Starting phenix.real_space_refine on Mon Mar 11 10:53:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3j_32282/03_2024/7w3j_32282_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3j_32282/03_2024/7w3j_32282.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/7w3j_32282/03_2024/7w3j_32282.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3j_32282/03_2024/7w3j_32282.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3j_32282/03_2024/7w3j_32282_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w3j_32282/03_2024/7w3j_32282_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 69883 2.51 5 N 18975 2.21 5 O 21045 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.21s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 110559 Number of models: 1 Model: "" Number of chains: 55 Chain: "E" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3097 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 19, 'TRANS': 369} Chain: "F" Number of atoms: 3133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3133 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 18, 'TRANS': 381} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 1867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1867 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 231} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1801 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 221} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "I" Number of atoms: 1933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1933 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 242} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1861 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 232} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "K" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1813 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 229} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "L" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1876 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 229} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "M" Number of atoms: 1890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1890 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 236} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "N" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1521 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 7, 'TRANS': 195} Chain: "O" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1645 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 210} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "P" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1587 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "Q" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1588 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 190} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1559 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 2, 'TRANS': 198} Chain: "S" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1641 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 206} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "T" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1683 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 208} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "g" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1879 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 235} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "h" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1805 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 221} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "i" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1955 Classifications: {'peptide': 250} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 244} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "j" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1861 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 232} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "k" Number of atoms: 1782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1782 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 225} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "l" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1861 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 227} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "m" Number of atoms: 1881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1881 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 5, 'TRANS': 234} Chain: "n" Number of atoms: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1510 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 195} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "o" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1659 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 9, 'TRANS': 210} Chain: "p" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1591 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain: "q" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1578 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 8, 'TRANS': 190} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "r" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1549 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 198} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "s" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1650 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 206} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "t" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1687 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 7, 'TRANS': 208} Chain: "x" Number of atoms: 3929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3929 Classifications: {'peptide': 494} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 472} Chain: "y" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "A" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3164 Classifications: {'peptide': 406} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 383} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 3207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3207 Classifications: {'peptide': 411} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 21, 'TRANS': 389} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3097 Classifications: {'peptide': 395} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 378} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 3039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3039 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 17, 'TRANS': 362} Chain: "U" Number of atoms: 6828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 872, 6828 Classifications: {'peptide': 872} Link IDs: {'PTRANS': 31, 'TRANS': 840} Chain breaks: 1 Chain: "W" Number of atoms: 3635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3635 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 437} Chain: "X" Number of atoms: 3009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3009 Classifications: {'peptide': 380} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 369} Chain: "Y" Number of atoms: 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: "V" Number of atoms: 3612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3612 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 15, 'TRANS': 428} Chain: "e" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 425 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "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: "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: "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: 36.87, per 1000 atoms: 0.33 Number of scatterers: 110559 At special positions: 0 Unit cell: (330.17, 226.05, 219.2, 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 21045 8.00 N 18975 7.00 C 69883 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 270 " distance=2.04 Simple disulfide: pdb=" SG CYS U 633 " - pdb=" SG CYS U 659 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 31.02 Conformation dependent library (CDL) restraints added in 15.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN c 401 " pdb="ZN ZN c 401 " - pdb=" NE2 HIS c 113 " pdb="ZN ZN c 401 " - pdb=" NE2 HIS c 115 " 27942 Ramachandran restraints generated. 13971 Oldfield, 0 Emsley, 13971 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 26302 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: 513 helices and 94 sheets defined 54.4% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 53.91 Creating SS restraints... Processing helix chain 'E' and resid 5 through 51 removed outlier: 5.681A pdb=" N LEU E 9 " --> pdb=" O ARG E 5 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLN E 10 " --> pdb=" O ASP E 6 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU E 16 " --> pdb=" O TYR E 12 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LEU E 17 " --> pdb=" O ARG E 13 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LYS E 20 " --> pdb=" O LEU E 16 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU E 21 " --> pdb=" O LEU E 17 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N GLY E 24 " --> pdb=" O LYS E 20 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ARG E 25 " --> pdb=" O GLU E 21 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N LEU E 26 " --> pdb=" O ILE E 22 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LYS E 27 " --> pdb=" O ASP E 23 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLN E 51 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 93 removed outlier: 3.657A pdb=" N LYS E 93 " --> pdb=" O LYS E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 126 removed outlier: 4.172A pdb=" N ASN E 121 " --> pdb=" O PRO E 117 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N MET E 122 " --> pdb=" O LEU E 118 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N GLU E 125 " --> pdb=" O ASN E 121 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ASP E 126 " --> pdb=" O MET E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 155 removed outlier: 3.581A pdb=" N VAL E 148 " --> pdb=" O GLU E 144 " (cutoff:3.500A) removed outlier: 4.600A 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: 3.652A pdb=" N ALA E 184 " --> pdb=" O LYS E 180 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLN E 190 " --> pdb=" O ALA E 186 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU E 191 " --> pdb=" O VAL E 187 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ASP E 192 " --> pdb=" O ALA E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 204 removed outlier: 6.575A pdb=" N ILE E 203 " --> pdb=" O VAL E 199 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL E 204 " --> pdb=" O SER E 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 199 through 204' Processing helix chain 'E' and resid 209 through 226 removed outlier: 3.522A pdb=" N LEU E 214 " --> pdb=" O GLU E 210 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE E 215 " --> pdb=" O SER E 211 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLN E 226 " --> pdb=" O ALA E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 239 removed outlier: 4.597A pdb=" N ILE E 238 " --> pdb=" O GLU E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 265 removed outlier: 4.026A pdb=" N ARG E 251 " --> pdb=" O THR E 247 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLU E 252 " --> pdb=" O SER E 248 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE E 253 " --> pdb=" O ALA E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 291 Processing helix chain 'E' and resid 305 through 318 removed outlier: 3.667A pdb=" N GLY E 318 " --> pdb=" O LYS E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 336 removed outlier: 4.523A pdb=" N ILE E 331 " --> pdb=" O ASP E 327 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ASP E 336 " --> pdb=" O VAL E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 358 removed outlier: 5.208A pdb=" N ALA E 357 " --> pdb=" O PHE E 353 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASP E 358 " --> pdb=" O ALA E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 379 removed outlier: 4.297A pdb=" N PHE E 367 " --> pdb=" O VAL E 363 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET E 368 " --> pdb=" O GLN E 364 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS E 369 " --> pdb=" O GLU E 365 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LYS E 379 " --> pdb=" O ALA E 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 36 removed outlier: 4.712A pdb=" N LYS F 35 " --> pdb=" O GLU