_final: 0.3699 (tpt) REVERT: x 101 MET cc_start: 0.7257 (ptp) cc_final: 0.6946 (ptp) REVERT: x 488 MET cc_start: 0.6460 (ppp) cc_final: 0.5621 (mmt) REVERT: U 486 MET cc_start: 0.8092 (tmm) cc_final: 0.7816 (tmm) REVERT: V 175 MET cc_start: 0.9053 (tpp) cc_final: 0.8739 (tpp) REVERT: Y 73 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.8180 (mpp) REVERT: Y 105 MET cc_start: 0.9110 (mmm) cc_final: 0.8889 (mmm) REVERT: Z 244 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.6282 (pm20) REVERT: a 127 ASP cc_start: 0.6675 (OUTLIER) cc_final: 0.6469 (p0) REVERT: b 107 MET cc_start: 0.5883 (tpp) cc_final: 0.5439 (tpp) REVERT: c 54 MET cc_start: 0.8822 (ppp) cc_final: 0.8540 (ppp) REVERT: d 196 ARG cc_start: 0.7871 (mmm160) cc_final: 0.7602 (mmm160) REVERT: f 505 MET cc_start: 0.4695 (tmm) cc_final: 0.4432 (ttp) REVERT: f 543 MET cc_start: 0.6800 (tmm) cc_final: 0.5799 (mpp) REVERT: f 744 MET cc_start: 0.8990 (tmm) cc_final: 0.8764 (tpp) outliers start: 141 outliers final: 62 residues processed: 565 average time/residue: 0.8779 time to fit residues: 893.0056 Evaluate side-chains 519 residues out of total 12043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 451 time to evaluate : 10.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain G residue 196 GLU Chi-restraints excluded: chain I residue 201 MET Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 184 ASP Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain L residue 225 ASP Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain P residue 12 MET Chi-restraints excluded: chain P residue 149 MET Chi-restraints excluded: chain Q residue 28 MET Chi-restraints excluded: chain R residue 93 MET Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain g residue 138 MET Chi-restraints excluded: chain h residue 45 VAL Chi-restraints excluded: chain h residue 181 ASP Chi-restraints excluded: chain l residue 159 MET Chi-restraints excluded: chain l residue 180 MET Chi-restraints excluded: chain q residue 180 VAL Chi-restraints excluded: chain r residue 56 GLU Chi-restraints excluded: chain t residue 3 ASN Chi-restraints excluded: chain t residue 127 MET Chi-restraints excluded: chain x residue 355 MET Chi-restraints excluded: chain y residue 14 THR Chi-restraints excluded: chain U residue 92 ASP Chi-restraints excluded: chain U residue 239 GLU Chi-restraints excluded: chain U residue 629 THR Chi-restraints excluded: chain U residue 663 THR Chi-restraints excluded: chain V residue 101 LEU Chi-restraints excluded: chain V residue 484 LEU Chi-restraints excluded: chain W residue 81 ASP Chi-restraints excluded: chain W residue 213 PHE Chi-restraints excluded: chain W residue 387 ASP Chi-restraints excluded: chain X residue 342 PHE Chi-restraints excluded: chain Y residue 73 MET Chi-restraints excluded: chain Y residue 209 THR Chi-restraints excluded: chain Y residue 299 MET Chi-restraints excluded: chain Z residue 145 HIS Chi-restraints excluded: chain Z residue 244 GLU Chi-restraints excluded: chain a residue 127 ASP Chi-restraints excluded: chain a residue 248 PHE Chi-restraints excluded: chain a residue 312 MET Chi-restraints excluded: chain b residue 8 VAL Chi-restraints excluded: chain c residue 67 VAL Chi-restraints excluded: chain c residue 169 VAL Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain d residue 41 THR Chi-restraints excluded: chain f residue 47 GLU Chi-restraints excluded: chain f residue 321 MET Chi-restraints excluded: chain f residue 340 MET Chi-restraints excluded: chain f residue 512 MET Chi-restraints excluded: chain f residue 655 LEU Chi-restraints excluded: chain e residue 65 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1393 random chunks: chunk 1121 optimal weight: 7.9990 chunk 764 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 1002 optimal weight: 3.9990 chunk 555 optimal weight: 6.9990 chunk 1149 optimal weight: 10.0000 chunk 930 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 687 optimal weight: 20.0000 chunk 1208 optimal weight: 10.0000 chunk 339 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 63 ASN ** x 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 707 ASN ** W 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 268 GLN Z 77 ASN ** Z 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 372 HIS ** f 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 815 HIS ** e 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 47 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 112802 Z= 0.151 Angle : 0.528 14.649 152390 Z= 0.270 Chirality : 0.041 0.351 17249 Planarity : 0.003 0.051 19646 Dihedral : 5.968 168.225 15541 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.33 % Favored : 93.58 % Rotamer: Outliers : 1.14 % Allowed : 14.30 % Favored : 84.57 % 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: 0.28 (0.07), residues: 13990 helix: 1.63 (0.07), residues: 6239 sheet: 0.34 (0.11), residues: 2102 loop : -1.60 (0.08), residues: 5649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP x 58 HIS 0.008 0.001 HIS U 70 PHE 0.021 0.001 PHE a 67 TYR 0.023 0.001 TYR Y 259 ARG 0.004 0.000 ARG F 362 *********************** 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 588 residues out of total 12043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 452 time to evaluate : 10.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LYS cc_start: 0.7416 (ptmt) cc_final: 0.7063 (tptt) REVERT: A 62 LEU cc_start: 0.4006 (OUTLIER) cc_final: 0.2935 (mt) REVERT: A 420 TYR cc_start: 0.6499 (m-80) cc_final: 0.6183 (m-80) REVERT: C 138 MET cc_start: 0.6335 (mmm) cc_final: 0.5800 (mmm) REVERT: C 230 MET cc_start: 0.8679 (ttm) cc_final: 0.8382 (tpp) REVERT: C 391 MET cc_start: 0.8611 (pmm) cc_final: 0.8325 (pmm) REVERT: C 399 MET cc_start: 0.8051 (pmm) cc_final: 0.7687 (pmm) REVERT: D 296 MET cc_start: 0.9100 (ppp) cc_final: 0.8757 (tmm) REVERT: N 164 MET cc_start: 0.8606 (mmm) cc_final: 0.8120 (mtp) REVERT: j 211 MET cc_start: 0.7237 (ttt) cc_final: 0.7002 (ttm) REVERT: k 59 MET cc_start: 0.8006 (mmm) cc_final: 0.7701 (tpp) REVERT: l 26 MET cc_start: 0.6586 (mmt) cc_final: 0.5773 (mtp) REVERT: t 103 MET cc_start: 0.8675 (mmm) cc_final: 0.8462 (mmm) REVERT: x 47 MET cc_start: 0.1436 (mmp) cc_final: 0.1062 (mmp) REVERT: x 92 MET cc_start: 0.7083 (OUTLIER) cc_final: 0.6689 (tmm) REVERT: x 488 MET cc_start: 0.6435 (ppp) cc_final: 0.5648 (mmt) REVERT: U 486 MET cc_start: 0.8034 (tmm) cc_final: 0.7744 (tmm) REVERT: V 175 MET cc_start: 0.8971 (tpp) cc_final: 0.8721 (tpp) REVERT: W 106 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8671 (mp10) REVERT: W 375 MET cc_start: 0.7812 (mmp) cc_final: 0.7420 (mmp) REVERT: Y 73 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.8178 (mpp) REVERT: Z 250 TYR cc_start: 0.5258 (OUTLIER) cc_final: 0.4268 (m-80) REVERT: a 372 HIS cc_start: 0.8650 (OUTLIER) cc_final: 0.8081 (m-70) REVERT: b 107 MET cc_start: 0.5972 (tpp) cc_final: 0.5581 (tpp) REVERT: f 505 MET cc_start: 0.4712 (tmm) cc_final: 0.4485 (ttp) REVERT: f 543 MET cc_start: 0.6773 (tmm) cc_final: 0.5842 (mpp) REVERT: f 744 MET cc_start: 0.8981 (tmm) cc_final: 0.8777 (tpp) outliers start: 136 outliers final: 74 residues processed: 561 average time/residue: 0.9227 time to fit residues: 938.5928 Evaluate side-chains 531 residues out of total 12043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 451 time to evaluate : 9.