Starting phenix.real_space_refine on Mon Mar 11 10:52:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3i_32281/03_2024/7w3i_32281_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3i_32281/03_2024/7w3i_32281.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/7w3i_32281/03_2024/7w3i_32281.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3i_32281/03_2024/7w3i_32281.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3i_32281/03_2024/7w3i_32281_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3i_32281/03_2024/7w3i_32281_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 639 5.16 5 C 69826 2.51 5 N 18971 2.21 5 O 21028 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "x PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x GLU 335": "OE1" <-> "OE2" Residue "F ASP 98": "OD1" <-> "OD2" Residue "J GLU 235": "OE1" <-> "OE2" Residue "P PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 33": "OD1" <-> "OD2" Residue "e GLU 34": "OE1" <-> "OE2" Residue "e ASP 35": "OD1" <-> "OD2" Time to flip residues: 0.23s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 110481 Number of models: 1 Model: "" Number of chains: 55 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: "A" Number of atoms: 3229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3229 Classifications: {'peptide': 413} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 23, 'TRANS': 389} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 3112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3112 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 378} 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: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3017 Classifications: {'peptide': 386} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 369} 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: 1889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1889 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 235} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1805 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 221} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "I" Number of atoms: 1958 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 250, 1955 Classifications: {'peptide': 250} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 244} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 250, 1955 Classifications: {'peptide': 250} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 244} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 1981 Chain: "J" Number of atoms: 1880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1880 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 232} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1777 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 225} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "L" Number of atoms: 1866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1866 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 227} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "M" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1876 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 234} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "N" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1514 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 6, 'TRANS': 195} Chain: "O" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1649 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 210} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "P" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1587 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "Q" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1588 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 190} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1559 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 2, 'TRANS': 198} Chain: "S" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1641 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 206} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "T" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1683 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 208} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "g" Number of atoms: 1880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1880 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 235} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "h" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1805 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 221} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "i" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1955 Classifications: {'peptide': 250} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 244} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "j" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1861 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 232} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "k" Number of atoms: 1782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1782 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 225} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "l" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1861 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 227} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "m" Number of atoms: 1881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1881 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 5, 'TRANS': 234} Chain: "n" Number of atoms: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1510 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 195} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "o" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1659 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 210} Chain: "p" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1591 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain: "q" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1588 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 190} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "r" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1559 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 2, 'TRANS': 198} Chain: "s" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1654 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 206} Chain: "t" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1687 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 7, 'TRANS': 208} Chain: "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: 3115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3115 Classifications: {'peptide': 378} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 370} Chain: "Z" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2281 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 9, 'TRANS': 276} Chain: "a" Number of atoms: 2995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2995 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 360} Chain: "b" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1458 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 9, 'TRANS': 181} Chain: "c" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2260 Classifications: {'peptide': 287} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 276} Chain: "d" Number of atoms: 2116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2116 Classifications: {'peptide': 257} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 245} Chain: "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: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 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: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 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: 40.83, per 1000 atoms: 0.37 Number of scatterers: 110481 At special positions: 0 Unit cell: (332.225, 212.35, 219.885, 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 639 16.00 P 16 15.00 O 21028 8.00 N 18971 7.00 C 69826 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=2.05 Simple disulfide: pdb=" SG CYS U 633 " - pdb=" SG CYS U 659 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 30.34 Conformation dependent library (CDL) restraints added in 14.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN c 401 " pdb="ZN ZN c 401 " - pdb=" NE2 HIS c 115 " pdb="ZN ZN c 401 " - pdb=" NE2 HIS c 113 " 27910 Ramachandran restraints generated. 13955 Oldfield, 0 Emsley, 13955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 26274 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: 506 helices and 86 sheets defined 53.5% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 46.61 Creating SS restraints... Processing helix chain 'x' and resid 25 through 37 Processing helix chain 'x' and resid 40 through 45 removed outlier: 4.600A pdb=" N GLN x 44 " --> pdb=" O GLN x 40 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LYS x 45 " --> pdb=" O PRO x 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 40 through 45' Processing helix chain 'x' and resid 94 through 100 removed outlier: 3.515A pdb=" N ALA x 98 " --> pdb=" O GLU x 94 " (cutoff:3.500A) Processing helix chain 'x' and resid 113 through 127 removed outlier: 4.437A pdb=" N ASN x 117 " --> pdb=" O THR x 113 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL x 126 " --> pdb=" O CYS x 122 " (cutoff:3.500A) Proline residue: x 127 - end of helix Processing helix chain 'x' and resid 128 through 136 Processing helix chain 'x' and resid 144 through 166 removed outlier: 4.327A pdb=" N SER x 148 " --> pdb=" O GLY x 144 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ALA x 149 " --> pdb=" O GLU x 145 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N GLN x 150 " --> pdb=" O MET x 146 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N TYR x 151 " --> pdb=" O ALA x 147 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU x 159 " --> pdb=" O ALA x 155 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N PHE x 160 " --> pdb=" O LEU x 156 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASP x 161 " --> pdb=" O ARG x 157 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER x 162 " --> pdb=" O ASP x 158 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS x 165 " --> pdb=" O ASP x 161 " (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 215 Processing helix chain 'x' and resid 220 through 226 removed outlier: 4.574A pdb=" N THR x 226 " --> pdb=" O SER x 222 " (cutoff:3.500A) Processing helix chain 'x' and resid 241 through 247 removed outlier: 3.627A pdb=" N GLN x 245 " --> pdb=" O SER x 241 " (cutoff:3.500A) Processing helix chain 'x' and resid 285 through 295 removed outlier: 4.211A pdb=" N GLN x 295 " --> pdb=" O LYS x 291 " (cutoff:3.500A) Processing helix chain 'x' and resid 365 through 382 removed outlier: 4.464A pdb=" N SER x 369 " --> pdb=" O GLU x 365 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N PHE x 370 " --> pdb=" O LYS x 366 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS x 373 " --> pdb=" O SER x 369 " (cutoff:3.500A) Processing helix chain 'x' and resid 459 through 467 removed outlier: 3.577A pdb=" N ILE x 463 " --> pdb=" O THR x 459 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N SER x 467 " --> pdb=" O ILE x 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 37 removed outlier: 4.269A pdb=" N THR A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N TYR A 36 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N GLY A 37 " --> pdb=" O LEU A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 59 removed outlier: 4.662A pdb=" N GLN A 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N VAL A 48 " --> pdb=" O GLN A 44 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ASP A 51 " --> pdb=" O GLN A 47 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE A 52 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N GLN A 53 " --> pdb=" O GLU A 49 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N GLN A 54 " --> pdb=" O ASP A 50 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU A 55 " --> pdb=" O ASP A 51 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LEU A 56 " --> pdb=" O ILE A 52 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS A 57 " --> pdb=" O GLN A 53 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N LYS A 58 " --> pdb=" O GLN A 54 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ILE A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 89 removed outlier: 4.608A pdb=" N LYS A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLN A 85 " --> pdb=" O ALA A 81 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N LEU A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N GLN A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 165 removed outlier: 3.732A pdb=" N THR A 162 " --> pdb=" O ASP A 158 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N MET A 163 " --> pdb=" O PRO A 159 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N MET A 164 " --> pdb=" O THR A 160 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN A 165 " --> pdb=" O VAL A 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 158 through 165' Processing helix chain 'A' and resid 173 through 178 removed outlier: 3.695A pdb=" N VAL A 177 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 3.770A 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: 4.148A pdb=" N THR A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Proline residue: A 194 - end of helix Processing helix chain 'A' and resid 198 through 205 removed outlier: 5.024A pdb=" N VAL A 202 " --> pdb=" O PRO A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 233 removed outlier: 3.655A pdb=" N THR A 233 " --> pdb=" O VAL A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 268 removed outlier: 3.606A pdb=" N LYS A 267 " --> pdb=" O MET A 263 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LYS A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 281 removed outlier: 4.145A pdb=" N ILE A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 308 removed outlier: 5.388A pdb=" N GLN A 296 " --> pdb=" O ASP A 292 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLY A 308 " --> pdb=" O ASN A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 334 removed outlier: 3.902A pdb=" N MET A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG A 333 " --> pdb=" O PRO A 329 " (cutoff:3.500A) Proline residue: A 334 - end of helix No H-bonds generated for 'chain 'A' and resid 328 through 334' Processing helix chain 'A' and resid 347 through 363 removed outlier: 5.738A pdb=" N ARG A 351 " --> pdb=" O ASP A 347 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR A 352 " --> pdb=" O LEU A 348 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N SER A 361 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N MET A 362 " --> pdb=" O HIS A 358 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N SER A 363 " --> pdb=" O ALA A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 378 removed outlier: 4.901A pdb=" N LEU A 373 " --> pdb=" O ARG A 369 " (cutoff:3.500A) removed outlier: 3.657A 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: 4.043A pdb=" N ALA A 399 " --> pdb=" O PHE A 395 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ARG A 400 " --> pdb=" O ALA A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 418 removed outlier: 3.573A pdb=" N PHE A 409 " --> pdb=" O THR A 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 83 removed outlier: 3.661A pdb=" N LYS B 64 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN B 82 " --> pdb=" O PHE B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 104 removed outlier: 3.768A pdb=" N LYS B 98 " --> pdb=" O GLU B 94 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU B 102 " --> pdb=" O LYS B 98 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG B 103 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N GLY B 104 " --> pdb=" O ASP B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 145 removed outlier: 4.470A pdb=" N LEU B 144 " --> pdb=" O ASP B 140 " (cutoff:3.500A) removed outlier: 7.524A 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 175 removed outlier: 4.559A pdb=" N THR B 172 " --> pdb=" O ASP B 168 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N VAL B 173 " --> pdb=" O PRO B 169 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N MET B 174 " --> pdb=" O LEU B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 206 removed outlier: 5.031A 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: 3.814A pdb=" N GLU B 212 " --> pdb=" O PRO B 208 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLU B 213 " --> pdb=" O GLU B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 243 removed outlier: 3.835A pdb=" N GLN B 242 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N THR B 243 " --> pdb=" O VAL B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 278 removed outlier: 4.627A pdb=" N ALA B 278 " --> pdb=" O ALA B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 293 removed outlier: 4.353A pdb=" N ILE B 290 " --> pdb=" O GLU B 286 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N GLY B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 317 removed outlier: 4.173A pdb=" N ILE B 305 " --> pdb=" O GLY B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 338 removed outlier: 5.101A pdb=" N LEU B 337 " --> pdb=" O ARG B 333 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N ASP B 338 " --> pdb=" O ILE B 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 333 through 338' Processing helix chain 'B' and resid 357 through 373 removed outlier: 4.276A pdb=" N ARG B 371 " --> pdb=" O ILE B 367 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N MET B 372 " --> pdb=" O HIS B 368 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N THR B 373 " --> pdb=" O THR B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 385 removed outlier: 4.197A pdb=" N LEU B 383 " --> pdb=" O THR B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 410 removed outlier: 3.561A pdb=" N GLU B 409 " --> pdb=" O MET B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 428 Processing helix chain 'B' and resid 34 through 39 removed outlier: 3.611A pdb=" N LYS B 39 " --> pdb=" O LYS B 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 65 removed outlier: 4.828A pdb=" N GLU C 29 " --> pdb=" O LEU C 25 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLU C 30 " --> pdb=" O SER C 26 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG C 44 " --> pdb=" O GLN C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 171 removed outlier: 4.537A pdb=" N LEU C 167 " --> pdb=" O GLU C 163 " (cutoff:3.500A) Proline residue: C 168 - end of helix Processing helix chain 'C' and resid 172 through 179 removed outlier: 3.798A pdb=" N GLU C 176 " --> pdb=" O PRO C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 208 removed outlier: 3.945A pdb=" N ASP C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 238 removed outlier: 4.829A pdb=" N PHE C 235 " --> pdb=" O VAL C 231 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL C 236 " --> pdb=" O ARG C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 282 removed outlier: 4.005A pdb=" N GLN C 270 " --> pdb=" O ASP C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 334 Processing helix chain 'C' and resid 343 through 351 removed outlier: 4.286A pdb=" N ILE C 347 " --> pdb=" O ASN C 343 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET C 351 " --> pdb=" O ILE C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 374 removed outlier: 6.963A pdb=" N VAL C 359 " --> pdb=" O SER C 355 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LYS C 360 " --> pdb=" O GLY C 356 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLY C 361 " --> pdb=" O ALA C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 392 removed outlier: 3.789A pdb=" N GLN C 392 " --> pdb=" O ALA C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 18 removed outlier: 4.467A pdb=" N SER C 18 " --> pdb=" O GLU C 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 83 removed outlier: 3.575A pdb=" N LYS D 45 " --> pdb=" O TYR D 41 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU D 47 " --> pdb=" O ARG D 43 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU D 52 " --> pdb=" O GLN D 48 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLN D 57 " --> pdb=" O PHE D 53 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE D 82 " --> pdb=" O GLU D 78 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLN D 83 " --> pdb=" O VAL D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 149 removed outlier: 4.220A pdb=" N ASP D 148 " --> pdb=" O PRO D 144 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N SER D 149 " --> pdb=" O PRO D 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 144 through 149' Processing helix chain 'D' and resid 163 through 168 removed outlier: 3.867A pdb=" N ILE D 167 " --> pdb=" O MET D 163 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N GLY D 168 " --> pdb=" O TYR D 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 163 through 168' Processing helix chain 'D' and resid 170 through 188 removed outlier: 3.634A pdb=" N LYS D 174 " --> pdb=" O MET D 170 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU D 183 " --> pdb=" O GLU D 179 " (cutoff:3.500A) Proline residue: D 184 - end of helix Processing helix chain 'D' and resid 189 through 195 Processing helix chain 'D' and resid 212 through 223 removed outlier: 6.390A pdb=" N ALA D 216 " --> pdb=" O LYS D 212 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LYS D 217 " --> pdb=" O THR D 213 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ALA D 218 " --> pdb=" O MET D 214 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL D 219 " --> pdb=" O LEU D 215 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS D 222 " --> pdb=" O ALA D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 257 removed outlier: 3.552A pdb=" N ARG D 245 " --> pdb=" O GLY D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 272 removed outlier: 5.048A pdb=" N THR D 272 " --> pdb=" O ASP D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 299 removed outlier: 4.112A pdb=" N GLY D 298 " --> pdb=" O ASN D 294 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N PHE D 299 " --> pdb=" O GLN D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 323 removed outlier: 3.735A pdb=" N LEU D 322 " --> pdb=" O ASP D 318 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ARG D 323 " --> pdb=" O PRO D 319 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 318 through 323' Processing helix chain 'D' and resid 338 through 353 removed outlier: 4.208A pdb=" N ARG D 342 " --> pdb=" O ARG D 338 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU D 343 " --> pdb=" O ARG D 339 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LYS D 351 " --> pdb=" O THR D 347 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N MET D 352 " --> pdb=" O ILE D 348 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ASN D 353 " --> pdb=" O THR D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 365 removed outlier: 4.300A pdb=" N TYR D 363 " --> pdb=" O ASP D 359 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N VAL D 364 " --> pdb=" O LEU D 360 " (cutoff:3.500A) removed outlier: 4.953A 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: 3.819A pdb=" N ILE D 375 " --> pdb=" O SER D 371 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASN D 376 " --> pdb=" O GLY D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 407 removed outlier: 3.516A pdb=" N PHE D 399 " --> pdb=" O LEU D 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 52 removed outlier: 4.218A pdb=" N LEU E 17 " --> pdb=" O ARG E 13 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLU E 18 " --> pdb=" O LYS E 14 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE E 22 " --> pdb=" O GLU E 18 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ASP E 23 " --> pdb=" O HIS E 19 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLY E 24 " --> pdb=" O LYS E 20 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ARG E 25 " --> pdb=" O GLU E 21 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LEU E 26 " --> pdb=" O ILE E 22 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLN E 51 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N SER E 52 " --> pdb=" O LYS E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 93 removed outlier: 3.579A pdb=" N LEU E 92 " --> pdb=" O ASP E 88 " (cutoff:3.500A) removed outlier: 5.008A 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 117 through 126 removed outlier: 5.028A pdb=" N ASN E 121 " --> pdb=" O PRO E 117 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N MET E 122 " --> pdb=" O LEU E 118 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N GLU E 125 " --> pdb=" O ASN E 121 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ASP E 126 " --> pdb=" O MET E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 136 removed outlier: 3.933A pdb=" N ILE E 135 " --> pdb=" O SER E 131 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N GLY E 136 " --> pdb=" O TYR E 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 131 through 136' Processing helix chain 'E' and resid 138 through 154 removed outlier: 5.303A pdb=" N ILE E 142 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU E 151 " --> pdb=" O GLU E 147 " (cutoff:3.500A) Proline residue: E 152 - end of helix Processing helix chain 'E' and resid 156 through 163 Processing helix chain 'E' and resid 179 through 192 removed outlier: 3.854A pdb=" N GLN E 190 " --> pdb=" O ALA E 186 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU E 191 " --> pdb=" O VAL E 187 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ASP E 192 " --> pdb=" O ALA E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 204 removed outlier: 6.662A pdb=" N ILE E 203 " --> pdb=" O VAL E 199 " (cutoff:3.500A) removed outlier: 6.264A 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: 4.135A pdb=" N GLN E 226 " --> pdb=" O ALA E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 239 removed outlier: 4.438A pdb=" N ILE E 238 " --> pdb=" O GLU E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 266 Processing helix chain 'E' and resid 286 through 291 removed outlier: 3.617A pdb=" N ARG E 291 " --> pdb=" O PRO E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 318 removed outlier: 3.869A pdb=" N GLY E 318 " --> pdb=" O LYS E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 336 removed outlier: 4.716A pdb=" N ILE E 331 " --> pdb=" O ASP E 327 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ASP E 336 " --> pdb=" O VAL E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 358 removed outlier: 4.910A pdb=" N ALA E 357 " --> pdb=" O PHE E 353 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASP E 358 " --> pdb=" O ALA E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 379 removed outlier: 3.691A pdb=" N PHE E 367 " --> pdb=" O VAL E 363 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS E 379 " --> pdb=" O ALA E 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 31 removed outlier: 4.668A pdb=" N GLY F 30 " --> pdb=" O GLN F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 42 removed outlier: 6.496A pdb=" N GLU F 40 " --> pdb=" O MET F 36 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ILE F 41 " --> pdb=" O SER F 37 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE F 42 " --> pdb=" O THR F 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 36 through 42' Processing helix chain 'F' and resid 48 through 85 removed outlier: 4.034A pdb=" N ILE F 52 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N THR F 85 " --> pdb=" O LYS F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 176 removed outlier: 4.702A 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: 5.098A 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: 4.493A pdb=" N LEU F 204 " --> pdb=" O GLU F 200 " (cutoff:3.500A) Proline residue: F 205 - end of helix Processing helix chain 'F' and resid 209 through 216 Processing helix chain 'F' and resid 232 through 244 removed outlier: 4.048A pdb=" N LEU F 236 " --> pdb=" O GLY F 232 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ALA F 237 " --> pdb=" O LYS F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 279 removed outlier: 6.160A pdb=" N LYS F 266 " --> pdb=" O GLY F 262 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU F 267 " --> pdb=" O ASP F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 292 removed outlier: 4.468A pdb=" N ILE F 291 " --> pdb=" O GLU F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 318 removed outlier: 5.419A pdb=" N GLN F 307 " --> pdb=" O ASP F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 339 removed outlier: 4.625A pdb=" N LEU F 338 " --> pdb=" O ARG F 334 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ASP F 339 " --> pdb=" O VAL F 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 334 through 339' Processing helix chain 'F' and resid 344 through 349 removed outlier: 3.508A pdb=" N ASP F 349 " --> pdb=" O SER F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 371 removed outlier: 5.729A pdb=" N ARG F 362 " --> pdb=" O ASN F 358 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA F 363 " --> pdb=" O GLU F 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 389 removed outlier: 3.952A pdb=" N LEU F 384 " --> pdb=" O ASN F 380 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASP F 389 " --> pdb=" O ALA F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 411 removed outlier: 3.741A pdb=" N ARG F 410 " --> pdb=" O ILE F 406 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY F 411 " --> pdb=" O ALA F 407 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 429 removed outlier: 3.565A pdb=" N ALA F 429 " --> pdb=" O LEU F 425 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 35 removed outlier: 3.603A pdb=" N ILE G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ASN G 33 " --> pdb=" O PHE G 29 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N GLN G 34 " --> pdb=" O LYS G 30 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N GLY G 35 " --> pdb=" O ALA G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 67 removed outlier: 4.144A pdb=" N VAL G 66 " --> pdb=" O ASP G 62 " (cutoff:3.500A) removed outlier: 5.208A 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: 3.947A pdb=" N VAL G 124 " --> pdb=" O ASP G 120 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N TYR G 125 " --> pdb=" O ILE G 121 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR G 126 " --> pdb=" O SER G 122 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN G 127 " --> pdb=" O GLN G 123 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ALA G 129 " --> pdb=" O TYR G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 186 removed outlier: 3.593A pdb=" N LYS G 184 " --> pdb=" O GLU G 180 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS G 185 " --> pdb=" O LYS G 181 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N LYS G 186 " --> pdb=" O LYS G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 207 removed outlier: 3.745A pdb=" N LEU G 202 " --> pdb=" O ALA G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 231 through 245 removed outlier: 3.596A pdb=" N GLU G 244 " --> pdb=" O VAL G 240 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG G 245 " --> pdb=" O ALA G 241 " (cutoff:3.500A) Processing helix chain 'g' and resid 22 through 35 removed outlier: 3.721A pdb=" N ILE g 32 " --> pdb=" O ALA g 28 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ASN g 33 " --> pdb=" O PHE g 29 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLN g 34 " --> pdb=" O LYS g 30 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N GLY g 35 " --> pdb=" O ALA g 31 " (cutoff:3.500A) Processing