F 31 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N MET F 36 " --> pdb=" O GLU F 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 31 through 36' Processing helix chain 'F' and resid 39 through 50 removed outlier: 3.925A pdb=" N GLN F 43 " --> pdb=" O GLU F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 85 removed outlier: 4.965A pdb=" N THR F 85 " --> pdb=" O LYS F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 146 removed outlier: 5.646A pdb=" N LYS F 146 " --> pdb=" O ALA F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 176 removed outlier: 4.878A pdb=" N GLU F 176 " --> pdb=" O VAL F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 189 removed outlier: 4.098A pdb=" N ILE F 188 " --> pdb=" O GLN F 184 " (cutoff:3.500A) removed outlier: 5.013A 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: 4.402A 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 233 through 244 removed outlier: 4.141A pdb=" N ALA F 237 " --> pdb=" O LYS F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 279 removed outlier: 6.052A pdb=" N LYS F 266 " --> pdb=" O GLY F 262 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU F 267 " --> pdb=" O ASP F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 292 removed outlier: 4.696A pdb=" N ILE F 291 " --> pdb=" O GLU F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 318 removed outlier: 5.497A pdb=" N GLN F 307 " --> pdb=" O ASP F 303 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG F 308 " --> pdb=" O ARG F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 344 removed outlier: 3.982A pdb=" N LEU F 343 " --> pdb=" O ASP F 339 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ARG F 344 " --> pdb=" O PRO F 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 339 through 344' Processing helix chain 'F' and resid 358 through 371 removed outlier: 5.179A pdb=" N ARG F 362 " --> pdb=" O ASN F 358 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA F 363 " --> pdb=" O GLU F 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 389 removed outlier: 4.675A pdb=" N ASP F 389 " --> pdb=" O ALA F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 411 removed outlier: 3.627A pdb=" N ARG F 410 " --> pdb=" O ILE F 406 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY F 411 " --> pdb=" O ALA F 407 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 429 removed outlier: 4.106A pdb=" N ALA F 429 " --> pdb=" O LEU F 425 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 36 removed outlier: 3.584A pdb=" N GLU G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA G 28 " --> pdb=" O GLN G 24 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE G 29 " --> pdb=" O VAL G 25 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYS G 30 " --> pdb=" O GLU G 26 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA G 31 " --> pdb=" O TYR G 27 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASN G 33 " --> pdb=" O PHE G 29 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLN G 34 " --> pdb=" O LYS G 30 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLY G 35 " --> pdb=" O ALA G 31 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLY G 36 " --> pdb=" O ILE G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 67 removed outlier: 4.275A pdb=" N VAL G 66 " --> pdb=" O ASP G 62 " (cutoff:3.500A) removed outlier: 4.987A 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: 3.717A pdb=" N TYR G 125 " --> pdb=" O ILE G 121 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR G 126 " --> pdb=" O SER G 122 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN G 127 " --> pdb=" O GLN G 123 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN G 128 " --> pdb=" O VAL G 124 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ALA G 129 " --> pdb=" O TYR G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 186 removed outlier: 4.401A pdb=" N LYS G 185 " --> pdb=" O LYS G 181 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LYS G 186 " --> pdb=" O LYS G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 207 removed outlier: 3.678A pdb=" N VAL G 195 " --> pdb=" O PHE G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 231 through 245 removed outlier: 3.604A pdb=" N GLU G 244 " --> pdb=" O VAL G 240 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ARG G 245 " --> pdb=" O ALA G 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 12 removed outlier: 6.091A pdb=" N ASP G 10 " --> pdb=" O ALA G 7 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ARG G 11 " --> pdb=" O GLY G 8 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N HIS G 12 " --> pdb=" O PHE G 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 7 through 12' Processing helix chain 'H' and resid 3 through 8 removed outlier: 4.190A pdb=" N SER H 7 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N PHE H 8 " --> pdb=" O ARG H 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 3 through 8' Processing helix chain 'H' and resid 19 through 33 removed outlier: 5.111A pdb=" N GLU H 23 " --> pdb=" O LEU H 19 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR H 24 " --> pdb=" O VAL H 20 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY H 32 " --> pdb=" O ALA H 28 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ALA H 33 " --> pdb=" O VAL H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 102 removed outlier: 3.684A pdb=" N TYR H 83 " --> pdb=" O MET H 79 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG H 84 " --> pdb=" O GLY H 80 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL H 85 " --> pdb=" O PRO H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 124 removed outlier: 3.774A pdb=" N GLU H 120 " --> pdb=" O SER H 116 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TYR H 121 " --> pdb=" O VAL H 117 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N THR H 122 " --> pdb=" O MET H 118 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLN H 123 " --> pdb=" O GLN H 119 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N SER H 124 " --> pdb=" O GLU H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 178 removed outlier: 3.636A pdb=" N GLY H 170 " --> pdb=" O ASN H 166 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 199 removed outlier: 4.417A pdb=" N SER H 198 " --> pdb=" O THR H 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 209 removed outlier: 4.374A pdb=" N ILE H 208 " --> pdb=" O THR H 204 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N GLU H 209 " --> pdb=" O GLU H 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 204 through 209' Processing helix chain 'H' and resid 222 through 234 Processing helix chain 'h' and resid 19 through 33 removed outlier: 3.844A pdb=" N GLY h 32 " --> pdb=" O ALA h 28 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ALA h 33 " --> pdb=" O VAL h 29 " (cutoff:3.500A) Processing helix chain 'h' and resid 58 through 63 removed outlier: 4.588A pdb=" N VAL h 62 " --> pdb=" O ASP h 58 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N HIS h 63 " --> pdb=" O GLU h 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 58 through 63' Processing helix chain 'h' and resid 79 through 102 removed outlier: 3.663A pdb=" N TYR h 83 " --> pdb=" O MET h 79 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG h 84 " --> pdb=" O GLY h 80 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL h 85 " --> pdb=" O PRO h 81 " (cutoff:3.500A) Processing helix chain 'h' and resid 106 through 124 removed outlier: 3.931A pdb=" N TYR h 121 " --> pdb=" O VAL h 117 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N THR h 122 " --> pdb=" O MET h 118 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN h 123 " --> pdb=" O GLN h 119 " (cutoff:3.500A) Processing helix chain 'h' and resid 166 through 178 Processing helix chain 'h' and resid 183 through 199 removed outlier: 3.609A pdb=" N ALA h 187 " --> pdb=" O GLU h 183 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N SER h 198 " --> pdb=" O THR h 194 " (cutoff:3.500A) Processing helix chain 'h' and resid 222 through 234 removed outlier: 3.672A pdb=" N ALA h 234 " --> pdb=" O LEU h 230 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 32 removed outlier: 5.473A pdb=" N GLU I 22 " --> pdb=" O LEU I 18 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR I 23 " --> pdb=" O TYR I 19 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA I 24 " --> pdb=" O GLN I 20 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N HIS I 30 " --> pdb=" O GLU I 26 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ALA I 31 " --> pdb=" O ALA I 27 " (cutoff:3.500A) removed outlier: 5.491A 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: 3.642A pdb=" N ALA I 120 " --> pdb=" O ASP I 116 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N TYR I 121 " --> pdb=" O ILE I 117 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR I 122 " --> pdb=" O LYS I 118 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 179 removed outlier: 3.560A pdb=" N GLN I 177 " --> pdb=" O SER I 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 185 through 201 removed outlier: 3.772A pdb=" N MET I 201 " --> pdb=" O LEU I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 207 through 212 removed outlier: 4.159A pdb=" N VAL I 211 " --> pdb=" O SER I 207 " (cutoff:3.500A) removed outlier: 5.448A 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 248 removed outlier: 3.831A pdb=" N GLU I 234 " --> pdb=" O GLN I 230 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLN I 235 " --> pdb=" O LYS I 231 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU I 236 " --> pdb=" O GLU I 232 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU I 248 " --> pdb=" O GLU I 244 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 29 removed outlier: 3.548A pdb=" N VAL J 26 " --> pdb=" O ALA J 22 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS J 27 " --> pdb=" O GLN J 23 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS J 28 " --> pdb=" O GLU J 24 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLY J 29 " --> pdb=" O ALA J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 99 Processing helix chain 'J' and resid 103 through 121 removed outlier: 3.743A pdb=" N TYR J 118 " --> pdb=" O LEU J 114 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR J 119 " --> pdb=" O LYS J 115 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN J 120 " --> pdb=" O GLN J 116 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N SER J 121 " --> pdb=" O ARG J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 164 through 176 removed outlier: 3.737A pdb=" N VAL J 168 " --> pdb=" O GLY J 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 177 through 183 removed outlier: 4.121A pdb=" N ILE J 181 " --> pdb=" O THR J 177 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU J 182 " --> pdb=" O ASP J 178 " (cutoff:3.500A) removed outlier: 5.036A 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: 4.064A pdb=" N VAL J 198 " --> pdb=" O ALA J 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 221 through 240 removed outlier: 3.560A pdb=" N GLU J 240 " --> pdb=" O LYS J 236 " (cutoff:3.500A) Processing helix chain 'j' and resid 16 through 29 removed outlier: 3.621A pdb=" N LYS j 28 " --> pdb=" O GLU j 24 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLY j 29 " --> pdb=" O ALA j 25 " (cutoff:3.500A) Processing helix chain 'j' and resid 55 through 60 removed outlier: 4.274A pdb=" N VAL j 59 " --> pdb=" O ASP j 55 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ARG j 60 " --> pdb=" O GLU j 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 55 through 60' Processing helix chain 'j' and resid 76 through 99 Processing helix chain 'j' and resid 103 through 121 removed outlier: 3.613A pdb=" N TYR j 118 " --> pdb=" O LEU j 114 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR j 119 " --> pdb=" O LYS j 115 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN j 120 " --> pdb=" O GLN j 116 " (cutoff:3.500A) Processing helix chain 'j' and resid 164 through 176 removed outlier: 5.069A pdb=" N LYS j 174 " --> pdb=" O GLU j 170 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASN j 175 " --> pdb=" O PHE j 171 " (cutoff:3.500A) Processing helix chain 'j' and resid 177 through 183 removed outlier: 3.821A pdb=" N ILE j 181 " --> pdb=" O THR j 177 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR j 183 " --> pdb=" O GLU j 179 " (cutoff:3.500A) Processing helix chain 'j' and resid 184 through 199 removed outlier: 3.923A pdb=" N ILE j 188 " --> pdb=" O ASP j 184 