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 374 ASP Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 196 GLU Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 201 MET Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain L residue 225 ASP Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain P residue 12 MET Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 149 MET Chi-restraints excluded: chain Q residue 28 MET Chi-restraints excluded: chain Q residue 190 ASP Chi-restraints excluded: chain R residue 93 MET Chi-restraints excluded: chain h residue 45 VAL Chi-restraints excluded: chain h residue 181 ASP Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain l residue 159 MET Chi-restraints excluded: chain l residue 180 MET Chi-restraints excluded: chain m residue 200 VAL Chi-restraints excluded: chain o residue 65 LEU Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 180 VAL Chi-restraints excluded: chain r residue 56 GLU Chi-restraints excluded: chain t residue 127 MET Chi-restraints excluded: chain x residue 67 MET Chi-restraints excluded: chain x residue 92 MET Chi-restraints excluded: chain x residue 355 MET Chi-restraints excluded: chain U residue 239 GLU Chi-restraints excluded: chain U residue 405 THR Chi-restraints excluded: chain U residue 629 THR Chi-restraints excluded: chain U residue 636 VAL Chi-restraints excluded: chain U residue 654 MET Chi-restraints excluded: chain V residue 112 VAL Chi-restraints excluded: chain W residue 106 GLN Chi-restraints excluded: chain W residue 213 PHE Chi-restraints excluded: chain W residue 310 THR Chi-restraints excluded: chain X residue 342 PHE Chi-restraints excluded: chain Y residue 73 MET Chi-restraints excluded: chain Y residue 189 VAL Chi-restraints excluded: chain Y residue 209 THR Chi-restraints excluded: chain Y residue 278 VAL Chi-restraints excluded: chain Y residue 299 MET Chi-restraints excluded: chain Z residue 145 HIS Chi-restraints excluded: chain Z residue 198 LEU Chi-restraints excluded: chain Z residue 250 TYR Chi-restraints excluded: chain a residue 183 VAL Chi-restraints excluded: chain a residue 248 PHE Chi-restraints excluded: chain a residue 312 MET Chi-restraints excluded: chain a residue 372 HIS Chi-restraints excluded: chain b residue 8 VAL Chi-restraints excluded: chain b residue 150 THR Chi-restraints excluded: chain c residue 99 LEU Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 169 VAL Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain f residue 47 GLU Chi-restraints excluded: chain f residue 321 MET Chi-restraints excluded: chain f residue 324 VAL Chi-restraints excluded: chain f residue 340 MET Chi-restraints excluded: chain f residue 655 LEU Chi-restraints excluded: chain e residue 65 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1393 random chunks: chunk 453 optimal weight: 10.0000 chunk 1212 optimal weight: 0.7980 chunk 266 optimal weight: 0.0370 chunk 790 optimal weight: 20.0000 chunk 332 optimal weight: 0.7980 chunk 1347 optimal weight: 10.0000 chunk 1118 optimal weight: 9.9990 chunk 624 optimal weight: 30.0000 chunk 112 optimal weight: 20.0000 chunk 445 optimal weight: 6.9990 chunk 707 optimal weight: 30.0000 overall best weight: 3.7262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 128 GLN ** U 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 218 GLN ** U 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 596 ASN ** U 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 707 ASN ** W 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 77 ASN ** Z 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 372 HIS ** f 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 747 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 112802 Z= 0.164 Angle : 0.533 16.001 152390 Z= 0.271 Chirality : 0.041 0.281 17249 Planarity : 0.003 0.052 19646 Dihedral : 5.884 169.688 15540 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.48 % Favored : 93.43 % Rotamer: Outliers : 1.33 % Allowed : 14.99 % Favored : 83.68 % 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: 0.33 (0.07), residues: 13990 helix: 1.71 (0.07), residues: 6239 sheet: 0.33 (0.11), residues: 2105 loop : -1.59 (0.08), residues: 5646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP f 154 HIS 0.020 0.001 HIS a 372 PHE 0.020 0.001 PHE a 67 TYR 0.021 0.001 TYR d 249 ARG 0.003 0.000 ARG b 25 *********************** 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 610 residues out of total 12043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 451 time to evaluate : 10.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LYS cc_start: 0.7414 (ptmt) cc_final: 0.7062 (tptt) REVERT: A 62 LEU cc_start: 0.3931 (OUTLIER) cc_final: 0.2859 (mt) REVERT: A 420 TYR cc_start: 0.6542 (m-80) cc_final: 0.6194 (m-80) REVERT: C 138 MET cc_start: 0.6446 (mmm) cc_final: 0.5967 (mmm) REVERT: C 230 MET cc_start: 0.8719 (ttm) cc_final: 0.8429 (tpp) REVERT: C 298 ILE cc_start: 0.9135 (OUTLIER) cc_final: 0.8712 (tp) REVERT: C 391 MET cc_start: 0.8638 (pmm) cc_final: 0.8197 (pmm) REVERT: C 399 MET cc_start: 0.8062 (pmm) cc_final: 0.7535 (pmm) REVERT: D 296 MET cc_start: 0.9109 (ppp) cc_final: 0.8766 (tmm) REVERT: N 164 MET cc_start: 0.8527 (mmm) cc_final: 0.8102 (mtp) REVERT: j 211 MET cc_start: 0.7220 (ttt) cc_final: 0.7017 (ttm) REVERT: l 26 MET cc_start: 0.6598 (mmt) cc_final: 0.5809 (mtp) REVERT: t 103 MET cc_start: 0.8689 (mmm) cc_final: 0.8464 (mmm) REVERT: x 47 MET cc_start: 0.1432 (mmp) cc_final: 0.1054 (mmp) REVERT: x 92 MET cc_start: 0.7069 (OUTLIER) cc_final: 0.6692 (tmm) REVERT: x 488 MET cc_start: 0.6505 (ppp) cc_final: 0.5697 (mmt) REVERT: U 486 MET cc_start: 0.8012 (tmm) cc_final: 0.7748 (tmm) REVERT: V 175 MET cc_start: 0.8952 (tpp) cc_final: 0.8722 (tpp) REVERT: W 106 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8665 (mp10) REVERT: W 334 GLU cc_start: 0.4901 (OUTLIER) cc_final: 0.4222 (tt0) REVERT: W 375 MET cc_start: 0.7903 (mmp) cc_final: 0.7588 (mmp) REVERT: Z 244 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.6241 (pm20) REVERT: Z 250 TYR cc_start: 0.5253 (OUTLIER) cc_final: 0.4261 (m-80) REVERT: b 107 MET cc_start: 0.5924 (tpp) cc_final: 0.5534 (tpp) REVERT: f 505 MET cc_start: 0.4771 (tmm) cc_final: 0.4554 (ttp) REVERT: f 543 MET cc_start: 0.6769 (tmm) cc_final: 0.5834 (mpp) outliers start: 159 outliers final: 94 residues processed: 583 average time/residue: 0.8801 time to fit residues: 926.9314 Evaluate side-chains 552 residues out of total 12043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 451 time to evaluate : 9.