helix chain 'g' and resid 62 through 67 removed outlier: 4.789A pdb=" N VAL g 66 " --> pdb=" O ASP g 62 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N THR g 67 " --> pdb=" O SER g 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 62 through 67' Processing helix chain 'g' and resid 83 through 105 Processing helix chain 'g' and resid 110 through 129 removed outlier: 4.040A pdb=" N VAL g 124 " --> pdb=" O ASP g 120 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N TYR g 125 " --> pdb=" O ILE g 121 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR g 126 " --> pdb=" O SER g 122 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ALA g 129 " --> pdb=" O TYR g 125 " (cutoff:3.500A) Processing helix chain 'g' and resid 171 through 186 removed outlier: 3.807A pdb=" N LYS g 184 " --> pdb=" O GLU g 180 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LYS g 185 " --> pdb=" O LYS g 181 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LYS g 186 " --> pdb=" O LYS g 182 " (cutoff:3.500A) Processing helix chain 'g' and resid 190 through 207 removed outlier: 3.769A pdb=" N LEU g 202 " --> pdb=" O ALA g 198 " (cutoff:3.500A) Processing helix chain 'g' and resid 231 through 245 removed outlier: 4.876A pdb=" N GLU g 244 " --> pdb=" O VAL g 240 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ARG g 245 " --> pdb=" O ALA g 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 32 removed outlier: 3.599A pdb=" N GLY H 31 " --> pdb=" O ALA H 27 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLY H 32 " --> pdb=" O ALA H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 102 Processing helix chain 'H' and resid 106 through 124 removed outlier: 3.587A pdb=" N THR H 122 " --> pdb=" O MET H 118 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN H 123 " --> pdb=" O GLN H 119 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER H 124 " --> pdb=" O GLU H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 178 removed outlier: 3.871A pdb=" N GLY H 170 " --> pdb=" O ASN H 166 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 199 removed outlier: 4.245A pdb=" N SER H 198 " --> pdb=" O THR H 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 233 removed outlier: 4.920A pdb=" N ALA H 232 " --> pdb=" O ASP H 228 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ILE H 233 " --> pdb=" O TYR H 229 " (cutoff:3.500A) Processing helix chain 'h' and resid 19 through 32 removed outlier: 3.641A pdb=" N GLY h 31 " --> pdb=" O ALA h 27 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLY h 32 " --> pdb=" O ALA h 28 " (cutoff:3.500A) Processing helix chain 'h' and resid 79 through 102 Processing helix chain 'h' and resid 106 through 124 removed outlier: 4.170A pdb=" N THR h 122 " --> pdb=" O MET h 118 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER h 124 " --> pdb=" O GLU h 120 " (cutoff:3.500A) Processing helix chain 'h' and resid 166 through 178 removed outlier: 3.552A pdb=" N LYS h 176 " --> pdb=" O THR h 172 " (cutoff:3.500A) Processing helix chain 'h' and resid 183 through 199 removed outlier: 4.372A pdb=" N SER h 198 " --> pdb=" O THR h 194 " (cutoff:3.500A) Processing helix chain 'h' and resid 222 through 233 Processing helix chain 'I' and resid 2 through 7 removed outlier: 3.884A pdb=" N ASP I 6 " --> pdb=" O SER I 2 " (cutoff:3.500A) removed outlier: 5.751A 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: 3.604A pdb=" N GLU I 22 " --> pdb=" O LEU I 18 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N HIS I 30 " --> pdb=" O GLU I 26 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA I 31 " --> pdb=" O ALA I 27 " (cutoff:3.500A) removed outlier: 5.525A 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: 3.797A pdb=" N ILE I 117 " --> pdb=" O ALA I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 179 Processing helix chain 'I' and resid 185 through 201 removed outlier: 3.607A pdb=" N MET I 201 " --> pdb=" O LEU I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 207 through 212 removed outlier: 3.727A pdb=" N VAL I 211 " --> pdb=" O SER I 207 " (cutoff:3.500A) removed outlier: 5.553A 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: 3.662A pdb=" N VAL I 233 " --> pdb=" O LYS I 229 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS I 251 " --> pdb=" O ALA I 247 " (cutoff:3.500A) Processing helix chain 'i' and resid 2 through 7 removed outlier: 3.751A pdb=" N ASP i 6 " --> pdb=" O SER i 2 " (cutoff:3.500A) removed outlier: 6.083A 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: 4.130A pdb=" N HIS i 30 " --> pdb=" O GLU i 26 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA i 31 " --> pdb=" O ALA i 27 " (cutoff:3.500A) removed outlier: 5.526A 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: 3.596A pdb=" N LEU i 110 " --> pdb=" O PRO i 106 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE i 124 " --> pdb=" O ALA i 120 " (cutoff:3.500A) Processing helix chain 'i' and resid 167 through 179 Processing helix chain 'i' and resid 185 through 201 removed outlier: 3.703A pdb=" N MET i 201 " --> pdb=" O LEU i 197 " (cutoff:3.500A) Processing helix chain 'i' and resid 207 through 212 removed outlier: 4.351A pdb=" N VAL i 211 " --> pdb=" O SER i 207 " (cutoff:3.500A) removed outlier: 5.899A 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: 3.571A pdb=" N LYS i 251 " --> pdb=" O ALA i 247 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 29 removed outlier: 3.690A pdb=" N LYS J 28 " --> pdb=" O GLU J 24 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLY J 29 " --> pdb=" O ALA J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 removed outlier: 3.964A pdb=" N VAL J 59 " --> pdb=" O ASP J 55 " (cutoff:3.500A) removed outlier: 4.239A 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 98 Processing helix chain 'J' and resid 103 through 121 removed outlier: 3.676A pdb=" N ILE J 107 " --> pdb=" O THR J 103 " (cutoff:3.500A) removed outlier: 3.826A 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: 3.769A pdb=" N ILE J 181 " --> pdb=" O THR J 177 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU J 182 " --> pdb=" O ASP J 178 " (cutoff:3.500A) removed outlier: 5.578A 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 199 removed outlier: 3.943A pdb=" N VAL J 198 " --> pdb=" O ALA J 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 221 through 240 removed outlier: 5.071A pdb=" N GLU J 240 " --> pdb=" O LYS J 236 " (cutoff:3.500A) Processing helix chain 'j' and resid 16 through 29 removed outlier: 3.814A pdb=" N LYS j 28 " --> pdb=" O GLU j 24 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLY j 29 " --> pdb=" O ALA j 25 " (cutoff:3.500A) Processing helix chain 'j' and resid 55 through 60 removed outlier: 4.434A pdb=" N VAL j 59 " --> pdb=" O ASP j 55 " (cutoff:3.500A) removed outlier: 4.390A 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 98 Processing helix chain 'j' and resid 103 through 121 removed outlier: 3.734A pdb=" N TYR j 118 " --> pdb=" O LEU j 114 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N THR j 119 " --> pdb=" O LYS j 115 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN j 120 " --> pdb=" O GLN j 116 " (cutoff:3.500A) removed outlier: 3.900A 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: 3.800A pdb=" N ILE j 181 " --> pdb=" O THR j 177 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU j 182 " --> pdb=" O ASP j 178 " (cutoff:3.500A) removed outlier: 4.451A 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 199 removed outlier: 3.739A pdb=" N GLU j 197 " --> pdb=" O LYS j 193 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N VAL j 198 " --> pdb=" O ALA j 194 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL j 199 " --> pdb=" O LEU j 195 " (cutoff:3.500A) Processing helix chain 'j' and resid 221 through 240 Processing helix chain 'K' and resid 21 through 34 removed outlier: 3.698A pdb=" N GLU K 25 " --> pdb=" O LEU K 21 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS K 32 " --> pdb=" O ILE K 28 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LEU K 33 " --> pdb=" O GLU K 29 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N GLY K 34 " --> pdb=" O ALA K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 103 removed outlier: 3.743A pdb=" N ALA K 85 " --> pdb=" O LEU K 81 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS K 86 " --> pdb=" O ILE K 82 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N THR K 87 " --> pdb=" O ALA K 83 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU K 88 " --> pdb=" O ASP K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 121 removed outlier: 4.137A pdb=" N LEU K 119 " --> pdb=" O ALA K 115 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA K 120 " --> pdb=" O VAL K 116 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N LEU K 121 " --> pdb=" O SER K 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 173 through 185 removed outlier: 3.709A 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 230 through 241 removed outlier: 3.926A pdb=" N VAL K 237 " --> pdb=" O GLU K 233 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS K 239 " --> pdb=" O GLU K 235 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ASP K 240 " --> pdb=" O GLU K 236 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE K 241 " --> pdb=" O VAL K 237 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 65 removed outlier: 3.682A pdb=" N ILE K 64 " --> pdb=" O PRO K 61 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N GLU K 65 " --> pdb=" O SER K 62 " (cutoff:3.500A) Processing helix chain 'k' and resid 21 through 34 removed outlier: 3.518A pdb=" N GLU k 25 " --> pdb=" O LEU k 21 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS k 32 " --> pdb=" O ILE k 28 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LEU k 33 " --> pdb=" O GLU k 29 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLY k 34 " --> pdb=" O ALA k 30 " (cutoff:3.500A) Processing helix chain 'k' and resid 81 through 103 removed outlier: 3.877A pdb=" N ALA k 85 " --> pdb=" O LEU k 81 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LYS k 86 " --> pdb=" O ILE k 82 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N THR k 87 " --> pdb=" O ALA k 83 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LEU k 88 " --> pdb=" O ASP k 84 " (cutoff:3.500A) Processing helix chain 'k' and resid 108 through 121 removed outlier: 4.079A pdb=" N LEU k 119 " --> pdb=" O ALA k 115 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA k 120 " --> pdb=" O VAL k 116 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N LEU k 121 " --> pdb=" O SER k 117 " (cutoff:3.500A) Processing helix chain 'k' and resid 173 through 185 removed outlier: 3.973A pdb=" N ALA k 177 " --> pdb=" O ALA k 173 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N SER k 179 " --> pdb=" O GLU k 175 " (cutoff:3.500A) Processing helix chain 'k' and resid 190 through 206 Processing helix chain 'k' and resid 230 through 241 removed outlier: 3.601A pdb=" N ASP k 240 " --> pdb=" O GLU k 236 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ILE k 241 " --> pdb=" O VAL k 237 " (cutoff:3.500A) Processing helix chain 'k' and resid 60 through 65 removed outlier: 5.214A pdb=" N GLU k 65 " --> pdb=" O SER k 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 32 removed outlier: 3.693A pdb=" N ALA L 28 " --> pdb=" O TYR L 24 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL L 29 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS L 30 " --> pdb=" O MET L 26 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN L 31 " --> pdb=" O GLU L 27 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLY L 32 " --> pdb=" O ALA L 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 99 removed outlier: 3.658A pdb=" N ALA L 81 " --> pdb=" O LEU L 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 104 through 123 removed outlier: 4.043A pdb=" N ILE L 118 " --> pdb=" O SER L 114 " (cutoff:3.500A) Proline residue: L 119 - end of helix removed outlier: 3.811A pdb=" N ARG L 122 " --> pdb=" O ILE L 118 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N TYR L 123 " --> pdb=" O PRO L 119 " (cutoff:3.500A) Processing helix chain 'L' and resid 164 through 176 removed outlier: 4.736A pdb=" N ALA L 168 " --> pdb=" O ARG L 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 200 removed outlier: 3.983A pdb=" N GLU L 197 " --> pdb=" O ARG L 193 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N THR L 198 " --> pdb=" O ALA L 194 " (cutoff:3.500A) removed outlier: 4.209A 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 227 through 234 Proline residue: L 231 - end of helix removed outlier: 3.749A pdb=" N GLU L 234 " --> pdb=" O SER L 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 227 through 234' Processing helix chain 'l' and resid 19 through 32 removed outlier: 3.626A pdb=" N GLU l 23 " --> pdb=" O ILE l 19 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS l 30 " --> pdb=" O MET l 26 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN l 31 " --> pdb=" O GLU l 27 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLY l 32 " --> pdb=" O ALA l 28 " (cutoff:3.500A) Processing helix chain 'l' and resid 77 through 99 removed outlier: 4.148A pdb=" N ALA l 81 " --> pdb=" O LEU l 77 " (cutoff:3.500A) Processing helix chain 'l' and resid 104 through 123 removed outlier: 3.932A pdb=" N ILE l 118 " --> pdb=" O SER l 114 " (cutoff:3.500A) Proline residue: l 119 - end of helix removed outlier: 3.636A pdb=" N ARG l 122 " --> pdb=" O ILE l 118 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N TYR l 123 " --> pdb=" O PRO l 119 " (cutoff:3.500A) Processing helix chain 'l' and resid 164 through 176 removed outlier: 4.610A pdb=" N ALA l 168 " --> pdb=" O ARG l 164 " (cutoff:3.500A) Processing helix chain 'l' and resid 183 through 200 removed outlier: 3.758A pdb=" N GLU l 197 " --> pdb=" O ARG l 193 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N THR l 198 " --> pdb=" O ALA l 194 " (cutoff:3.500A) removed outlier: 4.110A 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 227 through 234 Proline residue: l 231 - end of helix Processing helix chain 'M' and resid 20 through 33 removed outlier: 3.759A pdb=" N GLU M 24 " --> pdb=" O VAL M 20 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN M 32 " --> pdb=" O LYS M 28 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N SER M 33 " --> pdb=" O ALA M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 102 Processing helix chain 'M' and resid 107 through 124 removed outlier: 4.102A pdb=" N TYR M 122 " --> pdb=" O TYR M 118 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N THR M 123 " --> pdb=" O VAL M 119 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LEU M 124 " --> pdb=" O HIS M 120 " (cutoff:3.500A) Processing helix chain 'M' and resid 168 through 179 removed outlier: 4.404A pdb=" N LYS M 178 " --> pdb=" O THR M 174 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LEU M 179 " --> pdb=" O GLU M 175 " (cutoff:3.500A) Processing helix chain 'M' and resid 185 through 201 removed outlier: 3.558A pdb=" N ILE M 189 " --> pdb=" O THR M 185 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL M 190 " --> pdb=" O CYS M 186 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LYS M 191 " --> pdb=" O ARG M 187 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU M 192 " --> pdb=" O ASP M 188 " (cutoff:3.500A) Processing helix chain 'M' and resid 228 through 244 removed outlier: 3.820A pdb=" N LYS M 244 " --> pdb=" O LYS M 240 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 10 removed outlier: 6.217A pdb=" N ASP M 8 " --> pdb=" O THR M 5 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N LEU M 9 " --> pdb=" O GLY M 6 " (cutoff:3.500A) removed outlier: 5.151A 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 'm' and resid 20 through 33 removed outlier: 3.687A pdb=" N GLU m 24 " --> pdb=" O VAL m 20 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN m 32 " --> pdb=" O LYS m 28 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N SER m 33 " --> pdb=" O ALA m 29 " (cutoff:3.500A) Processing helix chain 'm' and resid 80 through 102 Processing helix chain 'm' and resid 107 through 124 removed outlier: 4.190A pdb=" N TYR m 122 " --> pdb=" O TYR m 118 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N THR m 123 " --> pdb=" O VAL m 119 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LEU m 124 " --> pdb=" O HIS m 120 " (cutoff:3.500A) Processing helix chain 'm' and resid 168 through 179 removed outlier: 5.301A pdb=" N LYS m 178 " --> pdb=" O THR m 174 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LEU m 179 " --> pdb=" O GLU m 175 " (cutoff:3.500A) Processing helix chain 'm' and resid 185 through 201 removed outlier: 3.884A pdb=" N LYS m 191 " --> pdb=" O ARG m 187 " (cutoff:3.500A) Processing helix chain 'm' and resid 228 through 244 Processing helix chain 'm' and resid 5 through 10 removed outlier: 5.403A pdb=" N ASP m 8 " --> pdb=" O THR m 5 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N LEU m 9 " --> pdb=" O GLY m 6 " (cutoff:3.500A) removed outlier: 5.344A 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: 3.572A pdb=" N ALA N 79 " --> pdb=" O LEU N 75 " (cutoff:3.500A) Processing helix chain 'N' and resid 131 through 143 removed outlier: 4.763A pdb=" N ILE N 135 " --> pdb=" O GLY N 131 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N TYR N 136 " --> pdb=" O SER N 132 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N GLY N 137 " --> pdb=" O SER N 133 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N TYR N 138 " --> pdb=" O TYR N 134 " (cutoff:3.500A) Processing helix chain 'N' and resid 148 through 167 Processing helix chain 'n' and resid 48 through 71 Processing helix chain 'n' and resid 75 through 91 removed outlier: 3.945A pdb=" N TYR n 90 " --> pdb=" O MET n 86 " (cutoff:3.500A) Processing helix chain 'n' and resid 131 through 143 removed outlier: 4.722A pdb=" N ILE n 135 " --> pdb=" O GLY n 131 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N TYR n 136 " --> pdb=" O SER n 132 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N GLY n 137 " --> pdb=" O SER n 133 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N TYR n 138 " --> pdb=" O TYR n 134 " (cutoff:3.500A) Processing helix chain 'n' and resid 148 through 167 Processing helix chain 'O' and resid 48 through 71 Processing helix chain 'O' and resid 75 through 91 removed outlier: 3.667A pdb=" N ALA O 79 " --> pdb=" O ARG O 75 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR O 90 " --> pdb=" O MET O 86 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN O 91 " --> pdb=" O LEU O 87 " (cutoff:3.500A) Processing helix chain 'O' and resid 130 through 142 removed outlier: 3.641A pdb=" N VAL O 137 " --> pdb=" O ALA O 133 " (cutoff:3.500A) Processing helix chain 'O' and resid 147 through 166 Processing helix chain 'o' and resid 48 through 71 Processing helix chain 'o' and resid 75 through 91 removed outlier: 3.627A pdb=" N ALA o 79 " --> pdb=" O ARG o 75 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR o 90 " --> pdb=" O MET o 86 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN o 91 " --> pdb=" O LEU o 87 " (cutoff:3.500A) Processing helix chain 'o' and resid 130 through 142 Processing helix chain 'o' and resid 147 through 166 removed outlier: 3.509A pdb=" N ASN o 165 " --> pdb=" O ALA o 161 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP o 166 " --> pdb=" O GLY o 162 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 8 removed outlier: 3.625A pdb=" N TYR P 6 " --> pdb=" O SER P 2 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ASN P 7 " --> pdb=" O ILE P 3 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY P 8 " --> pdb=" O MET P 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 2 through 8' Processing helix chain 'P' and resid 56 through 79 Processing helix chain 'P' and resid 83 through 99 removed outlier: 4.308A pdb=" N LYS P 98 " --> pdb=" O LEU P 94 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ARG P 99 " --> pdb=" O LEU P 95 " (cutoff:3.500A) Processing helix chain 'P' and resid 142 through 154 removed outlier: 3.844A pdb=" N SER P 152 " --> pdb=" O GLY P 148 " (cutoff:3.500A) Processing helix chain 'P' and resid 159 through 179 removed outlier: 3.988A pdb=" N ARG P 177 " --> pdb=" O ASN P 173 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP P 178 " --> pdb=" O ALA P 174 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N ALA P 179 " --> pdb=" O VAL P 175 " (cutoff:3.500A) Processing helix chain 'p' and resid 2 through 8 removed outlier: 3.988A pdb=" N TYR p 6 " --> pdb=" O SER p 2 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ASN p 7 " --> pdb=" O ILE p 3 " (cutoff:3.500A) removed outlier: 4.405A 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: 3.677A pdb=" N LEU p 73 " --> pdb=" O PHE p 69 " (cutoff:3.500A) Processing helix chain 'p' and resid 83 through 99 removed outlier: 4.227A pdb=" N LYS p 98 " --> pdb=" O LEU p 94 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ARG p 99 " --> pdb=" O LEU p 95 " (cutoff:3.500A) Processing helix chain 'p' and resid 142 through 154 removed outlier: 3.865A pdb=" N SER p 152 " --> pdb=" O GLY p 148 " (cutoff:3.500A) Processing helix chain 'p' and resid 159 through 179 removed outlier: 4.229A pdb=" N ARG p 177 " --> pdb=" O ASN p 173 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP p 178 " --> pdb=" O ALA p 174 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N ALA p 179 " --> pdb=" O VAL p 175 " (cutoff:3.500A) Processing helix chain 'Q' and resid 49 through 72 removed outlier: 3.591A pdb=" N THR Q 53 " --> pdb=" O GLU Q 49 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL Q 54 " --> pdb=" O ALA Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 93 removed outlier: 3.515A pdb=" N CYS Q 91 " --> pdb=" O ASN Q 87 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU Q 92 " --> pdb=" O LEU Q 88 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ARG Q 93 " --> pdb=" O ALA Q 89 " (cutoff:3.500A) Processing helix chain 'Q' and resid 133 through 147 removed outlier: 4.481A pdb=" N PHE Q 137 " --> pdb=" O GLY Q 133 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU Q 138 " --> pdb=" O TYR Q 134 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N SER Q 141 " --> pdb=" O PHE Q 137 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ILE Q 142 " --> pdb=" O LEU Q 138 " (cutoff:3.500A) Processing helix chain 'Q' and resid 152 through 171 Processing helix chain 'q' and resid 49 through 72 removed outlier: 3.589A pdb=" N THR q 53 " --> pdb=" O GLU q 49 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N VAL q 54 " --> pdb=" O ALA q 50 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN q 55 " --> pdb=" O GLY q 51 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE q 56 " --> pdb=" O ASP q 52 " (cutoff:3.500A) Processing helix chain 'q' and resid 76 through 93 removed outlier: 3.952A pdb=" N CYS q 91 " --> pdb=" O ASN q 87 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU q 92 " --> pdb=" O LEU q 88 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ARG q 93 " --> pdb=" O ALA q 89 " (cutoff:3.500A) Processing helix chain 'q' and resid 133 through 147 removed outlier: 4.664A pdb=" N PHE q 137 " --> pdb=" O GLY q 133 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU q 138 " --> pdb=" O TYR q 134 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N SER q 141 " --> pdb=" O PHE q 137 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE q 142 " --> pdb=" O LEU q 138 " (cutoff:3.500A) Processing helix chain 'q' and resid 152 through 171 Processing helix chain 'R' and resid 48 through 71 Processing helix chain 'R' and resid 75 through 91 removed outlier: 4.026A pdb=" N GLN R 89 " --> pdb=" O ASN R 85 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TYR R 90 " --> pdb=" O MET R 86 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS R 91 " --> pdb=" O VAL R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 143 removed outlier: 3.730A pdb=" N ALA R 135 " --> pdb=" O GLY R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 148 through 167 Processing helix chain 'R' and resid 191 through 201 Processing helix chain 'r' and resid 48 through 71 Processing helix chain 'r' and resid 75 through 91 removed outlier: 4.207A pdb=" N GLN r 89 " --> pdb=" O ASN r 85 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N TYR r 90 " --> pdb=" O MET r 86 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LYS r 91 " --> pdb=" O VAL r 87 " (cutoff:3.500A) Processing helix chain 'r' and resid 131 through 143 removed outlier: 3.644A pdb=" N ALA r 135 " --> pdb=" O GLY r 131 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG r 141 " --> pdb=" O GLY r 137 " (cutoff:3.500A) Processing helix chain 'r' and resid 148 through 167 Processing helix chain 'r' and resid 191 through 201 Processing helix chain 'S' and resid 57 through 79 Processing helix chain 'S' and resid 84 through 101 removed outlier: 3.934A pdb=" N ARG S 99 " --> pdb=" O ILE S 95 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ARG S 100 " --> pdb=" O LEU S 96 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N PHE S 101 " --> pdb=" O TYR S 97 " (cutoff:3.500A) Processing helix chain 'S' and resid 141 through 153 Proline residue: S 147 - end of helix Processing helix chain 'S' and resid 167 through 186 removed outlier: 3.751A pdb=" N ARG S 185 " --> pdb=" O SER S 181 " (cutoff:3.500A) Processing helix chain 's' and resid 57 through 79 Processing helix chain 's' and resid 84 through 101 removed outlier: 4.024A pdb=" N ARG s 99 " --> pdb=" O ILE s 95 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ARG s 100 " --> pdb=" O LEU s 96 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N PHE s 101 " --> pdb=" O TYR s 97 " (cutoff:3.500A) Processing helix chain 's' and resid 141 through 153 Proline residue: s 147 - end of helix Processing helix chain 's' and resid 167 through 186 removed outlier: 3.778A pdb=" N GLU s 184 " --> pdb=" O ILE s 180 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ARG s 185 " --> pdb=" O SER s 181 " (cutoff:3.500A) Processing helix chain 'T' and resid 56 through 78 removed outlier: 3.833A pdb=" N LEU T 77 " --> pdb=" O ASP T 73 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLY T 78 " --> pdb=" O GLU T 74 " (cutoff:3.500A) Processing helix chain 'T' and resid 84 through 103 removed outlier: 3.607A pdb=" N LYS T 102 " --> pdb=" O SER T 98 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N MET T 103 " --> pdb=" O ARG T 99 " (cutoff:3.500A) Processing helix chain 'T' and resid 140 through 158 removed outlier: 4.188A pdb=" N TYR T 144 " --> pdb=" O GLY T 140 " (cutoff:3.500A) removed outlier: 4.796A 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: 4.959A pdb=" N HIS T 213 " --> pdb=" O TRP T 209 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N MET T 214 " --> pdb=" O ASP T 210 " (cutoff:3.500A) removed outlier: 4.534A 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: 3.531A pdb=" N PHE t 60 " --> pdb=" O ASP t 56 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU t 77 " --> pdb=" O ASP t 73 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLY t 78 " --> pdb=" O GLU t 74 " (cutoff:3.500A) Processing helix chain 't' and resid 84 through 103 removed outlier: 3.626A pdb=" N LYS t 102 " --> pdb=" O SER t 98 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N MET t 103 " --> pdb=" O ARG t 99 " (cutoff:3.500A) Processing helix chain 't' and resid 140 through 158 removed outlier: 4.339A pdb=" N TYR t 144 " --> pdb=" O GLY t 140 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLN t 147 " --> pdb=" O ALA t 143 " (cutoff:3.500A) Proline residue: t 148 - end of helix removed outlier: 3.695A 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: 4.969A pdb=" N HIS t 213 " --> pdb=" O TRP t 209 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N MET t 214 " --> pdb=" O ASP t 210 " (cutoff:3.500A) removed outlier: 3.974A 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 'y' and resid 22 through 34 Processing helix chain 'y' and resid 37 through 42 removed outlier: 3.883A pdb=" N GLN y 41 " --> pdb=" O PRO y 37 " (cutoff:3.500A) removed outlier: 5.286A 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 'U' and resid 8 through 14 removed outlier: 4.379A pdb=" N LEU U 12 " --> pdb=" O ILE U 8 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP U 13 " --> pdb=" O ILE U 9 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLU U 14 " --> pdb=" O SER U 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 8 through 14' Processing helix chain 'U' and resid 16 through 31 removed outlier: 3.990A pdb=" N LYS U 26 " --> pdb=" O PHE U 22 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU U 27 " --> pdb=" O ALA U 23 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASN U 28 " --> pdb=" O LEU U 24 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ALA U 29 " --> pdb=" O HIS U 25 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL U 30 " --> pdb=" O LYS U 26 " (cutoff:3.500A) Processing helix chain 'U' and resid 34 through 42 removed outlier: 3.600A pdb=" N ILE U 38 " --> pdb=" O PHE U 34 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER U 39 " --> pdb=" O TRP U 35 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU U 40 " --> pdb=" O ALA U 36 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N SER U 41 " --> pdb=" O GLU U 37 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL U 42 " --> pdb=" O ILE U 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 34 through 42' Processing helix chain 'U' and resid 43 through 51 Processing helix chain 'U' and resid 56 through 72 Processing helix chain 'U' and resid 73 through 85 removed outlier: 3.594A pdb=" N SER U 77 " --> pdb=" O ALA U 73 " (cutoff:3.500A) Processing helix chain 'U' and resid 86 through 91 removed outlier: 4.027A pdb=" N VAL U 90 " --> pdb=" O ASP U 86 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ASN U 91 " --> pdb=" O LEU U 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 86 through 91' Processing helix chain 'U' and resid 94 through 119 Proline residue: U 119 - end of helix Processing helix chain 'U' and resid 127 through 145 removed outlier: 3.878A pdb=" N GLU U 131 " --> pdb=" O ASP U 127 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS U 136 " --> pdb=" O GLY U 132 " (cutoff:3.500A) Processing helix chain 'U' and resid 146 through 158 removed outlier: 3.940A pdb=" N GLU U 156 " --> pdb=" O GLY U 152 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ARG U 158 " --> pdb=" O ALA U 154 " (cutoff:3.500A) Processing helix chain 'U' and resid 159 through 169 removed outlier: 3.689A pdb=" N PHE U 163 " --> pdb=" O ARG U 159 " (cutoff:3.500A) Processing helix chain 'U' and resid 174 through 187 removed outlier: 4.712A pdb=" N ALA U 178 " --> pdb=" O PRO U 174 " (cutoff:3.500A) Processing helix chain 'U' and resid 191 through 209 removed outlier: 3.959A pdb=" N ASN U 195 " --> pdb=" O LYS U 191 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LYS U 196 " --> pdb=" O GLN U 192 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL U 202 " --> pdb=" O LEU U 198 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N LYS U 203 " --> pdb=" O ARG U 199 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE U 204 " --> pdb=" O VAL U 200 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU U 208 " --> pdb=" O ILE U 204 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N GLU U 209 " --> pdb=" O TYR U 205 " (cutoff:3.500A) Processing helix chain 'U' and resid 214 through 224 removed outlier: 3.525A pdb=" N GLN U 218 " --> pdb=" O ILE U 214 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU U 220 " --> pdb=" O VAL U 216 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ILE U 221 " --> pdb=" O CYS U 217 " (cutoff:3.500A) Processing helix chain 'U' and resid 225 through 240 removed outlier: 3.931A pdb=" N VAL U 229 " --> pdb=" O ASP U 225 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP U 240 " --> pdb=" O LEU U 236 " (cutoff:3.500A) Processing helix chain 'U' and resid 241 through 256 Processing helix chain 'U' and resid 257 through 270 removed outlier: 3.941A pdb=" N LEU U 261 " --> pdb=" O SER U 257 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N SER U 262 " --> pdb=" O GLN U 258 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER U 263 " --> pdb=" O GLN U 259 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR U 270 " --> pdb=" O GLN U 266 " (cutoff:3.500A) Processing helix chain 'U' and resid 320 through 331 removed outlier: 3.553A pdb=" N LYS U 324 " --> pdb=" O ASP U 320 " (cutoff:3.500A) Processing helix chain 'U' and resid 332 through 346 removed outlier: 4.059A pdb=" N ASN U 346 " --> pdb=" O LEU U 342 " (cutoff:3.500A) Processing helix chain 'U' and resid 349 through 360 removed outlier: 4.165A pdb=" N LEU U 353 " --> pdb=" O ASP U 349 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL U 360 " --> pdb=" O THR U 356 " (cutoff:3.500A) Processing helix chain 'U' and resid 364 through 378 removed outlier: 3.785A pdb=" N ALA U 368 " --> pdb=" O VAL U 364 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N SER U 374 " --> pdb=" O VAL U 370 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE U 375 " --> pdb=" O ILE U 371 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N MET U 376 " --> pdb=" O ALA U 372 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N HIS U 377 " --> pdb=" O ASN U 373 " (cutoff:3.500A) Processing helix chain 'U' and resid 383 through 388 removed outlier: 3.597A pdb=" N ARG U 387 " --> pdb=" O ASP U 383 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASP U 388 " --> pdb=" O GLN U 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 383 through 388' Processing helix chain 'U' and resid 389 through 396 removed outlier: 5.325A pdb=" N LEU U 393 " --> pdb=" O ASN U 389 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ALA U 396 " --> pdb=" O TRP U 392 " (cutoff:3.500A) Processing helix chain 'U' and resid 398 through 413 removed outlier: 6.251A pdb=" N PHE U 402 " --> pdb=" O ASN U 398 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR U 403 " --> pdb=" O TRP U 399 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR U 405 " --> pdb=" O LYS U 401 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY U 409 " --> pdb=" O THR U 405 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL U 410 " --> pdb=" O ALA U 406 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N HIS U 412 " --> pdb=" O LEU U 408 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS U 413 " --> pdb=" O GLY U 409 " (cutoff:3.500A) Processing helix chain 'U' and resid 418 through 433 removed outlier: 3.526A pdb=" N LEU U 427 " --> pdb=" O MET U 423 " (cutoff:3.500A) Proline residue: U 428 - end of helix removed outlier: 3.654A pdb=" N THR U 431 " --> pdb=" O LEU U 427 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N SER U 432 " --> pdb=" O PRO U 428 " (cutoff:3.500A) Proline residue: U 433 - end of helix Processing helix chain 'U' and resid 435 through 451 removed outlier: 4.150A pdb=" N GLU U 439 " --> pdb=" O SER U 435 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA U 451 " --> pdb=" O GLY U 447 " (cutoff:3.500A) Processing helix chain 'U' and resid 455 through 468 removed outlier: 3.716A pdb=" N GLN U 464 " --> pdb=" O TYR U 460 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA U 468 " --> pdb=" O GLN U 464 " (cutoff:3.500A) Processing helix chain 'U' and resid 472 through 486 Processing helix chain 'U' and resid 490 through 504 removed outlier: 3.876A pdb=" N GLN U 503 " --> pdb=" O THR U 499 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ASP U 504 " --> pdb=" O ASN U 500 " (cutoff:3.500A) Processing helix chain 'U' and resid 505 through 521 removed outlier: 4.958A pdb=" N GLU U 510 " --> pdb=" O ALA U 506 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ALA U 511 " --> pdb=" O VAL U 507 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N MET U 520 " --> pdb=" O LEU U 516 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU U 521 " --> pdb=" O GLY U 517 " (cutoff:3.500A) Processing helix chain 'U' and resid 525 through 539 removed outlier: 3.878A pdb=" N GLN U 537 " --> pdb=" O VAL U 533 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLU U 538 " --> pdb=" O GLY U 534 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N THR U 539 " --> pdb=" O TYR U 535 " (cutoff:3.500A) Processing helix chain 'U' and resid 541 through 557 removed outlier: 4.807A pdb=" N LEU U 545 " --> pdb=" O HIS U 541 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET U 556 " --> pdb=" O ILE U 552 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N TYR U 557 " --> pdb=" O ALA U 553 " (cutoff:3.500A) Processing helix chain 'U' and resid 563 through 573 removed outlier: 4.137A pdb=" N ARG U 572 " --> pdb=" O GLU U 568 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASP U 573 " --> pdb=" O SER U 569 " (cutoff:3.500A) Processing helix chain 'U' and resid 575 through 591 removed outlier: 3.521A pdb=" N CYS U 591 " --> pdb=" O ALA U 587 " (cutoff:3.500A) Processing helix chain 'U' and resid 595 through 609 removed outlier: 4.183A pdb=" N VAL U 607 " --> pdb=" O LEU U 603 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP U 609 " --> pdb=" O VAL U 605 " (cutoff:3.500A) Processing helix chain 'U' and resid 611 through 627 removed outlier: 4.169A pdb=" N LEU U 622 " --> pdb=" O ALA U 618 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N GLY U 623 " --> pdb=" O VAL U 619 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N PHE U 624 " --> pdb=" O GLU U 620 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ILE U 625 " --> pdb=" O SER U 621 " (cutoff:3.500A) Processing helix chain 'U' and resid 629 through 643 removed outlier: 3.705A pdb=" N CYS U 633 " --> pdb=" O THR U 629 " (cutoff:3.500A) Proline residue: U 634 - end of helix removed outlier: 5.736A pdb=" N LEU U 639 " --> pdb=" O SER U 635 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N LEU U 640 " --> pdb=" O VAL U 636 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLU U 642 " --> pdb=" O SER U 638 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N SER U 643 " --> pdb=" O LEU U 639 " (cutoff:3.500A) Processing helix chain 'U' and resid 645 through 661 removed outlier: 3.607A pdb=" N ARG U 649 " --> pdb=" O ASN U 645 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ALA U 661 " --> pdb=" O GLY U 657 " (cutoff:3.500A) Processing helix chain 'U' and resid 665 through 677 removed outlier: 6.538A pdb=" N ILE U 669 " --> pdb=" O ASN U 665 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ASN U 670 " --> pdb=" O LYS U 666 " (cutoff:3.500A) Proline residue: U 674 - end of helix removed outlier: 4.904A pdb=" N ASN U 677 " --> pdb=" O GLU U 673 " (cutoff:3.500A) Processing helix chain 'U' and resid 680 through 696 removed outlier: 3.565A pdb=" N ARG U 684 " --> pdb=" O VAL U 680 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET U 695 " --> pdb=" O SER U 691 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ILE U 696 " --> pdb=" O ALA U 692 " (cutoff:3.500A) Processing helix chain 'U' and resid 699 through 704 removed outlier: 3.803A 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 removed outlier: 3.729A pdb=" N ASN U 718 " --> pdb=" O SER U 714 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP U 719 " --> pdb=" O LYS U 715 " (cutoff:3.500A) Processing helix chain 'U' and resid 723 through 739 removed outlier: 3.666A pdb=" N ASP U 738 " --> pdb=" O GLN U 734 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA U 739 " --> pdb=" O GLY U 735 " (cutoff:3.500A) Processing helix chain 'U' and resid 756 through 773 removed outlier: 4.515A pdb=" N PHE U 769 " --> pdb=" O VAL U 765 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N TRP U 770 " --> pdb=" O PHE U 766 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N PHE U 771 " --> pdb=" O THR U 767 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N TRP U 772 " --> pdb=" O GLN U 768 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE U 773 " --> pdb=" O PHE U 769 " (cutoff:3.500A) Processing helix chain 'U' and resid 778 through 784 removed outlier: 4.152A pdb=" N ALA U 782 " --> pdb=" O PHE U 778 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N THR U 784 " --> pdb=" O SER U 780 " (cutoff:3.500A) Processing helix chain 'U' and resid 838 through 852 removed outlier: 3.789A pdb=" N LYS U 842 " --> pdb=" O LYS U 838 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLU U 843 " --> pdb=" O ALA U 839 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LYS U 849 " --> pdb=" O GLU U 845 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N GLU U 850 " --> pdb=" O LYS U 846 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLU U 851 " --> pdb=" O GLU U 847 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU U 852 " --> pdb=" O LYS U 848 " (cutoff:3.500A) Processing helix chain 'U' and resid 863 through 872 removed outlier: 3.850A pdb=" N LYS U 867 " --> pdb=" O GLU U 863 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LYS U 868 " --> pdb=" O GLU U 864 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLU U 870 " --> pdb=" O GLU U 866 " (cutoff:3.500A) Proline residue: U 871 - end of helix Processing helix chain 'U' and resid 885 through 890 removed outlier: 4.221A pdb=" N LYS U 890 " --> pdb=" O PRO U 886 " (cutoff:3.500A) Processing helix chain 'V' and resid 54 through 89 Processing helix chain 'V' and resid 90 through 105 removed outlier: 4.310A pdb=" N VAL V 94 " --> pdb=" O GLU V 90 " (cutoff:3.500A) Proline residue: V 102 - end of helix Processing helix chain 'V' and resid 109 through 121 Processing helix chain 'V' and resid 125 through 136 removed outlier: 3.840A pdb=" N ASP V 129 " --> pdb=" O ASN V 125 " (cutoff:3.500A) Proline residue: V 133 - end of helix removed outlier: 5.326A 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 181 through 199 removed outlier: 4.087A pdb=" N GLN V 198 " --> pdb=" O LYS V 194 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ASN V 199 " --> pdb=" O ILE V 195 " (cutoff:3.500A) Processing helix chain 'V' and resid 200 through 222 removed outlier: 4.281A pdb=" N ASP V 204 " --> pdb=" O ARG V 200 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N LEU V 205 " --> pdb=" O ARG V 201 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N VAL V 206 " --> pdb=" O ALA V 202 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS V 209 " --> pdb=" O LEU V 205 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE V 220 " --> pdb=" O ARG V 216 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU V 221 " --> pdb=" O VAL V 217 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP V 222 " --> pdb=" O TYR V 218 " (cutoff:3.500A) Processing helix chain 'V' and resid 225 through 242 removed outlier: 4.450A pdb=" N SER V 229 " --> pdb=" O ASP V 225 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N PHE V 230 " --> pdb=" O VAL V 226 " (cutoff:3.500A) Processing helix chain 'V' and resid 243 through 262 Processing helix chain 'V' and resid 263 through 274 removed outlier: 3.750A pdb=" N LYS V 273 " --> pdb=" O LYS V 269 " (cutoff:3.500A) Processing helix chain 'V' and resid 281 through 300 removed outlier: 3.695A pdb=" N LEU V 300 " --> pdb=" O LYS V 296 " (cutoff:3.500A) Processing helix chain 'V' and resid 301 through 316 Processing helix chain 'V' and resid 321 through 340 Processing helix chain 'V' and resid 344 through 350 removed outlier: 4.504A pdb=" N PHE V 348 " --> pdb=" O ASP V 344 " (cutoff:3.500A) removed outlier: 3.853A 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 Processing helix chain 'V' and resid 384 through 390 removed outlier: 3.557A pdb=" N ASP V 389 " --> pdb=" O LYS V 385 " (cutoff:3.500A) Processing helix chain 'V' and resid 391 through 415 removed outlier: 3.512A pdb=" N ILE V 395 " --> pdb=" O THR V 391 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N HIS V 400 " --> pdb=" O ILE V 396 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ILE V 403 " --> pdb=" O ARG V 399 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N LYS V 404 " --> pdb=" O HIS V 400 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N THR V 405 " --> pdb=" O ASN V 401 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLY V 406 " --> pdb=" O VAL V 402 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N SER V 415 " --> pdb=" O SER V 411 " (cutoff:3.500A) Processing helix chain 'V' and resid 418 through 427 Processing helix chain 'V' and resid 430 through 445 removed outlier: 3.861A pdb=" N ALA V 434 " --> pdb=" O SER V 430 " (cutoff:3.500A) Processing helix chain 'V' and resid 465 through 494 removed outlier: 4.582A pdb=" N THR V 469 " --> pdb=" O ASP V 465 " (cutoff:3.500A) Proline residue: V 472 - end of helix removed outlier: 4.781A pdb=" N GLN V 478 " --> pdb=" O LEU V 474 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ARG V 479 " --> pdb=" O ALA V 475 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ILE V 480 " --> pdb=" O PHE V 476 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N SER V 481 " --> pdb=" O HIS V 477 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N PHE V 482 " --> pdb=" O GLN V 478 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N CYS V 483 " --> pdb=" O ARG V 479 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU V 484 " --> pdb=" O ILE V 480 " (cutoff:3.500A) Processing helix chain 'W' and resid 20 through 36 removed outlier: 3.625A pdb=" N VAL W 24 " --> pdb=" O TYR W 20 " (cutoff:3.500A) Proline residue: W 29 - end of helix removed outlier: 5.050A pdb=" N LYS W 36 " --> pdb=" O ALA W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 58 Processing helix chain 'W' and resid 59 through 78 removed outlier: 4.811A pdb=" N THR W 63 " --> pdb=" O ASP W 59 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS W 78 " --> pdb=" O CYS W 74 " (cutoff:3.500A) Processing helix chain 'W' and resid 79 through 94 removed outlier: 4.334A pdb=" N GLU W 85 " --> pdb=" O ASP W 81 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARG W 94 " --> pdb=" O LEU W 90 " (cutoff:3.500A) Processing helix chain 'W' and resid 97 through 113 removed outlier: 3.534A pdb=" N VAL W 101 " --> pdb=" O LEU W 97 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLU W 113 " --> pdb=" O CYS W 109 " (cutoff:3.500A) Processing helix chain 'W' and resid 117 through 135 removed outlier: 4.298A pdb=" N LYS W 121 " --> pdb=" O ASP W 117 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR W 132 " --> pdb=" O LEU W 128 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLU W 133 " --> pdb=" O ARG W 129 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLY W 134 " --> pdb=" O MET W 130 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N LYS W 135 " --> pdb=" O VAL W 131 " (cutoff:3.500A) Processing helix chain 'W' and resid 140 through 156 removed outlier: 4.773A pdb=" N ARG W 144 " --> pdb=" O ILE W 140 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU W 145 " --> pdb=" O GLU W 141 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLN W 155 " --> pdb=" O THR W 151 " (cutoff:3.500A) Processing helix chain 'W' and resid 158 through 175 removed outlier: 4.174A pdb=" N LEU W 169 " --> pdb=" O ILE W 165 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N GLN W 170 " --> pdb=" O LEU W 166 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL W 171 " --> pdb=" O GLN W 167 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR W 173 " --> pdb=" O LEU W 169 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N TYR W 174 " --> pdb=" O GLN W 170 " (cutoff:3.500A) Processing helix chain 'W' and resid 179 through 197 removed outlier: 4.801A pdb=" N VAL W 183 " --> pdb=" O LYS W 179 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N MET W 190 " --> pdb=" O ILE W 186 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ARG W 191 " --> pdb=" O LEU W 187 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU W 192 " --> pdb=" O GLU W 188 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N CYS W 193 " --> pdb=" O GLN W 189 " (cutoff:3.500A) Processing helix chain 'W' and resid 200 through 213 removed outlier: 4.114A pdb=" N ILE W 204 " --> pdb=" O ILE W 200 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ILE W 205 " --> pdb=" O ARG W 201 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N PHE W 213 " --> pdb=" O ILE W 209 " (cutoff:3.500A) Processing helix chain 'W' and resid 215 through 220 removed outlier: 3.923A pdb=" N THR W 219 " --> pdb=" O GLN W 215 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N GLU W 220 " --> pdb=" O GLU W 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 215 through 220' Processing helix chain 'W' and resid 223 through 236 removed outlier: 3.593A pdb=" N TYR W 227 " --> pdb=" O LYS W 223 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ASN W 228 " --> pdb=" O LEU W 224 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N LEU W 229 " --> pdb=" O LYS W 225 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N MET W 230 " --> pdb=" O TYR W 226 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N HIS W 236 " --> pdb=" O GLN W 232 " (cutoff:3.500A) Processing helix chain 'W' and resid 239 through 258 removed outlier: 5.398A pdb=" N ILE W 243 " --> pdb=" O SER W 239 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N CYS W 244 " --> pdb=" O TYR W 240 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ASP W 252 " --> pdb=" O ARG W 248 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N THR W 253 " --> pdb=" O ALA W 249 " (cutoff:3.500A) Proline residue: W 254 - end of helix removed outlier: 3.608A pdb=" N ALA W 258 " --> pdb=" O PRO W 254 " (cutoff:3.500A) Processing helix chain 'W' and resid 259 through 272 Processing helix chain 'W' and resid 280 through 291 Processing helix chain 'W' and resid 299 through 310 removed outlier: 3.968A pdb=" N LYS W 303 " --> pdb=" O ILE W 299 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE W 309 " --> pdb=" O LEU W 305 " (cutoff:3.500A) Processing helix chain 'W' and resid 316 through 323 removed outlier: 3.885A pdb=" N GLU W 322 " --> pdb=" O SER W 318 " (cutoff:3.500A) Processing helix chain 'W' and resid 325 through 330 removed outlier: 3.868A pdb=" N ARG W 329 " --> pdb=" O GLY W 325 " (cutoff:3.500A) removed outlier: 3.502A 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 345 through 370 removed outlier: 3.654A pdb=" N LYS W 349 " --> pdb=" O GLU W 345 " (cutoff:3.500A) Processing helix chain 'W' and resid 374 through 383 removed outlier: 3.720A pdb=" N MET W 378 " --> pdb=" O THR W 374 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASP W 383 " --> pdb=" O ALA W 379 " (cutoff:3.500A) Processing helix chain 'W' and resid 385 through 400 Processing helix chain 'W' and resid 420 through 456 removed outlier: 4.226A pdb=" N GLN W 456 " --> pdb=" O ILE W 452 " (cutoff:3.500A) Processing helix chain 'X' and resid 45 through 61 removed outlier: 3.834A pdb=" N SER X 49 " --> pdb=" O VAL X 45 " (cutoff:3.500A) Processing helix chain 'X' and resid 62 through 78 removed outlier: 4.289A pdb=" N LEU X 66 " --> pdb=" O GLN X 62 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG X 74 " --> pdb=" O LEU X 70 " (cutoff:3.500A) Proline residue: X 75 - end of helix removed outlier: 4.524A pdb=" N ASN X 78 " --> pdb=" O ARG X 74 " (cutoff:3.500A) Processing helix chain 'X' and resid 81 through 100 removed outlier: 3.887A pdb=" N GLU X 100 " --> pdb=" O PHE X 96 " (cutoff:3.500A) Processing helix chain 'X' and resid 105 through 121 Processing helix chain 'X' and resid 122 through 141 Processing helix chain 'X' and resid 143 through 158 removed outlier: 3.666A pdb=" N LYS X 158 " --> pdb=" O LEU X 154 " (cutoff:3.500A) Processing helix chain 'X' and resid 162 through 181 removed outlier: 4.777A pdb=" N LEU X 166 " --> pdb=" O ASP X 162 " (cutoff:3.500A) Processing helix chain 'X' and resid 182 through 201 removed outlier: 3.628A pdb=" N ASN X 198 " --> pdb=" O ARG X 194 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ALA X 199 " --> pdb=" O THR X 195 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ILE X 200 " --> pdb=" O THR X 196 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N TYR X 201 " --> pdb=" O ALA X 197 " (cutoff:3.500A) Processing helix chain 'X' and resid 203 through 222 Processing helix chain 'X' and resid 224 through 240 removed outlier: 4.907A pdb=" N ALA X 228 " --> pdb=" O ASP X 224 " (cutoff:3.500A) Processing helix chain 'X' and resid 243 through 262 removed outlier: 4.398A pdb=" N THR X 249 " --> pdb=" O PRO X 245 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN X 262 " --> pdb=" O LYS X 258 " (cutoff:3.500A) Processing helix chain 'X' and resid 266 through 273 removed outlier: 4.088A 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 removed outlier: 3.654A pdb=" N GLU X 285 " --> pdb=" O GLY X 281 " (cutoff:3.500A) Processing helix chain 'X' and resid 298 through 310 removed outlier: 3.757A pdb=" N TYR X 309 " --> pdb=" O ALA X 305 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG X 310 " --> pdb=" O LEU X 306 " (cutoff:3.500A) Processing helix chain 'X' and resid 311 through 316 removed outlier: 5.059A pdb=" N ASP X 316 " --> pdb=" O GLU X 312 " (cutoff:3.500A) Processing helix chain 'X' and resid 318 through 340 removed outlier: 3.726A pdb=" N HIS X 322 " --> pdb=" O ILE X 318 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL X 338 " --> pdb=" O ASN X 334 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE X 339 " --> pdb=" O LEU X 335 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N GLU X 340 " --> pdb=" O ILE X 336 " (cutoff:3.500A) Processing helix chain 'X' and resid 346 through 355 removed outlier: 3.532A pdb=" N ILE X 350 " --> pdb=" O GLN X 346 " (cutoff:3.500A) Processing helix chain 'X' and resid 357 through 372 Processing helix chain 'X' and resid 394 through 422 removed outlier: 3.677A pdb=" N GLU X 398 " --> pdb=" O ASP X 394 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N THR X 422 " --> pdb=" O ALA X 418 " (cutoff:3.500A) Processing helix chain 'Y' and resid 13 through 30 Proline residue: Y 29 - end of helix Processing helix chain 'Y' and resid 37 through 46 removed outlier: 6.337A pdb=" N LEU Y 41 " --> pdb=" O VAL Y 37 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N MET Y 42 " --> pdb=" O ARG Y 38 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ALA Y 44 " --> pdb=" O GLU Y 40 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N VAL Y 45 " --> pdb=" O LEU Y 41 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG Y 46 " --> pdb=" O MET Y 42 " (cutoff:3.500A) Processing helix chain 'Y' and resid 50 through 60 removed outlier: 3.964A pdb=" N TYR Y 54 " --> pdb=" O MET Y 50 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLU Y 55 " --> pdb=" O ALA Y 51 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ALA Y 56 " --> pdb=" O PRO Y 52 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER Y 60 " --> pdb=" O ALA Y 56 " (cutoff:3.500A) Processing helix chain 'Y' and resid 68 through 93 removed outlier: 4.603A pdb=" N LYS Y 93 " --> pdb=" O GLU Y 89 " (cutoff:3.500A) Processing helix chain 'Y' and resid 99 through 114 removed outlier: 3.943A pdb=" N ALA Y 103 " --> pdb=" O GLU Y 99 " (cutoff:3.500A) Processing helix chain 'Y' and resid 116 through 131 removed outlier: 3.686A pdb=" N ALA Y 120 " --> pdb=" O ASP Y 116 " (cutoff:3.500A) Processing helix chain 'Y' and resid 133 through 152 removed outlier: 3.852A pdb=" N TYR Y 151 " --> pdb=" O ILE Y 147 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET Y 152 " --> pdb=" O GLY Y 148 " (cutoff:3.500A) Processing helix chain 'Y' and resid 153 through 168 Processing helix chain 'Y' and resid 173 through 189 removed outlier: 6.351A pdb=" N ARG Y 177 " --> pdb=" O ASP Y 173 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N ASN Y 178 " --> pdb=" O TRP Y 174 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ARG Y 179 " --> pdb=" O ASP Y 175 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU Y 180 " --> pdb=" O ARG Y 176 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N LYS Y 181 " --> pdb=" O ARG Y 177 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N VAL Y 182 " --> pdb=" O ASN Y 178 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU Y 186 " --> pdb=" O VAL Y 182 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N TYR Y 187 " --> pdb=" O TYR Y 183 " (cutoff:3.500A) Processing helix chain 'Y' and resid 194 through 203 removed outlier: 4.928A pdb=" N ALA Y 198 " --> pdb=" O PHE Y 194 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU Y 202 " --> pdb=" O ALA Y 198 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ASP Y 203 " --> pdb=" O GLU Y 199 " (cutoff:3.500A) Processing helix chain 'Y' and resid 215 through 231 removed outlier: 3.637A pdb=" N LEU Y 231 " --> pdb=" O SER Y 227 " (cutoff:3.500A) Processing helix chain 'Y' and resid 235 through 240 removed outlier: 4.150A pdb=" N LYS Y 239 " --> pdb=" O ASP Y 235 " (cutoff:3.500A) Processing helix chain 'Y' and resid 243 through 254 removed outlier: 3.541A pdb=" N LEU Y 247 " --> pdb=" O GLY Y 243 " (cutoff:3.500A) Proline residue: Y 254 - end of helix Processing helix chain 'Y' and resid 255 through 266 removed outlier: 3.585A pdb=" N CYS Y 266 " --> pdb=" O SER Y 262 " (cutoff:3.500A) Processing helix chain 'Y' and resid 268 through 283 removed outlier: 3.708A pdb=" N GLN Y 273 " --> pdb=" O SER Y 269 " (cutoff:3.500A) Processing helix chain 'Y' and resid 287 through 309 removed outlier: 6.169A pdb=" N ARG Y 293 " --> pdb=" O ALA Y 289 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N TYR Y 294 " --> pdb=" O PRO Y 290 " (cutoff:3.500A) Processing helix chain 'Y' and resid 315 through 322 removed outlier: 4.140A pdb=" N MET Y 319 " --> pdb=" O THR Y 315 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU Y 321 " --> pdb=" O GLY Y 317 " (cutoff:3.500A) Processing helix chain 'Y' and resid 326 through 341 removed outlier: 3.550A pdb=" N ILE Y 330 " --> pdb=" O GLY Y 326 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY Y 341 " --> pdb=" O PHE Y 337 " (cutoff:3.500A) Processing helix chain 'Y' and resid 360 through 387 removed outlier: 3.604A pdb=" N ILE Y 387 " --> pdb=" O LEU Y 383 " (cutoff:3.500A) Processing helix chain 'Z' and resid 12 through 31 removed outlier: 4.565A pdb=" N LEU Z 16 " --> pdb=" O HIS Z 12 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LEU Z 17 " --> pdb=" O PRO Z 13 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N LYS Z 28 " --> pdb=" O ASN Z 24 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N VAL Z 29 " --> pdb=" O ARG Z 25 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ASN Z 31 " --> pdb=" O GLY Z 27 " (cutoff:3.500A) Processing helix chain 'Z' and resid 71 through 86 Processing helix chain 'Z' and resid 102 through 116 removed outlier: 4.231A pdb=" N ILE Z 106 " --> pdb=" O HIS Z 102 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA Z 107 " --> pdb=" O LYS Z 103 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG Z 114 " --> pdb=" O GLU Z 110 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N TYR Z 115 " --> pdb=" O LEU Z 111 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N CYS Z 116 " --> pdb=" O MET Z 112 " (cutoff:3.500A) Processing helix chain 'Z' and resid 166 through 177 removed outlier: 6.829A pdb=" N VAL Z 170 " --> pdb=" O GLU Z 166 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N GLY Z 171 " --> pdb=" O ALA Z 167 " (cutoff:3.500A) Processing helix chain 'Z' and resid 185 through 218 removed outlier: 3.869A pdb=" N THR Z 217 " --> pdb=" O GLU Z 213 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLY Z 218 " --> pdb=" O LYS Z 214 " (cutoff:3.500A) Processing helix chain 'Z' and resid 226 through 238 removed outlier: 3.566A pdb=" N LEU Z 230 " --> pdb=" O ILE Z 226 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLN Z 231 " --> pdb=" O ILE Z 227 " (cutoff:3.500A) Proline residue: Z 238 - end of helix Processing helix chain 'Z' and resid 241 through 290 removed outlier: 4.570A pdb=" N PHE Z 245 " --> pdb=" O SER Z 241 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N VAL Z 246 " --> pdb=" O LEU Z 242 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N LYS Z 247 " --> pdb=" O GLN Z 243 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N PHE Z 249 " --> pdb=" O PHE Z 245 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N TYR Z 250 " --> pdb=" O VAL Z 246 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N LEU Z 251 " --> pdb=" O LYS Z 247 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LYS Z 252 " --> pdb=" O ALA Z 248 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASN Z 254 " --> pdb=" O TYR Z 250 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LEU Z 262 " --> pdb=" O VAL Z 258 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA Z 263 " --> pdb=" O VAL Z 259 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LEU Z 265 " --> pdb=" O TYR Z 261 " (cutoff:3.500A) Processing helix chain 'a' and resid 4 through 12 removed outlier: 3.848A pdb=" N LEU a 8 " --> pdb=" O VAL a 4 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN a 9 " --> pdb=" O PRO a 5 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER a 11 " --> pdb=" O PHE a 7 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N GLN a 12 " --> pdb=" O LEU a 8 " (cutoff:3.500A) Processing helix chain 'a' and resid 17 through 32 removed outlier: 4.396A pdb=" N VAL a 21 " --> pdb=" O GLY a 17 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ARG a 24 " --> pdb=" O ALA a 20 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU a 27 " --> pdb=" O HIS a 23 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N TYR a 29 " --> pdb=" O LEU a 25 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N THR a 30 " --> pdb=" O GLU a 26 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS a 31 " --> pdb=" O GLU a 27 " (cutoff:3.500A) Processing helix chain 'a' and resid 34 through 41 removed outlier: 4.120A pdb=" N THR a 38 " --> pdb=" O TRP a 34 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU a 39 " --> pdb=" O HIS a 35 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N VAL a 41 " --> pdb=" O LEU a 37 " (cutoff:3.500A) Processing helix chain 'a' and resid 54 through 68 removed outlier: 4.307A pdb=" N LEU a 59 " --> pdb=" O GLY a 55 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TYR a 60 " --> pdb=" O LEU a 56 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE a 67 " --> pdb=" O PHE a 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 72 through 88 Processing helix chain 'a' and resid 90 through 105 removed outlier: 4.357A pdb=" N THR a 95 " --> pdb=" O ASN a 91 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N LYS a 105 " --> pdb=" O ARG a 101 " (cutoff:3.500A) Processing helix chain 'a' and resid 109 through 123 removed outlier: 4.052A pdb=" N LEU a 113 " --> pdb=" O GLU a 109 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU a 123 " --> pdb=" O GLY a 119 " (cutoff:3.500A) Processing helix chain 'a' and resid 130 through 143 removed outlier: 4.085A pdb=" N VAL a 138 " --> pdb=" O THR a 134 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLU a 139 " --> pdb=" O ILE a 135 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N MET a 141 " --> pdb=" O ASP a 137 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU a 142 " --> pdb=" O VAL a 138 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ASN a 143 " --> pdb=" O GLU a 139 " (cutoff:3.500A) Processing helix chain 'a' and resid 148 through 163 removed