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU j 197 " --> pdb=" O LYS j 193 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N VAL j 198 " --> pdb=" O ALA j 194 " (cutoff:3.500A) Processing helix chain 'j' and resid 221 through 240 Processing helix chain 'K' and resid 21 through 35 removed outlier: 3.596A pdb=" N GLU K 25 " --> pdb=" O LEU K 21 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE K 31 " --> pdb=" O ALA K 27 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LYS K 32 " --> pdb=" O ILE K 28 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N LEU K 33 " --> pdb=" O GLU K 29 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N GLY K 34 " --> pdb=" O ALA K 30 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N SER K 35 " --> pdb=" O ILE K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 103 removed outlier: 3.511A pdb=" N ALA K 85 " --> pdb=" O LEU K 81 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LYS K 86 " --> pdb=" O ILE K 82 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N THR K 87 " --> pdb=" O ALA K 83 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU K 88 " --> pdb=" O ASP K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 122 removed outlier: 4.072A pdb=" N LEU K 121 " --> pdb=" O SER K 117 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N GLN K 122 " --> pdb=" O ASN K 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 173 through 185 removed outlier: 3.649A pdb=" N GLN K 182 " --> pdb=" O GLN K 178 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLU K 183 " --> pdb=" O SER K 179 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL K 184 " --> pdb=" O SER K 180 " (cutoff:3.500A) Processing helix chain 'K' and resid 190 through 206 Processing helix chain 'K' and resid 211 through 216 removed outlier: 4.353A pdb=" N ILE K 215 " --> pdb=" O ASN K 211 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLU K 216 " --> pdb=" O ALA K 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 211 through 216' Processing helix chain 'K' and resid 230 through 241 removed outlier: 3.530A pdb=" N LYS K 239 " --> pdb=" O GLU K 235 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ASP K 240 " --> pdb=" O GLU K 236 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ILE K 241 " --> pdb=" O VAL K 237 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 65 removed outlier: 4.786A pdb=" N GLU K 65 " --> pdb=" O SER K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 125 through 130 removed outlier: 4.130A pdb=" N ALA K 128 " --> pdb=" O GLU K 125 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASP K 129 " --> pdb=" O GLU K 126 " (cutoff:3.500A) Proline residue: K 130 - end of helix No H-bonds generated for 'chain 'K' and resid 125 through 130' Processing helix chain 'L' and resid 2 through 8 removed outlier: 4.198A pdb=" N TYR L 6 " --> pdb=" O PHE L 2 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ASP L 7 " --> pdb=" O ARG L 3 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N ASN L 8 " --> pdb=" O ASN L 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 2 through 8' Processing helix chain 'L' and resid 19 through 32 removed outlier: 3.803A pdb=" N GLU L 27 " --> pdb=" O GLU L 23 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA L 28 " --> pdb=" O TYR L 24 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL L 29 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS L 30 " --> pdb=" O MET L 26 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN L 31 " --> pdb=" O GLU L 27 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLY L 32 " --> pdb=" O ALA L 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 99 Processing helix chain 'L' and resid 104 through 123 removed outlier: 3.896A pdb=" N ILE L 118 " --> pdb=" O SER L 114 " (cutoff:3.500A) Proline residue: L 119 - end of helix removed outlier: 3.630A pdb=" N ARG L 122 " --> pdb=" O ILE L 118 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N TYR L 123 " --> pdb=" O PRO L 119 " (cutoff:3.500A) Processing helix chain 'L' and resid 164 through 180 removed outlier: 4.719A pdb=" N ALA L 168 " --> pdb=" O ARG L 164 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N SER L 177 " --> pdb=" O GLU L 173 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLU L 178 " --> pdb=" O ARG L 174 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N PHE L 179 " --> pdb=" O HIS L 175 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N MET L 180 " --> pdb=" O MET L 176 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 200 removed outlier: 3.868A pdb=" N THR L 198 " --> pdb=" O ALA L 194 " (cutoff:3.500A) removed outlier: 3.856A 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 206 through 211 removed outlier: 3.967A pdb=" N VAL L 210 " --> pdb=" O THR L 206 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N SER L 211 " --> pdb=" O THR L 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 206 through 211' Processing helix chain 'L' and resid 225 through 237 removed outlier: 4.542A pdb=" N SER L 230 " --> pdb=" O ASP L 226 " (cutoff:3.500A) Proline residue: L 231 - end of helix removed outlier: 4.693A pdb=" N GLY L 235 " --> pdb=" O PRO L 231 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LEU L 236 " --> pdb=" O PHE L 232 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N GLU L 237 " --> pdb=" O LEU L 233 " (cutoff:3.500A) Processing helix chain 'M' and resid 20 through 33 removed outlier: 3.770A pdb=" N GLU M 24 " --> pdb=" O VAL M 20 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN M 32 " --> pdb=" O LYS M 28 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N SER M 33 " --> pdb=" O ALA M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 102 Processing helix chain 'M' and resid 107 through 125 removed outlier: 3.980A pdb=" N TYR M 122 " --> pdb=" O TYR M 118 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N THR M 123 " --> pdb=" O VAL M 119 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LEU M 124 " --> pdb=" O HIS M 120 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N TYR M 125 " --> pdb=" O ALA M 121 " (cutoff:3.500A) Processing helix chain 'M' and resid 168 through 179 removed outlier: 3.522A pdb=" N ALA M 172 " --> pdb=" O ALA M 168 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS M 178 " --> pdb=" O THR M 174 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU M 179 " --> pdb=" O GLU M 175 " (cutoff:3.500A) Processing helix chain 'M' and resid 185 through 202 removed outlier: 3.521A pdb=" N HIS M 201 " --> pdb=" O ILE M 197 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ASP M 202 " --> pdb=" O TYR M 198 " (cutoff:3.500A) Processing helix chain 'M' and resid 228 through 244 removed outlier: 3.642A pdb=" N LYS M 244 " --> pdb=" O LYS M 240 " (cutoff:3.500A) Processing helix chain 'N' and resid 48 through 71 Processing helix chain 'N' and resid 75 through 91 removed outlier: 3.578A pdb=" N TYR N 90 " --> pdb=" O MET N 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 131 through 143 removed outlier: 4.621A pdb=" N ILE N 135 " --> pdb=" O GLY N 131 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N TYR N 136 " --> pdb=" O SER N 132 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLY N 137 " --> pdb=" O SER N 133 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N TYR N 138 " --> pdb=" O TYR N 134 " (cutoff:3.500A) Processing helix chain 'N' and resid 148 through 167 removed outlier: 3.530A pdb=" N GLU N 165 " --> pdb=" O ALA N 161 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG N 166 " --> pdb=" O LEU N 162 " (cutoff:3.500A) Processing helix chain 'O' and resid 48 through 71 Processing helix chain 'O' and resid 75 through 91 removed outlier: 3.630A pdb=" N ALA O 79 " --> pdb=" O ARG O 75 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG O 89 " --> pdb=" O GLN O 85 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N TYR O 90 " --> pdb=" O MET O 86 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN O 91 " --> pdb=" O LEU O 87 " (cutoff:3.500A) Processing helix chain 'O' and resid 130 through 142 removed outlier: 3.871A pdb=" N ALA O 134 " --> pdb=" O GLY O 130 " (cutoff:3.500A) Processing helix chain 'O' and resid 147 through 166 removed outlier: 3.555A pdb=" N ASP O 166 " --> pdb=" O GLY O 162 " (cutoff:3.500A) Processing helix chain 'o' and resid 48 through 71 Processing helix chain 'o' and resid 75 through 91 removed outlier: 3.616A pdb=" N ALA o 79 " --> pdb=" O ARG o 75 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG o 89 " --> pdb=" O GLN o 85 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N TYR o 90 " --> pdb=" O MET o 86 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLN o 91 " --> pdb=" O LEU o 87 " (cutoff:3.500A) Processing helix chain 'o' and resid 130 through 142 removed outlier: 3.863A pdb=" N ALA o 134 " --> pdb=" O GLY o 130 " (cutoff:3.500A) Processing helix chain 'o' and resid 147 through 166 removed outlier: 3.551A pdb=" N ASP o 166 " --> pdb=" O GLY o 162 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 8 removed outlier: 3.979A pdb=" N TYR P 6 " --> pdb=" O SER P 2 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ASN P 7 " --> pdb=" O ILE P 3 " (cutoff:3.500A) removed outlier: 4.436A 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: 3.632A pdb=" N LEU P 73 " --> pdb=" O PHE P 69 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 99 removed outlier: 3.575A pdb=" N GLU P 97 " --> pdb=" O ASN P 93 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N LYS P 98 " --> pdb=" O LEU P 94 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ARG P 99 " --> pdb=" O LEU P 95 " (cutoff:3.500A) Processing helix chain 'P' and resid 142 through 154 removed outlier: 4.019A pdb=" N SER P 152 " --> pdb=" O GLY P 148 " (cutoff:3.500A) Processing helix chain 'P' and resid 159 through 179 removed outlier: 3.516A pdb=" N GLU P 165 " --> pdb=" O ASP P 161 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG P 177 " --> pdb=" O ASN P 173 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP P 178 " --> pdb=" O ALA P 174 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N ALA P 179 " --> pdb=" O VAL P 175 " (cutoff:3.500A) Processing helix chain 'p' and resid 2 through 8 removed outlier: 3.639A pdb=" N TYR p 6 " --> pdb=" O SER p 2 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N ASN p 7 " --> pdb=" O ILE p 3 " (cutoff:3.500A) removed outlier: 4.173A 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: 3.643A pdb=" N LEU p 73 " --> pdb=" O PHE p 69 " (cutoff:3.500A) Processing helix chain 'p' and resid 83 through 99 removed outlier: 4.146A pdb=" N LYS p 98 " --> pdb=" O LEU p 94 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ARG p 99 " --> pdb=" O LEU p 95 " (cutoff:3.500A) Processing helix chain 'p' and resid 142 through 154 removed outlier: 4.168A pdb=" N SER p 152 " --> pdb=" O GLY p 148 " (cutoff:3.500A) Processing helix chain 'p' and resid 159 through 179 removed outlier: 3.647A pdb=" N ASP p 176 " --> pdb=" O LEU p 172 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ARG p 177 " --> pdb=" O ASN p 173 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASP p 178 " --> pdb=" O ALA p 174 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ALA p 179 " --> pdb=" O VAL p 175 " (cutoff:3.500A) Processing helix chain 'Q' and resid 51 through 72 removed outlier: 3.553A pdb=" N GLN Q 55 " --> pdb=" O GLY Q 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 95 removed outlier: 3.938A pdb=" N CYS Q 91 " --> pdb=" O ASN Q 87 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU Q 92 " --> pdb=" O LEU Q 88 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ARG Q 93 " --> pdb=" O ALA Q 89 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N SER Q 94 " --> pdb=" O ASP Q 90 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ARG Q 95 " --> pdb=" O CYS Q 91 " (cutoff:3.500A) Processing helix chain 'Q' and resid 134 through 147 removed outlier: 4.275A pdb=" N LEU Q 138 " --> pdb=" O TYR Q 134 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N SER Q 141 " --> pdb=" O PHE Q 137 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ILE Q 142 " --> pdb=" O LEU Q 138 " (cutoff:3.500A) Processing helix chain 'Q' and resid 152 through 170 Processing helix chain 'q' and resid 51 through 72 removed outlier: 3.520A pdb=" N GLN q 55 " --> pdb=" O GLY q 51 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU q 58 " --> pdb=" O VAL q 54 " (cutoff:3.500A) Processing helix chain 'q' and resid 76 through 95 removed outlier: 3.533A pdb=" N CYS q 91 " --> pdb=" O ASN q 87 