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 374 ASP Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 196 GLU Chi-restraints excluded: chain H residue 207 ASN Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 201 MET Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 184 ASP Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain K residue 84 ASP Chi-restraints excluded: chain L residue 225 ASP Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 216 VAL Chi-restraints excluded: chain P residue 12 MET Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain Q residue 28 MET Chi-restraints excluded: chain R residue 93 MET Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain g residue 111 VAL Chi-restraints excluded: chain h residue 45 VAL Chi-restraints excluded: chain h residue 181 ASP Chi-restraints excluded: chain i residue 21 VAL Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain l residue 159 MET Chi-restraints excluded: chain l residue 180 MET Chi-restraints excluded: chain m residue 200 VAL Chi-restraints excluded: chain o residue 65 LEU Chi-restraints excluded: chain q residue 180 VAL Chi-restraints excluded: chain r residue 56 GLU Chi-restraints excluded: chain r residue 187 VAL Chi-restraints excluded: chain t residue 3 ASN Chi-restraints excluded: chain t residue 127 MET Chi-restraints excluded: chain x residue 67 MET Chi-restraints excluded: chain x residue 92 MET Chi-restraints excluded: chain x residue 355 MET Chi-restraints excluded: chain y residue 14 THR Chi-restraints excluded: chain U residue 92 ASP Chi-restraints excluded: chain U residue 162 VAL Chi-restraints excluded: chain U residue 239 GLU Chi-restraints excluded: chain U residue 405 THR Chi-restraints excluded: chain U residue 629 THR Chi-restraints excluded: chain U residue 636 VAL Chi-restraints excluded: chain U residue 654 MET Chi-restraints excluded: chain U residue 676 THR Chi-restraints excluded: chain U residue 884 VAL Chi-restraints excluded: chain V residue 101 LEU Chi-restraints excluded: chain V residue 112 VAL Chi-restraints excluded: chain W residue 81 ASP Chi-restraints excluded: chain W residue 106 GLN Chi-restraints excluded: chain W residue 213 PHE Chi-restraints excluded: chain W residue 309 PHE Chi-restraints excluded: chain W residue 310 THR Chi-restraints excluded: chain W residue 334 GLU Chi-restraints excluded: chain X residue 166 LEU Chi-restraints excluded: chain X residue 342 PHE Chi-restraints excluded: chain Y residue 73 MET Chi-restraints excluded: chain Y residue 189 VAL Chi-restraints excluded: chain Y residue 209 THR Chi-restraints excluded: chain Y residue 278 VAL Chi-restraints excluded: chain Y residue 291 HIS Chi-restraints excluded: chain Y residue 299 MET Chi-restraints excluded: chain Z residue 106 ILE Chi-restraints excluded: chain Z residue 145 HIS Chi-restraints excluded: chain Z residue 244 GLU Chi-restraints excluded: chain Z residue 250 TYR Chi-restraints excluded: chain a residue 183 VAL Chi-restraints excluded: chain a residue 248 PHE Chi-restraints excluded: chain a residue 312 MET Chi-restraints excluded: chain b residue 8 VAL Chi-restraints excluded: chain b residue 150 THR Chi-restraints excluded: chain c residue 67 VAL Chi-restraints excluded: chain c residue 122 LEU Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 275 VAL Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain d residue 41 THR Chi-restraints excluded: chain f residue 47 GLU Chi-restraints excluded: chain f residue 340 MET Chi-restraints excluded: chain f residue 655 LEU Chi-restraints excluded: chain e residue 65 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1393 random chunks: chunk 1299 optimal weight: 9.9990 chunk 151 optimal weight: 5.9990 chunk 767 optimal weight: 8.9990 chunk 984 optimal weight: 5.9990 chunk 762 optimal weight: 5.9990 chunk 1134 optimal weight: 8.9990 chunk 752 optimal weight: 4.9990 chunk 1342 optimal weight: 20.0000 chunk 840 optimal weight: 20.0000 chunk 818 optimal weight: 7.9990 chunk 619 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 412 HIS ** U 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 707 ASN ** W 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 77 ASN ** Z 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 193 GLN ** f 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 118 ASN ** e 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 112802 Z= 0.227 Angle : 0.564 14.732 152390 Z= 0.289 Chirality : 0.041 0.281 17249 Planarity : 0.003 0.052 19646 Dihedral : 5.924 170.059 15540 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.90 % Favored : 93.01 % Rotamer: Outliers : 1.42 % Allowed : 15.58 % Favored : 83.00 % 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: 0.31 (0.07), residues: 13990 helix: 1.68 (0.07), residues: 6252 sheet: 0.29 (0.11), residues: 2122 loop : -1.59 (0.08), residues: 5616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP f 154 HIS 0.009 0.001 HIS U 70 PHE 0.021 0.001 PHE a 67 TYR 0.023 0.001 TYR A 429 ARG 0.004 0.000 ARG U 883 *********************** 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 622 residues out of total 12043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 452 time to evaluate : 10.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LYS cc_start: 0.7434 (ptmt) cc_final: 0.7093 (tptt) REVERT: A 62 LEU cc_start: 0.3728 (OUTLIER) cc_final: 0.2646 (mt) REVERT: A 362 MET cc_start: 0.8535 (ttt) cc_final: 0.8274 (ttp) REVERT: C 138 MET cc_start: 0.6517 (mmm) cc_final: 0.6086 (mmm) REVERT: C 230 MET cc_start: 0.8710 (ttm) cc_final: 0.8420 (tpp) REVERT: C 298 ILE cc_start: 0.9141 (OUTLIER) cc_final: 0.8720 (tp) REVERT: C 391 MET cc_start: 0.8664 (pmm) cc_final: 0.8122 (pmm) REVERT: D 296 MET cc_start: 0.9133 (ppp) cc_final: 0.8773 (tmm) REVERT: E 33 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8508 (mm) REVERT: E 277 MET cc_start: 0.8277 (mmp) cc_final: 0.7992 (mmp) REVERT: N 164 MET cc_start: 0.8469 (mmm) cc_final: 0.8138 (mtp) REVERT: j 211 MET cc_start: 0.7247 (ttt) cc_final: 0.7033 (ttm) REVERT: k 59 MET cc_start: 0.8074 (tmm) cc_final: 0.7602 (tmm) REVERT: l 26 MET cc_start: 0.6685 (mmt) cc_final: 0.5940 (mtp) REVERT: t 103 MET cc_start: 0.8701 (mmm) cc_final: 0.8468 (mmm) REVERT: x 92 MET cc_start: 0.7111 (OUTLIER) cc_final: 0.6701 (tmm) REVERT: x 101 MET cc_start: 0.7419 (ptp) cc_final: 0.7149 (ptp) REVERT: x 370 PHE cc_start: 0.8990 (OUTLIER) cc_final: 0.8677 (t80) REVERT: x 488 MET cc_start: 0.6498 (ppp) cc_final: 0.5690 (mmt) REVERT: U 376 MET cc_start: 0.8195 (mmm) cc_final: 0.7745 (mmm) REVERT: W 106 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8672 (mp10) REVERT: W 334 GLU cc_start: 0.5102 (OUTLIER) cc_final: 0.4413 (tt0) REVERT: W 375 MET cc_start: 0.7990 (mmp) cc_final: 0.7753 (mmp) REVERT: Y 105 MET cc_start: 0.9055 (mmm) cc_final: 0.8836 (mmm) REVERT: Z 244 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.6288 (pm20) REVERT: Z 250 TYR cc_start: 0.5318 (OUTLIER) cc_final: 0.4335 (m-80) REVERT: a 211 PHE cc_start: 0.5468 (OUTLIER) cc_final: 0.5128 (p90) REVERT: b 7 MET cc_start: 0.7601 (tpt) cc_final: 0.6980 (tpt) REVERT: b 107 MET cc_start: 0.5942 (tpp) cc_final: 0.5437 (tpp) REVERT: f 216 MET cc_start: 0.6727 (mmm) cc_final: 0.6483 (mmp) REVERT: f 505 MET cc_start: 0.4758 (tmm) cc_final: 0.4535 (ttp) outliers start: 170 outliers final: 111 residues processed: 592 average time/residue: 0.8824 time to fit residues: 945.0025 Evaluate side-chains 572 residues out of total 12043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 451 time to evaluate : 10.