outlier: 6.369A pdb=" N HIS a 152 " --> pdb=" O VAL a 148 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N SER a 153 " --> pdb=" O THR a 149 " (cutoff:3.500A) Processing helix chain 'a' and resid 169 through 184 removed outlier: 3.677A pdb=" N VAL a 183 " --> pdb=" O PHE a 179 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ASP a 184 " --> pdb=" O LEU a 180 " (cutoff:3.500A) Processing helix chain 'a' and resid 189 through 207 removed outlier: 3.666A pdb=" N GLN a 193 " --> pdb=" O PRO a 189 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N GLU a 195 " --> pdb=" O SER a 191 " (cutoff:3.500A) Processing helix chain 'a' and resid 214 through 220 removed outlier: 7.427A pdb=" N MET a 218 " --> pdb=" O GLY a 214 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N HIS a 219 " --> pdb=" O GLU a 215 " (cutoff:3.500A) Proline residue: a 220 - end of helix No H-bonds generated for 'chain 'a' and resid 214 through 220' Processing helix chain 'a' and resid 223 through 228 removed outlier: 4.188A pdb=" N ASN a 227 " --> pdb=" O GLU a 223 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR a 228 " --> pdb=" O SER a 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 223 through 228' Processing helix chain 'a' and resid 230 through 243 removed outlier: 4.363A pdb=" N ILE a 234 " --> pdb=" O ARG a 230 " (cutoff:3.500A) Processing helix chain 'a' and resid 246 through 258 removed outlier: 3.759A pdb=" N THR a 250 " --> pdb=" O GLU a 246 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ALA a 254 " --> pdb=" O THR a 250 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N TRP a 255 " --> pdb=" O LEU a 251 " (cutoff:3.500A) Processing helix chain 'a' and resid 259 through 265 removed outlier: 7.014A pdb=" N ALA a 263 " --> pdb=" O PRO a 259 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ASN a 264 " --> pdb=" O ASP a 260 " (cutoff:3.500A) Processing helix chain 'a' and resid 266 through 285 removed outlier: 4.577A pdb=" N CYS a 276 " --> pdb=" O ILE a 272 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N LEU a 277 " --> pdb=" O GLN a 273 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N MET a 278 " --> pdb=" O LEU a 274 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N GLU a 279 " --> pdb=" O LEU a 275 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET a 280 " --> pdb=" O CYS a 276 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG a 284 " --> pdb=" O MET a 280 " (cutoff:3.500A) Proline residue: a 285 - end of helix Processing helix chain 'a' and resid 292 through 301 removed outlier: 3.536A pdb=" N ILE a 296 " --> pdb=" O THR a 292 " (cutoff:3.500A) Processing helix chain 'a' and resid 303 through 318 removed outlier: 3.869A pdb=" N VAL a 307 " --> pdb=" O THR a 303 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLU a 308 " --> pdb=" O VAL a 304 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU a 309 " --> pdb=" O ASN a 305 " (cutoff:3.500A) Processing helix chain 'a' and resid 344 through 376 removed outlier: 4.329A pdb=" N GLY a 348 " --> pdb=" O GLN a 344 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP a 351 " --> pdb=" O LYS a 347 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ARG a 352 " --> pdb=" O GLY a 348 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU a 353 " --> pdb=" O MET a 349 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N TRP a 356 " --> pdb=" O ARG a 352 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N THR a 358 " --> pdb=" O GLU a 354 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP a 359 " --> pdb=" O PHE a 355 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ASP a 373 " --> pdb=" O HIS a 369 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ILE a 374 " --> pdb=" O GLN a 370 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR a 376 " --> pdb=" O HIS a 372 " (cutoff:3.500A) Processing helix chain 'b' and resid 13 through 18 removed outlier: 4.066A pdb=" N ARG b 17 " --> pdb=" O SER b 13 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ASN b 18 " --> pdb=" O GLU b 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 13 through 18' Processing helix chain 'b' and resid 24 through 45 Proline residue: b 45 - end of helix Processing helix chain 'b' and resid 68 through 76 removed outlier: 4.234A pdb=" N HIS b 76 " --> pdb=" O LEU b 72 " (cutoff:3.500A) Processing helix chain 'b' and resid 85 through 100 removed outlier: 3.681A pdb=" N GLY b 89 " --> pdb=" O THR b 85 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ILE b 90 " --> pdb=" O PHE b 86 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ARG b 91 " --> pdb=" O CYS b 87 " (cutoff:3.500A) removed outlier: 3.539A 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 removed outlier: 3.900A pdb=" N GLY b 162 " --> pdb=" O ASN b 158 " (cutoff:3.500A) Processing helix chain 'b' and resid 179 through 190 removed outlier: 4.785A pdb=" N LEU b 183 " --> pdb=" O LEU b 179 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE b 184 " --> pdb=" O ALA b 180 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N SER b 185 " --> pdb=" O ASP b 181 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N SER b 186 " --> pdb=" O ALA b 182 " (cutoff:3.500A) Proline residue: b 187 - end of helix Processing helix chain 'c' and resid 34 through 49 removed outlier: 3.740A pdb=" N GLY c 48 " --> pdb=" O HIS c 44 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL c 49 " --> pdb=" O GLY c 45 " (cutoff:3.500A) Processing helix chain 'c' and resid 88 through 103 removed outlier: 4.424A pdb=" N LYS c 100 " --> pdb=" O LEU c 96 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N GLN c 101 " --> pdb=" O ASP c 97 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N THR c 102 " --> pdb=" O MET c 98 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLY c 103 " --> pdb=" O LEU c 99 " (cutoff:3.500A) Processing helix chain 'c' and resid 123 through 137 removed outlier: 4.160A pdb=" N SER c 132 " --> pdb=" O ASN c 128 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE c 133 " --> pdb=" O THR c 129 " (cutoff:3.500A) Processing helix chain 'c' and resid 165 through 171 removed outlier: 4.482A pdb=" N VAL c 169 " --> pdb=" O ALA c 165 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLY c 171 " --> pdb=" O MET c 167 " (cutoff:3.500A) Processing helix chain 'c' and resid 180 through 185 removed outlier: 5.204A pdb=" N LEU c 184 " --> pdb=" O ASN c 180 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASN c 185 " --> pdb=" O LEU c 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 180 through 185' Processing helix chain 'c' and resid 188 through 195 removed outlier: 3.508A pdb=" N HIS c 194 " --> pdb=" O GLN c 190 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N GLY c 195 " --> pdb=" O ALA c 191 " (cutoff:3.500A) Processing helix chain 'c' and resid 210 through 223 removed outlier: 4.102A pdb=" N GLN c 214 " --> pdb=" O ASN c 210 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LYS c 215 " --> pdb=" O GLU c 211 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N MET c 216 " --> pdb=" O LEU c 212 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LYS c 222 " --> pdb=" O LEU c 218 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS c 223 " --> pdb=" O ASN c 219 " (cutoff:3.500A) Processing helix chain 'c' and resid 225 through 230 removed outlier: 3.964A pdb=" N LEU c 229 " --> pdb=" O TRP c 225 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR c 230 " --> pdb=" O MET c 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 225 through 230' Processing helix chain 'c' and resid 236 through 260 Processing helix chain 'c' and resid 266 through 275 removed outlier: 4.665A pdb=" N LEU c 270 " --> pdb=" O THR c 266 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS c 273 " --> pdb=" O GLN c 269 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN c 274 " --> pdb=" O LEU c 270 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL c 275 " --> pdb=" O ALA c 271 " (cutoff:3.500A) Processing helix chain 'c' and resid 285 through 310 removed outlier: 3.716A pdb=" N PHE c 309 " --> pdb=" O ASP c 305 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N LYS c 310 " --> pdb=" O THR c 306 " (cutoff:3.500A) Processing helix chain 'd' and resid 7 through 12 removed outlier: 3.785A pdb=" N ARG d 11 " --> pdb=" O GLY d 7 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N LYS d 12 " --> pdb=" O GLU d 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 7 through 12' Processing helix chain 'd' and resid 15 through 32 removed outlier: 4.478A pdb=" N CYS d 19 " --> pdb=" O ASN d 15 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU d 31 " --> pdb=" O LYS d 27 " (cutoff:3.500A) Processing helix chain 'd' and resid 43 through 66 removed outlier: 4.485A pdb=" N GLN d 47 " --> pdb=" O LEU d 43 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ILE d 49 " --> pdb=" O LYS d 45 " (cutoff:3.500A) Processing helix chain 'd' and resid 67 through 84 Processing helix chain 'd' and resid 92 through 110 removed outlier: 4.956A pdb=" N HIS d 96 " --> pdb=" O SER d 92 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N GLN d 97 " --> pdb=" O ALA d 93 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU d 98 " --> pdb=" O TYR d 94 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN d 110 " --> pdb=" O LEU d 106 " (cutoff:3.500A) Processing helix chain 'd' and resid 111 through 123 removed outlier: 3.578A pdb=" N LEU d 119 " --> pdb=" O PHE d 115 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N GLU d 120 " --> pdb=" O HIS d 116 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG d 121 " --> pdb=" O THR d 117 " (cutoff:3.500A) Proline residue: d 123 - end of helix Processing helix chain 'd' and resid 130 through 145 Proline residue: d 136 - end of helix removed outlier: 4.600A pdb=" N GLU d 145 " --> pdb=" O GLN d 141 " (cutoff:3.500A) Processing helix chain 'd' and resid 147 through 158 removed outlier: 5.069A pdb=" N VAL d 151 " --> pdb=" O SER d 147 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY d 156 " --> pdb=" O PHE d 152 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN d 157 " --> pdb=" O LEU d 153 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ILE d 158 " --> pdb=" O ALA d 154 " (cutoff:3.500A) Processing helix chain 'd' and resid 163 through 184 removed outlier: 3.561A pdb=" N ILE d 167 " --> pdb=" O TYR d 163 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ASP d 168 " --> pdb=" O THR d 164 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ILE d 169 " --> pdb=" O PHE d 165 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LYS d 184 " --> pdb=" O GLY d 180 " (cutoff:3.500A) Processing helix chain 'd' and resid 203 through 214 removed outlier: 3.984A pdb=" N THR d 207 " --> pdb=" O PRO d 203 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLY d 214 " --> pdb=" O ALA d 210 " (cutoff:3.500A) Processing helix chain 'd' and resid 235 through 255 removed outlier: 4.696A pdb=" N SER d 239 " --> pdb=" O THR d 235 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N THR d 240 " --> pdb=" O THR d 236 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N GLU d 241 " --> pdb=" O ILE d 237 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N MET d 255 " --> pdb=" O ARG d 251 " (cutoff:3.500A) Processing helix chain 'f' and resid 6 through 27 Proline residue: f 10 - end of helix Proline residue: f 13 - end of helix removed outlier: 3.985A 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 removed outlier: 3.592A pdb=" N ASP f 25 " --> pdb=" O PRO f 21 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N GLU f 26 " --> pdb=" O GLY f 22 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LYS f 27 " --> pdb=" O GLY f 23 " (cutoff:3.500A) Processing helix chain 'f' and resid 28 through 47 removed outlier: 4.974A pdb=" N ARG f 34 " --> pdb=" O GLY f 30 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ASP f 35 " --> pdb=" O LYS f 31 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU f 45 " --> pdb=" O LYS f 41 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER f 46 " --> pdb=" O GLU f 42 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU f 47 " --> pdb=" O GLN f 43 " (cutoff:3.500A) Processing helix chain 'f' and resid 54 through 59 Processing helix chain 'f' and resid 62 through 75 removed outlier: 5.625A pdb=" N LYS f 66 " --> pdb=" O ARG f 62 " (cutoff:3.500A) Proline residue: f 73 - end of helix Processing helix chain 'f' and resid 80 through 95 removed outlier: 4.065A pdb=" N SER f 84 " --> pdb=" O ARG f 80 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N SER f 85 " --> pdb=" O GLN f 81 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL f 92 " --> pdb=" O SER f 88 " (cutoff:3.500A) Proline residue: f 93 - end of helix Processing helix chain 'f' and resid 99 through 104 removed outlier: 4.587A pdb=" N TYR f 103 " --> pdb=" O LEU f 99 " (cutoff:3.500A) Processing helix chain 'f' and resid 106 through 112 Processing helix chain 'f' and resid 115 through 120 removed outlier: 6.470A pdb=" N LYS f 119 " --> pdb=" O PRO f 115 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG f 120 " --> pdb=" O GLY f 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 115 through 120' Processing helix chain 'f' and resid 128 through 148 removed outlier: 4.710A pdb=" N THR f 132 " --> pdb=" O VAL f 128 " (cutoff:3.500A) Processing helix chain 'f' and resid 153 through 172 Processing helix chain 'f' and resid 176 through 182 removed outlier: 5.065A pdb=" N GLN f 180 " --> pdb=" O ALA f 176 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ARG f 181 " --> pdb=" O GLU f 177 " (cutoff:3.500A) Processing helix chain 'f' and resid 185 through 190 removed outlier: 4.757A pdb=" N GLU f 190 " --> pdb=" O THR f 186 " (cutoff:3.500A) Processing helix chain 'f' and resid 194 through 209 removed outlier: 3.669A pdb=" N MET f 209 " --> pdb=" O CYS f 205 " (cutoff:3.500A) Processing helix chain 'f' and resid 212 through 227 removed outlier: 5.026A pdb=" N MET f 216 " --> pdb=" O GLU f 212 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR f 226 " --> pdb=" O ASP f 222 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ALA f 227 " --> pdb=" O GLU f 223 " (cutoff:3.500A) Processing helix chain 'f' and resid 231 through 241 removed outlier: 4.682A pdb=" N SER f 235 " --> pdb=" O LEU f 231 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ASN f 238 " --> pdb=" O THR f 234 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N TYR f 239 " --> pdb=" O SER f 235 " (cutoff:3.500A) Proline residue: f 241 - end of helix Processing helix chain 'f' and resid 253 through 264 removed outlier: 3.651A pdb=" N ARG f 257 " --> pdb=" O LEU f 253 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG f 261 " --> pdb=" O ARG f 257 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N PHE f 262 " --> pdb=" O LYS f 258 " (cutoff:3.500A) Proline residue: f 263 - end of helix Processing helix chain 'f' and resid 268 through 279 removed outlier: 3.581A pdb=" N GLU f 276 " --> pdb=" O LEU f 272 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU f 277 " --> pdb=" O ASN f 273 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N VAL f 278 " --> pdb=" O ASP f 274 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLU f 279 " --> pdb=" O MET f 275 " (cutoff:3.500A) Processing helix chain 'f' and resid 287 through 294 removed outlier: 3.582A pdb=" N GLN f 291 " --> pdb=" O ASP f 287 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLN f 293 " --> pdb=" O VAL f 289 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N MET f 294 " --> pdb=" O VAL f 290 " (cutoff:3.500A) Processing helix chain 'f' and resid 295 through 302 removed outlier: 4.708A pdb=" N GLY f 299 " --> pdb=" O ALA f 295 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N HIS f 301 " --> pdb=" O MET f 297 " (cutoff:3.500A) Processing helix chain 'f' and resid 325 through 336 removed outlier: 4.555A pdb=" N ASN f 329 " --> pdb=" O GLN f 325 " (cutoff:3.500A) Processing helix chain 'f' and resid 347 through 353 removed outlier: 3.903A pdb=" N THR f 351 " --> pdb=" O ASP f 347 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N HIS f 352 " --> pdb=" O ILE f 348 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N LEU f 353 " --> pdb=" O TYR f 349 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 347 through 353' Processing helix chain 'f' and resid 354 through 359 removed outlier: 3.759A pdb=" N PHE f 358 " --> pdb=" O GLU f 354 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N GLY f 359 " --> pdb=" O ASN f 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 354 through 359' Processing helix chain 'f' and resid 367 through 383 removed outlier: 3.501A pdb=" N ASN f 371 " --> pdb=" O SER f 367 " (cutoff:3.500A) Processing helix chain 'f' and resid 389 through 394 removed outlier: 4.886A pdb=" N ASP f 393 " --> pdb=" O LYS f 389 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ASP f 394 " --> pdb=" O LEU f 390 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 389 through 394' Processing helix chain 'f' and resid 395 through 402 removed outlier: 3.823A pdb=" N ASN f 402 " --> pdb=" O TRP f 398 " (cutoff:3.500A) Processing helix chain 'f' and resid 406 through 419 removed outlier: 4.103A pdb=" N LEU f 418 " --> pdb=" O LEU f 414 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU f 419 " --> pdb=" O GLY f 415 " (cutoff:3.500A) Processing helix chain 'f' and resid 423 through 433 removed outlier: 4.370A pdb=" N GLN f 428 " --> pdb=" O GLY f 424 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE f 429 " --> pdb=" O GLY f 425 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ASP f 430 " --> pdb=" O LEU f 426 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYS f 431 " --> pdb=" O THR f 427 " (cutoff:3.500A) Processing helix chain 'f' and resid 437 through 456 removed outlier: 3.531A pdb=" N SER f 453 " --> pdb=" O GLY f 449 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N GLY f 454 " --> pdb=" O ILE f 450 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N VAL f 455 " --> pdb=" O VAL f 451 " (cutoff:3.500A) Processing helix chain 'f' and resid 463 through 473 removed outlier: 4.298A pdb=" N ASP f 468 " --> pdb=" O ALA f 464 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N VAL f 470 " --> pdb=" O LEU f 466 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N LEU f 471 " --> pdb=" O SER f 467 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N HIS f 472 " --> pdb=" O ASP f 468 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ASN f 473 " --> pdb=" O TYR f 469 " (cutoff:3.500A) Processing helix chain 'f' and resid 474 through 490 removed outlier: 4.525A pdb=" N ILE f 482 " --> pdb=" O ARG f 478 " (cutoff:3.500A) Processing helix chain 'f' and resid 495 through 506 removed outlier: 4.106A pdb=" N THR f 499 " --> pdb=" O GLU f 495 " (cutoff:3.500A) Proline residue: f 503 - end of helix Processing helix chain 'f' and resid 514 through 527 removed outlier: 3.827A pdb=" N THR f 518 " --> pdb=" O VAL f 514 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA f 519 " --> pdb=" O ALA f 515 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA f 526 " --> pdb=" O CYS f 522 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL f 527 " --> pdb=" O GLY f 523 " (cutoff:3.500A) Processing helix chain 'f' and resid 530 through 544 removed outlier: 3.950A pdb=" N VAL f 534 " --> pdb=" O CYS f 530 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR f 535 " --> pdb=" O ASN f 531 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ILE f 538 " --> pdb=" O VAL f 534 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET f 543 " --> pdb=" O LEU f 539 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU f 544 " --> pdb=" O GLN f 540 " (cutoff:3.500A) Processing helix chain 'f' and resid 545 through 551 removed outlier: 3.762A pdb=" N GLU f 549 " --> pdb=" O LYS f 545 " (cutoff:3.500A) Processing helix chain 'f' and resid 554 through 567 removed outlier: 4.556A pdb=" N LEU f 558 " --> pdb=" O TYR f 554 " (cutoff:3.500A) Proline residue: f 559 - end of helix removed outlier: 4.186A pdb=" N LEU f 562 " --> pdb=" O LEU f 558 " (cutoff:3.500A) Processing helix chain 'f' and resid 572 through 583 removed outlier: 5.779A pdb=" N ILE f 576 " --> pdb=" O ALA f 572 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL f 582 " --> pdb=" O ALA f 578 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N VAL f 583 " --> pdb=" O ALA f 579 " (cutoff:3.500A) Processing helix chain 'f' and resid 587 through 601 removed outlier: 3.998A pdb=" N ALA f 591 " --> pdb=" O PHE f 587 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N THR f 593 " --> pdb=" O SER f 589 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N TYR f 600 " --> pdb=" O ASP f 596 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ALA f 601 " --> pdb=" O VAL f 597 " (cutoff:3.500A) Processing helix chain 'f' and resid 606 through 614 Processing helix chain 'f' and resid 615 through 620 removed outlier: 4.638A pdb=" N HIS f 619 " --> pdb=" O ILE f 615 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE f 620 " --> pdb=" O CYS f 616 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 615 through 620' Processing helix chain 'f' and resid 642 through 647 removed outlier: 6.913A pdb=" N MET f 646 " --> pdb=" O ALA f 642 " (cutoff:3.500A) Processing helix chain 'f' and resid 648 through 657 removed outlier: 4.180A pdb=" N LEU f 655 " --> pdb=" O GLY f 651 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE f 657 " --> pdb=" O ALA f 653 " (cutoff:3.500A) Processing helix chain 'f' and resid 667 through 678 removed outlier: 5.910A pdb=" N ALA f 671 " --> pdb=" O GLY f 667 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N LEU f 672 " --> pdb=" O ALA f 668 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N ARG f 673 " --> pdb=" O GLU f 669 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N THR f 674 " --> pdb=" O MET f 670 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE f 675 " --> pdb=" O ALA f 671 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N GLY f 676 " --> pdb=" O LEU f 672 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N HIS f 677 " --> pdb=" O ARG f 673 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU f 678 " --> pdb=" O THR f 674 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 667 through 678' Processing helix chain 'f' and resid 688 through 698 removed outlier: 5.367A pdb=" N LEU f 696 " --> pdb=" O LEU f 692 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE f 697 " --> pdb=" O ALA f 693 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N SER f 698 " --> pdb=" O LEU f 694 " (cutoff:3.500A) Processing helix chain 'f' and resid 701 through 715 removed outlier: 4.042A pdb=" N ASN f 705 " --> pdb=" O ASN f 701 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N SER f 714 " --> pdb=" O LEU f 710 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N HIS f 715 " --> pdb=" O SER f 711 " (cutoff:3.500A) Processing helix chain 'f' and resid 722 through 732 removed outlier: 6.781A pdb=" N ILE f 726 " --> pdb=" O SER f 722 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N PHE f 727 " --> pdb=" O TYR f 723 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL f 732 " --> pdb=" O ALA f 728 " (cutoff:3.500A) Processing helix chain 'f' and resid 739 through 754 removed outlier: 3.856A pdb=" N LEU f 745 " --> pdb=" O LEU f 741 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG f 746 " --> pdb=" O ALA f 742 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU f 748 " --> pdb=" O MET f 744 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA f 749 " --> pdb=" O LEU f 745 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLN f 750 " --> pdb=" O ARG f 746 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N TYR f 751 " --> pdb=" O GLN f 747 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LYS f 754 " --> pdb=" O GLN f 750 " (cutoff:3.500A) Processing helix chain 'f' and resid 774 through 782 removed outlier: 4.799A pdb=" N LEU f 778 " --> pdb=" O GLY f 774 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N CYS f 779 " --> pdb=" O THR f 775 " (cutoff:3.500A) Proline residue: f 780 - end of helix No H-bonds generated for 'chain 'f' and resid 774 through 782' Processing helix chain 'f' and resid 797 through 803 removed outlier: 3.958A pdb=" N VAL f 801 " --> pdb=" O LEU f 797 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N PHE f 803 " --> pdb=" O VAL f 799 " (cutoff:3.500A) Processing helix chain 'f' and resid 242 through 247 removed outlier: 4.112A pdb=" N ASN f 245 " --> pdb=" O GLU f 242 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ALA f 247 " --> pdb=" O GLU f 244 " (cutoff:3.500A) Processing helix chain 'f' and resid 628 through 633 removed outlier: 5.249A pdb=" N LYS f 631 " --> pdb=" O ASP f 628 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LYS f 632 " --> pdb=" O LYS f 629 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLU f 633 " --> pdb=" O ASP f 630 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 628 through 633' Processing helix chain 'f' and resid 314 through 319 removed outlier: 3.866A pdb=" N GLU f 319 " --> pdb=" O TYR f 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 314 through 319' Processing helix chain 'e' and resid 51 through 64 removed outlier: 5.025A pdb=" N GLN e 55 " --> pdb=" O ASP e 51 " (cutoff:3.500A) Processing helix chain 'e' and resid 42 through 47 removed outlier: 3.783A pdb=" N ASP e 45 " --> pdb=" O ASN e 42 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASP e 46 " --> pdb=" O TRP e 43 " (cutoff:3.500A) removed outlier: 5.486A 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 'x' and resid 2 through 6 removed outlier: 5.327A pdb=" N THR x 22 " --> pdb=" O PRO x 2 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL x 18 " --> pdb=" O VAL x 6 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'x' and resid 274 through 278 removed outlier: 3.639A pdb=" N CYS x 277 " --> pdb=" O GLN x 327 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL x 329 " --> pdb=" O CYS x 277 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ARG x 330 " --> pdb=" O VAL x 343 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'x' and resid 296 through 301 removed outlier: 3.646A pdb=" N LYS x 256 " --> pdb=" O ILE x 312 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N GLY x 248 " --> pdb=" O PRO x 321 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG x 319 " --> pdb=" O GLU x 250 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'x' and resid 417 through 421 removed outlier: 6.286A pdb=" N TYR x 417 " --> pdb=" O ARG x 483 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU x 479 " --> pdb=" O GLN x 421 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'x' and resid 454 through 458 removed outlier: 6.520A pdb=" N GLU x 446 " --> pdb=" O ARG x 442 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER x 438 " --> pdb=" O PHE x 450 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN x 427 " --> pdb=" O HIS x 435 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU x 424 " --> pdb=" O TYR x 476 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'x' and resid 323 through 327 Processing sheet with id= 7, first strand: chain 'A' and resid 120 through 124 removed outlier: 3.524A pdb=" N PHE A 121 " --> pdb=" O ILE A 113 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE A 112 " --> pdb=" O ILE A 102 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'A' and resid 236 through 240 removed outlier: 3.870A pdb=" N CYS A 236 " --> pdb=" O ALA A 269 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASP A 275 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N CYS A 270 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS A 316 " --> pdb=" O CYS A 270 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA A 320 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL A 212 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLY A 216 " --> pdb=" O THR A 321 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE A 215 " --> pdb=" O ILE A 341 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'B' and resid 107 through 111 Processing sheet with id= 10, first strand: chain 'B' and resid 246 through 251 removed outlier: 5.926A pdb=" N THR B 246 " --> pdb=" O PRO B 279 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE B 281 " --> pdb=" O THR B 246 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU B 248 " --> pdb=" O ILE B 281 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER B 280 " --> pdb=" O ASP B 324 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'C' and resid 94 through 98 removed outlier: 3.713A pdb=" N PHE C 95 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL C 85 " --> pdb=" O VAL C 97 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N LEU C 86 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N GLU C 75 " --> pdb=" O LYS C 88 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY C 74 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N CYS C 112 " --> pdb=" O VAL C 76 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'C' and resid 210 through 214 removed outlier: 3.630A pdb=" N VAL C 214 " --> pdb=" O PHE C 247 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ASP C 249 " --> pdb=" O VAL C 214 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER C 244 " --> pdb=" O ASN C 288 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS C 290 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET C 248 " --> pdb=" O ILE C 292 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA C 294 " --> pdb=" O MET C 248 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLU C 250 " --> pdb=" O ALA C 294 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ASN C 296 " --> pdb=" O GLU C 250 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL C 186 " --> pdb=" O VAL C 291 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG C 313 " --> pdb=" O GLY C 185 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR C 189 " --> pdb=" O ILE C 315 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'D' and resid 109 through 115 removed outlier: 3.836A pdb=" N SER D 109 " --> pdb=" O SER D 105 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE D 115 " --> pdb=" O ASN D 99 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ASN D 99 " --> pdb=" O ILE D 115 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ILE D 102 " --> pdb=" O LEU D 93 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ALA D 128 " --> pdb=" O PHE D 92 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'D' and resid 226 through 230 removed outlier: 4.452A pdb=" N ALA D 226 " --> pdb=" O PRO D 259 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP D 265 " --> pdb=" O VAL D 230 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA D 310 " --> pdb=" O ILE D 264 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLY D 206 " --> pdb=" O THR D 311 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG D 329 " --> pdb=" O GLY D 201 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE D 331 " --> pdb=" O LEU D 203 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'E' and resid 77 through 82 removed outlier: 7.305A pdb=" N ILE E 70 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N THR E 96 " --> pdb=" O VAL E 60 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'E' and resid 194 through 198 removed outlier: 5.660A pdb=" N ASN E 194 " --> pdb=" O PRO E 227 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS E 274 " --> pdb=" O CYS E 228 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA E 278 " --> pdb=" O MET E 232 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N CYS E 170 " --> pdb=" O MET E 275 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLY E 174 " --> pdb=" O THR E 279 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR E 173 " --> pdb=" O ILE E 299 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'F' and resid 88 through 91 removed outlier: 6.285A pdb=" N GLY F 152 " --> pdb=" O LEU F 161 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LEU F 159 " --> pdb=" O ASN F 154 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'F' and resid 121 through 125 Processing sheet with id= 19, first strand: chain 'F' and resid 246 through 252 removed outlier: 3.830A pdb=" N LYS F 327 " --> pdb=" O SER F 281 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLY F 227 " --> pdb=" O THR F 332 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'G' and resid 68 through 72 removed outlier: 6.537A pdb=" N HIS G 68 " --> pdb=" O MET G 80 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE G 76 " --> pdb=" O ILE G 72 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL G 151 " --> pdb=" O PHE G 163 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N TYR G 159 " --> pdb=" O ASP G 155 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'G' and resid 164 through 169 removed outlier: 6.708A pdb=" N LYS G 164 " --> pdb=" O ARG G 43 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N THR G 38 " --> pdb=" O GLN G 53 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN G 53 " --> pdb=" O THR G 38 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N GLU G 214 " --> pdb=" O LYS G 54 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'g' and resid 68 through 72 removed outlier: 6.173A pdb=" N HIS g 68 " --> pdb=" O MET g 80 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE g 76 " --> pdb=" O ILE g 72 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N MET g 138 " --> pdb=" O CYS g 154 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL g 151 " --> pdb=" O PHE g 163 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS g 153 " --> pdb=" O CYS g 161 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N CYS g 161 " --> pdb=" O LYS g 153 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP g 155 " --> pdb=" O TYR g 159 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N TYR g 159 " --> pdb=" O ASP g 155 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'g' and resid 164 through 169 removed outlier: 6.789A pdb=" N LYS g 164 " --> pdb=" O ARG g 43 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N THR g 38 " --> pdb=" O GLN g 53 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN g 53 " --> pdb=" O THR g 38 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N GLU g 214 " --> pdb=" O LYS g 54 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'H' and resid 65 through 68 removed outlier: 6.492A pdb=" N ILE H 72 " --> pdb=" O ILE H 68 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N LEU H 146 " --> pdb=" O TRP H 158 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN H 148 " --> pdb=" O PHE H 156 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'H' and resid 160 through 164 removed outlier: 3.771A pdb=" N GLU H 49 " --> pdb=" O PRO H 34 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ASN H 207 " --> pdb=" O LYS H 50 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N VAL H 210 " --> pdb=" O LEU H 221 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN H 214 " --> pdb=" O GLY H 217 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'h' and resid 65 through 68 removed outlier: 6.499A pdb=" N ILE h 72 " --> pdb=" O ILE h 68 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N LEU h 146 " --> pdb=" O TRP h 158 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'h' and resid 160 through 164 removed outlier: 4.956A pdb=" N ASN h 207 " --> pdb=" O LYS h 50 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N VAL h 210 " --> pdb=" O LEU h 221 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN h 214 " --> pdb=" O GLY h 217 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'I' and resid 33 through 39 removed outlier: 5.332A pdb=" N THR I 33 " --> pdb=" O GLU I 48 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY I 42 " --> pdb=" O ALA I 39 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ILE I 213 " --> pdb=" O LEU I 228 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'I' and resid 65 through 68 removed outlier: 6.593A pdb=" N MET I 72 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY I 138 " --> pdb=" O GLN I 146 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LEU I 147 " --> pdb=" O TRP I 159 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ASN I 155 " --> pdb=" O ASP I 151 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'i' and resid 33 through 39 removed outlier: 5.074A pdb=" N THR i 33 " --> pdb=" O GLU i 48 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY i 42 " --> pdb=" O ALA i 39 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ILE i 213 " --> pdb=" O LEU i 228 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'i' and resid 65 through 68 removed outlier: 6.642A pdb=" N MET i 72 " --> pdb=" O LEU i 68 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU i 134 " --> pdb=" O SER i 150 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY i 138 " --> pdb=" O GLN i 146 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU i 147 " --> pdb=" O TRP i 159 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP i 151 " --> pdb=" O ASN i 155 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ASN i 155 " --> pdb=" O ASP i 151 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'J' and resid 62 through 65 removed outlier: 6.582A pdb=" N VAL J 69 " --> pdb=" O LEU J 65 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP J 148 " --> pdb=" O THR J 152 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N THR J 152 " --> pdb=" O ASP J 148 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'J' and resid 158 through 162 removed outlier: 4.927A pdb=" N THR J 31 " --> pdb=" O GLU J 46 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ASN J 205 " --> pdb=" O LYS J 47 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N LEU J 208 " --> pdb=" O LEU J 220 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'j' and resid 62 through 65 removed outlier: 6.466A pdb=" N VAL j 69 " --> pdb=" O LEU j 65 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY j 135 " --> pdb=" O ARG j 143 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS j 154 " --> pdb=" O GLN j 146 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP j 148 " --> pdb=" O THR j 152 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N THR j 152 " --> pdb=" O ASP j 148 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'j' and resid 158 through 162 removed outlier: 5.539A pdb=" N THR j 31 " --> pdb=" O GLU j 46 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N ASN j 205 " --> pdb=" O LYS j 47 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LEU j 208 " --> pdb=" O LEU j 220 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS j 218 " --> pdb=" O VAL j 210 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'K' and resid 66 through 70 removed outlier: 6.663A pdb=" N LYS K 66 " --> pdb=" O MET K 78 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE K 74 " --> pdb=" O ILE K 70 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N HIS K 73 " --> pdb=" O VAL K 146 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY K 144 " --> pdb=" O GLY K 75 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'K' and resid 166 through 171 removed outlier: 6.388A pdb=" N ASP K 166 " --> pdb=" O GLN K 41 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N THR K 36 " --> pdb=" O GLU K 51 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLY K 45 " --> pdb=" O THR K 42 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ASN K 214 " --> pdb=" O LYS K 52 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N LEU K 217 " --> pdb=" O PHE K 229 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'k' and resid 66 through 70 removed outlier: 6.584A pdb=" N LYS k 66 " --> pdb=" O MET k 78 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE k 74 " --> pdb=" O ILE k 70 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N HIS k 73 " --> pdb=" O VAL k 146 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU k 141 " --> pdb=" O MET k 156 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'k' and resid 166 through 171 removed outlier: 6.582A pdb=" N ASP k 166 " --> pdb=" O GLN k 41 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N THR k 36 " --> pdb=" O GLU k 51 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY k 45 " --> pdb=" O THR k 42 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N ASN k 214 " --> pdb=" O LYS k 52 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N LEU k 217 " --> pdb=" O PHE k 229 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'L' and resid 63 through 66 removed outlier: 6.453A pdb=" N ILE L 70 " --> pdb=" O VAL L 66 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N HIS L 69 " --> pdb=" O TYR L 137 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ILE L 144 " --> pdb=" O CYS L 156 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASN L 152 " --> pdb=" O CYS L 148 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'L' and resid 158 through 162 removed outlier: 4.642A pdb=" N ALA L 34 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ASN L 209 " --> pdb=" O LYS L 50 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE L 212 " --> pdb=" O TYR L 224 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'l' and resid 63 through 66 removed outlier: 6.452A pdb=" N ILE l 70 " --> pdb=" O VAL l 66 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N HIS l 69 " --> pdb=" O TYR l 137 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU l 132 " --> pdb=" O THR l 147 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ILE l 144 " --> pdb=" O CYS l 156 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASN l 152 " --> pdb=" O CYS l 148 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'l' and resid 158 through 162 removed outlier: 5.240A pdb=" N ALA l 34 " --> pdb=" O LEU l 49 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ASN l 209 " --> pdb=" O LYS l 50 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'M' and resid 66 through 69 removed outlier: 6.425A pdb=" N VAL M 73 " --> pdb=" O VAL M 69 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER M 141 " --> pdb=" O GLY M 145 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'M' and resid 162 through 166 removed outlier: 4.684A pdb=" N THR M 35 " --> pdb=" O GLU M 50 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'm' and resid 66 through 69 removed outlier: 6.676A pdb=" N VAL m 73 " --> pdb=" O VAL m 69 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER m 141 " --> pdb=" O GLY m 145 " (cutoff:3.500A) Processing sheet with id= 47, 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= 48, first strand: chain 'N' and resid 34 through 37 removed outlier: 6.482A pdb=" N ILE N 41 " --> pdb=" O ILE N 37 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N ARG N 40 " --> pdb=" O TRP N 103 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA N 101 " --> pdb=" O PHE N 42 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'N' and resid 125 through 129 removed outlier: 6.450A pdb=" N THR N 2 " --> pdb=" O ASP N 17 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER N 18 " --> pdb=" O VAL N 173 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL N 173 " --> pdb=" O SER N 18 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY N 183 " --> pdb=" O ALA N 180 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'n' and resid 34 through 37 removed outlier: 6.683A pdb=" N ILE n 41 " --> pdb=" O ILE n 37 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ARG n 40 " --> pdb=" O TRP n 103 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'n' and resid 125 through 129 removed outlier: 6.587A pdb=" N THR n 2 " --> pdb=" O ASP n 17 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER n 18 " --> pdb=" O VAL n 173 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N VAL n 173 " --> pdb=" O SER n 18 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY n 183 " --> pdb=" O ALA n 180 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'O' and resid 34 through 37 removed outlier: 6.389A pdb=" N ILE O 41 " --> pdb=" O ILE O 37 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'O' and resid 124 through 128 removed outlier: 6.444A pdb=" N THR O 2 " --> pdb=" O ASP O 17 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR O 18 " --> pdb=" O ASN O 172 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ASN O 172 " --> pdb=" O THR O 18 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LYS O 182 " --> pdb=" O SER O 179 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'o' and resid 34 through 37 removed outlier: 6.592A pdb=" N ILE o 41 " --> pdb=" O ILE o 37 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'o' and resid 124 through 128 removed outlier: 3.506A pdb=" N ILE o 3 " --> pdb=" O MET o 127 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N THR o 2 " --> pdb=" O ASP o 17 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP o 17 " --> pdb=" O THR o 2 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N THR o 18 " --> pdb=" O ASN o 172 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ASN o 172 " --> pdb=" O THR o 18 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LYS o 182 " --> pdb=" O SER o 179 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'P' and resid 42 through 45 removed outlier: 6.045A pdb=" N LEU P 49 " --> pdb=" O MET P 45 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ARG P 48 " --> pdb=" O LEU P 112 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA P 54 " --> pdb=" O GLU P 106 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'P' and resid 136 through 140 removed outlier: 6.480A pdb=" N ALA P 10 " --> pdb=" O ASP P 25 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N GLY P 184 " --> pdb=" O ARG P 26 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N VAL P 185 " --> pdb=" O LEU P 200 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LYS P 194 " --> pdb=" O GLU P 191 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'p' and resid 42 through 45 removed outlier: 5.060A pdb=" N LEU p 49 " --> pdb=" O MET p 45 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ARG p 48 " --> pdb=" O LEU p 112 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU p 112 " --> pdb=" O ARG p 48 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALA p 54 " --> pdb=" O GLU p 106 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'p' and resid 136 through 140 removed outlier: 6.017A pdb=" N ALA p 10 " --> pdb=" O ASP p 25 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLY p 184 " --> pdb=" O ARG p 26 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N VAL p 185 " --> pdb=" O LEU p 200 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS p 194 " --> pdb=" O GLU p 191 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'Q' and resid 35 through 38 removed outlier: 6.457A pdb=" N ILE Q 42 " --> pdb=" O MET Q 38 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N LYS Q 41 " --> pdb=" O TYR Q 107 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'Q' and resid 129 through 132 removed outlier: 3.614A pdb=" N LEU Q 4 " --> pdb=" O HIS Q 132 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TYR Q 3 " --> pdb=" O ASP Q 18 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'q' and resid 35 through 38 removed outlier: 6.530A pdb=" N ILE q 42 " --> pdb=" O MET q 38 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N LYS q 41 " --> pdb=" O TYR q 107 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'q' and resid 129 through 132 removed outlier: 4.082A pdb=" N LEU q 4 " --> pdb=" O HIS q 132 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N TYR q 3 " --> pdb=" O ASP q 18 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'R' and resid 34 through 37 removed outlier: 3.551A pdb=" N ILE R 37 " --> pdb=" O LEU R 41 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU R 41 " --> pdb=" O ILE R 37 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'R' and resid 125 through 129 removed outlier: 6.433A pdb=" N THR R 2 " --> pdb=" O ASP R 17 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY R 11 " --> pdb=" O PHE R 8 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ALA R 173 " --> pdb=" O SER R 18 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LEU R 176 " --> pdb=" O VAL R 187 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY R 183 " --> pdb=" O ARG R 180 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'r' and resid 34 through 37 removed outlier: 6.579A pdb=" N LEU r 41 " --> pdb=" O ILE r 37 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'r' and resid 125 through 129 removed outlier: 6.326A pdb=" N THR r 2 " --> pdb=" O ASP r 17 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY r 11 " --> pdb=" O PHE r 8 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER r 18 " --> pdb=" O ALA r 173 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ALA r 173 " --> pdb=" O SER r 18 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LEU r 176 " --> pdb=" O VAL r 187 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'S' and resid 43 through 46 removed outlier: 6.615A pdb=" N THR S 50 " --> pdb=" O LEU S 46 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LYS S 49 " --> pdb=" O LEU S 113 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'S' and resid 135 through 139 removed outlier: 5.246A pdb=" N THR S 11 " --> pdb=" O ASP S 26 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N THR S 27 " --> pdb=" O ALA S 192 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA S 192 " --> pdb=" O THR S 27 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 's' and resid 43 through 46 removed outlier: 6.630A pdb=" N THR s 50 " --> pdb=" O LEU s 46 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LYS s 49 " --> pdb=" O LEU s 113 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 's' and resid 135 through 139 removed outlier: 6.141A pdb=" N THR s 11 " --> pdb=" O ASP s 26 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N THR s 27 " --> pdb=" O ALA s 192 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ALA s 192 " --> pdb=" O THR s 27 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY s 202 " --> pdb=" O THR s 199 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'T' and resid 42 through 45 removed outlier: 6.621A pdb=" N THR T 49 " --> pdb=" O VAL T 45 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N SER T 48 " --> pdb=" O TYR T 115 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'T' and resid 136 through 139 removed outlier: 4.140A pdb=" N VAL T 11 " --> pdb=" O THR T 139 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL T 6 " --> pdb=" O SER T 29 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N SER T 29 " --> pdb=" O VAL T 6 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N GLY T 8 " --> pdb=" O LEU T 27 " (cutoff:3.500A) removed outlier: 8.765A pdb=" N LEU T 27 " --> pdb=" O GLY T 8 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N SER T 10 " --> pdb=" O ASP T 25 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ASP T 25 " --> pdb=" O SER T 10 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 't' and resid 42 through 45 removed outlier: 6.741A pdb=" N THR t 49 " --> pdb=" O VAL t 45 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N SER t 48 " --> pdb=" O TYR t 115 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR t 109 " --> pdb=" O SER t 54 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 't' and resid 136 through 139 removed outlier: 4.444A pdb=" N VAL t 11 " --> pdb=" O THR t 139 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N VAL t 6 " --> pdb=" O SER t 29 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N SER t 29 " --> pdb=" O VAL t 6 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N GLY t 8 " --> pdb=" O LEU t 27 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N LEU t 27 " --> pdb=" O GLY t 8 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N SER t 10 " --> pdb=" O ASP t 25 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ASP t 25 " --> pdb=" O SER t 10 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA t 23 " --> pdb=" O LEU t 12 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ILE t 189 " --> pdb=" O GLU t 200 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY t 196 " --> pdb=" O THR t 193 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'y' and resid 1 through 7 removed outlier: 3.579A pdb=" N LYS y 11 " --> pdb=" O THR y 7 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'U' and resid 802 through 805 No H-bonds generated for sheet with id= 77 Processing sheet with id= 78, first strand: chain 'V' and resid 449 through 453 Processing sheet with id= 79, first strand: chain 'X' and resid 376 through 380 Processing sheet with id= 80, first strand: chain 'Y' and resid 345 through 349 removed outlier: 3.534A pdb=" N ILE Y 353 " --> pdb=" O ASP Y 348 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'Z' and resid 46 through 50 removed outlier: 9.161A pdb=" N GLN Z 7 " --> pdb=" O HIS Z 157 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N THR Z 159 " --> pdb=" O GLN Z 7 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N SER Z 140 " --> pdb=" O SER Z 119 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N SER Z 119 " --> pdb=" O SER Z 140 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL Z 120 " --> pdb=" O VAL Z 92 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N VAL Z 35 " --> pdb=" O THR Z 97 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASN Z 52 " --> pdb=" O LEU Z 40 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'a' and resid 320 through 326 removed outlier: 5.424A pdb=" N THR a 334 " --> pdb=" O LYS a 321 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'b' and resid 4 through 10 removed outlier: 3.635A pdb=" N GLY b 50 " --> pdb=" O THR b 6 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'b' and resid 107 through 114 Processing sheet with id= 85, first strand: chain 'c' and resid 66 through 69 removed outlier: 3.525A pdb=" N VAL c 67 " --> pdb=" O GLN c 30 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL c 31 " --> pdb=" O THR c 204 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE c 33 " --> pdb=" O ASN c 206 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'c' and resid 141 through 145 removed outlier: 3.670A pdb=" N VAL c 144 " --> pdb=" O ASP c 158 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP c 158 " --> pdb=" O VAL c 144 " (cutoff:3.500A) 5506 hydrogen bonds defined for protein. 16428 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 45.57 Time building geometry restraints manager: 33.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 36400 1.34 - 1.46: 24167 1.46 - 1.59: 50740 1.59 - 1.71: 13 1.71 - 1.84: 1069 Bond restraints: 112389 Sorted by residual: bond pdb=" N ILE W 115 " pdb=" CA ILE W 115 " ideal model delta sigma weight residual 1.455 1.498 -0.043 1.18e-02 7.18e+03 1.34e+01 bond pdb=" CA THR W 116 " pdb=" C THR W 116 " ideal model delta sigma weight residual 1.523 1.572 -0.049 1.34e-02 5.57e+03 1.33e+01 bond pdb=" N ASP W 117 " pdb=" CA ASP W 117 " ideal model delta sigma weight residual 1.457 1.503 -0.046 1.29e-02 6.01e+03 1.26e+01 bond pdb=" CA ASP W 117 " pdb=" C ASP W 117 " ideal model delta sigma weight residual 1.523 1.564 -0.041 1.34e-02 5.57e+03 9.24e+00 bond pdb=" N LEU W 118 " pdb=" CA LEU W 118 " ideal model delta sigma weight residual 1.457 1.498 -0.042 1.41e-02 5.03e+03 8.69e+00 ... (remaining 112384 not shown) Histogram of bond angle deviations from ideal: 93.48 - 102.75: 630 102.75 - 112.01: 54598 112.01 - 121.27: 68107 121.27 - 130.54: 28029 130.54 - 139.80: 446 Bond angle restraints: 151810 Sorted by residual: angle pdb=" N VAL A 48 " pdb=" CA VAL A 48 " pdb=" C VAL A 48 " ideal model delta sigma weight residual 112.96 107.42 5.54 1.00e+00 1.00e+00 3.07e+01 angle pdb=" N GLY A 37 " pdb=" CA GLY A 37 " pdb=" C GLY A 37 " ideal model delta sigma weight residual 114.46 104.95 9.51 1.81e+00 3.05e-01 2.76e+01 angle pdb=" C PRO X 317 " pdb=" N ILE X 318 " pdb=" CA ILE X 318 " ideal model delta sigma weight residual 121.97 131.31 -9.34 1.80e+00 3.09e-01 2.69e+01 angle pdb=" N ASP W 117 " pdb=" CA ASP W 117 " pdb=" C ASP W 117 " ideal model delta sigma weight residual 110.80 121.08 -10.28 2.13e+00 2.20e-01 2.33e+01 angle pdb=" N THR W 116 " pdb=" CA THR W 116 " pdb=" C THR W 116 " ideal model delta sigma weight residual 110.80 120.92 -10.12 2.13e+00 2.20e-01 2.26e+01 ... (remaining 151805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.08: 66217 30.08 - 60.17: 2318 60.17 - 90.25: 208 90.25 - 120.34: 2 120.34 - 150.42: 1 Dihedral angle restraints: 68746 sinusoidal: 27926 harmonic: 40820 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 300.00 149.58 150.42 1 2.00e+01 2.50e-03 4.49e+01 dihedral pdb=" O2A ADP C 501 " pdb=" O3A ADP C 501 " pdb=" PA ADP C 501 " pdb=" PB ADP C 501 " ideal model delta sinusoidal sigma weight residual -60.00 58.46 -118.46 1 2.00e+01 2.50e-03 3.54e+01 dihedral pdb=" CA VAL g 222 " pdb=" C VAL g 222 " pdb=" N GLU g 223 " pdb=" CA GLU g 223 " ideal model delta harmonic sigma weight residual 180.00 150.55 29.45 0 5.00e+00 4.00e-02 3.47e+01 ... (remaining 68743 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 16489 0.111 - 0.222: 663 0.222 - 0.333: 17 0.333 - 0.443: 0 0.443 - 0.554: 2 Chirality restraints: 17171 Sorted by residual: chirality pdb=" CB ILE I 52 " pdb=" CA ILE I 52 " pdb=" CG1 ILE I 52 " pdb=" CG2 ILE I 52 " both_signs ideal model delta sigma weight residual False 2.64 2.09 0.55 2.00e-01 2.50e+01 7.68e+00 chirality pdb=" CB ILE C 151 " pdb=" CA ILE C 151 " pdb=" CG1 ILE C 151 " pdb=" CG2 ILE C 151 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.48 2.00e-01 2.50e+01 5.72e+00 chirality pdb=" CB ILE W 140 " pdb=" CA ILE W 140 " pdb=" CG1 ILE W 140 " pdb=" CG2 ILE W 140 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 17168 not shown) Planarity restraints: 19566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP M 215 " 0.027 2.00e-02 2.50e+03 3.08e-02 2.37e+01 pdb=" CG TRP M 215 " -0.081 2.00e-02 2.50e+03 pdb=" CD1 TRP M 215 " 0.044 2.00e-02 2.50e+03 pdb=" CD2 TRP M 215 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP M 215 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP M 215 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP M 215 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 215 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 215 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP M 215 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU W 113 " -0.023 2.00e-02 2.50e+03 4.61e-02 2.13e+01 pdb=" C GLU W 113 " 0.080 2.00e-02 2.50e+03 pdb=" O GLU W 113 " -0.029 2.00e-02 2.50e+03 pdb=" N GLU W 114 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP m 215 " -0.032 2.00e-02 2.50e+03 2.64e-02 1.74e+01 pdb=" CG TRP m 215 " 0.069 2.00e-02 2.50e+03 pdb=" CD1 TRP m 215 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP m 215 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP m 215 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP m 215 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP m 215 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP m 215 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP m 215 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP m 215 " -0.010 2.00e-02 2.50e+03 ... (remaining 19563 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.34: 100 2.34 - 2.98: 50808 2.98 - 3.62: 169040 3.62 - 4.26: 246941 4.26 - 4.90: 414154 Nonbonded interactions: 881043 Sorted by model distance: nonbonded pdb=" OD2 ASP c 126 " pdb="ZN ZN c 401 " model vdw 1.702 2.230 nonbonded pdb=" CG ASP c 126 " pdb="ZN ZN c 401 " model vdw 2.134 2.460 nonbonded pdb=" OH TYR f 349 " pdb=" OG SER f 374 " model vdw 2.204 2.440 nonbonded pdb=" O GLU G 196 " pdb=" OG1 THR G 200 " model vdw 2.235 2.440 nonbonded pdb=" O ILE V 464 " pdb=" OH TYR Z 250 " model vdw 2.238 2.440 ... (remaining 881038 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'G' and (resid 2 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 through 195 or (resid 196 and (n \ ame N or name CA or name C or name O or name CB )) or resid 197 through 222 or ( \ resid 223 and (name N or name CA or name C or name O or name CB )) or resid 224 \ through 245)) selection = (chain 'g' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB )) or resid 4 through 245)) } ncs_group { reference = (chain 'H' and (resid 3 through 140 or (resid 141 and (name N or name CA or name \ C or name O or name CB )) or resid 142 through 199 or (resid 200 and (name N or \ name CA or name C or name O or name CB )) or resid 201 through 234)) selection = (chain 'h' and (resid 3 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB )) or resid 71 through 175 or (resid 176 and (name N or na \ me CA or name C or name O or name CB )) or resid 177 through 234)) } ncs_group { reference = (chain 'I' and (resid 2 through 6 or resid 8 through 198 or (resid 199 and (name \ N or name CA or name C or name O or name CB )) or resid 200 through 204 or (res \ id 205 and (name N or name CA or name C or name O or name CB )) or resid 206 thr \ ough 251)) selection = (chain 'i' and (resid 2 through 6 or resid 8 through 228 or (resid 229 and (name \ N or name CA or name C or name O or name CB )) or resid 230 or (resid 231 and ( \ name N or name CA or name C or name O or name CB )) or resid 232 through 251)) } ncs_group { reference = (chain 'J' and (resid 2 through 169 or (resid 170 and (name N or name CA or name \ C or name O or name CB )) or resid 171 through 206 or (resid 207 and (name N or \ name CA or name C or name O or name CB )) or resid 208 through 223 or (resid 22 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 225 through \ 231 or (resid 232 and (name N or name CA or name C or name O or name CB )) or re \ sid 233 through 238 or (resid 239 through 240 and (name N or name CA or name C o \ r name O or name CB )))) selection = (chain 'j' and (resid 2 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 240)) } ncs_group { reference = (chain 'K' and (resid 8 through 240 or (resid 241 and (name N or name CA or name \ C or name O or name CB or name CG1 or name CG2 or name CD1)))) selection = (chain 'k' and (resid 8 through 126 or (resid 127 through 129 and (name N or nam \ e CA or name C or name O or name CB )) or resid 130 through 241)) } ncs_group { reference = (chain 'L' and (resid 4 through 207 or (resid 208 and (name N or name CA or name \ C or name O or name CB )) or resid 209 through 237 or (resid 238 and (name N or \ name CA or name C or name O or name CB )) or resid 239 through 241)) selection = (chain 'l' and (resid 4 through 217 or (resid 218 and (name N or name CA or name \ C or name O or name CB )) or resid 219 through 241)) } ncs_group { reference = chain 'M' selection = (chain 'm' and ((resid 5 and (name N or name CA or name C or name O or name CB ) \ ) or resid 6 through 187 or (resid 188 and (name N or name CA or name C or name \ O or name CB )) or resid 189 through 244)) } ncs_group { reference = (chain 'N' and (resid 1 through 149 or (resid 150 and (name N or name CA or name \ C or name O or name CB )) or resid 151 through 202)) selection = chain 'n' } ncs_group { reference = chain 'O' selection = (chain 'o' and (resid 1 through 193 or (resid 194 and (name N or name CA or name \ C or name O or name CB )) or resid 195 through 202 or (resid 203 and (name N or \ name CA or name C or name O or name CB )) or resid 204 through 220)) } ncs_group { reference = chain 'P' selection = (chain 'p' and (resid 2 through 191 or (resid 192 and (name N or name CA or name \ C or name O or name CB )) or resid 193 through 205)) } ncs_group { reference = chain 'Q' selection = chain 'q' } ncs_group { reference = chain 'R' selection = chain 'r' } ncs_group { reference = chain 'S' selection = (chain 's' and ((resid 1 and (name N or name CA or name C or name O or name CB ) \ ) or resid 2 through 161 or (resid 162 and (name N or name CA or name C or name \ O or name CB )) or resid 163 through 168 or (resid 169 and (name N or name CA or \ name C or name O or name CB )) or resid 170 through 213)) } ncs_group { reference = chain 'T' selection = (chain 't' and (resid 1 through 205 or (resid 206 and (name N or name CA or name \ C or name O or name CB )) or resid 207 through 216)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.150 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: 0.060 Extract box with map and model: 51.430 Check model and map are aligned: 1.180 Set scattering table: 0.720 Process input model: 266.540 Find NCS groups from input model: 6.580 Set up NCS constraints: 0.620 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 338.