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ARG q 93 " --> pdb=" O ALA q 89 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N SER q 94 " --> pdb=" O ASP q 90 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ARG q 95 " --> pdb=" O CYS q 91 " (cutoff:3.500A) Processing helix chain 'q' and resid 134 through 147 removed outlier: 4.242A pdb=" N LEU q 138 " --> pdb=" O TYR q 134 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N SER q 141 " --> pdb=" O PHE q 137 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ILE q 142 " --> pdb=" O LEU q 138 " (cutoff:3.500A) Processing helix chain 'q' and resid 152 through 170 Processing helix chain 'R' and resid 48 through 71 removed outlier: 4.578A pdb=" N CYS R 52 " --> pdb=" O GLY R 48 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 91 removed outlier: 3.941A pdb=" N GLN R 89 " --> pdb=" O ASN R 85 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N TYR R 90 " --> pdb=" O MET R 86 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS R 91 " --> pdb=" O VAL R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 143 removed outlier: 3.785A pdb=" N GLY R 137 " --> pdb=" O VAL R 133 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL R 138 " --> pdb=" O TYR R 134 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG R 141 " --> pdb=" O GLY R 137 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY R 142 " --> pdb=" O VAL R 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 148 through 167 Processing helix chain 'R' and resid 191 through 201 Processing helix chain 'r' and resid 48 through 71 Processing helix chain 'r' and resid 75 through 91 removed outlier: 4.042A pdb=" N GLN r 89 " --> pdb=" O ASN r 85 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N TYR r 90 " --> pdb=" O MET r 86 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LYS r 91 " --> pdb=" O VAL r 87 " (cutoff:3.500A) Processing helix chain 'r' and resid 131 through 143 removed outlier: 3.551A pdb=" N VAL r 138 " --> pdb=" O TYR r 134 " (cutoff:3.500A) removed outlier: 3.857A 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 removed outlier: 3.787A pdb=" N GLU r 197 " --> pdb=" O ALA r 193 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLY r 201 " --> pdb=" O GLU r 197 " (cutoff:3.500A) Processing helix chain 'S' and resid 57 through 80 Processing helix chain 'S' and resid 84 through 100 removed outlier: 4.040A pdb=" N ARG S 99 " --> pdb=" O ILE S 95 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ARG S 100 " --> pdb=" O LEU S 96 " (cutoff:3.500A) Processing helix chain 'S' and resid 141 through 153 Proline residue: S 147 - end of helix Processing helix chain 'S' and resid 167 through 186 removed outlier: 3.981A pdb=" N GLU S 184 " --> pdb=" O ILE S 180 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG S 185 " --> pdb=" O SER S 181 " (cutoff:3.500A) Processing helix chain 's' and resid 57 through 80 Processing helix chain 's' and resid 84 through 100 removed outlier: 4.070A pdb=" N ARG s 99 " --> pdb=" O ILE s 95 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ARG s 100 " --> pdb=" O LEU s 96 " (cutoff:3.500A) Processing helix chain 's' and resid 141 through 153 Proline residue: s 147 - end of helix Processing helix chain 's' and resid 167 through 186 removed outlier: 3.912A pdb=" N GLU s 184 " --> pdb=" O ILE s 180 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ARG s 185 " --> pdb=" O SER s 181 " (cutoff:3.500A) Processing helix chain 'T' and resid 56 through 78 removed outlier: 3.521A pdb=" N PHE T 60 " --> pdb=" O ASP T 56 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU T 77 " --> pdb=" O ASP T 73 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLY T 78 " --> pdb=" O GLU T 74 " (cutoff:3.500A) Processing helix chain 'T' and resid 84 through 103 removed outlier: 3.614A pdb=" N LYS T 102 " --> pdb=" O SER T 98 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N MET T 103 " --> pdb=" O ARG T 99 " (cutoff:3.500A) Processing helix chain 'T' and resid 140 through 157 removed outlier: 4.533A pdb=" N TYR T 144 " --> pdb=" O GLY T 140 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLN T 147 " --> pdb=" O ALA T 143 " (cutoff:3.500A) Proline residue: T 148 - end of helix removed outlier: 3.972A pdb=" N LYS T 156 " --> pdb=" O GLU T 152 " (cutoff:3.500A) Processing helix chain 'T' and resid 161 through 180 Processing helix chain 'T' and resid 209 through 215 removed outlier: 4.487A pdb=" N HIS T 213 " --> pdb=" O TRP T 209 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N MET T 214 " --> pdb=" O ASP T 210 " (cutoff:3.500A) removed outlier: 4.620A 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: 3.980A pdb=" N LEU t 77 " --> pdb=" O ASP t 73 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLY t 78 " --> pdb=" O GLU t 74 " (cutoff:3.500A) Processing helix chain 't' and resid 84 through 103 removed outlier: 3.701A pdb=" N MET t 103 " --> pdb=" O ARG t 99 " (cutoff:3.500A) Processing helix chain 't' and resid 140 through 157 removed outlier: 4.708A pdb=" N TYR t 144 " --> pdb=" O GLY t 140 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLN t 147 " --> pdb=" O ALA t 143 " (cutoff:3.500A) Proline residue: t 148 - end of helix removed outlier: 3.879A pdb=" N VAL t 153 " --> pdb=" O LEU t 149 " (cutoff:3.500A) Processing helix chain 't' and resid 161 through 180 Processing helix chain 't' and resid 209 through 215 removed outlier: 5.217A pdb=" N HIS t 213 " --> pdb=" O TRP t 209 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N MET t 214 " --> pdb=" O ASP t 210 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE t 215 " --> pdb=" O ILE t 211 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 209 through 215' Processing helix chain 'g' and resid 22 through 35 removed outlier: 3.584A pdb=" N GLU g 26 " --> pdb=" O LEU g 22 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE g 32 " --> pdb=" O ALA g 28 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASN g 33 " --> pdb=" O PHE g 29 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLN g 34 " --> pdb=" O LYS g 30 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N GLY g 35 " --> pdb=" O ALA g 31 " (cutoff:3.500A) Processing helix chain 'g' and resid 62 through 67 removed outlier: 4.519A pdb=" N VAL g 66 " --> pdb=" O ASP g 62 " (cutoff:3.500A) removed outlier: 5.516A 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 removed outlier: 3.514A pdb=" N SER g 89 " --> pdb=" O ALA g 85 " (cutoff:3.500A) Processing helix chain 'g' and resid 110 through 129 removed outlier: 4.378A pdb=" N TYR g 125 " --> pdb=" O ILE g 121 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N THR g 126 " --> pdb=" O SER g 122 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN g 127 " --> pdb=" O GLN g 123 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN g 128 " --> pdb=" O VAL g 124 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ALA g 129 " --> pdb=" O TYR g 125 " (cutoff:3.500A) Processing helix chain 'g' and resid 171 through 186 removed outlier: 3.747A pdb=" N LYS g 184 " --> pdb=" O GLU g 180 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LYS g 185 " --> pdb=" O LYS g 181 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LYS g 186 " --> pdb=" O LYS g 182 " (cutoff:3.500A) Processing helix chain 'g' and resid 190 through 207 removed outlier: 3.679A pdb=" N LEU g 202 " --> pdb=" O ALA g 198 " (cutoff:3.500A) Processing helix chain 'g' and resid 231 through 245 removed outlier: 3.854A pdb=" N GLU g 244 " --> pdb=" O VAL g 240 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG g 245 " --> pdb=" O ALA g 241 " (cutoff:3.500A) Processing helix chain 'i' and resid 18 through 32 removed outlier: 3.522A pdb=" N GLU i 22 " --> pdb=" O LEU i 18 " (cutoff:3.500A) removed outlier: 3.925A 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: 5.688A pdb=" N GLY i 32 " --> pdb=" O ILE i 28 " (cutoff:3.500A) Processing helix chain 'i' and resid 79 through 102 removed outlier: 3.532A pdb=" N ALA i 83 " --> pdb=" O ILE i 79 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASN i 84 " --> pdb=" O THR i 80 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL i 85 " --> pdb=" O SER i 81 " (cutoff:3.500A) Processing helix chain 'i' and resid 106 through 124 removed outlier: 3.706A pdb=" N TYR i 121 " --> pdb=" O ILE i 117 " (cutoff:3.500A) Processing helix chain 'i' and resid 167 through 179 removed outlier: 3.936A pdb=" N GLN i 177 " --> pdb=" O SER i 173 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP i 178 " --> pdb=" O MET i 174 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR i 179 " --> pdb=" O LEU i 175 " (cutoff:3.500A) Processing helix chain 'i' and resid 185 through 202 removed outlier: 3.522A pdb=" N ALA i 189 " --> pdb=" O THR i 185 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N MET i 201 " --> pdb=" O LEU i 197 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP i 202 " --> pdb=" O ASN i 198 " (cutoff:3.500A) Processing helix chain 'i' and resid 207 through 212 removed outlier: 3.970A pdb=" N VAL i 211 " --> pdb=" O SER i 207 " (cutoff:3.500A) removed outlier: 5.863A 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 250 removed outlier: 3.768A pdb=" N GLU i 248 " --> pdb=" O GLU i 244 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG i 249 " --> pdb=" O ALA i 245 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N GLU i 250 " --> pdb=" O LYS i 246 " (cutoff:3.500A) Processing helix chain 'k' and resid 21 through 35 removed outlier: 3.508A pdb=" N GLU k 25 " --> pdb=" O LEU k 21 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS k 32 " --> pdb=" O ILE k 28 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU k 33 " --> pdb=" O GLU k 29 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLY k 34 " --> pdb=" O ALA k 30 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N SER k 35 " --> pdb=" O ILE k 31 " (cutoff:3.500A) Processing helix chain 'k' and resid 81 through 103 removed outlier: 3.709A pdb=" N ALA k 85 " --> pdb=" O LEU k 81 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LYS k 86 " --> pdb=" O ILE k 82 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N THR k 87 " --> pdb=" O ALA k 83 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU k 88 " --> pdb=" O ASP k 84 " (cutoff:3.500A) Processing helix chain 'k' and resid 108 through 121 removed outlier: 4.126A pdb=" N LEU k 119 " --> pdb=" O ALA k 115 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA k 120 " --> pdb=" O VAL k 116 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N LEU k 121 " --> pdb=" O SER k 117 " (cutoff:3.500A) Processing helix chain 'k' and resid 173 through 185 removed outlier: 3.641A pdb=" N ALA k 177 " --> pdb=" O ALA k 173 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N SER k 179 " --> pdb=" O GLU k 175 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU k 183 " --> pdb=" O SER k 179 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR k 185 " --> pdb=" O LEU k 181 " (cutoff:3.500A) Processing helix chain 'k' and resid 190 through 206 Processing helix chain 'k' and resid 211 through 216 removed outlier: 4.254A pdb=" N ILE k 215 " --> pdb=" O ASN k 211 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLU k 216 " --> pdb=" O ALA k 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 211 through 216' Processing helix chain 'k' and resid 230 through 241 removed outlier: 3.848A pdb=" N ASP k 240 " --> pdb=" O GLU k 236 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE k 241 " --> pdb=" O VAL k 237 " (cutoff:3.500A) Processing helix chain 'l' and resid 19 through 32 removed outlier: 3.774A pdb=" N GLU l 23 " --> pdb=" O ILE l 19 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS l 30 " --> pdb=" O MET l 26 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLN l 31 " --> pdb=" O GLU l 27 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N GLY l 32 " --> pdb=" O ALA l 28 " (cutoff:3.500A) Processing helix chain 'l' and resid 77 through 99 Processing helix chain 'l' and resid 104 through 122 removed outlier: 4.097A pdb=" N ILE l 118 " --> pdb=" O SER l 114 " (cutoff:3.500A) Proline residue: l 119 - end of helix removed outlier: 3.597A pdb=" N ARG l 122 " --> pdb=" O ILE l 118 " (cutoff:3.500A) Processing helix chain 'l' and resid 164 through 180 removed outlier: 4.602A pdb=" N ALA l 168 " --> pdb=" O ARG l 164 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N SER l 177 " --> pdb=" O GLU l 173 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLU l 178 " --> pdb=" O ARG l 174 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N PHE l 179 " --> pdb=" O HIS l 175 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N MET l 180 " --> pdb=" O MET l 176 " (cutoff:3.500A) Processing helix chain 'l' and resid 183 through 200 removed outlier: 3.988A pdb=" N THR l 198 " --> pdb=" O ALA l 194 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU l 199 " --> pdb=" O LEU l 195 " (cutoff:3.500A) Proline residue: l 200 - end of helix Processing helix chain 'l' and resid 225 through 234 removed outlier: 4.298A pdb=" N SER l 230 " --> pdb=" O ASP l 226 " (cutoff:3.500A) Proline residue: l 231 - end of helix removed outlier: 4.284A pdb=" N GLU l 234 " --> pdb=" O SER l 230 " (cutoff:3.500A) Processing helix chain 'm' and resid 20 through 33 removed outlier: 3.693A pdb=" N GLU m 24 " --> pdb=" O VAL m 20 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA m 29 " --> pdb=" O TYR m 25 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL m 30 " --> pdb=" O ALA m 26 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU m 31 " --> pdb=" O MET m 27 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASN m 32 " --> pdb=" O LYS m 28 " (cutoff:3.500A) removed outlier: 4.560A 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: 4.193A pdb=" N TYR m 122 " --> pdb=" O TYR m 118 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR m 123 " --> pdb=" O VAL m 119 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LEU m 124 " --> pdb=" O HIS m 120 " (cutoff:3.500A) Processing helix chain 'm' and resid 168 through 179 removed outlier: 4.175A pdb=" N LYS m 178 " --> pdb=" O THR m 174 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU m 179 " --> pdb=" O GLU m 175 " (cutoff:3.500A) Processing helix chain 'm' and resid 180 through 185 removed outlier: 4.342A pdb=" N MET m 184 " --> pdb=" O GLN m 180 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N THR m 185 " --> pdb=" O MET m 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 180 through 185' Processing helix chain 'm' and resid 186 through 201 removed outlier: 4.549A pdb=" N LYS m 191 " --> pdb=" O ARG m 187 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N HIS m 201 " --> pdb=" O ILE m 197 " (cutoff:3.500A) Processing helix chain 'm' and resid 228 through 244 removed outlier: 3.936A pdb=" N LYS m 244 " --> pdb=" O LYS m 240 " (cutoff:3.500A) Processing helix chain 'm' and resid 5 through 10 removed outlier: 5.650A pdb=" N ASP m 8 " --> pdb=" O THR m 5 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N LEU m 9 " --> pdb=" O GLY m 6 " (cutoff:3.500A) removed outlier: 5.064A 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 removed outlier: 3.820A pdb=" N ILE n 68 " --> pdb=" O GLY n 64 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLU n 69 " --> pdb=" O PHE n 65 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU n 70 " --> pdb=" O HIS n 66 " (cutoff:3.500A) Processing helix chain 'n' and resid 75 through 91 removed outlier: 3.523A pdb=" N ALA n 79 " --> pdb=" O LEU n 75 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR n 90 " --> pdb=" O MET n 86 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG n 91 " --> pdb=" O CYS n 87 " (cutoff:3.500A) Processing helix chain 'n' and resid 131 through 143 removed outlier: 4.697A pdb=" N ILE n 135 " --> pdb=" O GLY n 131 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TYR n 136 " --> pdb=" O SER n 132 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N GLY n 137 " --> pdb=" O SER n 133 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N TYR n 138 " --> pdb=" O TYR n 134 " (cutoff:3.500A) Processing helix chain 'n' and resid 148 through 167 Processing helix chain 'x' and resid 25 through 37 removed outlier: 3.566A pdb=" N PHE x 29 " --> pdb=" O PRO x 25 " (cutoff:3.500A) Processing helix chain 'x' and resid 94 through 101 Processing helix chain 'x' and resid 113 through 127 removed outlier: 4.782A pdb=" N ASN x 117 " --> pdb=" O THR x 113 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL x 126 " --> pdb=" O CYS x 122 " (cutoff:3.500A) Proline residue: x 127 - end of helix Processing helix chain 'x' and resid 128 through 137 removed outlier: 5.450A pdb=" N ALA x 137 " --> pdb=" O LEU x 133 " (cutoff:3.500A) Processing helix chain 'x' and resid 144 through 166 removed outlier: 3.768A pdb=" N ALA x 149 " --> pdb=" O GLU x 145 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLN x 150 " --> pdb=" O MET x 146 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N TYR x 151 " --> pdb=" O ALA x 147 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE x 152 " --> pdb=" O SER x 148 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP x 161 " --> pdb=" O ARG x 157 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR x 166 " --> pdb=" O SER x 162 " (cutoff:3.500A) Processing helix chain 'x' and resid 172 through 184 Proline residue: x 184 - end of helix Processing helix chain 'x' and resid 199 through 215 removed outlier: 3.607A pdb=" N CYS x 203 " --> pdb=" O ASP x 199 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU x 215 " --> pdb=" O LEU x 211 " (cutoff:3.500A) Processing helix chain 'x' and resid 220 through 225 removed outlier: 3.762A pdb=" N LYS x 224 " --> pdb=" O ASP x 220 " (cutoff:3.500A) Processing helix chain 'x' and resid 241 through 247 removed outlier: 3.520A pdb=" N GLN x 245 " --> pdb=" O SER x 241 " (cutoff:3.500A) Processing helix chain 'x' and resid 285 through 296 removed outlier: 3.808A pdb=" N GLN x 295 " --> pdb=" O LYS x 291 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N GLU x 296 " --> pdb=" O LEU x 292 " (cutoff:3.500A) Processing helix chain 'x' and resid 362 through 383 removed outlier: 4.187A pdb=" N PHE x 370 " --> pdb=" O LYS x 366 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N LYS x 373 " --> pdb=" O SER x 369 " (cutoff:3.500A) Processing helix chain 'x' and resid 459 through 467 removed outlier: 3.575A pdb=" N ILE x 463 " --> pdb=" O THR x 459 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N SER x 467 " --> pdb=" O ILE x 463 " (cutoff:3.500A) Processing helix chain 'y' and resid 22 through 34 Processing helix chain 'y' and resid 55 through 60 removed outlier: 3.795A pdb=" N ASP y 58 " --> pdb=" O THR y 55 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN y 60 " --> pdb=" O SER y 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 36 removed outlier: 3.551A pdb=" N THR A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 60 removed outlier: 4.421A pdb=" N ARG A 43 " --> pdb=" O SER A 39 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N GLN A 44 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN A 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N VAL A 48 " --> pdb=" O GLN A 44 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLU A 49 " --> pdb=" O ILE A 45 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ASP A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ASP A 51 " --> pdb=" O GLN A 47 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ILE A 52 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N GLN A 53 " --> pdb=" O GLU A 49 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 56 " --> pdb=" O ILE A 52 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS A 57 " --> pdb=" O GLN A 53 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LYS A 58 " --> pdb=" O GLN A 54 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ILE A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 70 removed outlier: 3.549A pdb=" N ASP A 69 " --> pdb=" O ILE A 65 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N THR A 70 " --> pdb=" O LYS A 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 65 through 70' Processing helix chain 'A' and resid 74 through 79 Processing helix chain 'A' and resid 158 through 165 removed outlier: 3.903A pdb=" N MET A 163 " --> pdb=" O PRO A 159 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N MET A 164 " --> pdb=" O THR A 160 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN A 165 " --> pdb=" O VAL A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 178 removed outlier: 4.433A pdb=" N VAL A 177 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 4.788A 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: 4.342A 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: 4.826A pdb=" N VAL A 202 " --> pdb=" O PRO A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 233 removed outlier: 4.090A pdb=" N THR A 233 " --> pdb=" O VAL A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 268 removed outlier: 3.520A pdb=" N ARG A 255 " --> pdb=" O GLY A 251 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A 267 " --> pdb=" O MET A 263 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LYS A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 281 removed outlier: 3.780A pdb=" N ILE A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 308 removed outlier: 5.235A pdb=" N GLN A 296 " --> pdb=" O ASP A 292 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLY A 308 " --> pdb=" O ASN A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 333 Processing helix chain 'A' and resid 347 through 363 removed outlier: 5.282A pdb=" N ARG A 351 " --> pdb=" O ASP A 347 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR A 352 " --> pdb=" O LEU A 348 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N SER A 361 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N MET A 362 " --> pdb=" O HIS A 358 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N SER A 363 " --> pdb=" O ALA A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 378 removed outlier: 5.214A pdb=" N LEU A 373 " --> pdb=" O ARG A 369 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N CYS A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 381 through 400 removed outlier: 3.661A pdb=" N ALA A 399 " --> pdb=" O PHE A 395 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ARG A 400 " --> pdb=" O ALA A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 419 removed outlier: 3.532A pdb=" N PHE A 409 " --> pdb=" O THR A 405 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER A 419 " --> pdb=" O LYS A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 91 removed outlier: 3.593A pdb=" N SER A 89 " --> pdb=" O LYS A 84 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N GLN A 91 " --> pdb=" O THR A 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 39 removed outlier: 4.056A pdb=" N LYS B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LYS B 39 " --> pdb=" O LYS B 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 34 through 39' Processing helix chain 'B' and resid 58 through 82 removed outlier: 4.067A pdb=" N GLN B 82 " --> pdb=" O PHE B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 6.559A pdb=" N SER B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS B 98 " --> pdb=" O GLU B 94 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N VAL B 99 " --> pdb=" O GLU B 95 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU B 102 " --> pdb=" O LYS B 98 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG B 103 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N GLY B 104 " --> pdb=" O ASP B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 176 removed outlier: 3.869A pdb=" N THR B 172 " --> pdb=" O ASP B 168 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N VAL B 173 " --> pdb=" O PRO B 169 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N MET B 174 " --> pdb=" O LEU B 170 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS B 175 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N VAL B 176 " --> pdb=" O THR B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 168 through 176' Processing helix chain 'B' and resid 190 through 201 Processing helix chain 'B' and resid 208 through 215 removed outlier: 4.727A pdb=" N GLU B 212 " --> pdb=" O PRO B 208 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N MET B 214 " --> pdb=" O TYR B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 243 removed outlier: 3.973A pdb=" N THR B 243 " --> pdb=" O VAL B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 278 removed outlier: 4.758A pdb=" N ALA B 278 " --> pdb=" O ALA B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 293 removed outlier: 4.564A pdb=" N ILE B 290 " --> pdb=" O GLU B 286 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N GLY B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 317 removed outlier: 3.997A pdb=" N ILE B 305 " --> pdb=" O GLY B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 344 removed outlier: 3.740A pdb=" N ILE B 342 " --> pdb=" O ASP B 338 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG B 343 " --> pdb=" O PRO B 339 " (cutoff:3.500A) Proline residue: B 344 - end of helix No H-bonds generated for 'chain 'B' and resid 338 through 344' Processing helix chain 'B' and resid 357 through 373 removed outlier: 4.490A pdb=" N ARG B 371 " --> pdb=" O ILE B 367 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N MET B 372 " --> pdb=" O HIS B 368 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N THR B 373 " --> pdb=" O THR B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 386 removed outlier: 4.351A pdb=" N LEU B 383 " --> pdb=" O THR B 379 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N MET B 385 " --> pdb=" O ASP B 381 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ALA B 386 " --> pdb=" O ASP B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 410 removed outlier: 3.582A pdb=" N GLY B 403 " --> pdb=" O CYS B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 432 removed outlier: 3.789A pdb=" N GLN B 431 " --> pdb=" O LEU B 427 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N GLU B 432 " --> pdb=" O TYR B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 207 removed outlier: 4.192A pdb=" N HIS B 207 " --> pdb=" O GLU B 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 202 through 207' Processing helix chain 'C' and resid 12 through 65 removed outlier: 6.968A pdb=" N GLY C 19 " --> pdb=" O LYS C 15 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LEU C 20 " --> pdb=" O ALA C 16 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N TYR C 23 " --> pdb=" O GLY C 19 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLU C 29 " --> pdb=" O LEU C 25 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU C 30 " --> pdb=" O SER C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 152 removed outlier: 4.506A pdb=" N ILE C 151 " --> pdb=" O THR C 147 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLY C 152 " --> pdb=" O TYR C 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 147 through 152' Processing helix chain 'C' and resid 154 through 170 removed outlier: 4.601A 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 171 through 179 removed outlier: 4.725A pdb=" N PHE C 175 " --> pdb=" O HIS C 171 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU C 176 " --> pdb=" O PRO C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 208 removed outlier: 4.022A pdb=" N ALA C 200 " --> pdb=" O LYS C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 222 removed outlier: 4.382A pdb=" N GLN C 221 " --> pdb=" O SER C 217 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 217 through 222' Processing helix chain 'C' and resid 232 through 238 removed outlier: 4.559A pdb=" N VAL C 236 " --> pdb=" O ARG C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 282 removed outlier: 4.318A pdb=" N GLN C 270 " --> pdb=" O ASP C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 312 removed outlier: 4.120A pdb=" N ILE C 311 " --> pdb=" O ARG C 307 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP C 312 " --> pdb=" O PRO C 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 307 through 312' Processing helix chain 'C' and resid 321 through 334 removed outlier: 3.822A pdb=" N ARG C 334 " --> pdb=" O LYS C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 351 removed outlier: 5.218A pdb=" N ILE C 347 " --> pdb=" O ASN C 343 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU C 350 " --> pdb=" O LYS C 346 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N MET C 351 " --> pdb=" O ILE C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 374 removed outlier: 3.696A pdb=" N GLY C 361 " --> pdb=" O ALA C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 392 removed outlier: 4.923A pdb=" N GLN C 392 " --> pdb=" O ALA C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 405 removed outlier: 4.710A pdb=" N TRP C 405 " --> pdb=" O ILE C 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 84 removed outlier: 3.609A pdb=" N ARG D 43 " --> pdb=" O ASP D 39 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU D 52 " --> pdb=" O GLN D 48 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLN D 57 " --> pdb=" O PHE D 53 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU D 58 " --> pdb=" O LEU D 54 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS D 66 " --> pdb=" O LYS D 62 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLN D 83 " --> pdb=" O VAL D 79 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N SER D 84 " --> pdb=" O LYS D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 125 removed outlier: 3.963A pdb=" N LEU D 124 " --> pdb=" O ASP D 120 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N LYS D 125 " --> pdb=" O ARG D 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 120 through 125' Processing helix chain 'D' and resid 170 through 187 removed outlier: 4.215A pdb=" N LEU D 183 " --> pdb=" O GLU D 179 " (cutoff:3.500A) Proline residue: D 184 - end of helix Processing helix chain 'D' and resid 188 through 195 Processing helix chain 'D' and resid 211 through 223 removed outlier: 3.908A pdb=" N ALA D 216 " --> pdb=" O LYS D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 258 removed outlier: 3.555A pdb=" N ALA D 258 " --> pdb=" O ALA D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 272 removed outlier: 5.525A pdb=" N THR D 272 " --> pdb=" O ASP D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 299 removed outlier: 3.952A pdb=" N VAL D 285 " --> pdb=" O ALA D 281 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLY D 298 " --> pdb=" O ASN D 294 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE D 299 " --> pdb=" O GLN D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 323 removed outlier: 3.626A pdb=" N LEU D 322 " --> pdb=" O ASP D 318 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ARG D 323 " --> pdb=" O PRO D 319 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 318 through 323' Processing helix chain 'D' and resid 337 through 353 removed outlier: 4.394A pdb=" N LYS D 351 " --> pdb=" O THR D 347 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N MET D 352 " --> pdb=" O ILE D 348 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ASN D 353 " --> pdb=" O THR D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 365 removed outlier: 4.031A pdb=" N TYR D 363 " --> pdb=" O ASP D 359 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL D 364 " --> pdb=" O LEU D 360 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA D 365 " --> pdb=" O GLU D 361 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 359 through 365' Processing helix chain 'D' and resid 371 through 390 removed outlier: 4.227A pdb=" N ILE D 375 " --> pdb=" O SER D 371 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ASN D 376 " --> pdb=" O GLY D 372 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 406 removed outlier: 4.329A pdb=" N PHE D 399 " --> pdb=" O LEU D 395 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLU D 400 " --> pdb=" O ALA D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 149 removed outlier: 4.365A pdb=" N ASP D 148 " --> pdb=" O PRO D 145 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N SER D 149 " --> pdb=" O GLU D 146 " (cutoff:3.500A) Processing helix chain 'U' and resid 8 through 14 removed outlier: 3.967A pdb=" N LEU U 12 " --> pdb=" O ILE U 8 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP U 13 " --> pdb=" O ILE U 9 " (cutoff:3.500A) removed outlier: 3.919A 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: 4.973A pdb=" N LYS U 26 " --> pdb=" O PHE U 22 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU U 27 " --> pdb=" O ALA U 23 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ASN U 28 " --> pdb=" O LEU U 24 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ALA U 29 " --> pdb=" O HIS U 25 " (cutoff:3.500A) Processing helix chain 'U' and resid 34 through 42 removed outlier: 3.533A pdb=" N ILE U 38 " --> pdb=" O PHE U 34 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER U 39 " --> pdb=" O TRP U 35 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLU U 40 " --> pdb=" O ALA U 36 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N SER U 41 " --> pdb=" O GLU U 37 " (cutoff:3.500A) removed outlier: 3.654A 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 52 removed outlier: 5.279A pdb=" N GLU U 52 " --> pdb=" O LEU U 48 " (cutoff:3.500A) Processing helix chain 'U' and resid 56 through 72 Processing helix chain 'U' and resid 73 through 85 removed outlier: 3.643A pdb=" N SER U 77 " --> pdb=" O ALA U 73 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY U 85 " --> pdb=" O ALA U 81 " (cutoff:3.500A) Processing helix chain 'U' and resid 86 through 91 removed outlier: 4.297A pdb=" N VAL U 90 " --> pdb=" O ASP U 86 " (cutoff:3.500A) removed outlier: 5.535A 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: 3.908A pdb=" N GLU U 131 " --> pdb=" O ASP U 127 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE U 133 " --> pdb=" O ARG U 129 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS U 136 " --> pdb=" O GLY U 132 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASP U 144 " --> pdb=" O ARG U 140 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N HIS U 145 " --> pdb=" O CYS U 141 " (cutoff:3.500A) Processing helix chain 'U' and resid 146 through 158 removed outlier: 3.820A pdb=" N ALA U 150 " --> pdb=" O LYS U 146 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY U 152 " --> pdb=" O LYS U 148 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE U 153 " --> pdb=" O GLN U 149 " (cutoff:3.500A) Processing helix chain 'U' and resid 159 through 171 removed outlier: 5.377A pdb=" N SER U 170 " --> pdb=" O THR U 166 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ASN U 171 " --> pdb=" O ILE U 167 " (cutoff:3.500A) Processing helix chain 'U' and resid 174 through 186 removed outlier: 4.147A pdb=" N ALA U 178 " --> pdb=" O PRO U 174 " (cutoff:3.500A) Processing helix chain 'U' and resid 190 through 209 removed outlier: 4.173A pdb=" N ASN U 195 " --> pdb=" O LYS U 191 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N LYS U 196 " --> pdb=" O GLN U 192 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS U 203 " --> pdb=" O ARG U 199 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE U 204 " --> pdb=" O VAL U 200 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N GLU U 209 " --> pdb=" O TYR U 205 " (cutoff:3.500A) Processing helix chain 'U' and resid 212 through 224 removed outlier: 4.836A pdb=" N VAL U 216 " --> pdb=" O ASP U 212 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LEU U 220 " --> pdb=" O VAL U 216 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ILE U 221 " --> pdb=" O CYS U 217 " (cutoff:3.500A) Processing helix chain 'U' and resid 225 through 240 removed outlier: 3.610A pdb=" N GLU U 239 " --> pdb=" O LYS U 235 " (cutoff:3.500A) removed outlier: 3.615A 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: 3.502A pdb=" N LEU U 261 " --> pdb=" O SER U 257 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N SER U 262 " --> pdb=" O GLN U 258 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER U 263 " --> pdb=" O GLN U 259 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR U 270 " --> pdb=" O GLN U 266 " (cutoff:3.500A) Processing helix chain 'U' and resid 320 through 331 removed outlier: 3.565A pdb=" N LYS U 324 " --> pdb=" O ASP U 320 " (cutoff:3.500A) Processing helix chain 'U' and resid 332 through 346 removed outlier: 3.646A pdb=" N ASN U 346 " --> pdb=" O LEU U 342 " (cutoff:3.500A) Processing helix chain 'U' and resid 349 through 361 removed outlier: 4.115A pdb=" N LEU U 353 " --> pdb=" O ASP U 349 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA U 359 " --> pdb=" O ASN U 355 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL U 360 " --> pdb=" O THR U 356 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ARG U 361 " --> pdb=" O LYS U 357 " (cutoff:3.500A) Processing helix chain 'U' and resid 364 through 378 removed outlier: 3.652A pdb=" N ALA U 368 " --> pdb=" O VAL U 364 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N SER U 374 " --> pdb=" O VAL U 370 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE U 375 " --> pdb=" O ILE U 371 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N MET U 376 " --> pdb=" O ALA U 372 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N HIS U 377 " --> pdb=" O ASN U 373 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N CYS U 378 " --> pdb=" O SER U 374 " (cutoff:3.500A) Processing helix chain 'U' and resid 383 through 389 removed