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 374 ASP Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 196 GLU Chi-restraints excluded: chain H residue 207 ASN Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 201 MET Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 184 ASP Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain K residue 84 ASP Chi-restraints excluded: chain L residue 167 SER Chi-restraints excluded: chain L residue 225 ASP Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 216 VAL Chi-restraints excluded: chain P residue 12 MET Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain Q residue 28 MET Chi-restraints excluded: chain Q residue 190 ASP Chi-restraints excluded: chain R residue 93 MET Chi-restraints excluded: chain R residue 196 HIS Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain g residue 111 VAL Chi-restraints excluded: chain h residue 45 VAL Chi-restraints excluded: chain h residue 181 ASP Chi-restraints excluded: chain i residue 21 VAL Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain l residue 159 MET Chi-restraints excluded: chain l residue 180 MET Chi-restraints excluded: chain m residue 200 VAL Chi-restraints excluded: chain o residue 6 VAL Chi-restraints excluded: chain o residue 65 LEU Chi-restraints excluded: chain p residue 90 MET Chi-restraints excluded: chain q residue 180 VAL Chi-restraints excluded: chain r residue 56 GLU Chi-restraints excluded: chain r residue 187 VAL Chi-restraints excluded: chain t residue 3 ASN Chi-restraints excluded: chain t residue 127 MET Chi-restraints excluded: chain x residue 67 MET Chi-restraints excluded: chain x residue 92 MET Chi-restraints excluded: chain x residue 355 MET Chi-restraints excluded: chain x residue 370 PHE Chi-restraints excluded: chain y residue 14 THR Chi-restraints excluded: chain U residue 92 ASP Chi-restraints excluded: chain U residue 162 VAL Chi-restraints excluded: chain U residue 239 GLU Chi-restraints excluded: chain U residue 564 ASP Chi-restraints excluded: chain U residue 629 THR Chi-restraints excluded: chain U residue 636 VAL Chi-restraints excluded: chain U residue 663 THR Chi-restraints excluded: chain U residue 676 THR Chi-restraints excluded: chain U residue 884 VAL Chi-restraints excluded: chain V residue 101 LEU Chi-restraints excluded: chain V residue 112 VAL Chi-restraints excluded: chain V residue 484 LEU Chi-restraints excluded: chain W residue 81 ASP Chi-restraints excluded: chain W residue 106 GLN Chi-restraints excluded: chain W residue 213 PHE Chi-restraints excluded: chain W residue 309 PHE Chi-restraints excluded: chain W residue 310 THR Chi-restraints excluded: chain W residue 334 GLU Chi-restraints excluded: chain W residue 387 ASP Chi-restraints excluded: chain W residue 422 ASN Chi-restraints excluded: chain X residue 166 LEU Chi-restraints excluded: chain X residue 342 PHE Chi-restraints excluded: chain Y residue 73 MET Chi-restraints excluded: chain Y residue 189 VAL Chi-restraints excluded: chain Y residue 278 VAL Chi-restraints excluded: chain Y residue 291 HIS Chi-restraints excluded: chain Y residue 299 MET Chi-restraints excluded: chain Z residue 96 HIS Chi-restraints excluded: chain Z residue 106 ILE Chi-restraints excluded: chain Z residue 145 HIS Chi-restraints excluded: chain Z residue 157 HIS Chi-restraints excluded: chain Z residue 198 LEU Chi-restraints excluded: chain Z residue 244 GLU Chi-restraints excluded: chain Z residue 250 TYR Chi-restraints excluded: chain a residue 183 VAL Chi-restraints excluded: chain a residue 211 PHE Chi-restraints excluded: chain a residue 248 PHE Chi-restraints excluded: chain a residue 312 MET Chi-restraints excluded: chain b residue 8 VAL Chi-restraints excluded: chain c residue 67 VAL Chi-restraints excluded: chain c residue 99 LEU Chi-restraints excluded: chain c residue 122 LEU Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 169 VAL Chi-restraints excluded: chain c residue 275 VAL Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain d residue 41 THR Chi-restraints excluded: chain f residue 47 GLU Chi-restraints excluded: chain f residue 133 MET Chi-restraints excluded: chain f residue 324 VAL Chi-restraints excluded: chain f residue 340 MET Chi-restraints excluded: chain f residue 582 VAL Chi-restraints excluded: chain f residue 655 LEU Chi-restraints excluded: chain f residue 799 VAL Chi-restraints excluded: chain f residue 801 VAL Chi-restraints excluded: chain e residue 32 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1393 random chunks: chunk 830 optimal weight: 9.9990 chunk 536 optimal weight: 20.0000 chunk 801 optimal weight: 10.0000 chunk 404 optimal weight: 7.9990 chunk 263 optimal weight: 7.9990 chunk 260 optimal weight: 6.9990 chunk 853 optimal weight: 50.0000 chunk 914 optimal weight: 0.9990 chunk 663 optimal weight: 20.0000 chunk 125 optimal weight: 8.9990 chunk 1055 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN ** x 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 207 ASN U 218 GLN ** U 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 707 ASN ** W 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 264 ASN d 149 ASN ** f 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 614 HIS ** f 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 112802 Z= 0.237 Angle : 0.575 16.115 152390 Z= 0.294 Chirality : 0.041 0.251 17249 Planarity : 0.004 0.052 19646 Dihedral : 5.930 168.331 15539 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.86 % Favored : 93.05 % Rotamer: Outliers : 1.33 % Allowed : 16.02 % Favored : 82.65 % 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: 0.30 (0.07), residues: 13990 helix: 1.67 (0.07), residues: 6246 sheet: 0.31 (0.11), residues: 2112 loop : -1.59 (0.08), residues: 5632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP m 215 HIS 0.009 0.001 HIS U 70 PHE 0.021 0.001 PHE a 67 TYR 0.023 0.001 TYR A 429 ARG 0.003 0.000 ARG D 391 *********************** REFINEMENT MACRO_CYCLE 8 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 611 residues out of total 12043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 452 time to evaluate : 9.