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 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 : 0.005 0.068 112389 Z= 0.314 Angle : 0.821 13.121 151810 Z= 0.418 Chirality : 0.051 0.554 17171 Planarity : 0.006 0.092 19566 Dihedral : 14.742 150.424 42466 Min Nonbonded Distance : 1.702 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.72 % Favored : 93.22 % Rotamer: Outliers : 0.26 % Allowed : 0.58 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % 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: -1.17 (0.07), residues: 13955 helix: 0.05 (0.06), residues: 6060 sheet: -0.11 (0.12), residues: 2029 loop : -1.89 (0.08), residues: 5866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.081 0.002 TRP M 215 HIS 0.018 0.001 HIS U 70 PHE 0.033 0.002 PHE D 235 TYR 0.034 0.002 TYR A 432 ARG 0.013 0.001 ARG Y 46 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27910 Ramachandran restraints generated. 13955 Oldfield, 0 Emsley, 13955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27910 Ramachandran restraints generated. 13955 Oldfield, 0 Emsley, 13955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 12009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 477 time to evaluate : 9.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: x 181 MET cc_start: 0.6124 (mmp) cc_final: 0.5126 (ptm) REVERT: C 80 MET cc_start: 0.8396 (tmm) cc_final: 0.8181 (tmm) REVERT: D 296 MET cc_start: 0.8859 (ppp) cc_final: 0.8498 (ppp) REVERT: E 218 MET cc_start: 0.9381 (ttp) cc_final: 0.9109 (ptm) REVERT: K 156 MET cc_start: 0.8296 (tpt) cc_final: 0.7967 (tpt) REVERT: U 206 MET cc_start: 0.7546 (tmm) cc_final: 0.6914 (mmt) REVERT: U 423 MET cc_start: 0.7940 (mmm) cc_final: 0.7722 (mmt) REVERT: V 175 MET cc_start: 0.5439 (ppp) cc_final: 0.4762 (ppp) REVERT: V 358 MET cc_start: 0.8321 (tmm) cc_final: 0.8109 (ppp) REVERT: V 409 MET cc_start: 0.8233 (mmp) cc_final: 0.7648 (tmm) REVERT: W 28 LEU cc_start: 0.6197 (mt) cc_final: 0.5883 (tp) REVERT: W 190 MET cc_start: -0.0420 (mmm) cc_final: -0.1051 (ttt) REVERT: W 378 MET cc_start: 0.7137 (mmt) cc_final: 0.6831 (mmp) REVERT: X 254 MET cc_start: 0.5721 (mmt) cc_final: 0.4517 (mmt) REVERT: X 260 MET cc_start: 0.6863 (pmm) cc_final: 0.6199 (pmm) REVERT: Z 257 MET cc_start: 0.8928 (tmm) cc_final: 0.8706 (tmm) REVERT: b 16 MET cc_start: 0.6001 (ptm) cc_final: 0.5779 (ptm) REVERT: c 51 MET cc_start: 0.8552 (mmt) cc_final: 0.7669 (mmm) REVERT: c 95 MET cc_start: 0.7720 (mmt) cc_final: 0.7107 (mmt) REVERT: c 98 MET cc_start: 0.7561 (tmm) cc_final: 0.7101 (tmm) REVERT: c 216 MET cc_start: 0.8398 (ppp) cc_final: 0.8134 (ppp) REVERT: c 292 MET cc_start: 0.8530 (ppp) cc_final: 0.8219 (tmm) REVERT: f 1 MET cc_start: 0.5643 (tpt) cc_final: 0.5064 (tpt) REVERT: f 58 MET cc_start: 0.2380 (mtt) cc_final: 0.2070 (mtm) REVERT: f 89 MET cc_start: 0.5506 (tpt) cc_final: 0.4801 (mmt) REVERT: f 729 MET cc_start: 0.5383 (tpt) cc_final: 0.5125 (mtp) REVERT: f 744 MET cc_start: 0.1511 (mmm) cc_final: 0.1236 (mtp) REVERT: f 761 MET cc_start: 0.4872 (mmp) cc_final: 0.4390 (tpt) outliers start: 30 outliers final: 8 residues processed: 506 average time/residue: 0.9880 time to fit residues: 892.7057 Evaluate side-chains 451 residues out of total 12009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 443 time to evaluate : 9.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 327 GLN Chi-restraints excluded: chain A residue 38 GLN 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 F residue 416 THR Chi-restraints excluded: chain e residue 27 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1386 random chunks: chunk 1170 optimal weight: 9.9990 chunk 1050 optimal weight: 50.0000 chunk 582 optimal weight: 9.9990 chunk 358 optimal weight: 30.0000 chunk 708 optimal weight: 3.9990 chunk 561 optimal weight: 6.9990 chunk 1086 optimal weight: 40.0000 chunk 420 optimal weight: 9.9990 chunk 660 optimal weight: 10.0000 chunk 808 optimal weight: 6.9990 chunk 1258 optimal weight: 9.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 201 ASN x 327 GLN A 85 GLN A 203 ASN B 314 ASN C 377 HIS ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 10 GLN ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 81 HIS h 123 GLN ** q 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 452 ASN U 665 ASN ** U 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 110 HIS W 444 HIS ** Z 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 225 GLN a 287 ASN ** b 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 197 ASN f 198 HIS ** f 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 565 ASN f 649 HIS ** f 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 112389 Z= 0.244 Angle : 0.589 13.463 151810 Z= 0.307 Chirality : 0.042 0.322 17171 Planarity : 0.004 0.062 19566 Dihedral : 6.114 148.021 15482 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.06 % Favored : 93.91 % Rotamer: Outliers : 0.28 % Allowed : 6.74 % Favored : 92.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 13955 helix: 1.00 (0.07), residues: 6176 sheet: 0.16 (0.12), residues: 1977 loop : -1.76 (0.08), residues: 5802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP M 215 HIS 0.014 0.001 HIS T 81 PHE 0.027 0.001 PHE X 76 TYR 0.016 0.001 TYR Y 143 ARG 0.008 0.000 ARG C 307 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27910 Ramachandran restraints generated. 13955 Oldfield, 0 Emsley, 13955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27910 Ramachandran restraints generated. 13955 Oldfield, 0 Emsley, 13955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 12009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 446 time to evaluate : 9.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: x 181 MET cc_start: 0.6158 (mmp) cc_final: 0.5133 (ptm) REVERT: x 327 GLN cc_start: 0.6700 (OUTLIER) cc_final: 0.6461 (pt0) REVERT: D 204 MET cc_start: 0.7247 (ttt) cc_final: 0.6866 (ttt) REVERT: D 296 MET cc_start: 0.8874 (ppp) cc_final: 0.8571 (ppp) REVERT: D 352 MET cc_start: 0.6379 (tpp) cc_final: 0.6024 (tpp) REVERT: E 218 MET cc_start: 0.9337 (ttp) cc_final: 0.9126 (ptm) REVERT: F 36 MET cc_start: 0.0569 (mmt) cc_final: 0.0110 (ptt) REVERT: K 206 MET cc_start: 0.7749 (mmm) cc_final: 0.7258 (tmm) REVERT: Q 118 MET cc_start: 0.7781 (ttm) cc_final: 0.7538 (ttm) REVERT: m 117 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.7650 (mmp) REVERT: p 131 MET cc_start: 0.7764 (mmt) cc_final: 0.7490 (mmt) REVERT: s 158 MET cc_start: 0.8231 (mtt) cc_final: 0.8007 (mtm) REVERT: U 206 MET cc_start: 0.7559 (tmm) cc_final: 0.6887 (mmt) REVERT: U 239 GLU cc_start: 0.6233 (OUTLIER) cc_final: 0.5875 (mp0) REVERT: U 423 MET cc_start: 0.7976 (mmm) cc_final: 0.7667 (mmt) REVERT: V 175 MET cc_start: 0.5540 (ppp) cc_final: 0.5091 (ppp) REVERT: V 409 MET cc_start: 0.8260 (mmp) cc_final: 0.7626 (tmm) REVERT: W 378 MET cc_start: 0.7230 (mmt) cc_final: 0.6976 (mmp) REVERT: X 254 MET cc_start: 0.5706 (mmt) cc_final: 0.4301 (mmt) REVERT: X 368 MET cc_start: 0.6984 (tmm) cc_final: 0.6706 (tmm) REVERT: b 107 MET cc_start: 0.7276 (mmt) cc_final: 0.6898 (mmp) REVERT: c 51 MET cc_start: 0.8711 (mmt) cc_final: 0.7829 (mmm) REVERT: c 95 MET cc_start: 0.7702 (mmt) cc_final: 0.7467 (mmm) REVERT: c 98 MET cc_start: 0.7588 (tmm) cc_final: 0.7042 (tmm) REVERT: c 216 MET cc_start: 0.8505 (ppp) cc_final: 0.8126 (ppp) REVERT: f 58 MET cc_start: 0.2843 (mtt) cc_final: 0.2396 (mtp) REVERT: f 89 MET cc_start: 0.5402 (tpt) cc_final: 0.4538 (mmt) REVERT: f 729 MET cc_start: 0.5904 (tpt) cc_final: 0.5188 (mtp) REVERT: f 744 MET cc_start: 0.1442 (mmm) cc_final: 0.1126 (mtp) REVERT: f 761 MET cc_start: 0.5142 (mmp) cc_final: 0.4818 (tpt) REVERT: f 825 MET cc_start: 0.5405 (mmm) cc_final: 0.5043 (mmp) outliers start: 32 outliers final: 12 residues processed: 464 average time/residue: 0.8750 time to fit residues: 732.2533 Evaluate side-chains 456 residues out of total 12009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 441 time to evaluate : 9.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 327 GLN Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain S residue 191 ASP Chi-restraints excluded: chain m residue 117 MET Chi-restraints excluded: chain o residue 146 MET Chi-restraints excluded: chain U residue 239 GLU Chi-restraints excluded: chain W residue 117 ASP Chi-restraints excluded: chain Y residue 104 MET Chi-restraints excluded: chain Z residue 144 VAL Chi-restraints excluded: chain c residue 122 LEU Chi-restraints excluded: chain e residue 27 TRP Chi-restraints excluded: chain e residue 65 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1386 random chunks: chunk 699 optimal weight: 7.9990 chunk 390 optimal weight: 5.9990 chunk 1047 optimal weight: 50.0000 chunk 857 optimal weight: 20.0000 chunk 347 optimal weight: 20.0000 chunk 1260 optimal weight: 4.9990 chunk 1362 optimal weight: 7.9990 chunk 1122 optimal weight: 7.9990 chunk 1250 optimal weight: 30.0000 chunk 429 optimal weight: 9.9990 chunk 1011 optimal weight: 50.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 281 GLN ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 ASN B 242 GLN C 332 HIS C 377 HIS ** D 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 258 GLN ** F 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 119 ASN ** k 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 166 GLN o 193 ASN ** q 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 41 GLN U 438 GLN ** U 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 718 ASN ** U 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 444 HIS Z 193 ASN ** Z 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 475 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 112389 Z= 0.223 Angle : 0.559 10.362 151810 Z= 0.290 Chirality : 0.042 0.342 17171 Planarity : 0.004 0.063 19566 Dihedral : 5.860 145.080 15478 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.30 % Favored : 93.66 % Rotamer: Outliers : 0.62 % Allowed : 10.26 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.05 (0.07), residues: 13955 helix: 1.35 (0.07), residues: 6180 sheet: 0.16 (0.12), residues: 1997 loop : -1.70 (0.08), residues: 5778 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 0.017 0.001 PHE s 179 TYR 0.029 0.001 TYR A 36 ARG 0.007 0.000 ARG C 307 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27910 Ramachandran restraints generated. 13955 Oldfield, 0 Emsley, 13955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27910 Ramachandran restraints generated. 13955 Oldfield, 0 Emsley, 13955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 12009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 445 time to evaluate : 9.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: x 181 MET cc_start: 0.6110 (mmp) cc_final: 0.5114 (ptm) REVERT: D 153 MET cc_start: 0.6419 (tpt) cc_final: 0.6176 (tpt) REVERT: D 296 MET cc_start: 0.8916 (ppp) cc_final: 0.8650 (ppp) REVERT: D 309 MET cc_start: 0.7782 (mmm) cc_final: 0.7300 (mmm) REVERT: D 352 MET cc_start: 0.6559 (tpp) cc_final: 0.6268 (tpp) REVERT: F 36 MET cc_start: 0.0730 (mmt) cc_final: 0.0330 (ptt) REVERT: F 55 MET cc_start: 0.7495 (tmm) cc_final: 0.7159 (tmm) REVERT: K 78 MET cc_start: 0.8260 (ptt) cc_final: 0.7977 (ptt) REVERT: K 206 MET cc_start: 0.7702 (mmm) cc_final: 0.7256 (tmm) REVERT: s 158 MET cc_start: 0.8229 (mtt) cc_final: 0.8024 (mtm) REVERT: t 110 MET cc_start: 0.8754 (mpp) cc_final: 0.8336 (mpp) REVERT: U 206 MET cc_start: 0.7569 (tmm) cc_final: 0.6864 (mmt) REVERT: U 239 GLU cc_start: 0.6396 (OUTLIER) cc_final: 0.6076 (mp0) REVERT: U 423 MET cc_start: 0.8020 (mmm) cc_final: 0.7753 (mmt) REVERT: U 583 MET cc_start: 0.8649 (mmm) cc_final: 0.8189 (mmm) REVERT: V 175 MET cc_start: 0.6448 (OUTLIER) cc_final: 0.6101 (tmm) REVERT: V 409 MET cc_start: 0.8274 (mmp) cc_final: 0.7663 (tmm) REVERT: W 375 MET cc_start: 0.7455 (mmm) cc_final: 0.7218 (mmp) REVERT: X 254 MET cc_start: 0.5771 (mmt) cc_final: 0.4848 (mmt) REVERT: X 368 MET cc_start: 0.7046 (tmm) cc_final: 0.6637 (tmm) REVERT: b 107 MET cc_start: 0.7034 (mmt) cc_final: 0.6693 (mmp) REVERT: c 51 MET cc_start: 0.8725 (mmt) cc_final: 0.7795 (mmm) REVERT: c 95 MET cc_start: 0.7679 (mmt) cc_final: 0.7476 (mmt) REVERT: c 216 MET cc_start: 0.8477 (ppp) cc_final: 0.8134 (ppp) REVERT: d 4 GLN cc_start: 0.5030 (OUTLIER) cc_final: 0.4078 (tt0) REVERT: f 58 MET cc_start: 0.2828 (mtt) cc_final: 0.2467 (mtm) REVERT: f 89 MET cc_start: 0.5394 (tpt) cc_final: 0.4407 (mmt) REVERT: f 761 MET cc_start: 0.5126 (mmp) cc_final: 0.4911 (tpt) REVERT: f 825 MET cc_start: 0.5367 (mmm) cc_final: 0.4539 (mmm) outliers start: 73 outliers final: 23 residues processed: 498 average time/residue: 0.9334 time to fit residues: 845.1535 Evaluate side-chains 464 residues out of total 12009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 438 time to evaluate : 10.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 327 GLN Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain E residue 348 THR Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain T residue 205 THR Chi-restraints excluded: chain i residue 202 ASP Chi-restraints excluded: chain n residue 192 ASP Chi-restraints excluded: chain U residue 239 GLU Chi-restraints excluded: chain U residue 629 THR Chi-restraints excluded: chain U residue 854 MET Chi-restraints excluded: chain V residue 175 MET Chi-restraints excluded: chain W residue 117 ASP Chi-restraints excluded: chain W residue 158 ASP Chi-restraints excluded: chain W residue 442 THR Chi-restraints excluded: chain X residue 80 ILE Chi-restraints excluded: chain X residue 190 LEU Chi-restraints excluded: chain Y residue 37 VAL Chi-restraints excluded: chain Y residue 104 MET Chi-restraints excluded: chain Z residue 126 VAL Chi-restraints excluded: chain Z residue 144 VAL Chi-restraints excluded: chain b residue 60 VAL Chi-restraints excluded: chain c residue 275 VAL Chi-restraints excluded: chain d residue 4 GLN Chi-restraints excluded: chain d residue 43 LEU Chi-restraints excluded: chain e residue 27 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1386 random chunks: chunk 1245 optimal weight: 20.0000 chunk 948 optimal weight: 50.0000 chunk 654 optimal weight: 20.0000 chunk 139 optimal weight: 20.0000 chunk 601 optimal weight: 9.9990 chunk 846 optimal weight: 30.0000 chunk 1265 optimal weight: 7.9990 chunk 1339 optimal weight: 50.0000 chunk 661 optimal weight: 30.0000 chunk 1199 optimal weight: 20.0000 chunk 361 optimal weight: 9.9990 overall best weight: 13.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 96 GLN ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 GLN ** C 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 353 ASN ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 271 HIS ** E 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 142 HIS Q 8 GLN ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 62 GLN j 215 GLN ** k 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 110 GLN U 218 GLN ** U 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 453 HIS ** U 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 424 GLN W 444 HIS Y 196 GLN Z 193 ASN ** Z 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 225 GLN ** a 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 79 GLN ** b 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 142 ASN f 213 GLN ** f 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 475 ASN ** f 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 112389 Z= 0.405 Angle : 0.692 10.279 151810 Z= 0.361 Chirality : 0.045 0.337 17171 Planarity : 0.005 0.060 19566 Dihedral : 6.259 150.511 15476 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.40 % Favored : 92.56 % Rotamer: Outliers : 1.74 % Allowed : 13.43 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.20 % Twisted General : 0.01 % 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: -0.36 (0.07), residues: 13955 helix: 1.08 (0.07), residues: 6164 sheet: -0.02 (0.11), residues: 2004 loop : -1.82 (0.08), residues: 5787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP m 215 HIS 0.012 0.002 HIS U 70 PHE 0.039 0.002 PHE S 124 TYR 0.023 0.002 TYR n 136 ARG 0.018 0.001 ARG C 307 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27910 Ramachandran restraints generated. 13955 Oldfield, 0 Emsley, 13955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27910 Ramachandran restraints generated. 13955 Oldfield, 0 Emsley, 13955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 12009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 441 time to evaluate : 9.521 Fit side-chains revert: symmetry clash REVERT: x 181 MET cc_start: 0.6046 (mmp) cc_final: 0.4980 (ptm) REVERT: x 207 MET cc_start: 0.7057 (tmm) cc_final: 0.6696 (tmm) REVERT: x 221 ASP cc_start: 0.5411 (m-30) cc_final: 0.4828 (p0) REVERT: D 153 MET cc_start: 0.7068 (tpt) cc_final: 0.6853 (tpt) REVERT: D 296 MET cc_start: 0.8935 (ppp) cc_final: 0.8650 (ppp) REVERT: D 309 MET cc_start: 0.7919 (mmm) cc_final: 0.7348 (mmm) REVERT: E 218 MET cc_start: 0.9315 (ptm) cc_final: 0.9029 (ppp) REVERT: F 36 MET cc_start: 0.1020 (mmt) cc_final: 0.0573 (ptt) REVERT: F 55 MET cc_start: 0.7487 (tmm) cc_final: 0.7069 (tmm) REVERT: K 206 MET cc_start: 0.7681 (mmm) cc_final: 0.7365 (tmm) REVERT: M 52 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.9024 (pp) REVERT: Q 1 MET cc_start: 0.6606 (mmm) cc_final: 0.6254 (mmm) REVERT: S 201 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.7960 (mm-30) REVERT: j 211 MET cc_start: 0.6477 (mtt) cc_final: 0.6194 (ttm) REVERT: p 4 MET cc_start: 0.8180 (mmm) cc_final: 0.7937 (mmt) REVERT: p 12 MET cc_start: 0.7974 (OUTLIER) cc_final: 0.7614 (ttp) REVERT: q 11 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7311 (p0) REVERT: y 1 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.6530 (tmm) REVERT: U 206 MET cc_start: 0.7522 (tmm) cc_final: 0.6890 (mmt) REVERT: U 239 GLU cc_start: 0.6447 (OUTLIER) cc_final: 0.6001 (mp0) REVERT: V 175 MET cc_start: 0.6322 (ppp) cc_final: 0.5587 (ppp) REVERT: V 409 MET cc_start: 0.8287 (mmp) cc_final: 0.7580 (tmm) REVERT: V 433 ASP cc_start: 0.7409 (OUTLIER) cc_final: 0.7054 (p0) REVERT: W 366 MET cc_start: 0.7623 (mpp) cc_final: 0.7414 (mpp) REVERT: X 254 MET cc_start: 0.5873 (mmt) cc_final: 0.5078 (mmt) REVERT: Y 214 MET cc_start: 0.6815 (mmp) cc_final: 0.6427 (mmm) REVERT: a 141 MET cc_start: 0.6771 (pmm) cc_final: 0.6209 (ptp) REVERT: a 278 MET cc_start: 0.7535 (pmm) cc_final: 0.7175 (pmm) REVERT: b 107 MET cc_start: 0.7025 (mmt) cc_final: 0.6618 (mmt) REVERT: c 51 MET cc_start: 0.8940 (mmt) cc_final: 0.8036 (mmm) REVERT: c 95 MET cc_start: 0.7833 (mmt) cc_final: 0.7555 (mmm) REVERT: c 216 MET cc_start: 0.8587 (ppp) cc_final: 0.8354 (ppp) REVERT: d 4 GLN cc_start: 0.5382 (OUTLIER) cc_final: 0.4542 (tt0) REVERT: d 158 ILE cc_start: 0.5264 (OUTLIER) cc_final: 0.4848 (mt) REVERT: f 26 GLU cc_start: 0.3895 (OUTLIER) cc_final: 0.3421 (pp20) REVERT: f 27 LYS cc_start: 0.6696 (mtpt) cc_final: 0.6411 (tttm) REVERT: f 58 MET cc_start: 0.2839 (mtt) cc_final: 0.2442 (mtp) REVERT: f 89 MET cc_start: 0.5433 (tpt) cc_final: 0.4355 (mmt) REVERT: f 825 MET cc_start: 0.5450 (mmm) cc_final: 0.4652 (mmm) outliers start: 207 outliers final: 85 residues processed: 620 average time/residue: 0.8343 time to fit residues: 942.3973 Evaluate side-chains 534 residues out of total 12009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 439 time to evaluate : 9.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 254 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 357 ASP Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 336 MET Chi-restraints excluded: chain D residue 110 ASN Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 374 ASP Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 348 THR Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 405 MET Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 202 LEU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain J residue 107 ILE Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain L residue 228 ASP Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain S residue 191 ASP Chi-restraints excluded: chain S residue 201 GLU Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 70 MET Chi-restraints excluded: chain T residue 117 ASP Chi-restraints excluded: chain T residue 193 THR Chi-restraints excluded: chain T residue 205 THR Chi-restraints excluded: chain g residue 175 SER Chi-restraints excluded: chain g residue 224 ASN Chi-restraints excluded: chain i residue 202 ASP Chi-restraints excluded: chain j residue 184 ASP Chi-restraints excluded: chain k residue 106 THR Chi-restraints excluded: chain k residue 146 VAL Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain l residue 176 MET Chi-restraints excluded: chain n residue 192 ASP Chi-restraints excluded: chain p residue 12 MET Chi-restraints excluded: chain p residue 122 CYS Chi-restraints excluded: chain q residue 11 ASP Chi-restraints excluded: chain t residue 127 MET Chi-restraints excluded: chain t residue 163 THR Chi-restraints excluded: chain y residue 1 MET Chi-restraints excluded: chain U residue 143 ASP Chi-restraints excluded: chain U residue 239 GLU Chi-restraints excluded: chain U residue 248 ILE Chi-restraints excluded: chain U residue 629 THR Chi-restraints excluded: chain U residue 695 MET Chi-restraints excluded: chain U residue 854 MET Chi-restraints excluded: chain V residue 433 ASP Chi-restraints excluded: chain W residue 117 ASP Chi-restraints excluded: chain W residue 158 ASP Chi-restraints excluded: chain W residue 425 LEU Chi-restraints excluded: chain W residue 442 THR Chi-restraints excluded: chain X residue 80 ILE Chi-restraints excluded: chain X residue 190 LEU Chi-restraints excluded: chain X residue 256 LEU Chi-restraints excluded: chain Y residue 37 VAL Chi-restraints excluded: chain Y residue 68 ASP Chi-restraints excluded: chain Y residue 104 MET Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain Z residue 126 VAL Chi-restraints excluded: chain Z residue 130 ASP Chi-restraints excluded: chain Z residue 144 VAL Chi-restraints excluded: chain a residue 111 VAL Chi-restraints excluded: chain b residue 16 MET Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain c residue 180 ASN Chi-restraints excluded: chain c residue 275 VAL Chi-restraints excluded: chain d residue 4 GLN Chi-restraints excluded: chain d residue 43 LEU Chi-restraints excluded: chain d residue 126 ASP Chi-restraints excluded: chain d residue 158 ILE Chi-restraints excluded: chain f residue 26 GLU Chi-restraints excluded: chain f residue 793 VAL Chi-restraints excluded: chain e residue 27 TRP Chi-restraints excluded: chain e residue 50 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1386 random chunks: chunk 1115 optimal weight: 10.0000 chunk 760 optimal weight: 20.0000 chunk 19 optimal weight: 40.0000 chunk 997 optimal weight: 30.0000 chunk 552 optimal weight: 20.0000 chunk 1143 optimal weight: 30.0000 chunk 926 optimal weight: 4.9990 chunk 1 optimal weight: 30.0000 chunk 684 optimal weight: 40.0000 chunk 1202 optimal weight: 20.0000 chunk 338 optimal weight: 10.0000 overall best weight: 12.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 ASN C 22 GLN ** C 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 345 ASN ** F 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 255 GLN ** F 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 162 GLN ** U 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 743 ASN ** U 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 218 ASN Y 14 ASN Z 12 HIS Z 157 HIS ** b 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 329 ASN ** f 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 475 ASN ** f 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 112389 Z= 0.362 Angle : 0.646 11.066 151810 Z= 0.337 Chirality : 0.044 0.298 17171 Planarity : 0.004 0.061 19566 Dihedral : 6.224 143.188 15472 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.99 % Favored : 92.97 % Rotamer: Outliers : 2.05 % Allowed : 15.78 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.37 (0.07), residues: 13955 helix: 1.10 (0.07), residues: 6166 sheet: 0.01 (0.12), residues: 1933 loop : -1.85 (0.08), residues: 5856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP M 215 HIS 0.010 0.001 HIS U 70 PHE 0.028 0.002 PHE s 179 TYR 0.026 0.002 TYR h 121 ARG 0.012 0.001 ARG C 307 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27910 Ramachandran restraints generated. 13955 Oldfield, 0 Emsley, 13955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27910 Ramachandran restraints generated. 13955 Oldfield, 0 Emsley, 13955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 12009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 442 time to evaluate : 8.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: x 178 PHE cc_start: 0.6081 (OUTLIER) cc_final: 0.5574 (m-80) REVERT: x 181 MET cc_start: 0.6023 (mmp) cc_final: 0.5014 (ptm) REVERT: x 207 MET cc_start: 0.7133 (tmm) cc_final: 0.6725 (tmm) REVERT: x 221 ASP cc_start: 0.5331 (m-30) cc_final: 0.4551 (p0) REVERT: B 107 MET cc_start: 0.7077 (ppp) cc_final: 0.6802 (ppp) REVERT: B 372 MET cc_start: 0.7479 (tpp) cc_final: 0.7261 (mpp) REVERT: D 296 MET cc_start: 0.8967 (ppp) cc_final: 0.8670 (ppp) REVERT: D 309 MET cc_start: 0.7888 (mmm) cc_final: 0.7381 (mmm) REVERT: E 218 MET cc_start: 0.9304 (ptm) cc_final: 0.9040 (ppp) REVERT: F 36 MET cc_start: 0.1245 (mmt) cc_final: 0.0761 (ptt) REVERT: F 55 MET cc_start: 0.7550 (tmm) cc_final: 0.7134 (tmm) REVERT: M 52 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.9080 (pp) REVERT: S 201 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.7974 (mm-30) REVERT: i 121 TYR cc_start: 0.8405 (OUTLIER) cc_final: 0.8111 (t80) REVERT: p 12 MET cc_start: 0.8017 (OUTLIER) cc_final: 0.7656 (ttp) REVERT: p 131 MET cc_start: 0.7872 (mmt) cc_final: 0.7398 (mmt) REVERT: q 11 ASP cc_start: 0.7852 (OUTLIER) cc_final: 0.7277 (p0) REVERT: y 1 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.6482 (tmm) REVERT: U 137 MET cc_start: 0.8488 (mmp) cc_final: 0.8174 (mmm) REVERT: U 206 MET cc_start: 0.7563 (tmm) cc_final: 0.6917 (mmt) REVERT: U 239 GLU cc_start: 0.6583 (OUTLIER) cc_final: 0.6311 (pm20) REVERT: U 583 MET cc_start: 0.8608 (mmm) cc_final: 0.8406 (tpp) REVERT: V 175 MET cc_start: 0.6454 (ppp) cc_final: 0.5727 (tmm) REVERT: V 409 MET cc_start: 0.8347 (mmp) cc_final: 0.7610 (tmm) REVERT: V 433 ASP cc_start: 0.7420 (OUTLIER) cc_final: 0.7107 (p0) REVERT: X 254 MET cc_start: 0.5843 (mmt) cc_final: 0.5118 (mmt) REVERT: Y 169 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6684 (mp0) REVERT: Y 214 MET cc_start: 0.6709 (mmp) cc_final: 0.6325 (mmm) REVERT: a 278 MET cc_start: 0.7650 (pmm) cc_final: 0.7230 (pmm) REVERT: b 107 MET cc_start: 0.7111 (mmt) cc_final: 0.6650 (mmt) REVERT: c 51 MET cc_start: 0.8900 (mmt) cc_final: 0.7980 (mmm) REVERT: d 4 GLN cc_start: 0.5625 (OUTLIER) cc_final: 0.4240 (tt0) REVERT: d 132 TYR cc_start: 0.6375 (OUTLIER) cc_final: 0.5796 (m-80) REVERT: d 158 ILE cc_start: 0.5350 (OUTLIER) cc_final: 0.4939 (mt) REVERT: f 26 GLU cc_start: 0.4003 (OUTLIER) cc_final: 0.3549 (pp20) REVERT: f 27 LYS cc_start: 0.6591 (mtpt) cc_final: 0.5847 (mtpt) REVERT: f 58 MET cc_start: 0.2803 (mtt) cc_final: 0.2421 (mtp) REVERT: f 89 MET cc_start: 0.5417 (tpt) cc_final: 0.4388 (mmt) REVERT: f 150 GLU cc_start: 0.2232 (OUTLIER) cc_final: 0.1890 (tm-30) REVERT: f 298 LEU cc_start: 0.3786 (OUTLIER) cc_final: 0.3415 (tp) REVERT: f 761 MET cc_start: 0.4887 (tpt) cc_final: 0.4546 (tpp) REVERT: f 825 MET cc_start: 0.5347 (mmm) cc_final: 0.4632 (mmm) outliers start: 244 outliers final: 109 residues processed: 664 average time/residue: 0.9046 time to fit residues: 1096.2477 Evaluate side-chains 566 residues out of total 12009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 441 time to evaluate : 9.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 48 VAL Chi-restraints excluded: chain x residue 178 PHE Chi-restraints excluded: chain x residue 279 ILE Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 110 ASN Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 224 ASP Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 405 MET Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain G residue 202 LEU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain L residue 206 THR Chi-restraints excluded: chain M residue 13 THR Chi-restraints excluded: chain M residue 37 ILE Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain S residue 191 ASP Chi-restraints excluded: chain S residue 201 GLU Chi-restraints excluded: chain T residue 70 MET Chi-restraints excluded: chain T residue 117 ASP Chi-restraints excluded: chain T residue 205 THR Chi-restraints excluded: chain g residue 13 ILE Chi-restraints excluded: chain g residue 134 LEU Chi-restraints excluded: chain g residue 190 THR Chi-restraints excluded: chain g residue 224 ASN Chi-restraints excluded: chain i residue 121 TYR Chi-restraints excluded: chain i residue 202 ASP Chi-restraints excluded: chain k residue 13 ASN Chi-restraints excluded: chain k residue 31 ILE Chi-restraints excluded: chain k residue 225 ASN Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain l residue 176 MET Chi-restraints excluded: chain m residue 77 VAL Chi-restraints excluded: chain m residue 184 MET Chi-restraints excluded: chain n residue 68 ILE Chi-restraints excluded: chain n residue 192 ASP Chi-restraints excluded: chain p residue 12 MET Chi-restraints excluded: chain p residue 58 THR Chi-restraints excluded: chain q residue 11 ASP Chi-restraints excluded: chain r residue 194 ASP Chi-restraints excluded: chain s residue 26 ASP Chi-restraints excluded: chain s residue 164 VAL Chi-restraints excluded: chain t residue 21 VAL Chi-restraints excluded: chain t residue 127 MET Chi-restraints excluded: chain t residue 141 TYR Chi-restraints excluded: chain y residue 1 MET Chi-restraints excluded: chain U residue 143 ASP Chi-restraints excluded: chain U residue 239 GLU Chi-restraints excluded: chain U residue 496 LEU Chi-restraints excluded: chain U residue 585 THR Chi-restraints excluded: chain U residue 629 THR Chi-restraints excluded: chain U residue 695 MET Chi-restraints excluded: chain U residue 854 MET Chi-restraints excluded: chain V residue 433 ASP Chi-restraints excluded: chain V residue 494 MET Chi-restraints excluded: chain W residue 117 ASP Chi-restraints excluded: chain W residue 158 ASP Chi-restraints excluded: chain W residue 171 VAL Chi-restraints excluded: chain W residue 425 LEU Chi-restraints excluded: chain X residue 80 ILE Chi-restraints excluded: chain X residue 190 LEU Chi-restraints excluded: chain X residue 256 LEU Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain Y residue 37 VAL Chi-restraints excluded: chain Y residue 104 MET Chi-restraints excluded: chain Y residue 134 LEU Chi-restraints excluded: chain Y residue 169 GLU Chi-restraints excluded: chain Y residue 299 MET Chi-restraints excluded: chain Z residue 10 VAL Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain Z residue 67 VAL Chi-restraints excluded: chain Z residue 126 VAL Chi-restraints excluded: chain Z residue 130 ASP Chi-restraints excluded: chain Z residue 144 VAL Chi-restraints excluded: chain a residue 102 GLU Chi-restraints excluded: chain a residue 221 VAL Chi-restraints excluded: chain b residue 60 VAL Chi-restraints excluded: chain b residue 117 VAL Chi-restraints excluded: chain c residue 36 LEU Chi-restraints excluded: chain c residue 275 VAL Chi-restraints excluded: chain d residue 4 GLN Chi-restraints excluded: chain d residue 43 LEU Chi-restraints excluded: chain d residue 126 ASP Chi-restraints excluded: chain d residue 132 TYR Chi-restraints excluded: chain d residue 158 ILE Chi-restraints excluded: chain d residue 197 ILE Chi-restraints excluded: chain f residue 24 THR Chi-restraints excluded: chain f residue 26 GLU Chi-restraints excluded: chain f residue 150 GLU Chi-restraints excluded: chain f residue 171 GLN Chi-restraints excluded: chain f residue 298 LEU Chi-restraints excluded: chain f residue 408 LEU Chi-restraints excluded: chain f residue 422 VAL Chi-restraints excluded: chain f residue 594 LEU Chi-restraints excluded: chain f residue 718 ASP Chi-restraints excluded: chain f residue 729 MET Chi-restraints excluded: chain e residue 27 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1386 random chunks: chunk 450 optimal weight: 4.9990 chunk 1206 optimal weight: 8.9990 chunk 264 optimal weight: 8.9990 chunk 786 optimal weight: 0.8980 chunk 330 optimal weight: 10.0000 chunk 1341 optimal weight: 50.0000 chunk 1113 optimal weight: 30.0000 chunk 620 optimal weight: 20.0000 chunk 111 optimal weight: 30.0000 chunk 443 optimal weight: 9.9990 chunk 704 optimal weight: 20.0000 overall best weight: 6.