outlier: 4.459A pdb=" N ARG U 387 " --> pdb=" O ASP U 383 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ASP U 388 " --> pdb=" O GLN U 384 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASN U 389 " --> pdb=" O PHE U 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 383 through 389' Processing helix chain 'U' and resid 390 through 396 removed outlier: 4.224A pdb=" N ALA U 396 " --> pdb=" O TRP U 392 " (cutoff:3.500A) Processing helix chain 'U' and resid 398 through 413 removed outlier: 6.136A pdb=" N PHE U 402 " --> pdb=" O ASN U 398 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N THR U 405 " --> pdb=" O LYS U 401 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLY U 409 " --> pdb=" O THR U 405 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL U 410 " --> pdb=" O ALA U 406 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N HIS U 412 " --> pdb=" O LEU U 408 " (cutoff:3.500A) Processing helix chain 'U' and resid 418 through 432 removed outlier: 4.810A pdb=" N TYR U 426 " --> pdb=" O LEU U 422 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LEU U 427 " --> pdb=" O MET U 423 " (cutoff:3.500A) Proline residue: U 428 - end of helix removed outlier: 4.604A pdb=" N THR U 431 " --> pdb=" O LEU U 427 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N SER U 432 " --> pdb=" O PRO U 428 " (cutoff:3.500A) Processing helix chain 'U' and resid 435 through 451 removed outlier: 4.772A pdb=" N GLU U 439 " --> pdb=" O SER U 435 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY U 440 " --> pdb=" O ALA U 436 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA U 451 " --> pdb=" O GLY U 447 " (cutoff:3.500A) Processing helix chain 'U' and resid 455 through 468 removed outlier: 3.514A pdb=" N ASP U 459 " --> pdb=" O GLY U 455 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLN U 464 " --> pdb=" O TYR U 460 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU U 465 " --> pdb=" O LEU U 461 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS U 466 " --> pdb=" O LEU U 462 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ALA U 468 " --> pdb=" O GLN U 464 " (cutoff:3.500A) Processing helix chain 'U' and resid 472 through 486 removed outlier: 3.583A pdb=" N GLY U 476 " --> pdb=" O ILE U 472 " (cutoff:3.500A) Processing helix chain 'U' and resid 490 through 504 removed outlier: 3.532A pdb=" N TYR U 494 " --> pdb=" O ARG U 490 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASP U 504 " --> pdb=" O ASN U 500 " (cutoff:3.500A) Processing helix chain 'U' and resid 508 through 521 removed outlier: 3.528A pdb=" N MET U 520 " --> pdb=" O LEU U 516 " (cutoff:3.500A) Processing helix chain 'U' and resid 525 through 539 removed outlier: 3.655A pdb=" N ALA U 536 " --> pdb=" O MET U 532 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLN U 537 " --> pdb=" O VAL U 533 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLU U 538 " --> pdb=" O GLY U 534 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR U 539 " --> pdb=" O TYR U 535 " (cutoff:3.500A) Processing helix chain 'U' and resid 541 through 557 removed outlier: 3.988A pdb=" N LEU U 545 " --> pdb=" O HIS U 541 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL U 550 " --> pdb=" O ARG U 546 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY U 551 " --> pdb=" O GLY U 547 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N MET U 556 " --> pdb=" O ILE U 552 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N TYR U 557 " --> pdb=" O ALA U 553 " (cutoff:3.500A) Processing helix chain 'U' and resid 563 through 573 removed outlier: 3.596A pdb=" N ARG U 572 " --> pdb=" O GLU U 568 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ASP U 573 " --> pdb=" O SER U 569 " (cutoff:3.500A) Processing helix chain 'U' and resid 575 through 591 removed outlier: 3.558A pdb=" N CYS U 591 " --> pdb=" O ALA U 587 " (cutoff:3.500A) Processing helix chain 'U' and resid 595 through 609 removed outlier: 4.128A pdb=" N VAL U 607 " --> pdb=" O LEU U 603 " (cutoff:3.500A) Processing helix chain 'U' and resid 611 through 627 removed outlier: 3.763A pdb=" N ARG U 615 " --> pdb=" O ASN U 611 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLY U 623 " --> pdb=" O VAL U 619 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N PHE U 624 " --> pdb=" O GLU U 620 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE U 625 " --> pdb=" O SER U 621 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE U 627 " --> pdb=" O GLY U 623 " (cutoff:3.500A) Processing helix chain 'U' and resid 629 through 643 removed outlier: 4.143A pdb=" N CYS U 633 " --> pdb=" O THR U 629 " (cutoff:3.500A) Proline residue: U 634 - end of helix removed outlier: 3.511A pdb=" N SER U 638 " --> pdb=" O PRO U 634 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N LEU U 639 " --> pdb=" O SER U 635 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N LEU U 640 " --> pdb=" O VAL U 636 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLU U 642 " --> pdb=" O SER U 638 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N SER U 643 " --> pdb=" O LEU U 639 " (cutoff:3.500A) Processing helix chain 'U' and resid 645 through 661 removed outlier: 3.561A pdb=" N CYS U 660 " --> pdb=" O LEU U 656 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ALA U 661 " --> pdb=" O GLY U 657 " (cutoff:3.500A) Processing helix chain 'U' and resid 665 through 676 removed outlier: 6.567A pdb=" N ILE U 669 " --> pdb=" O ASN U 665 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ASN U 670 " --> pdb=" O LYS U 666 " (cutoff:3.500A) Proline residue: U 674 - end of helix Processing helix chain 'U' and resid 680 through 696 removed outlier: 3.587A pdb=" N ARG U 684 " --> pdb=" O VAL U 680 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET U 695 " --> pdb=" O SER U 691 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE U 696 " --> pdb=" O ALA U 692 " (cutoff:3.500A) Processing helix chain 'U' and resid 699 through 704 removed outlier: 3.679A 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: 4.481A pdb=" N ASN U 718 " --> pdb=" O SER U 714 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASP U 719 " --> pdb=" O LYS U 715 " (cutoff:3.500A) Processing helix chain 'U' and resid 723 through 739 removed outlier: 3.647A pdb=" N GLY U 729 " --> pdb=" O MET U 725 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA U 730 " --> pdb=" O ALA U 726 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASP U 738 " --> pdb=" O GLN U 734 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA U 739 " --> pdb=" O GLY U 735 " (cutoff:3.500A) Processing helix chain 'U' and resid 756 through 769 removed outlier: 3.765A pdb=" N VAL U 761 " --> pdb=" O MET U 757 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN U 768 " --> pdb=" O LEU U 764 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N PHE U 769 " --> pdb=" O VAL U 765 " (cutoff:3.500A) Processing helix chain 'U' and resid 772 through 784 removed outlier: 4.473A pdb=" N SER U 776 " --> pdb=" O TRP U 772 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N HIS U 777 " --> pdb=" O PHE U 773 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N PHE U 778 " --> pdb=" O PRO U 774 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N LEU U 779 " --> pdb=" O LEU U 775 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N SER U 780 " --> pdb=" O SER U 776 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N LEU U 781 " --> pdb=" O HIS U 777 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ALA U 782 " --> pdb=" O PHE U 778 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR U 783 " --> pdb=" O LEU U 779 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N THR U 784 " --> pdb=" O SER U 780 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 772 through 784' Processing helix chain 'U' and resid 835 through 852 removed outlier: 4.138A pdb=" N ALA U 839 " --> pdb=" O ILE U 835 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LYS U 849 " --> pdb=" O GLU U 845 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLU U 850 " --> pdb=" O LYS U 846 " (cutoff:3.500A) Processing helix chain 'U' and resid 864 through 872 removed outlier: 3.827A pdb=" N LYS U 868 " --> pdb=" O GLU U 864 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU U 870 " --> pdb=" O GLU U 866 " (cutoff:3.500A) Proline residue: U 871 - end of helix Processing helix chain 'U' and resid 885 through 892 removed outlier: 3.547A pdb=" N LEU U 889 " --> pdb=" O MET U 885 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LYS U 890 " --> pdb=" O PRO U 886 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N VAL U 891 " --> pdb=" O ALA U 887 " (cutoff:3.500A) Processing helix chain 'W' and resid 20 through 36 removed outlier: 3.716A pdb=" N VAL W 24 " --> pdb=" O TYR W 20 " (cutoff:3.500A) Proline residue: W 29 - end of helix removed outlier: 3.709A pdb=" N LYS W 36 " --> pdb=" O ALA W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 39 through 58 removed outlier: 4.406A pdb=" N VAL W 43 " --> pdb=" O ARG W 39 " (cutoff:3.500A) Processing helix chain 'W' and resid 59 through 78 removed outlier: 4.298A pdb=" N THR W 63 " --> pdb=" O ASP W 59 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA W 77 " --> pdb=" O MET W 73 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS W 78 " --> pdb=" O CYS W 74 " (cutoff:3.500A) Processing helix chain 'W' and resid 79 through 94 removed outlier: 3.940A pdb=" N GLU W 85 " --> pdb=" O ASP W 81 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ARG W 94 " --> pdb=" O LEU W 90 " (cutoff:3.500A) Processing helix chain 'W' and resid 97 through 116 removed outlier: 4.028A pdb=" N GLU W 113 " --> pdb=" O CYS W 109 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N GLU W 114 " --> pdb=" O THR W 110 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE W 115 " --> pdb=" O TYR W 111 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N THR W 116 " --> pdb=" O VAL W 112 " (cutoff:3.500A) Processing helix chain 'W' and resid 117 through 132 removed outlier: 5.894A pdb=" N LYS W 121 " --> pdb=" O ASP W 117 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU W 122 " --> pdb=" O LEU W 118 " (cutoff:3.500A) Processing helix chain 'W' and resid 140 through 156 removed outlier: 4.488A pdb=" N GLN W 155 " --> pdb=" O THR W 151 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN W 156 " --> pdb=" O ILE W 152 " (cutoff:3.500A) Processing helix chain 'W' and resid 158 through 176 removed outlier: 4.170A pdb=" N GLN W 167 " --> pdb=" O ALA W 163 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLU W 168 " --> pdb=" O SER W 164 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LEU W 169 " --> pdb=" O ILE W 165 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLN W 170 " --> pdb=" O LEU W 166 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N VAL W 171 " --> pdb=" O GLN W 167 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU W 172 " --> pdb=" O GLU W 168 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N THR W 173 " --> pdb=" O LEU W 169 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N TYR W 174 " --> pdb=" O GLN W 170 " (cutoff:3.500A) Processing helix chain 'W' and resid 179 through 197 removed outlier: 4.684A pdb=" N VAL W 183 " --> pdb=" O LYS W 179 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU W 188 " --> pdb=" O GLU W 184 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLN W 189 " --> pdb=" O PHE W 185 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N MET W 190 " --> pdb=" O ILE W 186 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ARG W 191 " --> pdb=" O LEU W 187 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU W 192 " --> pdb=" O GLU W 188 " (cutoff:3.500A) Processing helix chain 'W' and resid 198 through 211 removed outlier: 3.760A pdb=" N GLN W 203 " --> pdb=" O TYR W 199 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ILE W 204 " --> pdb=" O ILE W 200 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE W 205 " --> pdb=" O ARG W 201 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N THR W 211 " --> pdb=" O LYS W 207 " (cutoff:3.500A) Processing helix chain 'W' and resid 215 through 220 removed outlier: 3.841A pdb=" N THR W 219 " --> pdb=" O GLN W 215 " (cutoff:3.500A) removed outlier: 5.525A 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 238 removed outlier: 5.311A pdb=" N ASN W 228 " --> pdb=" O LEU W 224 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU W 229 " --> pdb=" O LYS W 225 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N MET W 230 " --> pdb=" O TYR W 226 