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LYS cc_start: 0.7453 (ptmt) cc_final: 0.7122 (tptt) REVERT: A 62 LEU cc_start: 0.3879 (OUTLIER) cc_final: 0.2772 (mt) REVERT: A 362 MET cc_start: 0.8577 (ttt) cc_final: 0.8329 (ttp) REVERT: A 420 TYR cc_start: 0.6495 (m-80) cc_final: 0.6211 (m-80) REVERT: C 138 MET cc_start: 0.6631 (mmm) cc_final: 0.6340 (mmm) REVERT: C 230 MET cc_start: 0.8723 (ttm) cc_final: 0.8419 (tpp) REVERT: C 298 ILE cc_start: 0.9144 (OUTLIER) cc_final: 0.8732 (tp) REVERT: C 391 MET cc_start: 0.8687 (pmm) cc_final: 0.8162 (pmm) REVERT: D 296 MET cc_start: 0.9129 (ppp) cc_final: 0.8778 (tmm) REVERT: E 33 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8502 (mm) REVERT: N 164 MET cc_start: 0.8460 (mmm) cc_final: 0.8227 (mtp) REVERT: P 34 MET cc_start: 0.9112 (tmm) cc_final: 0.8886 (tmm) REVERT: j 211 MET cc_start: 0.7259 (ttt) cc_final: 0.7030 (ttm) REVERT: k 59 MET cc_start: 0.8092 (tmm) cc_final: 0.7748 (tmm) REVERT: l 26 MET cc_start: 0.6756 (mmt) cc_final: 0.5988 (mtp) REVERT: l 88 MET cc_start: 0.8571 (mmm) cc_final: 0.8360 (mtp) REVERT: t 103 MET cc_start: 0.8712 (mmm) cc_final: 0.8471 (mmm) REVERT: x 92 MET cc_start: 0.7114 (OUTLIER) cc_final: 0.6687 (tmm) REVERT: x 370 PHE cc_start: 0.9052 (OUTLIER) cc_final: 0.8688 (t80) REVERT: x 488 MET cc_start: 0.6514 (ppp) cc_final: 0.5710 (mmt) REVERT: U 380 THR cc_start: 0.9474 (OUTLIER) cc_final: 0.9132 (p) REVERT: W 106 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.8676 (mp10) REVERT: W 334 GLU cc_start: 0.5162 (OUTLIER) cc_final: 0.4538 (tt0) REVERT: X 254 MET cc_start: 0.8400 (mtm) cc_final: 0.8106 (mtm) REVERT: Z 244 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.6331 (pm20) REVERT: a 141 MET cc_start: 0.8797 (ppp) cc_final: 0.8411 (ppp) REVERT: a 211 PHE cc_start: 0.5429 (OUTLIER) cc_final: 0.5000 (p90) REVERT: b 107 MET cc_start: 0.6040 (tpp) cc_final: 0.5399 (tpp) REVERT: f 505 MET cc_start: 0.4784 (tmm) cc_final: 0.4574 (ttp) outliers start: 159 outliers final: 121 residues processed: 583 average time/residue: 0.8353 time to fit residues: 883.1990 Evaluate side-chains 583 residues out of total 12043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 452 time to evaluate : 10.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 374 ASP Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 196 GLU Chi-restraints excluded: chain H residue 207 ASN Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 201 MET Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 184 ASP Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain K residue 84 ASP Chi-restraints excluded: chain L residue 167 SER Chi-restraints excluded: chain L residue 225 ASP Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 216 VAL Chi-restraints excluded: chain P residue 12 MET Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain Q residue 28 MET Chi-restraints excluded: chain Q residue 190 ASP Chi-restraints excluded: chain R residue 93 MET Chi-restraints excluded: chain R residue 196 HIS Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain g residue 111 VAL Chi-restraints excluded: chain h residue 45 VAL Chi-restraints excluded: chain h residue 181 ASP Chi-restraints excluded: chain i residue 21 VAL Chi-restraints excluded: chain j residue 139 ASP Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain l residue 159 MET Chi-restraints excluded: chain l residue 180 MET Chi-restraints excluded: chain m residue 200 VAL Chi-restraints excluded: chain o residue 6 VAL Chi-restraints excluded: chain o residue 65 LEU Chi-restraints excluded: chain p residue 4 MET Chi-restraints excluded: chain p residue 90 MET Chi-restraints excluded: chain q residue 180 VAL Chi-restraints excluded: chain r residue 56 GLU Chi-restraints excluded: chain r residue 187 VAL Chi-restraints excluded: chain t residue 3 ASN Chi-restraints excluded: chain t residue 127 MET Chi-restraints excluded: chain x residue 67 MET Chi-restraints excluded: chain x residue 92 MET Chi-restraints excluded: chain x residue 355 MET Chi-restraints excluded: chain x residue 370 PHE Chi-restraints excluded: chain y residue 14 THR Chi-restraints excluded: chain U residue 92 ASP Chi-restraints excluded: chain U residue 162 VAL Chi-restraints excluded: chain U residue 239 GLU Chi-restraints excluded: chain U residue 380 THR Chi-restraints excluded: chain U residue 564 ASP Chi-restraints excluded: chain U residue 629 THR Chi-restraints excluded: chain U residue 636 VAL Chi-restraints excluded: chain U residue 663 THR Chi-restraints excluded: chain U residue 676 THR Chi-restraints excluded: chain U residue 884 VAL Chi-restraints excluded: chain V residue 101 LEU Chi-restraints excluded: chain V residue 112 VAL Chi-restraints excluded: chain V residue 484 LEU Chi-restraints excluded: chain W residue 81 ASP Chi-restraints excluded: chain W residue 106 GLN Chi-restraints excluded: chain W residue 171 VAL Chi-restraints excluded: chain W residue 213 PHE Chi-restraints excluded: chain W residue 310 THR Chi-restraints excluded: chain W residue 334 GLU Chi-restraints excluded: chain W residue 387 ASP Chi-restraints excluded: chain W residue 422 ASN Chi-restraints excluded: chain X residue 51 LEU Chi-restraints excluded: chain X residue 342 PHE Chi-restraints excluded: chain Y residue 73 MET Chi-restraints excluded: chain Y residue 189 VAL Chi-restraints excluded: chain Y residue 278 VAL Chi-restraints excluded: chain Y residue 291 HIS Chi-restraints excluded: chain Y residue 299 MET Chi-restraints excluded: chain Z residue 96 HIS Chi-restraints excluded: chain Z residue 145 HIS Chi-restraints excluded: chain Z residue 157 HIS Chi-restraints excluded: chain Z residue 198 LEU Chi-restraints excluded: chain Z residue 244 GLU Chi-restraints excluded: chain Z residue 250 TYR Chi-restraints excluded: chain a residue 175 ASP Chi-restraints excluded: chain a residue 183 VAL Chi-restraints excluded: chain a residue 211 PHE Chi-restraints excluded: chain a residue 248 PHE Chi-restraints excluded: chain a residue 292 THR Chi-restraints excluded: chain a residue 312 MET Chi-restraints excluded: chain b residue 8 VAL Chi-restraints excluded: chain c residue 67 VAL Chi-restraints excluded: chain c residue 99 LEU Chi-restraints excluded: chain c residue 108 VAL Chi-restraints excluded: chain c residue 122 LEU Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 169 VAL Chi-restraints excluded: chain c residue 275 VAL Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain d residue 41 THR Chi-restraints excluded: chain f residue 47 GLU Chi-restraints excluded: chain f residue 133 MET Chi-restraints excluded: chain f residue 324 VAL Chi-restraints excluded: chain f residue 340 MET Chi-restraints excluded: chain f residue 370 MET Chi-restraints excluded: chain f residue 582 