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 HIS A 247 GLN ** C 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 345 ASN ** F 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 8 GLN ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 132 HIS ** U 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 400 HIS ** W 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 112389 Z= 0.222 Angle : 0.579 12.302 151810 Z= 0.298 Chirality : 0.042 0.336 17171 Planarity : 0.004 0.057 19566 Dihedral : 5.979 138.043 15472 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.79 % Favored : 93.17 % Rotamer: Outliers : 1.79 % Allowed : 16.79 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.14 (0.07), residues: 13955 helix: 1.33 (0.07), residues: 6185 sheet: 0.04 (0.12), residues: 1935 loop : -1.76 (0.08), residues: 5835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP Y 63 HIS 0.008 0.001 HIS U 70 PHE 0.019 0.001 PHE P 69 TYR 0.020 0.001 TYR Y 259 ARG 0.008 0.000 ARG C 307 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27910 Ramachandran restraints generated. 13955 Oldfield, 0 Emsley, 13955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27910 Ramachandran restraints generated. 13955 Oldfield, 0 Emsley, 13955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 12009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 442 time to evaluate : 9.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: x 181 MET cc_start: 0.5980 (mmp) cc_final: 0.4988 (ptm) REVERT: x 207 MET cc_start: 0.7109 (tmm) cc_final: 0.6687 (tmm) REVERT: A 261 PHE cc_start: 0.8758 (OUTLIER) cc_final: 0.8509 (m-10) REVERT: B 107 MET cc_start: 0.7148 (ppp) cc_final: 0.6861 (ppp) REVERT: B 214 MET cc_start: 0.7433 (OUTLIER) cc_final: 0.6803 (tmm) REVERT: C 274 LEU cc_start: 0.9554 (OUTLIER) cc_final: 0.9313 (tt) REVERT: D 296 MET cc_start: 0.8966 (ppp) cc_final: 0.8656 (ppp) REVERT: D 309 MET cc_start: 0.7841 (mmm) cc_final: 0.7342 (mmm) REVERT: E 218 MET cc_start: 0.9332 (ptm) cc_final: 0.8987 (ppp) REVERT: E 247 THR cc_start: 0.9110 (OUTLIER) cc_final: 0.8567 (p) REVERT: F 36 MET cc_start: 0.1181 (mmt) cc_final: 0.0714 (ptt) REVERT: F 55 MET cc_start: 0.7572 (tmm) cc_final: 0.7150 (tmm) REVERT: i 249 ARG cc_start: 0.6665 (OUTLIER) cc_final: 0.6386 (ptt90) REVERT: j 211 MET cc_start: 0.6411 (OUTLIER) cc_final: 0.6074 (tpp) REVERT: k 59 MET cc_start: 0.7932 (tpp) cc_final: 0.7521 (mmt) REVERT: l 26 MET cc_start: 0.7688 (mmt) cc_final: 0.6947 (mmt) REVERT: t 110 MET cc_start: 0.8793 (mpp) cc_final: 0.8254 (mpp) REVERT: y 1 MET cc_start: 0.7855 (OUTLIER) cc_final: 0.6470 (tmm) REVERT: U 137 MET cc_start: 0.8499 (mmp) cc_final: 0.8153 (mmm) REVERT: U 206 MET cc_start: 0.7547 (tmm) cc_final: 0.6898 (mmt) REVERT: U 239 GLU cc_start: 0.6521 (OUTLIER) cc_final: 0.6277 (pm20) REVERT: U 423 MET cc_start: 0.7847 (mmt) cc_final: 0.7275 (tpt) REVERT: U 583 MET cc_start: 0.8557 (mmm) cc_final: 0.8309 (mmm) REVERT: V 175 MET cc_start: 0.6514 (OUTLIER) cc_final: 0.5797 (tmm) REVERT: V 409 MET cc_start: 0.8312 (mmp) cc_final: 0.7596 (tmm) REVERT: V 433 ASP cc_start: 0.7372 (OUTLIER) cc_final: 0.7080 (p0) REVERT: V 478 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.8283 (pp30) REVERT: W 63 THR cc_start: 0.6554 (OUTLIER) cc_final: 0.6342 (p) REVERT: X 254 MET cc_start: 0.5837 (mmt) cc_final: 0.4651 (mmt) REVERT: Y 63 TRP cc_start: 0.5180 (m100) cc_final: 0.4607 (t-100) REVERT: Y 214 MET cc_start: 0.6640 (mmp) cc_final: 0.6295 (mmm) REVERT: Y 389 MET cc_start: 0.7250 (tpt) cc_final: 0.6574 (pmm) REVERT: Z 236 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.6957 (mt) REVERT: a 246 GLU cc_start: 0.5202 (OUTLIER) cc_final: 0.4517 (tt0) REVERT: a 278 MET cc_start: 0.7746 (pmm) cc_final: 0.7295 (pmm) REVERT: b 107 MET cc_start: 0.7007 (mmt) cc_final: 0.6543 (mmt) REVERT: c 51 MET cc_start: 0.8886 (mmt) cc_final: 0.7923 (mmm) REVERT: c 167 MET cc_start: 0.6370 (tpp) cc_final: 0.5953 (tpt) REVERT: c 216 MET cc_start: 0.8296 (ppp) cc_final: 0.8003 (ppp) REVERT: d 4 GLN cc_start: 0.5254 (OUTLIER) cc_final: 0.4296 (tt0) REVERT: d 89 LEU cc_start: 0.5850 (OUTLIER) cc_final: 0.5541 (tt) REVERT: d 132 TYR cc_start: 0.6360 (OUTLIER) cc_final: 0.5818 (m-80) REVERT: f 26 GLU cc_start: 0.3982 (OUTLIER) cc_final: 0.3491 (pp20) REVERT: f 27 LYS cc_start: 0.6560 (mtpt) cc_final: 0.5801 (mtpt) REVERT: f 58 MET cc_start: 0.2756 (mtt) cc_final: 0.2386 (mtp) REVERT: f 89 MET cc_start: 0.5379 (tpt) cc_final: 0.4343 (mmt) REVERT: f 298 LEU cc_start: 0.3814 (OUTLIER) cc_final: 0.3296 (tt) REVERT: f 761 MET cc_start: 0.4946 (tpt) cc_final: 0.4599 (tpp) REVERT: f 825 MET cc_start: 0.5447 (mmm) cc_final: 0.4749 (mmm) outliers start: 213 outliers final: 114 residues processed: 632 average time/residue: 0.8455 time to fit residues: 965.7551 Evaluate side-chains 573 residues out of total 12009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 440 time to evaluate : 12.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 72 MET Chi-restraints excluded: chain x residue 279 ILE Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain C residue 171 HIS Chi-restraints excluded: chain C residue 209 CYS Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 336 MET Chi-restraints excluded: chain D residue 110 ASN Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 374 ASP Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 348 THR Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 202 LEU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain J residue 107 ILE Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain L residue 206 THR Chi-restraints excluded: chain L residue 228 ASP Chi-restraints excluded: chain M residue 93 GLU Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain S residue 191 ASP Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 70 MET Chi-restraints excluded: chain T residue 117 ASP Chi-restraints excluded: chain g residue 175 SER Chi-restraints excluded: chain g residue 190 THR Chi-restraints excluded: chain g residue 224 ASN Chi-restraints excluded: chain i residue 194 ILE Chi-restraints excluded: chain i residue 202 ASP Chi-restraints excluded: chain i residue 249 ARG Chi-restraints excluded: chain j residue 211 MET Chi-restraints excluded: chain k residue 13 ASN Chi-restraints excluded: chain k residue 87 THR Chi-restraints excluded: chain k residue 146 VAL Chi-restraints excluded: chain k residue 225 ASN Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain l residue 176 MET Chi-restraints excluded: chain m residue 50 GLU Chi-restraints excluded: chain m residue 77 VAL Chi-restraints excluded: chain m residue 204 VAL Chi-restraints excluded: chain n residue 60 THR Chi-restraints excluded: chain n residue 68 ILE Chi-restraints excluded: chain p residue 20 VAL Chi-restraints excluded: chain s residue 26 ASP Chi-restraints excluded: chain s residue 77 HIS Chi-restraints excluded: chain s residue 164 VAL Chi-restraints excluded: chain t residue 21 VAL Chi-restraints excluded: chain t residue 127 MET Chi-restraints excluded: chain t residue 141 TYR Chi-restraints excluded: chain y residue 1 MET Chi-restraints excluded: chain U residue 239 GLU Chi-restraints excluded: chain U residue 248 ILE Chi-restraints excluded: chain U residue 403 THR Chi-restraints excluded: chain U residue 629 THR Chi-restraints excluded: chain U residue 663 THR Chi-restraints excluded: chain U residue 695 MET Chi-restraints excluded: chain U residue 706 VAL Chi-restraints excluded: chain U residue 736 ILE Chi-restraints excluded: chain U residue 854 MET Chi-restraints excluded: chain V residue 175 MET Chi-restraints excluded: chain V residue 433 ASP Chi-restraints excluded: chain V residue 478 GLN Chi-restraints excluded: chain W residue 63 THR Chi-restraints excluded: chain W residue 117 ASP Chi-restraints excluded: chain W residue 158 ASP Chi-restraints excluded: chain W residue 171 VAL Chi-restraints excluded: chain W residue 425 LEU Chi-restraints excluded: chain X residue 80 ILE Chi-restraints excluded: chain X residue 177 TYR Chi-restraints excluded: chain X residue 190 LEU Chi-restraints excluded: chain X residue 256 LEU Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain Y residue 37 VAL Chi-restraints excluded: chain Y residue 45 VAL Chi-restraints excluded: chain Y residue 104 MET Chi-restraints excluded: chain Y residue 134 LEU Chi-restraints excluded: chain Y residue 299 MET Chi-restraints excluded: chain Z residue 10 VAL Chi-restraints excluded: chain Z residue 130 ASP Chi-restraints excluded: chain Z residue 144 VAL Chi-restraints excluded: chain Z residue 201 LEU Chi-restraints excluded: chain Z residue 236 LEU Chi-restraints excluded: chain a residue 111 VAL Chi-restraints excluded: chain a residue 169 HIS Chi-restraints excluded: chain a residue 246 GLU Chi-restraints excluded: chain b residue 60 VAL Chi-restraints excluded: chain b residue 117 VAL Chi-restraints excluded: chain c residue 36 LEU Chi-restraints excluded: chain c residue 177 THR Chi-restraints excluded: chain c residue 292 MET Chi-restraints excluded: chain d residue 4 GLN Chi-restraints excluded: chain d residue 43 LEU Chi-restraints excluded: chain d residue 89 LEU Chi-restraints excluded: chain d residue 132 TYR Chi-restraints excluded: chain d residue 197 ILE Chi-restraints excluded: chain f residue 24 THR Chi-restraints excluded: chain f residue 26 GLU Chi-restraints excluded: chain f residue 171 GLN Chi-restraints excluded: chain f residue 298 LEU Chi-restraints excluded: chain f residue 655 LEU Chi-restraints excluded: chain f residue 718 ASP Chi-restraints excluded: chain f residue 729 MET Chi-restraints excluded: chain f residue 793 VAL Chi-restraints excluded: chain e residue 27 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1386 random chunks: chunk 1292 optimal weight: 6.9990 chunk 151 optimal weight: 0.3980 chunk 764 optimal weight: 5.9990 chunk 979 optimal weight: 30.0000 chunk 758 optimal weight: 20.0000 chunk 1128 optimal weight: 8.9990 chunk 748 optimal weight: 20.0000 chunk 1335 optimal weight: 10.0000 chunk 836 optimal weight: 0.0970 chunk 814 optimal weight: 5.9990 chunk 616 optimal weight: 5.9990 overall best weight: 3.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 ASN ** C 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 166 ASN H 169 ASN ** K 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 110 HIS ** U 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 193 ASN ** b 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 99 HIS c 176 GLN ** f 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 112389 Z= 0.159 Angle : 0.553 11.840 151810 Z= 0.281 Chirality : 0.041 0.321 17171 Planarity : 0.004 0.058 19566 Dihedral : 5.728 131.273 15472 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.26 % Favored : 93.70 % Rotamer: Outliers : 1.62 % Allowed : 17.38 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.06 (0.07), residues: 13955 helix: 1.53 (0.07), residues: 6192 sheet: 0.10 (0.12), residues: 1957 loop : -1.68 (0.08), residues: 5806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP d 61 HIS 0.006 0.001 HIS V 214 PHE 0.019 0.001 PHE P 69 TYR 0.023 0.001 TYR Y 259 ARG 0.007 0.000 ARG n 89 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27910 Ramachandran restraints generated. 13955 Oldfield, 0 Emsley, 13955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27910 Ramachandran restraints generated. 13955 Oldfield, 0 Emsley, 13955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 12009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 445 time to evaluate : 9.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: x 72 MET cc_start: 0.5519 (OUTLIER) cc_final: 0.3495 (tpt) REVERT: x 95 GLU cc_start: -0.1060 (OUTLIER) cc_final: -0.1937 (mt-10) REVERT: x 101 MET cc_start: 0.4551 (OUTLIER) cc_final: 0.3674 (ppp) REVERT: x 181 MET cc_start: 0.5970 (mmp) cc_final: 0.4995 (ptm) REVERT: x 207 MET cc_start: 0.7109 (tmm) cc_final: 0.6722 (tmm) REVERT: A 261 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.8465 (m-10) REVERT: B 107 MET cc_start: 0.7080 (ppp) cc_final: 0.6806 (ppp) REVERT: B 214 MET cc_start: 0.7393 (OUTLIER) cc_final: 0.6833 (tmm) REVERT: C 139 MET cc_start: 0.8358 (tpp) cc_final: 0.7385 (tpp) REVERT: D 296 MET cc_start: 0.8964 (ppp) cc_final: 0.8642 (ppp) REVERT: D 309 MET cc_start: 0.7767 (mmm) cc_final: 0.7288 (mmm) REVERT: D 352 MET cc_start: 0.6659 (tpp) cc_final: 0.5691 (tpp) REVERT: E 218 MET cc_start: 0.9348 (ptm) cc_final: 0.9032 (ppp) REVERT: E 247 THR cc_start: 0.9073 (OUTLIER) cc_final: 0.8530 (p) REVERT: F 36 MET cc_start: 0.1195 (mmt) cc_final: 0.0730 (ptt) REVERT: F 55 MET cc_start: 0.7586 (tmm) cc_final: 0.7184 (tmm) REVERT: F 366 MET cc_start: 0.7963 (mmp) cc_final: 0.7738 (mmm) REVERT: R 197 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7654 (mp0) REVERT: g 111 VAL cc_start: 0.8172 (OUTLIER) cc_final: 0.7933 (t) REVERT: i 249 ARG cc_start: 0.6669 (OUTLIER) cc_final: 0.6453 (ptt90) REVERT: j 211 MET cc_start: 0.6352 (OUTLIER) cc_final: 0.5972 (tpp) REVERT: k 59 MET cc_start: 0.7854 (tpp) cc_final: 0.7411 (mmt) REVERT: p 12 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7655 (ttp) REVERT: q 11 ASP cc_start: 0.7794 (OUTLIER) cc_final: 0.7216 (p0) REVERT: t 110 MET cc_start: 0.8766 (mpp) cc_final: 0.8472 (mpp) REVERT: y 1 MET cc_start: 0.7881 (OUTLIER) cc_final: 0.6543 (tmm) REVERT: U 137 MET cc_start: 0.8475 (mmp) cc_final: 0.8142 (mmm) REVERT: U 206 MET cc_start: 0.7561 (tmm) cc_final: 0.6898 (mmt) REVERT: U 239 GLU cc_start: 0.6458 (OUTLIER) cc_final: 0.6085 (mp0) REVERT: U 415 HIS cc_start: 0.6536 (OUTLIER) cc_final: 0.5654 (t70) REVERT: U 583 MET cc_start: 0.8496 (mmm) cc_final: 0.8236 (mmm) REVERT: V 175 MET cc_start: 0.6576 (OUTLIER) cc_final: 0.5847 (tmm) REVERT: V 403 ILE cc_start: 0.7759 (OUTLIER) cc_final: 0.7339 (tp) REVERT: V 409 MET cc_start: 0.8281 (mmp) cc_final: 0.7594 (tmm) REVERT: V 433 ASP cc_start: 0.7370 (OUTLIER) cc_final: 0.7108 (p0) REVERT: V 462 GLU cc_start: 0.6498 (OUTLIER) cc_final: 0.5968 (tm-30) REVERT: W 73 MET cc_start: 0.4667 (ptm) cc_final: 0.4390 (ppp) REVERT: X 254 MET cc_start: 0.5944 (mmt) cc_final: 0.4870 (mmt) REVERT: Y 169 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6639 (mp0) REVERT: Y 214 MET cc_start: 0.6639 (mmp) cc_final: 0.6298 (mmm) REVERT: Y 389 MET cc_start: 0.7072 (tpt) cc_final: 0.6465 (pmm) REVERT: Z 236 LEU cc_start: 0.7149 (OUTLIER) cc_final: 0.6911 (mt) REVERT: a 246 GLU cc_start: 0.5203 (OUTLIER) cc_final: 0.4521 (tt0) REVERT: a 278 MET cc_start: 0.7719 (pmm) cc_final: 0.7275 (pmm) REVERT: c 51 MET cc_start: 0.8775 (mmt) cc_final: 0.7766 (mmm) REVERT: c 167 MET cc_start: 0.6554 (tpp) cc_final: 0.5749 (ttt) REVERT: d 4 GLN cc_start: 0.5390 (OUTLIER) cc_final: 0.4426 (tt0) REVERT: d 89 LEU cc_start: 0.5772 (OUTLIER) cc_final: 0.5459 (tt) REVERT: d 126 ASP cc_start: 0.6826 (OUTLIER) cc_final: 0.6451 (p0) REVERT: d 132 TYR cc_start: 0.6444 (OUTLIER) cc_final: 0.5807 (m-80) REVERT: f 26 GLU cc_start: 0.3863 (OUTLIER) cc_final: 0.3379 (pp20) REVERT: f 27 LYS cc_start: 0.6542 (mtpt) cc_final: 0.5784 (mtpt) REVERT: f 58 MET cc_start: 0.2803 (mtt) cc_final: 0.2427 (mtp) REVERT: f 89 MET cc_start: 0.5363 (tpt) cc_final: 0.4370 (mmt) REVERT: f 298 LEU cc_start: 0.3588 (OUTLIER) cc_final: 0.3137 (tt) REVERT: f 426 LEU cc_start: -0.3101 (OUTLIER) cc_final: -0.3609 (mm) REVERT: f 761 MET cc_start: 0.4941 (tpt) cc_final: 0.4631 (tpp) REVERT: f 825 MET cc_start: 0.5521 (mmm) cc_final: 0.4867 (mmm) outliers start: 193 outliers final: 112 residues processed: 613 average time/residue: 0.8491 time to fit residues: 942.7210 Evaluate side-chains 582 residues out of total 12009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 441 time to evaluate : 9.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 72 MET Chi-restraints excluded: chain x residue 95 GLU Chi-restraints excluded: chain x residue 101 MET Chi-restraints excluded: chain x residue 225 GLU Chi-restraints excluded: chain x residue 279 ILE Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain C residue 102 ASN Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 209 CYS Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 336 MET Chi-restraints excluded: chain D residue 44 TYR Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 374 ASP Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 202 LEU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain L residue 206 THR Chi-restraints excluded: chain M residue 93 GLU Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain R residue 197 GLU Chi-restraints excluded: chain S residue 191 ASP Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 70 MET Chi-restraints excluded: chain g residue 13 ILE Chi-restraints excluded: chain g residue 111 VAL Chi-restraints excluded: chain g residue 175 SER Chi-restraints excluded: chain g residue 190 THR Chi-restraints excluded: chain g residue 224 ASN Chi-restraints excluded: chain i residue 43 VAL Chi-restraints excluded: chain i residue 194 ILE Chi-restraints excluded: chain i residue 202 ASP Chi-restraints excluded: chain i residue 249 ARG Chi-restraints excluded: chain j residue 211 MET Chi-restraints excluded: chain j residue 217 LEU Chi-restraints excluded: chain k residue 13 ASN Chi-restraints excluded: chain k residue 225 ASN Chi-restraints excluded: chain l residue 176 MET Chi-restraints excluded: chain m residue 20 VAL Chi-restraints excluded: chain m residue 77 VAL Chi-restraints excluded: chain m residue 184 MET Chi-restraints excluded: chain n residue 60 THR Chi-restraints excluded: chain n residue 192 ASP Chi-restraints excluded: chain o residue 146 MET Chi-restraints excluded: chain p residue 12 MET Chi-restraints excluded: chain p residue 58 THR Chi-restraints excluded: chain q residue 11 ASP Chi-restraints excluded: chain s residue 26 ASP Chi-restraints excluded: chain s residue 77 HIS Chi-restraints excluded: chain s residue 199 THR Chi-restraints excluded: chain t residue 21 VAL Chi-restraints excluded: chain t residue 141 TYR Chi-restraints excluded: chain y residue 1 MET Chi-restraints excluded: chain U residue 239 GLU Chi-restraints excluded: chain U residue 415 HIS Chi-restraints excluded: chain U residue 629 THR Chi-restraints excluded: chain U residue 663 THR Chi-restraints excluded: chain U residue 695 MET Chi-restraints excluded: chain U residue 706 VAL Chi-restraints excluded: chain U residue 736 ILE Chi-restraints excluded: chain U residue 788 VAL Chi-restraints excluded: chain U residue 854 MET Chi-restraints excluded: chain V residue 175 MET Chi-restraints excluded: chain V residue 314 ARG Chi-restraints excluded: chain V residue 403 ILE Chi-restraints excluded: chain V residue 433 ASP Chi-restraints excluded: chain V residue 462 GLU Chi-restraints excluded: chain W residue 107 GLN Chi-restraints excluded: chain W residue 117 ASP Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain W residue 171 VAL Chi-restraints excluded: chain W residue 366 MET Chi-restraints excluded: chain W residue 425 LEU Chi-restraints excluded: chain X residue 80 ILE Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 177 TYR Chi-restraints excluded: chain X residue 190 LEU Chi-restraints excluded: chain X residue 256 LEU Chi-restraints excluded: chain Y residue 37 VAL Chi-restraints excluded: chain Y residue 68 ASP Chi-restraints excluded: chain Y residue 104 MET Chi-restraints excluded: chain Y residue 134 LEU Chi-restraints excluded: chain Y residue 169 GLU Chi-restraints excluded: chain Y residue 299 MET Chi-restraints excluded: chain Z residue 122 VAL Chi-restraints excluded: chain Z residue 126 VAL Chi-restraints excluded: chain Z residue 130 ASP Chi-restraints excluded: chain Z residue 144 VAL Chi-restraints excluded: chain Z residue 201 LEU Chi-restraints excluded: chain Z residue 236 LEU Chi-restraints excluded: chain Z residue 264 SER Chi-restraints excluded: chain a residue 102 GLU Chi-restraints excluded: chain a residue 149 THR Chi-restraints excluded: chain a residue 221 VAL Chi-restraints excluded: chain a residue 246 GLU Chi-restraints excluded: chain b residue 60 VAL Chi-restraints excluded: chain b residue 117 VAL Chi-restraints excluded: chain c residue 36 LEU Chi-restraints excluded: chain c residue 275 VAL Chi-restraints excluded: chain c residue 292 MET Chi-restraints excluded: chain d residue 4 GLN Chi-restraints excluded: chain d residue 43 LEU Chi-restraints excluded: chain d residue 89 LEU Chi-restraints excluded: chain d residue 126 ASP Chi-restraints excluded: chain d residue 132 TYR Chi-restraints excluded: chain d residue 197 ILE Chi-restraints excluded: chain f residue 26 GLU Chi-restraints excluded: chain f residue 171 GLN Chi-restraints excluded: chain f residue 298 LEU Chi-restraints excluded: chain f residue 426 LEU Chi-restraints excluded: chain f residue 655 LEU Chi-restraints excluded: chain f residue 718 ASP Chi-restraints excluded: chain f residue 729 MET Chi-restraints excluded: chain f residue 793 VAL Chi-restraints excluded: chain e residue 27 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1386 random chunks: chunk 826 optimal weight: 20.0000 chunk 533 optimal weight: 30.0000 chunk 797 optimal weight: 10.0000 chunk 402 optimal weight: 20.0000 chunk 262 optimal weight: 7.9990 chunk 258 optimal weight: 6.9990 chunk 849 optimal weight: 30.0000 chunk 910 optimal weight: 50.0000 chunk 660 optimal weight: 20.0000 chunk 124 optimal weight: 30.0000 chunk 1050 optimal weight: 50.0000 overall best weight: 12.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 345 ASN ** F 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 333 ASN ** F 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 166 ASN H 169 ASN ** K 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 221 GLN Q 8 GLN ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 10 HIS ** U 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 193 ASN ** a 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 214 GLN f 102 HIS ** f 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 112389 Z= 0.375 Angle : 0.665 12.140 151810 Z= 0.342 Chirality : 0.044 0.292 17171 Planarity : 0.004 0.059 19566 Dihedral : 6.085 142.272 15472 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.70 % Favored : 92.25 % Rotamer: Outliers : 2.09 % Allowed : 17.64 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.20 (0.07), residues: 13955 helix: 1.26 (0.07), residues: 6193 sheet: 0.05 (0.12), residues: 1944 loop : -1.78 (0.08), residues: 5818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP m 215 HIS 0.013 0.001 HIS D 222 PHE 0.022 0.002 PHE s 179 TYR 0.022 0.002 TYR X 177 ARG 0.015 0.001 ARG C 307 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27910 Ramachandran restraints generated. 13955 Oldfield, 0 Emsley, 13955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27910 Ramachandran restraints generated. 13955 Oldfield, 0 Emsley, 13955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 12009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 442 time to evaluate : 9.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: x 67 MET cc_start: 0.4016 (tpp) cc_final: 0.3728 (tpt) REVERT: x 95 GLU cc_start: -0.1088 (OUTLIER) cc_final: -0.1975 (mt-10) REVERT: x 101 MET cc_start: 0.4635 (OUTLIER) cc_final: 0.3761 (ppp) REVERT: x 181 MET cc_start: 0.6055 (mmp) cc_final: 0.5072 (ptm) REVERT: x 207 MET cc_start: 0.7170 (tmm) cc_final: 0.6784 (tmm) REVERT: A 261 PHE cc_start: 0.8816 (OUTLIER) cc_final: 0.8580 (m-10) REVERT: B 107 MET cc_start: 0.7125 (ppp) cc_final: 0.6911 (ppp) REVERT: B 214 MET cc_start: 0.7455 (OUTLIER) cc_final: 0.6762 (tmm) REVERT: D 296 MET cc_start: 0.8960 (ppp) cc_final: 0.8665 (ppp) REVERT: D 309 MET cc_start: 0.7902 (mmm) cc_final: 0.7443 (mmm) REVERT: E 218 MET cc_start: 0.9332 (ptm) cc_final: 0.9047 (ppp) REVERT: E 247 THR cc_start: 0.9141 (OUTLIER) cc_final: 0.8627 (p) REVERT: E 262 ASN cc_start: 0.8975 (OUTLIER) cc_final: 0.8502 (t0) REVERT: F 36 MET cc_start: 0.1331 (mmt) cc_final: 0.0854 (ptt) REVERT: F 55 MET cc_start: 0.7582 (tmm) cc_final: 0.7318 (tmm) REVERT: F 366 MET cc_start: 0.8148 (mmp) cc_final: 0.7904 (mmm) REVERT: i 121 TYR cc_start: 0.8160 (OUTLIER) cc_final: 0.7731 (t80) REVERT: i 249 ARG cc_start: 0.6688 (OUTLIER) cc_final: 0.6310 (ptt90) REVERT: j 211 MET cc_start: 0.6454 (OUTLIER) cc_final: 0.6090 (tpp) REVERT: k 59 MET cc_start: 0.8074 (tpp) cc_final: 0.7687 (mmt) REVERT: p 12 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7617 (ttp) REVERT: q 11 ASP cc_start: 0.7850 (OUTLIER) cc_final: 0.7288 (p0) REVERT: y 1 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.6486 (tmm) REVERT: y 19 PRO cc_start: 0.7421 (Cg_exo) cc_final: 0.7219 (Cg_endo) REVERT: U 137 MET cc_start: 0.8519 (mmp) cc_final: 0.8161 (mmm) REVERT: U 206 MET cc_start: 0.7558 (tmm) cc_final: 0.6937 (mmt) REVERT: U 239 GLU cc_start: 0.6530 (OUTLIER) cc_final: 0.6150 (mp0) REVERT: U 415 HIS cc_start: 0.6741 (OUTLIER) cc_final: 0.5791 (t70) REVERT: U 675 MET cc_start: 0.8058 (ppp) cc_final: 0.7616 (ppp) REVERT: V 175 MET cc_start: 0.6523 (OUTLIER) cc_final: 0.5762 (tmm) REVERT: V 403 ILE cc_start: 0.7761 (OUTLIER) cc_final: 0.7348 (tp) REVERT: V 409 MET cc_start: 0.8336 (mmp) cc_final: 0.7548 (tmm) REVERT: V 433 ASP cc_start: 0.7373 (OUTLIER) cc_final: 0.7130 (p0) REVERT: V 462 GLU cc_start: 0.6414 (OUTLIER) cc_final: 0.6125 (tm-30) REVERT: W 73 MET cc_start: 0.4648 (ptm) cc_final: 0.4352 (ppp) REVERT: X 254 MET cc_start: 0.6018 (mmt) cc_final: 0.4877 (mmt) REVERT: Y 53 TYR cc_start: 0.3605 (OUTLIER) cc_final: 0.3289 (p90) REVERT: Y 214 MET cc_start: 0.6648 (mmp) cc_final: 0.6257 (mmm) REVERT: Y 389 MET cc_start: 0.7179 (tpt) cc_final: 0.6518 (pmm) REVERT: Z 133 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8403 (mp) REVERT: Z 236 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6921 (mt) REVERT: a 246 GLU cc_start: 0.5315 (OUTLIER) cc_final: 0.4542 (tt0) REVERT: a 278 MET cc_start: 0.7848 (pmm) cc_final: 0.7428 (pmm) REVERT: c 51 MET cc_start: 0.8918 (mmt) cc_final: 0.8030 (mmm) REVERT: d 4 GLN cc_start: 0.5599 (OUTLIER) cc_final: 0.4647 (tt0) REVERT: d 89 LEU cc_start: 0.5927 (OUTLIER) cc_final: 0.5608 (tt) REVERT: d 132 TYR cc_start: 0.6525 (OUTLIER) cc_final: 0.5739 (m-80) REVERT: d 158 ILE cc_start: 0.5355 (OUTLIER) cc_final: 0.4929 (mt) REVERT: f 26 GLU cc_start: 0.4052 (OUTLIER) cc_final: 0.3557 (pp20) REVERT: f 27 LYS cc_start: 0.6651 (mtpt) cc_final: 0.5884 (mtpt) REVERT: f 58 MET cc_start: 0.2876 (mtt) cc_final: 0.2502 (mtp) REVERT: f 89 MET cc_start: 0.5440 (tpt) cc_final: 0.4388 (mmt) REVERT: f 196 MET cc_start: 0.6181 (OUTLIER) cc_final: 0.5919 (mmt) REVERT: f 298 LEU cc_start: 0.3706 (OUTLIER) cc_final: 0.3226 (tt) REVERT: f 761 MET cc_start: 0.4986 (tpt) cc_final: 0.4632 (tpp) REVERT: f 825 MET cc_start: 0.5427 (mmm) cc_final: 0.4809 (mmm) outliers start: 249 outliers final: 163 residues processed: 660 average time/residue: 0.8443 time to fit residues: 1014.8810 Evaluate side-chains 634 residues out of total 12009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 442 time to evaluate : 9.