VAL Chi-restraints excluded: chain f residue 655 LEU Chi-restraints excluded: chain f residue 771 LEU Chi-restraints excluded: chain f residue 799 VAL Chi-restraints excluded: chain f residue 801 VAL Chi-restraints excluded: chain e residue 32 GLU Chi-restraints excluded: chain e residue 65 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1393 random chunks: chunk 1221 optimal weight: 8.9990 chunk 1286 optimal weight: 5.9990 chunk 1173 optimal weight: 7.9990 chunk 1251 optimal weight: 3.9990 chunk 1285 optimal weight: 6.9990 chunk 753 optimal weight: 8.9990 chunk 545 optimal weight: 20.0000 chunk 982 optimal weight: 9.9990 chunk 383 optimal weight: 7.9990 chunk 1130 optimal weight: 4.9990 chunk 1183 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 369 HIS ** x 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 128 GLN ** U 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 707 ASN ** W 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 44 GLN ** Z 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 614 HIS ** f 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 112802 Z= 0.212 Angle : 0.576 15.606 152390 Z= 0.292 Chirality : 0.041 0.229 17249 Planarity : 0.003 0.051 19646 Dihedral : 5.889 167.453 15539 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.88 % Favored : 93.04 % Rotamer: Outliers : 1.35 % Allowed : 16.23 % Favored : 82.42 % 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: 0.31 (0.07), residues: 13990 helix: 1.67 (0.07), residues: 6240 sheet: 0.32 (0.11), residues: 2099 loop : -1.58 (0.08), residues: 5651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP f 154 HIS 0.020 0.001 HIS f 614 PHE 0.022 0.001 PHE a 67 TYR 0.024 0.001 TYR A 429 ARG 0.003 0.000 ARG j 169 *********************** REFINEMENT MACRO_CYCLE 9 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 613 residues out of total 12043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 451 time to evaluate : 10.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LYS cc_start: 0.7440 (ptmt) cc_final: 0.7107 (tptt) REVERT: A 62 LEU cc_start: 0.3865 (OUTLIER) cc_final: 0.2782 (mt) REVERT: A 362 MET cc_start: 0.8548 (ttt) cc_final: 0.8307 (ttp) REVERT: A 420 TYR cc_start: 0.6516 (m-80) cc_final: 0.6189 (m-80) REVERT: C 138 MET cc_start: 0.6705 (mmm) cc_final: 0.6459 (mmm) REVERT: C 230 MET cc_start: 0.8727 (ttm) cc_final: 0.8419 (tpp) REVERT: C 298 ILE cc_start: 0.9141 (OUTLIER) cc_final: 0.8730 (tp) REVERT: C 391 MET cc_start: 0.8680 (pmm) cc_final: 0.8045 (pmm) REVERT: D 296 MET cc_start: 0.9135 (ppp) cc_final: 0.8794 (tmm) REVERT: E 33 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8503 (mm) REVERT: E 368 MET cc_start: 0.8500 (mmm) cc_final: 0.8261 (mmm) REVERT: N 164 MET cc_start: 0.8457 (mmm) cc_final: 0.8246 (mtp) REVERT: P 34 MET cc_start: 0.9099 (tmm) cc_final: 0.8861 (tmm) REVERT: k 59 MET cc_start: 0.8069 (tmm) cc_final: 0.7759 (tmm) REVERT: l 26 MET cc_start: 0.6751 (mmt) cc_final: 0.6004 (mtp) REVERT: t 103 MET cc_start: 0.8700 (mmm) cc_final: 0.8450 (mmm) REVERT: x 92 MET cc_start: 0.7145 (OUTLIER) cc_final: 0.6698 (tmm) REVERT: x 370 PHE cc_start: 0.9066 (OUTLIER) cc_final: 0.8738 (t80) REVERT: x 488 MET cc_start: 0.6539 (ppp) cc_final: 0.5735 (mmt) REVERT: U 376 MET cc_start: 0.8097 (mmm) cc_final: 0.7680 (mmm) REVERT: U 380 THR cc_start: 0.9472 (OUTLIER) cc_final: 0.9136 (p) REVERT: W 334 GLU cc_start: 0.5237 (OUTLIER) cc_final: 0.4558 (tt0) REVERT: W 375 MET cc_start: 0.7926 (mmp) cc_final: 0.7521 (mmp) REVERT: Z 244 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.6260 (pm20) REVERT: a 141 MET cc_start: 0.8781 (ppp) cc_final: 0.8442 (ppp) REVERT: a 211 PHE cc_start: 0.5428 (OUTLIER) cc_final: 0.4996 (p90) REVERT: b 7 MET cc_start: 0.7387 (tpt) cc_final: 0.6988 (tpt) REVERT: b 107 MET cc_start: 0.6091 (tpp) cc_final: 0.5468 (tpp) REVERT: c 226 MET cc_start: 0.7975 (mmt) cc_final: 0.7725 (mmt) REVERT: f 131 MET cc_start: 0.4797 (tpt) cc_final: 0.4575 (tpt) REVERT: f 216 MET cc_start: 0.6593 (mmm) cc_final: 0.6297 (mmp) REVERT: f 505 MET cc_start: 0.4831 (tmm) cc_final: 0.4622 (ttp) outliers start: 162 outliers final: 132 residues processed: 584 average time/residue: 0.8859 time to fit residues: 937.8507 Evaluate side-chains 591 residues out of total 12043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 450 time to evaluate : 10.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 374 ASP Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 196 GLU Chi-restraints excluded: chain H residue 207 ASN Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 201 MET Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 184 ASP Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain K residue 84 ASP Chi-restraints excluded: chain L residue 225 ASP Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 216 VAL Chi-restraints excluded: chain P residue 12 MET Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain Q residue 28 MET Chi-restraints excluded: chain Q residue 190 ASP Chi-restraints excluded: chain R residue 93 MET Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain R residue 196 HIS Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain g residue 111 VAL Chi-restraints excluded: chain h residue 45 VAL Chi-restraints excluded: chain h residue 181 ASP Chi-restraints excluded: chain i residue 21 VAL Chi-restraints excluded: chain j residue 139 ASP Chi-restraints excluded: chain j residue 173 GLU Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain l residue 159 MET Chi-restraints excluded: chain l residue 180 MET Chi-restraints excluded: chain m residue 200 VAL Chi-restraints excluded: chain n residue 76 VAL Chi-restraints excluded: chain o residue 6 VAL Chi-restraints excluded: chain o residue 65 LEU Chi-restraints excluded: chain p residue 4 MET Chi-restraints excluded: chain p residue 90 MET Chi-restraints excluded: chain q residue 180 VAL Chi-restraints excluded: chain r residue 56 GLU Chi-restraints excluded: chain r residue 187 VAL Chi-restraints excluded: chain t residue 3 ASN Chi-restraints excluded: chain t residue 127 MET Chi-restraints excluded: chain x residue 47 MET Chi-restraints excluded: chain x residue 67 MET Chi-restraints excluded: chain x residue 92 MET Chi-restraints excluded: chain x residue 355 MET Chi-restraints excluded: chain x residue 370 PHE Chi-restraints excluded: chain y residue 14 THR Chi-restraints excluded: chain U residue 92 ASP Chi-restraints excluded: chain U residue 162 VAL Chi-restraints excluded: chain U residue 239 GLU Chi-restraints excluded: chain U residue 380 THR Chi-restraints excluded: chain U residue 629 THR Chi-restraints excluded: chain U residue 636 VAL Chi-restraints excluded: chain U residue 663 THR Chi-restraints excluded: chain U residue 676 THR Chi-restraints excluded: chain U residue 884 VAL Chi-restraints excluded: chain V residue 101 LEU Chi-restraints excluded: chain V residue 112 VAL Chi-restraints excluded: chain V residue 484 LEU Chi-restraints excluded: chain W residue 76 GLU Chi-restraints excluded: chain W residue 81 ASP Chi-restraints excluded: chain W residue 106 GLN Chi-restraints excluded: chain W residue 171 VAL Chi-restraints excluded: chain W residue 213 PHE Chi-restraints excluded: chain W residue 310 THR Chi-restraints excluded: chain W residue 334 GLU Chi-restraints excluded: chain W residue 387 ASP Chi-restraints excluded: chain W residue 422 ASN Chi-restraints excluded: chain X residue 51 LEU Chi-restraints excluded: chain X residue 342 PHE Chi-restraints excluded: chain Y residue 73 MET Chi-restraints excluded: chain Y residue 189 VAL Chi-restraints excluded: chain Y residue 278 VAL Chi-restraints excluded: chain Y residue 291 HIS Chi-restraints excluded: chain Y residue 299 MET Chi-restraints excluded: chain Z residue 96 HIS Chi-restraints excluded: chain Z residue 145 HIS Chi-restraints excluded: chain Z residue 155 PHE Chi-restraints excluded: chain Z residue 157 HIS Chi-restraints excluded: chain Z residue 198 LEU Chi-restraints excluded: chain Z residue 244 GLU Chi-restraints excluded: chain Z residue 250 TYR Chi-restraints excluded: chain a residue 175 ASP Chi-restraints excluded: chain a residue 183 VAL Chi-restraints excluded: chain a residue 211 PHE Chi-restraints excluded: chain a residue 248 PHE Chi-restraints excluded: chain a residue 292 THR Chi-restraints excluded: chain a residue 312 MET Chi-restraints excluded: chain b residue 8 VAL Chi-restraints excluded: chain c residue 36 LEU Chi-restraints excluded: chain c residue 54 MET Chi-restraints excluded: chain c residue 67 VAL Chi-restraints excluded: chain c residue 98 MET Chi-restraints excluded: chain c residue 99 LEU Chi-restraints excluded: chain c residue 108 VAL Chi-restraints excluded: chain c residue 122 LEU Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 169 VAL Chi-restraints excluded: chain c residue 275 VAL Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain d residue 41 THR Chi-restraints excluded: chain f residue 47 GLU Chi-restraints excluded: chain f residue 133 MET Chi-restraints excluded: chain f residue 324 VAL Chi-restraints excluded: chain f residue 340 MET Chi-restraints excluded: chain f residue 370 MET Chi-restraints excluded: chain f residue 582 VAL Chi-restraints excluded: chain f residue 655 LEU Chi-restraints excluded: chain f residue 771 LEU Chi-restraints excluded: chain f residue 799 VAL Chi-restraints excluded: chain f residue 801 VAL Chi-restraints excluded: chain e residue 32 GLU Chi-restraints excluded: chain e residue 65 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1393 random chunks: chunk 1246 optimal weight: 50.0000 chunk 821 optimal weight: 5.9990 chunk 1323 optimal weight: 0.9980 chunk 807 optimal weight: 9.9990 chunk 627 optimal weight: 7.9990 chunk 919 optimal weight: 10.0000 chunk 1387 optimal weight: 8.9990 chunk 1277 optimal weight: 0.3980 chunk 1105 optimal weight: 5.9990 chunk 114 optimal weight: 8.9990 chunk 853 optimal weight: 50.0000 overall best weight: 4.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 707 ASN ** W 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 72 HIS ** Z 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 112802 Z= 0.180 Angle : 0.565 15.410 152390 Z= 0.285 Chirality : 0.041 0.195 17249 Planarity : 0.003 0.051 19646 Dihedral : 5.812 165.038 15539 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.70 % Favored : 93.21 % Rotamer: Outliers : 1.23 % Allowed : 16.51 % Favored : 82.27 % 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: 0.34 (0.07), residues: 13990 helix: 1.70 (0.07), residues: 6255 sheet: 0.34 (0.11), residues: 2092 loop : -1.57 (0.08), residues: 5643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP f 154 HIS 0.009 0.001 HIS U 70 PHE 0.022 0.001 PHE a 67 TYR 0.025 0.001 TYR A 429 ARG 0.003 0.000 ARG B 408 ********************** REFINEMENT MACRO_CYCLE 10 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 600 residues out of total 12043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 453 time to evaluate : 10.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LYS cc_start: 0.7401 (ptmt) cc_final: 0.7061 (tptt) REVERT: A 62 LEU cc_start: 0.3893 (OUTLIER) cc_final: 0.2847 (mt) REVERT: A 362 MET cc_start: 0.8556 (ttt) cc_final: 0.8317 (ttp) REVERT: A 420 TYR cc_start: 0.6441 (m-80) cc_final: 0.6107 (m-80) REVERT: C 138 MET cc_start: 0.6954 (mmm) cc_final: 0.6685 (mmm) REVERT: C 230 MET cc_start: 0.8727 (ttm) cc_final: 0.8416 (tpp) REVERT: C 298 ILE cc_start: 0.9143 (OUTLIER) cc_final: 0.8727 (tp) REVERT: C 391 MET cc_start: 0.8672 (pmm) cc_final: 0.7889 (pmm) REVERT: D 163 MET cc_start: 0.7410 (mmm) cc_final: 0.6934 (mmm) REVERT: D 296 MET cc_start: 0.9142 (ppp) cc_final: 0.8820 (tmm) REVERT: E 33 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8506 (mm) REVERT: E 368 MET cc_start: 0.8542 (mmm) cc_final: 0.8333 (mmm) REVERT: N 164 MET cc_start: 0.8422 (mmm) cc_final: 0.8192 (mtp) REVERT: P 34 MET cc_start: 0.9104 (tmm) cc_final: 0.8865 (tmm) REVERT: k 59 MET cc_start: 0.8040 (tmm) cc_final: 0.7725 (tmm) REVERT: l 26 MET cc_start: 0.6722 (mmt) cc_final: 0.5993 (mtp) REVERT: t 103 MET cc_start: 0.8687 (mmm) cc_final: 0.8441 (mmm) REVERT: x 92 MET cc_start: 0.7165 (OUTLIER) cc_final: 0.6716 (tmm) REVERT: x 370 PHE cc_start: 0.9053 (OUTLIER) cc_final: 0.8799 (t80) REVERT: x 488 MET cc_start: 0.6608 (ppp) cc_final: 0.5822 (mmt) REVERT: U 376 MET cc_start: 0.8101 (mmm) cc_final: 0.7683 (mmm) REVERT: U 380 THR cc_start: 0.9454 (OUTLIER) cc_final: 0.9133 (p) REVERT: W 106 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.8679 (mp10) REVERT: W 334 GLU cc_start: 0.5131 (OUTLIER) cc_final: 0.4480 (tt0) REVERT: Z 244 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.6226 (pm20) REVERT: a 141 MET cc_start: 0.8782 (ppp) cc_final: 0.8520 (ppp) REVERT: a 211 PHE cc_start: 0.5411 (OUTLIER) cc_final: 0.4973 (p90) REVERT: b 7 MET cc_start: 0.7393 (tpt) cc_final: 0.6981 (tpt) REVERT: b 107 MET cc_start: 0.6199 (tpp) cc_final: 0.5583 (tpp) REVERT: c 167 MET cc_start: 0.8668 (tpp) cc_final: 0.8350 (mmm) REVERT: c 226 MET cc_start: 0.7926 (mmt) cc_final: 0.7673 (mmt) REVERT: f 505 MET cc_start: 0.4872 (tmm) cc_final: 0.4669 (ttp) outliers start: 147 outliers final: 123 residues processed: 572 average time/residue: 0.8742 time to fit residues: 904.1020 Evaluate side-chains 584 residues out of total 12043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 451 time to evaluate : 10.