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 48 VAL Chi-restraints excluded: chain x residue 72 MET Chi-restraints excluded: chain x residue 95 GLU Chi-restraints excluded: chain x residue 101 MET Chi-restraints excluded: chain x residue 225 GLU Chi-restraints excluded: chain x residue 279 ILE Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain C residue 102 ASN Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 209 CYS Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 336 MET Chi-restraints excluded: chain D residue 44 TYR Chi-restraints excluded: chain D residue 110 ASN Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 374 ASP Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 262 ASN Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 202 LEU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain J residue 107 ILE Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain L residue 206 THR Chi-restraints excluded: chain L residue 228 ASP Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain S residue 191 ASP Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 70 MET Chi-restraints excluded: chain g residue 13 ILE Chi-restraints excluded: chain g residue 175 SER Chi-restraints excluded: chain g residue 190 THR Chi-restraints excluded: chain g residue 224 ASN Chi-restraints excluded: chain i residue 43 VAL Chi-restraints excluded: chain i residue 121 TYR Chi-restraints excluded: chain i residue 194 ILE Chi-restraints excluded: chain i residue 202 ASP Chi-restraints excluded: chain i residue 249 ARG Chi-restraints excluded: chain j residue 184 ASP Chi-restraints excluded: chain j residue 211 MET Chi-restraints excluded: chain j residue 217 LEU Chi-restraints excluded: chain k residue 13 ASN Chi-restraints excluded: chain k residue 31 ILE Chi-restraints excluded: chain k residue 87 THR Chi-restraints excluded: chain k residue 106 THR Chi-restraints excluded: chain k residue 146 VAL Chi-restraints excluded: chain k residue 225 ASN Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain l residue 49 LEU Chi-restraints excluded: chain l residue 176 MET Chi-restraints excluded: chain l residue 228 ASP Chi-restraints excluded: chain m residue 50 GLU Chi-restraints excluded: chain m residue 77 VAL Chi-restraints excluded: chain m residue 184 MET Chi-restraints excluded: chain m residue 204 VAL Chi-restraints excluded: chain n residue 60 THR Chi-restraints excluded: chain n residue 68 ILE Chi-restraints excluded: chain n residue 192 ASP Chi-restraints excluded: chain o residue 146 MET 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 p residue 122 CYS Chi-restraints excluded: chain q residue 11 ASP Chi-restraints excluded: chain s residue 26 ASP Chi-restraints excluded: chain s residue 164 VAL Chi-restraints excluded: chain s residue 199 THR Chi-restraints excluded: chain t residue 21 VAL Chi-restraints excluded: chain t residue 127 MET Chi-restraints excluded: chain t residue 141 TYR Chi-restraints excluded: chain y residue 1 MET Chi-restraints excluded: chain U residue 143 ASP Chi-restraints excluded: chain U residue 239 GLU Chi-restraints excluded: chain U residue 248 ILE Chi-restraints excluded: chain U residue 403 THR Chi-restraints excluded: chain U residue 415 HIS Chi-restraints excluded: chain U residue 496 LEU Chi-restraints excluded: chain U residue 629 THR Chi-restraints excluded: chain U residue 663 THR Chi-restraints excluded: chain U residue 695 MET Chi-restraints excluded: chain U residue 706 VAL Chi-restraints excluded: chain U residue 736 ILE Chi-restraints excluded: chain U residue 788 VAL Chi-restraints excluded: chain U residue 854 MET Chi-restraints excluded: chain V residue 175 MET Chi-restraints excluded: chain V residue 403 ILE Chi-restraints excluded: chain V residue 433 ASP Chi-restraints excluded: chain V residue 462 GLU Chi-restraints excluded: chain W residue 117 ASP Chi-restraints excluded: chain W residue 158 ASP Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain W residue 171 VAL Chi-restraints excluded: chain W residue 240 TYR Chi-restraints excluded: chain W residue 366 MET Chi-restraints excluded: chain W residue 425 LEU Chi-restraints excluded: chain X residue 80 ILE Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 177 TYR Chi-restraints excluded: chain X residue 190 LEU Chi-restraints excluded: chain X residue 256 LEU Chi-restraints excluded: chain X residue 350 ILE Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain Y residue 37 VAL Chi-restraints excluded: chain Y residue 53 TYR Chi-restraints excluded: chain Y residue 68 ASP Chi-restraints excluded: chain Y residue 104 MET Chi-restraints excluded: chain Y residue 134 LEU Chi-restraints excluded: chain Y residue 299 MET Chi-restraints excluded: chain Z residue 10 VAL Chi-restraints excluded: chain Z residue 67 VAL Chi-restraints excluded: chain Z residue 91 ILE Chi-restraints excluded: chain Z residue 122 VAL Chi-restraints excluded: chain Z residue 126 VAL Chi-restraints excluded: chain Z residue 130 ASP Chi-restraints excluded: chain Z residue 133 LEU Chi-restraints excluded: chain Z residue 144 VAL Chi-restraints excluded: chain Z residue 201 LEU Chi-restraints excluded: chain Z residue 236 LEU Chi-restraints excluded: chain Z residue 264 SER Chi-restraints excluded: chain a residue 54 ASP Chi-restraints excluded: chain a residue 102 GLU Chi-restraints excluded: chain a residue 111 VAL Chi-restraints excluded: chain a residue 149 THR Chi-restraints excluded: chain a residue 169 HIS Chi-restraints excluded: chain a residue 221 VAL Chi-restraints excluded: chain a residue 246 GLU Chi-restraints excluded: chain b residue 60 VAL Chi-restraints excluded: chain b residue 117 VAL Chi-restraints excluded: chain c residue 177 THR Chi-restraints excluded: chain c residue 275 VAL Chi-restraints excluded: chain c residue 292 MET Chi-restraints excluded: chain d residue 4 GLN Chi-restraints excluded: chain d residue 43 LEU Chi-restraints excluded: chain d residue 72 GLU Chi-restraints excluded: chain d residue 89 LEU Chi-restraints excluded: chain d residue 126 ASP Chi-restraints excluded: chain d residue 132 TYR Chi-restraints excluded: chain d residue 158 ILE Chi-restraints excluded: chain d residue 197 ILE Chi-restraints excluded: chain d residue 255 MET Chi-restraints excluded: chain f residue 24 THR Chi-restraints excluded: chain f residue 26 GLU Chi-restraints excluded: chain f residue 171 GLN Chi-restraints excluded: chain f residue 196 MET Chi-restraints excluded: chain f residue 215 ASP Chi-restraints excluded: chain f residue 298 LEU Chi-restraints excluded: chain f residue 580 LEU Chi-restraints excluded: chain f residue 655 LEU Chi-restraints excluded: chain f residue 718 ASP Chi-restraints excluded: chain f residue 729 MET Chi-restraints excluded: chain f residue 793 VAL Chi-restraints excluded: chain f residue 808 ASN Chi-restraints excluded: chain e residue 27 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1386 random chunks: chunk 1215 optimal weight: 5.9990 chunk 1279 optimal weight: 20.0000 chunk 1167 optimal weight: 9.9990 chunk 1244 optimal weight: 8.9990 chunk 749 optimal weight: 6.9990 chunk 542 optimal weight: 10.0000 chunk 977 optimal weight: 20.0000 chunk 382 optimal weight: 30.0000 chunk 1124 optimal weight: 50.0000 chunk 1177 optimal weight: 7.9990 chunk 1240 optimal weight: 20.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 8 GLN ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 102 HIS ** f 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 866 GLN ** e 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 112389 Z= 0.245 Angle : 0.601 12.393 151810 Z= 0.306 Chirality : 0.042 0.337 17171 Planarity : 0.004 0.058 19566 Dihedral : 5.964 134.855 15472 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.87 % Favored : 93.08 % Rotamer: Outliers : 1.90 % Allowed : 17.98 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.07), residues: 13955 helix: 1.36 (0.07), residues: 6196 sheet: 0.06 (0.12), residues: 1943 loop : -1.75 (0.08), residues: 5816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP Y 63 HIS 0.011 0.001 HIS f 102 PHE 0.019 0.001 PHE P 69 TYR 0.020 0.001 TYR h 121 ARG 0.009 0.000 ARG C 307 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27910 Ramachandran restraints generated. 13955 Oldfield, 0 Emsley, 13955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27910 Ramachandran restraints generated. 13955 Oldfield, 0 Emsley, 13955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 12009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 445 time to evaluate : 9.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: x 67 MET cc_start: 0.3937 (tpp) cc_final: 0.3667 (tpt) REVERT: x 95 GLU cc_start: -0.1121 (OUTLIER) cc_final: -0.1991 (mt-10) REVERT: x 101 MET cc_start: 0.4635 (OUTLIER) cc_final: 0.3804 (ppp) REVERT: x 178 PHE cc_start: 0.5952 (OUTLIER) cc_final: 0.5320 (m-80) REVERT: x 181 MET cc_start: 0.6033 (mmp) cc_final: 0.5123 (ptm) REVERT: x 207 MET cc_start: 0.7206 (tmm) cc_final: 0.6804 (tmm) REVERT: A 261 PHE cc_start: 0.8761 (OUTLIER) cc_final: 0.8505 (m-10) REVERT: B 214 MET cc_start: 0.7472 (OUTLIER) cc_final: 0.6794 (tmm) REVERT: D 124 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8324 (mm) REVERT: D 296 MET cc_start: 0.8962 (ppp) cc_final: 0.8649 (ppp) REVERT: D 309 MET cc_start: 0.7863 (mmm) cc_final: 0.7417 (mmm) REVERT: D 352 MET cc_start: 0.6657 (tpp) cc_final: 0.6275 (mpp) REVERT: E 218 MET cc_start: 0.9350 (ptm) cc_final: 0.9043 (ppp) REVERT: E 247 THR cc_start: 0.9135 (OUTLIER) cc_final: 0.8622 (p) REVERT: F 36 MET cc_start: 0.1354 (mmt) cc_final: 0.0886 (ptt) REVERT: F 55 MET cc_start: 0.7597 (tmm) cc_final: 0.7320 (tmm) REVERT: i 121 TYR cc_start: 0.8156 (OUTLIER) cc_final: 0.7627 (t80) REVERT: i 249 ARG cc_start: 0.6579 (OUTLIER) cc_final: 0.6222 (ptt90) REVERT: j 211 MET cc_start: 0.6407 (OUTLIER) cc_final: 0.6016 (tpp) REVERT: k 59 MET cc_start: 0.8032 (tpp) cc_final: 0.7668 (mmt) REVERT: p 12 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7639 (ttp) REVERT: q 11 ASP cc_start: 0.7816 (OUTLIER) cc_final: 0.7248 (p0) REVERT: y 1 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.6433 (tmm) REVERT: y 19 PRO cc_start: 0.7381 (Cg_exo) cc_final: 0.7166 (Cg_endo) REVERT: U 137 MET cc_start: 0.8518 (mmp) cc_final: 0.8130 (mmm) REVERT: U 206 MET cc_start: 0.7561 (tmm) cc_final: 0.6960 (mmt) REVERT: U 239 GLU cc_start: 0.6501 (OUTLIER) cc_final: 0.6135 (mp0) REVERT: U 415 HIS cc_start: 0.6663 (OUTLIER) cc_final: 0.5734 (t70) REVERT: U 423 MET cc_start: 0.7718 (mmt) cc_final: 0.6894 (tpt) REVERT: U 675 MET cc_start: 0.7968 (ppp) cc_final: 0.7501 (ppp) REVERT: U 757 MET cc_start: 0.8165 (tmm) cc_final: 0.7596 (ttm) REVERT: V 175 MET cc_start: 0.6587 (OUTLIER) cc_final: 0.5860 (tmm) REVERT: V 403 ILE cc_start: 0.7739 (OUTLIER) cc_final: 0.7326 (tp) REVERT: V 409 MET cc_start: 0.8309 (mmp) cc_final: 0.7561 (tmm) REVERT: V 433 ASP cc_start: 0.7325 (OUTLIER) cc_final: 0.7106 (p0) REVERT: V 462 GLU cc_start: 0.6441 (OUTLIER) cc_final: 0.6088 (tm-30) REVERT: W 73 MET cc_start: 0.4708 (ptm) cc_final: 0.4408 (ppp) REVERT: X 254 MET cc_start: 0.5938 (mmt) cc_final: 0.4855 (mmt) REVERT: Y 53 TYR cc_start: 0.3600 (OUTLIER) cc_final: 0.3360 (p90) REVERT: Y 63 TRP cc_start: 0.5209 (m100) cc_final: 0.4677 (t-100) REVERT: Y 214 MET cc_start: 0.6682 (mmp) cc_final: 0.6277 (mmm) REVERT: Y 389 MET cc_start: 0.7147 (tpt) cc_final: 0.6520 (pmm) REVERT: Z 236 LEU cc_start: 0.7279 (OUTLIER) cc_final: 0.6951 (mt) REVERT: a 246 GLU cc_start: 0.5327 (OUTLIER) cc_final: 0.4581 (tt0) REVERT: a 278 MET cc_start: 0.7853 (pmm) cc_final: 0.7399 (pmm) REVERT: c 51 MET cc_start: 0.8865 (mmt) cc_final: 0.7798 (mmm) REVERT: c 167 MET cc_start: 0.6299 (tpp) cc_final: 0.5842 (tpt) REVERT: c 216 MET cc_start: 0.8359 (ppp) cc_final: 0.8002 (ppp) REVERT: d 4 GLN cc_start: 0.5698 (OUTLIER) cc_final: 0.5080 (tt0) REVERT: d 89 LEU cc_start: 0.5861 (OUTLIER) cc_final: 0.5539 (tt) REVERT: d 126 ASP cc_start: 0.6931 (OUTLIER) cc_final: 0.6430 (p0) REVERT: d 132 TYR cc_start: 0.6622 (OUTLIER) cc_final: 0.5834 (m-80) REVERT: f 26 GLU cc_start: 0.4025 (OUTLIER) cc_final: 0.3543 (pp20) REVERT: f 27 LYS cc_start: 0.6621 (mtpt) cc_final: 0.5903 (mtpt) REVERT: f 58 MET cc_start: 0.2818 (mtt) cc_final: 0.2420 (mtp) REVERT: f 89 MET cc_start: 0.5398 (tpt) cc_final: 0.4370 (mmt) REVERT: f 196 MET cc_start: 0.6169 (OUTLIER) cc_final: 0.5903 (mmt) REVERT: f 298 LEU cc_start: 0.3600 (OUTLIER) cc_final: 0.3136 (tt) REVERT: f 761 MET cc_start: 0.5014 (tpt) cc_final: 0.4680 (tpp) REVERT: f 825 MET cc_start: 0.5440 (mmm) cc_final: 0.4837 (mmm) outliers start: 226 outliers final: 163 residues processed: 643 average time/residue: 0.8421 time to fit residues: 988.0725 Evaluate side-chains 634 residues out of total 12009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 442 time to evaluate : 9.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 37 THR Chi-restraints excluded: chain x residue 48 VAL Chi-restraints excluded: chain x residue 72 MET Chi-restraints excluded: chain x residue 95 GLU Chi-restraints excluded: chain x residue 101 MET Chi-restraints excluded: chain x residue 178 PHE Chi-restraints excluded: chain x residue 225 GLU Chi-restraints excluded: chain x residue 279 ILE Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain C residue 102 ASN Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 209 CYS Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 336 MET Chi-restraints excluded: chain D residue 44 TYR Chi-restraints excluded: chain D residue 110 ASN Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 374 ASP Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 202 LEU Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain J residue 107 ILE Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain L residue 206 THR Chi-restraints excluded: chain L residue 228 ASP Chi-restraints excluded: chain M residue 13 THR Chi-restraints excluded: chain M residue 37 ILE Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain S residue 191 ASP Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 70 MET Chi-restraints excluded: chain T residue 205 THR Chi-restraints excluded: chain g residue 13 ILE Chi-restraints excluded: chain g residue 175 SER Chi-restraints excluded: chain g residue 190 THR Chi-restraints excluded: chain g residue 224 ASN Chi-restraints excluded: chain i residue 43 VAL Chi-restraints excluded: chain i residue 121 TYR Chi-restraints excluded: chain i residue 194 ILE Chi-restraints excluded: chain i residue 202 ASP Chi-restraints excluded: chain i residue 249 ARG Chi-restraints excluded: chain j residue 211 MET Chi-restraints excluded: chain j residue 217 LEU Chi-restraints excluded: chain k residue 13 ASN Chi-restraints excluded: chain k residue 31 ILE Chi-restraints excluded: chain k residue 87 THR Chi-restraints excluded: chain k residue 106 THR Chi-restraints excluded: chain k residue 146 VAL Chi-restraints excluded: chain k residue 225 ASN Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain l residue 49 LEU Chi-restraints excluded: chain l residue 176 MET Chi-restraints excluded: chain m residue 9 LEU Chi-restraints excluded: chain m residue 50 GLU Chi-restraints excluded: chain m residue 77 VAL Chi-restraints excluded: chain m residue 204 VAL Chi-restraints excluded: chain n residue 60 THR Chi-restraints excluded: chain n residue 68 ILE Chi-restraints excluded: chain n residue 192 ASP Chi-restraints excluded: chain o residue 146 MET 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 p residue 122 CYS Chi-restraints excluded: chain q residue 11 ASP Chi-restraints excluded: chain s residue 26 ASP Chi-restraints excluded: chain s residue 77 HIS Chi-restraints excluded: chain s residue 164 VAL Chi-restraints excluded: chain s residue 199 THR Chi-restraints excluded: chain t residue 21 VAL Chi-restraints excluded: chain t residue 127 MET Chi-restraints excluded: chain t residue 141 TYR Chi-restraints excluded: chain y residue 1 MET Chi-restraints excluded: chain U residue 239 GLU Chi-restraints excluded: chain U residue 248 ILE Chi-restraints excluded: chain U residue 403 THR Chi-restraints excluded: chain U residue 415 HIS Chi-restraints excluded: chain U residue 629 THR Chi-restraints excluded: chain U residue 663 THR Chi-restraints excluded: chain U residue 695 MET Chi-restraints excluded: chain U residue 706 VAL Chi-restraints excluded: chain U residue 736 ILE Chi-restraints excluded: chain U residue 788 VAL Chi-restraints excluded: chain U residue 854 MET Chi-restraints excluded: chain V residue 175 MET Chi-restraints excluded: chain V residue 314 ARG Chi-restraints excluded: chain V residue 403 ILE Chi-restraints excluded: chain V residue 433 ASP Chi-restraints excluded: chain V residue 462 GLU Chi-restraints excluded: chain V residue 494 MET Chi-restraints excluded: chain W residue 117 ASP Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain W residue 171 VAL Chi-restraints excluded: chain W residue 240 TYR Chi-restraints excluded: chain W residue 425 LEU Chi-restraints excluded: chain X residue 80 ILE Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 177 TYR Chi-restraints excluded: chain X residue 190 LEU Chi-restraints excluded: chain X residue 256 LEU Chi-restraints excluded: chain Y residue 37 VAL Chi-restraints excluded: chain Y residue 53 TYR Chi-restraints excluded: chain Y residue 68 ASP Chi-restraints excluded: chain Y residue 104 MET Chi-restraints excluded: chain Y residue 134 LEU Chi-restraints excluded: chain Y residue 299 MET Chi-restraints excluded: chain Z residue 67 VAL Chi-restraints excluded: chain Z residue 91 ILE Chi-restraints excluded: chain Z residue 112 MET Chi-restraints excluded: chain Z residue 122 VAL Chi-restraints excluded: chain Z residue 126 VAL Chi-restraints excluded: chain Z residue 130 ASP Chi-restraints excluded: chain Z residue 144 VAL Chi-restraints excluded: chain Z residue 201 LEU Chi-restraints excluded: chain Z residue 236 LEU Chi-restraints excluded: chain Z residue 264 SER Chi-restraints excluded: chain a residue 102 GLU Chi-restraints excluded: chain a residue 111 VAL Chi-restraints excluded: chain a residue 149 THR Chi-restraints excluded: chain a residue 169 HIS Chi-restraints excluded: chain a residue 221 VAL Chi-restraints excluded: chain a residue 246 GLU Chi-restraints excluded: chain b residue 60 VAL Chi-restraints excluded: chain b residue 117 VAL Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain c residue 177 THR Chi-restraints excluded: chain c residue 275 VAL Chi-restraints excluded: chain c residue 292 MET Chi-restraints excluded: chain d residue 4 GLN Chi-restraints excluded: chain d residue 43 LEU Chi-restraints excluded: chain d residue 72 GLU Chi-restraints excluded: chain d residue 89 LEU Chi-restraints excluded: chain d residue 126 ASP Chi-restraints excluded: chain d residue 132 TYR Chi-restraints excluded: chain d residue 197 ILE Chi-restraints excluded: chain d residue 255 MET Chi-restraints excluded: chain f residue 24 THR Chi-restraints excluded: chain f residue 26 GLU Chi-restraints excluded: chain f residue 171 GLN Chi-restraints excluded: chain f residue 196 MET Chi-restraints excluded: chain f residue 298 LEU Chi-restraints excluded: chain f residue 580 LEU Chi-restraints excluded: chain f residue 594 LEU Chi-restraints excluded: chain f residue 655 LEU Chi-restraints excluded: chain f residue 718 ASP Chi-restraints excluded: chain f residue 729 MET Chi-restraints excluded: chain f residue 793 VAL Chi-restraints excluded: chain f residue 808 ASN Chi-restraints excluded: chain e residue 27 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1386 random chunks: chunk 817 optimal weight: 7.9990 chunk 1316 optimal weight: 9.9990 chunk 803 optimal weight: 8.9990 chunk 624 optimal weight: 9.9990 chunk 915 optimal weight: 8.9990 chunk 1380 optimal weight: 40.0000 chunk 1270 optimal weight: 6.9990 chunk 1099 optimal weight: 0.7980 chunk 114 optimal weight: 9.9990 chunk 849 optimal weight: 20.0000 chunk 674 optimal weight: 10.0000 overall best weight: 6.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 GLN C 53 ASN ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 166 ASN H 169 ASN ** K 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 242 HIS ** V 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 102 HIS ** f 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 112389 Z= 0.222 Angle : 0.595 16.104 151810 Z= 0.300 Chirality : 0.042 0.338 17171 Planarity : 0.004 0.057 19566 Dihedral : 5.867 132.757 15472 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.14 % Favored : 92.81 % Rotamer: Outliers : 1.75 % Allowed : 18.31 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.05 (0.07), residues: 13955 helix: 1.43 (0.07), residues: 6212 sheet: 0.05 (0.12), residues: 1959 loop : -1.75 (0.08), residues: 5784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP Y 63 HIS 0.010 0.001 HIS U 70 PHE 0.019 0.001 PHE P 69 TYR 0.019 0.001 TYR h 121 ARG 0.008 0.000 ARG C 307 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27910 Ramachandran restraints generated. 13955 Oldfield, 0 Emsley, 13955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27910 Ramachandran restraints generated. 13955 Oldfield, 0 Emsley, 13955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 12009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 441 time to evaluate : 9.162 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: x 95 GLU cc_start: -0.1070 (OUTLIER) cc_final: -0.1971 (mt-10) REVERT: x 101 MET cc_start: 0.4628 (OUTLIER) cc_final: 0.3795 (ppp) REVERT: x 181 MET cc_start: 0.6054 (mmp) cc_final: 0.5141 (ptm) REVERT: x 207 MET cc_start: 0.7166 (tmm) cc_final: 0.6773 (tmm) REVERT: A 261 PHE cc_start: 0.8756 (OUTLIER) cc_final: 0.8513 (m-10) REVERT: B 214 MET cc_start: 0.7466 (OUTLIER) cc_final: 0.6853 (tmm) REVERT: C 139 MET cc_start: 0.8138 (tpp) cc_final: 0.7100 (tpp) REVERT: D 124 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8317 (mm) REVERT: D 204 MET cc_start: 0.7019 (ttt) cc_final: 0.6743 (ttt) REVERT: D 296 MET cc_start: 0.8965 (ppp) cc_final: 0.8639 (ppp) REVERT: D 309 MET cc_start: 0.7833 (mmm) cc_final: 0.7401 (mmm) REVERT: E 218 MET cc_start: 0.9359 (ptm) cc_final: 0.9054 (ppp) REVERT: E 247 THR cc_start: 0.9091 (OUTLIER) cc_final: 0.8564 (p) REVERT: E 262 ASN cc_start: 0.8866 (OUTLIER) cc_final: 0.8398 (t0) REVERT: F 36 MET cc_start: 0.1448 (mmt) cc_final: 0.0926 (ptt) REVERT: F 55 MET cc_start: 0.7593 (tmm) cc_final: 0.7297 (tmm) REVERT: R 197 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7598 (mp0) REVERT: i 121 TYR cc_start: 0.8128 (OUTLIER) cc_final: 0.7557 (t80) REVERT: i 249 ARG cc_start: 0.6580 (OUTLIER) cc_final: 0.6243 (ptt90) REVERT: j 211 MET cc_start: 0.6359 (OUTLIER) cc_final: 0.5986 (tpp) REVERT: k 59 MET cc_start: 0.8040 (tpp) cc_final: 0.7680 (mmt) REVERT: p 12 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7644 (ttp) REVERT: q 11 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7253 (p0) REVERT: y 1 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.6502 (tmm) REVERT: y 19 PRO cc_start: 0.7324 (Cg_exo) cc_final: 0.7100 (Cg_endo) REVERT: U 137 MET cc_start: 0.8500 (mmp) cc_final: 0.8111 (mmm) REVERT: U 206 MET cc_start: 0.7580 (tmm) cc_final: 0.6942 (mmt) REVERT: U 239 GLU cc_start: 0.6471 (OUTLIER) cc_final: 0.6063 (mp0) REVERT: U 415 HIS cc_start: 0.6682 (OUTLIER) cc_final: 0.5703 (t70) REVERT: U 423 MET cc_start: 0.7662 (mmt) cc_final: 0.6846 (tpt) REVERT: U 675 MET cc_start: 0.7954 (ppp) cc_final: 0.7529 (ppp) REVERT: U 757 MET cc_start: 0.8121 (tmm) cc_final: 0.7416 (ttm) REVERT: V 175 MET cc_start: 0.6564 (OUTLIER) cc_final: 0.5833 (tmm) REVERT: V 403 ILE cc_start: 0.7746 (OUTLIER) cc_final: 0.7335 (tp) REVERT: V 409 MET cc_start: 0.8304 (mmp) cc_final: 0.7562 (tmm) REVERT: V 433 ASP cc_start: 0.7329 (OUTLIER) cc_final: 0.7117 (p0) REVERT: V 462 GLU cc_start: 0.6387 (OUTLIER) cc_final: 0.6048 (tm-30) REVERT: W 73 MET cc_start: 0.4758 (ptm) cc_final: 0.4458 (ppp) REVERT: X 254 MET cc_start: 0.5928 (mmt) cc_final: 0.4868 (mmt) REVERT: Y 214 MET cc_start: 0.6624 (mmp) cc_final: 0.6218 (mmm) REVERT: Y 389 MET cc_start: 0.7122 (tpt) cc_final: 0.6511 (pmm) REVERT: Z 236 LEU cc_start: 0.7230 (OUTLIER) cc_final: 0.6889 (mt) REVERT: a 246 GLU cc_start: 0.5248 (OUTLIER) cc_final: 0.4511 (tt0) REVERT: a 278 MET cc_start: 0.7858 (pmm) cc_final: 0.7393 (pmm) REVERT: c 167 MET cc_start: 0.6425 (tpp) cc_final: 0.5973 (tpt) REVERT: c 216 MET cc_start: 0.8328 (ppp) cc_final: 0.7955 (ppp) REVERT: d 4 GLN cc_start: 0.5547 (OUTLIER) cc_final: 0.5090 (tm-30) REVERT: d 89 LEU cc_start: 0.5811 (OUTLIER) cc_final: 0.5477 (tt) REVERT: f 26 GLU cc_start: 0.4046 (OUTLIER) cc_final: 0.3559 (pp20) REVERT: f 27 LYS cc_start: 0.6642 (mtpt) cc_final: 0.5911 (mtpt) REVERT: f 58 MET cc_start: 0.2802 (mtt) cc_final: 0.2431 (mtp) REVERT: f 89 MET cc_start: 0.5413 (tpt) cc_final: 0.4406 (mmt) REVERT: f 196 MET cc_start: 0.6073 (OUTLIER) cc_final: 0.5801 (mmt) REVERT: f 298 LEU cc_start: 0.3418 (OUTLIER) cc_final: 0.2972 (tt) REVERT: f 761 MET cc_start: 0.5010 (tpt) cc_final: 0.4663 (tpp) REVERT: f 825 MET cc_start: 0.5458 (mmm) cc_final: 0.4855 (mmm) outliers start: 208 outliers final: 162 residues processed: 623 average time/residue: 0.8906 time to fit residues: 1009.3569 Evaluate side-chains 630 residues out of total 12009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 441 time to evaluate : 9.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 37 THR Chi-restraints excluded: chain x residue 48 VAL Chi-restraints excluded: chain x residue 72 MET Chi-restraints excluded: chain x residue 95 GLU Chi-restraints excluded: chain x residue 101 MET Chi-restraints excluded: chain x residue 225 GLU Chi-restraints excluded: chain x residue 279 ILE Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 261 PHE Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain C residue 102 ASN Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 209 CYS Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 336 MET Chi-restraints excluded: chain D residue 44 TYR Chi-restraints excluded: chain D residue 110 ASN Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 124 LEU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 374 ASP Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 262 ASN Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain F residue 41 ILE Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 182 THR Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 202 LEU Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain J residue 107 ILE Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain L residue 206 THR Chi-restraints excluded: chain L residue 228 ASP Chi-restraints excluded: chain M residue 13 THR Chi-restraints excluded: chain M residue 37 ILE Chi-restraints excluded: chain M residue 93 GLU Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain P residue 58 THR Chi-restraints excluded: chain P residue 122 CYS Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain R residue 197 GLU Chi-restraints excluded: chain S residue 191 ASP Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 70 MET Chi-restraints excluded: chain T residue 205 THR Chi-restraints excluded: chain g residue 13 ILE Chi-restraints excluded: chain g residue 175 SER Chi-restraints excluded: chain g residue 190 THR Chi-restraints excluded: chain g residue 224 ASN Chi-restraints excluded: chain i residue 43 VAL Chi-restraints excluded: chain i residue 121 TYR Chi-restraints excluded: chain i residue 194 ILE Chi-restraints excluded: chain i residue 202 ASP Chi-restraints excluded: chain i residue 249 ARG Chi-restraints excluded: chain j residue 184 ASP Chi-restraints excluded: chain j residue 211 MET Chi-restraints excluded: chain j residue 217 LEU Chi-restraints excluded: chain k residue 13 ASN Chi-restraints excluded: chain k residue 87 THR Chi-restraints excluded: chain k residue 106 THR Chi-restraints excluded: chain k residue 225 ASN Chi-restraints excluded: chain l residue 49 LEU Chi-restraints excluded: chain l residue 176 MET Chi-restraints excluded: chain m residue 9 LEU Chi-restraints excluded: chain m residue 50 GLU Chi-restraints excluded: chain m residue 77 VAL Chi-restraints excluded: chain m residue 184 MET Chi-restraints excluded: chain m residue 204 VAL Chi-restraints excluded: chain n residue 60 THR Chi-restraints excluded: chain n residue 192 ASP Chi-restraints excluded: chain o residue 146 MET 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 p residue 122 CYS Chi-restraints excluded: chain q residue 11 ASP Chi-restraints excluded: chain s residue 26 ASP Chi-restraints excluded: chain s residue 164 VAL Chi-restraints excluded: chain s residue 199 THR Chi-restraints excluded: chain t residue 21 VAL Chi-restraints excluded: chain t residue 141 TYR Chi-restraints excluded: chain y residue 1 MET Chi-restraints excluded: chain U residue 239 GLU Chi-restraints excluded: chain U residue 248 ILE Chi-restraints excluded: chain U residue 403 THR Chi-restraints excluded: chain U residue 415 HIS Chi-restraints excluded: chain U residue 629 THR Chi-restraints excluded: chain U residue 663 THR Chi-restraints excluded: chain U residue 695 MET Chi-restraints excluded: chain U residue 706 VAL Chi-restraints excluded: chain U residue 736 ILE Chi-restraints excluded: chain U residue 788 VAL Chi-restraints excluded: chain U residue 854 MET Chi-restraints excluded: chain V residue 112 VAL Chi-restraints excluded: chain V residue 175 MET Chi-restraints excluded: chain V residue 314 ARG Chi-restraints excluded: chain V residue 403 ILE Chi-restraints excluded: chain V residue 433 ASP Chi-restraints excluded: chain V residue 462 GLU Chi-restraints excluded: chain V residue 494 MET Chi-restraints excluded: chain W residue 117 ASP Chi-restraints excluded: chain W residue 171 VAL Chi-restraints excluded: chain W residue 240 TYR Chi-restraints excluded: chain W residue 425 LEU Chi-restraints excluded: chain X residue 80 ILE Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 153 LEU Chi-restraints excluded: chain X residue 177 TYR Chi-restraints excluded: chain X residue 190 LEU Chi-restraints excluded: chain X residue 256 LEU Chi-restraints excluded: chain Y residue 37 VAL Chi-restraints excluded: chain Y residue 68 ASP Chi-restraints excluded: chain Y residue 104 MET Chi-restraints excluded: chain Y residue 134 LEU Chi-restraints excluded: chain Y residue 229 ILE Chi-restraints excluded: chain Y residue 299 MET Chi-restraints excluded: chain Z residue 10 VAL Chi-restraints excluded: chain Z residue 67 VAL Chi-restraints excluded: chain Z residue 112 MET Chi-restraints excluded: chain Z residue 122 VAL Chi-restraints excluded: chain Z residue 126 VAL Chi-restraints excluded: chain Z residue 130 ASP Chi-restraints excluded: chain Z residue 144 VAL Chi-restraints excluded: chain Z residue 201 LEU Chi-restraints excluded: chain Z residue 236 LEU Chi-restraints excluded: chain Z residue 264 SER Chi-restraints excluded: chain a residue 54 ASP Chi-restraints excluded: chain a residue 102 GLU Chi-restraints excluded: chain a residue 111 VAL Chi-restraints excluded: chain a residue 149 THR Chi-restraints excluded: chain a residue 169 HIS Chi-restraints excluded: chain a residue 221 VAL Chi-restraints excluded: chain a residue 246 GLU Chi-restraints excluded: chain b residue 60 VAL Chi-restraints excluded: chain b residue 117 VAL Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain c residue 177 THR Chi-restraints excluded: chain c residue 275 VAL Chi-restraints excluded: chain c residue 292 MET Chi-restraints excluded: chain d residue 4 GLN Chi-restraints excluded: chain d residue 43 LEU Chi-restraints excluded: chain d residue 72 GLU Chi-restraints excluded: chain d residue 89 LEU Chi-restraints excluded: chain d residue 132 TYR Chi-restraints excluded: chain d residue 197 ILE Chi-restraints excluded: chain d residue 255 MET Chi-restraints excluded: chain f residue 24 THR Chi-restraints excluded: chain f residue 26 GLU Chi-restraints excluded: chain f residue 171 GLN Chi-restraints excluded: chain f residue 196 MET Chi-restraints excluded: chain f residue 298 LEU Chi-restraints excluded: chain f residue 580 LEU Chi-restraints excluded: chain f residue 655 LEU Chi-restraints excluded: chain f residue 718 ASP Chi-restraints excluded: chain f residue 729 MET Chi-restraints excluded: chain f residue 793 VAL Chi-restraints excluded: chain e residue 27 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1386 random chunks: chunk 873 optimal weight: 4.9990 chunk 1171 optimal weight: 6.9990 chunk 336 optimal weight: 20.0000 chunk 1013 optimal weight: 50.0000 chunk 162 optimal weight: 8.9990 chunk 305 optimal weight: 0.9980 chunk 1101 optimal weight: 6.9990 chunk 460 optimal weight: 20.0000 chunk 1130 optimal weight: 20.0000 chunk 139 optimal weight: 30.0000 chunk 202 optimal weight: 9.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 ASN ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 166 ASN H 169 ASN ** K 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 874 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 102 HIS ** f 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 866 GLN ** e 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.049333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.042742 restraints weight = 1716186.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.043120 restraints weight = 1057854.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.043405 restraints weight = 759927.157| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3387 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3387 r_free = 0.3387 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3383 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 112389 Z= 0.199 Angle : 0.581 15.301 151810 Z= 0.293 Chirality : 0.042 0.341 17171 Planarity : 0.004 0.057 19566 Dihedral : 5.782 129.990 15472 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.65 % Favored : 93.31 % Rotamer: Outliers : 1.81 % Allowed : 18.30 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 13955 helix: 1.50 (0.07), residues: 6215 sheet: 0.05 (0.12), residues: 1976 loop : -1.72 (0.08), residues: 5764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP Y 63 HIS 0.010 0.001 HIS U 70 PHE 0.019 0.001 PHE P 69 TYR 0.019 0.001 TYR h 121 ARG 0.007 0.000 ARG C 307 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18924.29 seconds wall clock time: 337 minutes 1.06 seconds (20221.06 seconds total)