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 374 ASP Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain F residue 93 VAL Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 196 GLU Chi-restraints excluded: chain H residue 207 ASN Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 184 ASP Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain K residue 84 ASP Chi-restraints excluded: chain L residue 225 ASP Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 216 VAL Chi-restraints excluded: chain P residue 12 MET Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain Q residue 28 MET Chi-restraints excluded: chain R residue 93 MET Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain g residue 111 VAL Chi-restraints excluded: chain h residue 45 VAL Chi-restraints excluded: chain h residue 181 ASP Chi-restraints excluded: chain i residue 21 VAL Chi-restraints excluded: chain j residue 139 ASP Chi-restraints excluded: chain j residue 173 GLU Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain l residue 159 MET Chi-restraints excluded: chain l residue 180 MET Chi-restraints excluded: chain m residue 200 VAL Chi-restraints excluded: chain n residue 76 VAL Chi-restraints excluded: chain o residue 6 VAL Chi-restraints excluded: chain o residue 65 LEU Chi-restraints excluded: chain p residue 4 MET Chi-restraints excluded: chain p residue 90 MET Chi-restraints excluded: chain q residue 180 VAL Chi-restraints excluded: chain r residue 56 GLU Chi-restraints excluded: chain r residue 187 VAL Chi-restraints excluded: chain t residue 3 ASN Chi-restraints excluded: chain t residue 127 MET Chi-restraints excluded: chain x residue 47 MET Chi-restraints excluded: chain x residue 67 MET Chi-restraints excluded: chain x residue 92 MET Chi-restraints excluded: chain x residue 355 MET Chi-restraints excluded: chain x residue 370 PHE Chi-restraints excluded: chain y residue 14 THR Chi-restraints excluded: chain U residue 92 ASP Chi-restraints excluded: chain U residue 162 VAL Chi-restraints excluded: chain U residue 239 GLU Chi-restraints excluded: chain U residue 380 THR Chi-restraints excluded: chain U residue 629 THR Chi-restraints excluded: chain U residue 636 VAL Chi-restraints excluded: chain U residue 663 THR Chi-restraints excluded: chain U residue 676 THR Chi-restraints excluded: chain U residue 884 VAL Chi-restraints excluded: chain V residue 101 LEU Chi-restraints excluded: chain V residue 112 VAL Chi-restraints excluded: chain V residue 484 LEU Chi-restraints excluded: chain W residue 76 GLU Chi-restraints excluded: chain W residue 81 ASP Chi-restraints excluded: chain W residue 106 GLN Chi-restraints excluded: chain W residue 171 VAL Chi-restraints excluded: chain W residue 213 PHE Chi-restraints excluded: chain W residue 310 THR Chi-restraints excluded: chain W residue 334 GLU Chi-restraints excluded: chain W residue 387 ASP Chi-restraints excluded: chain W residue 422 ASN Chi-restraints excluded: chain X residue 51 LEU Chi-restraints excluded: chain X residue 342 PHE Chi-restraints excluded: chain Y residue 73 MET Chi-restraints excluded: chain Y residue 189 VAL Chi-restraints excluded: chain Y residue 278 VAL Chi-restraints excluded: chain Y residue 291 HIS Chi-restraints excluded: chain Y residue 299 MET Chi-restraints excluded: chain Z residue 96 HIS Chi-restraints excluded: chain Z residue 145 HIS Chi-restraints excluded: chain Z residue 155 PHE Chi-restraints excluded: chain Z residue 157 HIS Chi-restraints excluded: chain Z residue 244 GLU Chi-restraints excluded: chain Z residue 250 TYR Chi-restraints excluded: chain a residue 175 ASP Chi-restraints excluded: chain a residue 183 VAL Chi-restraints excluded: chain a residue 211 PHE Chi-restraints excluded: chain a residue 248 PHE Chi-restraints excluded: chain a residue 280 MET Chi-restraints excluded: chain a residue 292 THR Chi-restraints excluded: chain a residue 312 MET Chi-restraints excluded: chain b residue 8 VAL Chi-restraints excluded: chain c residue 67 VAL Chi-restraints excluded: chain c residue 98 MET Chi-restraints excluded: chain c residue 99 LEU Chi-restraints excluded: chain c residue 108 VAL Chi-restraints excluded: chain c residue 122 LEU Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 169 VAL Chi-restraints excluded: chain c residue 275 VAL Chi-restraints excluded: chain d residue 23 LEU Chi-restraints excluded: chain d residue 41 THR Chi-restraints excluded: chain f residue 47 GLU Chi-restraints excluded: chain f residue 133 MET Chi-restraints excluded: chain f residue 324 VAL Chi-restraints excluded: chain f residue 340 MET Chi-restraints excluded: chain f residue 370 MET Chi-restraints excluded: chain f residue 582 VAL Chi-restraints excluded: chain f residue 655 LEU Chi-restraints excluded: chain f residue 771 LEU Chi-restraints excluded: chain f residue 799 VAL Chi-restraints excluded: chain e residue 65 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1393 random chunks: chunk 677 optimal weight: 10.0000 chunk 877 optimal weight: 10.0000 chunk 1177 optimal weight: 3.9990 chunk 338 optimal weight: 30.0000 chunk 1018 optimal weight: 9.9990 chunk 163 optimal weight: 6.9990 chunk 307 optimal weight: 9.9990 chunk 1106 optimal weight: 10.0000 chunk 463 optimal weight: 20.0000 chunk 1136 optimal weight: 10.0000 chunk 140 optimal weight: 20.0000 overall best weight: 8.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 HIS D 301 GLN ** E 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 12 HIS I 142 HIS ** I 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 120 HIS ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 147 GLN ** x 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 707 ASN V 185 GLN ** W 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 256 ASN ** f 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 758 ASN f 770 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.033661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.026294 restraints weight = 1224250.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.026586 restraints weight = 826132.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.026774 restraints weight = 645973.096| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3098 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.024 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.024 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3094 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 112802 Z= 0.289 Angle : 0.620 15.091 152390 Z= 0.316 Chirality : 0.042 0.219 17249 Planarity : 0.004 0.052 19646 Dihedral : 5.949 157.846 15539 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.43 % Favored : 92.47 % Rotamer: Outliers : 1.25 % Allowed : 16.57 % Favored : 82.17 % 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: 0.22 (0.07), residues: 13990 helix: 1.55 (0.07), residues: 6269 sheet: 0.31 (0.11), residues: 2085 loop : -1.60 (0.08), residues: 5636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP m 215 HIS 0.009 0.001 HIS U 70 PHE 0.022 0.001 PHE a 67 TYR 0.024 0.001 TYR A 429 ARG 0.005 0.000 ARG d 175 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18396.98 seconds wall clock time: 328 minutes 4.00 seconds (19684.00 seconds total)