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS W 236 " --> pdb=" O GLN W 232 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLU W 237 " --> pdb=" O LEU W 233 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N GLY W 238 " --> pdb=" O ASP W 234 " (cutoff:3.500A) Processing helix chain 'W' and resid 239 through 258 removed outlier: 5.128A pdb=" N ILE W 243 " --> pdb=" O SER W 239 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ASP W 252 " --> pdb=" O ARG W 248 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N THR W 253 " --> pdb=" O ALA W 249 " (cutoff:3.500A) Proline residue: W 254 - end of helix Processing helix chain 'W' and resid 259 through 278 removed outlier: 4.257A pdb=" N TYR W 273 " --> pdb=" O SER W 269 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N VAL W 274 " --> pdb=" O VAL W 270 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N ILE W 275 " --> pdb=" O VAL W 271 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU W 276 " --> pdb=" O LEU W 272 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA W 277 " --> pdb=" O TYR W 273 " (cutoff:3.500A) Proline residue: W 278 - end of helix Processing helix chain 'W' and resid 280 through 291 Processing helix chain 'W' and resid 293 through 300 removed outlier: 4.899A pdb=" N GLU W 297 " --> pdb=" O ASP W 293 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N GLU W 298 " --> pdb=" O LYS W 294 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ILE W 299 " --> pdb=" O LYS W 295 " (cutoff:3.500A) Proline residue: W 300 - end of helix No H-bonds generated for 'chain 'W' and resid 293 through 300' Processing helix chain 'W' and resid 301 through 311 removed outlier: 3.742A pdb=" N LEU W 308 " --> pdb=" O ASP W 304 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR W 310 " --> pdb=" O LEU W 306 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N THR W 311 " --> pdb=" O LYS W 307 " (cutoff:3.500A) Processing helix chain 'W' and resid 316 through 324 removed outlier: 3.967A pdb=" N GLU W 322 " --> pdb=" O SER W 318 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR W 324 " --> pdb=" O LEU W 320 " (cutoff:3.500A) Processing helix chain 'W' and resid 325 through 330 removed outlier: 4.477A pdb=" N ARG W 329 " --> pdb=" O GLY W 325 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS W 330 " --> pdb=" O MET W 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 325 through 330' Processing helix chain 'W' and resid 334 through 341 Processing helix chain 'W' and resid 344 through 370 removed outlier: 4.758A pdb=" N GLU W 348 " --> pdb=" O THR W 344 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS W 349 " --> pdb=" O GLU W 345 " (cutoff:3.500A) Processing helix chain 'W' and resid 374 through 382 removed outlier: 3.575A pdb=" N MET W 378 " --> pdb=" O THR W 374 " (cutoff:3.500A) Processing helix chain 'W' and resid 385 through 400 removed outlier: 4.069A pdb=" N ASN W 399 " --> pdb=" O ASN W 395 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS W 400 " --> pdb=" O LEU W 396 " (cutoff:3.500A) Processing helix chain 'W' and resid 420 through 455 Processing helix chain 'X' and resid 43 through 61 removed outlier: 4.523A pdb=" N GLU X 47 " --> pdb=" O VAL X 43 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN X 48 " --> pdb=" O GLN X 44 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU X 51 " --> pdb=" O GLU X 47 " (cutoff:3.500A) Processing helix chain 'X' and resid 62 through 80 removed outlier: 4.333A pdb=" N LEU X 66 " --> pdb=" O GLN X 62 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ARG X 74 " --> pdb=" O LEU X 70 " (cutoff:3.500A) Proline residue: X 75 - end of helix removed outlier: 4.298A pdb=" N SER X 79 " --> pdb=" O PRO X 75 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ILE X 80 " --> pdb=" O PHE X 76 " (cutoff:3.500A) Processing helix chain 'X' and resid 81 through 101 removed outlier: 3.847A pdb=" N GLU X 100 " --> pdb=" O PHE X 96 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N ALA X 101 " --> pdb=" O LEU X 97 " (cutoff:3.500A) Processing helix chain 'X' and resid 102 through 121 removed outlier: 3.940A pdb=" N GLU X 106 " --> pdb=" O ALA X 102 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N VAL X 107 " --> pdb=" O THR X 103 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N GLU X 108 " --> pdb=" O GLY X 104 " (cutoff:3.500A) Processing helix chain 'X' and resid 122 through 141 Processing helix chain 'X' and resid 143 through 161 removed outlier: 4.037A pdb=" N LYS X 159 " --> pdb=" O ARG X 155 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N MET X 160 " --> pdb=" O GLU X 156 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ASP X 161 " --> pdb=" O LEU X 157 " (cutoff:3.500A) Processing helix chain 'X' and resid 162 through 181 removed outlier: 5.066A pdb=" N LEU X 166 " --> pdb=" O ASP X 162 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU X 180 " --> pdb=" O THR X 176 " (cutoff:3.500A) Processing helix chain 'X' and resid 182 through 198 removed outlier: 3.980A pdb=" N ASN X 198 " --> pdb=" O ARG X 194 " (cutoff:3.500A) Processing helix chain 'X' and resid 203 through 222 Processing helix chain 'X' and resid 224 through 240 removed outlier: 4.060A pdb=" N ALA X 228 " --> pdb=" O ASP X 224 " (cutoff:3.500A) Processing helix chain 'X' and resid 243 through 262 removed outlier: 4.129A pdb=" N THR X 249 " --> pdb=" O PRO X 245 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ASN X 262 " --> pdb=" O LYS X 258 " (cutoff:3.500A) Processing helix chain 'X' and resid 266 through 273 removed outlier: 3.882A pdb=" N GLY X 273 " --> pdb=" O ALA X 269 " (cutoff:3.500A) Processing helix chain 'X' and resid 274 through 280 removed outlier: 3.832A pdb=" N TYR X 279 " --> pdb=" O LEU X 275 " (cutoff:3.500A) Processing helix chain 'X' and resid 281 through 297 removed outlier: 3.643A pdb=" N GLU X 285 " --> pdb=" O GLY X 281 " (cutoff:3.500A) Processing helix chain 'X' and resid 298 through 310 removed outlier: 3.806A pdb=" N ARG X 310 " --> pdb=" O LEU X 306 " (cutoff:3.500A) Processing helix chain 'X' and resid 318 through 340 removed outlier: 3.670A pdb=" N HIS X 322 " --> pdb=" O ILE X 318 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLU X 340 " --> pdb=" O ILE X 336 " (cutoff:3.500A) Processing helix chain 'X' and resid 346 through 355 removed outlier: 3.536A pdb=" N ILE X 350 " --> pdb=" O GLN X 346 " (cutoff:3.500A) Processing helix chain 'X' and resid 357 through 372 removed outlier: 4.012A pdb=" N VAL X 361 " --> pdb=" O SER X 357 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LYS X 372 " --> pdb=" O MET X 368 " (cutoff:3.500A) Processing helix chain 'X' and resid 394 through 422 removed outlier: 3.844A pdb=" N GLU X 398 " --> pdb=" O ASP X 394 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR X 422 " --> pdb=" O ALA X 418 " (cutoff:3.500A) Processing helix chain 'Y' and resid 13 through 29 removed outlier: 4.804A pdb=" N LEU Y 17 " --> pdb=" O LYS Y 13 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ARG Y 18 " --> pdb=" O ASN Y 14 " (cutoff:3.500A) Proline residue: Y 29 - end of helix Processing helix chain 'Y' and resid 39 through 46 removed outlier: 4.343A pdb=" N ALA Y 43 " --> pdb=" O ASP Y 39 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL Y 45 " --> pdb=" O LEU Y 41 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG Y 46 " --> pdb=" O MET Y 42 " (cutoff:3.500A) Processing helix chain 'Y' and resid 50 through 61 removed outlier: 3.852A pdb=" N TYR Y 54 " --> pdb=" O MET Y 50 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLU Y 55 " --> pdb=" O ALA Y 51 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA Y 56 " --> pdb=" O PRO Y 52 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LEU Y 61 " --> pdb=" O LEU Y 57 " (cutoff:3.500A) Processing helix chain 'Y' and resid 66 through 93 removed outlier: 3.594A pdb=" N LEU Y 70 " --> pdb=" O ASP Y 66 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N LYS Y 93 " --> pdb=" O GLU Y 89 " (cutoff:3.500A) Processing helix chain 'Y' and resid 100 through 114 Processing helix chain 'Y' and resid 116 through 131 removed outlier: 3.767A pdb=" N ALA Y 120 " --> pdb=" O ASP Y 116 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASP Y 129 " --> pdb=" O ARG Y 125 " (cutoff:3.500A) Processing helix chain 'Y' and resid 133 through 152 Processing helix chain 'Y' and resid 153 through 169 removed outlier: 4.712A pdb=" N GLU Y 169 " --> pdb=" O LYS Y 165 " (cutoff:3.500A) Processing helix chain 'Y' and resid 172 through 191 removed outlier: 4.606A pdb=" N ARG Y 176 " --> pdb=" O GLY Y 172 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ARG Y 177 " --> pdb=" O ASP Y 173 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ASN Y 178 " --> pdb=" O TRP Y 174 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ARG Y 179 " --> pdb=" O ASP Y 175 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LEU Y 180 " --> pdb=" O ARG Y 176 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LYS Y 181 " --> pdb=" O ARG Y 177 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N VAL Y 182 " --> pdb=" O ASN Y 178 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU Y 186 " --> pdb=" O VAL Y 182 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TYR Y 187 " --> pdb=" O TYR Y 183 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ILE Y 191 " --> pdb=" O TYR Y 187 " (cutoff:3.500A) Processing helix chain 'Y' and resid 195 through 202 removed outlier: 3.950A pdb=" N LEU Y 202 " --> pdb=" O ALA Y 198 " (cutoff:3.500A) Processing helix chain 'Y' and resid 215 through 231 removed outlier: 4.288A pdb=" N MET Y 228 " --> pdb=" O VAL Y 224 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ILE Y 229 " --> pdb=" O TYR Y 225 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA Y 230 " --> pdb=" O VAL Y 226 " (cutoff:3.500A) Processing helix chain 'Y' and resid 235 through 240 Processing helix chain 'Y' and resid 243 through 254 Proline residue: Y 254 - end of helix Processing helix chain 'Y' and resid 255 through 266 removed outlier: 3.631A pdb=" N CYS Y 266 " --> pdb=" O SER Y 262 " (cutoff:3.500A) Processing helix chain 'Y' and resid 268 through 283 removed outlier: 3.786A pdb=" N GLN Y 273 " --> pdb=" O SER Y 269 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS Y 283 " --> pdb=" O GLU Y 279 " (cutoff:3.500A) Processing helix chain 'Y' and resid 287 through 310 removed outlier: 4.541A pdb=" N HIS Y 291 " --> pdb=" O LEU Y 287 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR Y 292 " --> pdb=" O PHE Y 288 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ARG Y 293 " --> pdb=" O ALA Y 289 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N TYR Y 294 " --> pdb=" O PRO Y 290 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ARG Y 297 " --> pdb=" O ARG Y 293 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU Y 309 " --> pdb=" O SER Y 305 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N SER Y 310 " --> pdb=" O GLN Y 306 " (cutoff:3.500A) Processing helix chain 'Y' and resid 315 through 322 removed outlier: 3.801A pdb=" N MET Y 319 " --> pdb=" O THR Y 315 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLU Y 321 " --> pdb=" O GLY Y 317 " (cutoff:3.500A) Processing helix chain 'Y' and resid 326 through 341 removed outlier: 3.758A pdb=" N GLY Y 341 " --> pdb=" O PHE Y 337 " (cutoff:3.500A) Processing helix chain 'Y' and resid 360 through 388 removed outlier: 4.232A pdb=" N ASN Y 388 " --> pdb=" O SER Y 384 " (cutoff:3.500A) Processing helix chain 'Z' and resid 12 through 27 removed outlier: 4.185A pdb=" N LEU Z 16 " --> pdb=" O HIS Z 12 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N LEU Z 17 " --> pdb=" O PRO Z 13 " (cutoff:3.500A) Processing helix chain 'Z' and resid 71 through 86 Processing helix chain 'Z' and resid 103 through 117 removed outlier: 4.713A pdb=" N ALA Z 107 " --> pdb=" O LYS Z 103 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ARG Z 114 " --> pdb=" O GLU Z 110 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N TYR Z 115 " --> pdb=" O LEU Z 111 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N CYS Z 116 " --> pdb=" O MET Z 112 " (cutoff:3.500A) Proline residue: Z 117 - end of helix Processing helix chain 'Z' and resid 165 through 177 removed outlier: 3.781A pdb=" N GLU Z 169 " --> pdb=" O GLU Z 165 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL Z 170 " --> pdb=" O GLU Z 166 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY Z 171 " --> pdb=" O ALA Z 167 " (cutoff:3.500A) Processing helix chain 'Z' and resid 186 through 218 removed outlier: 3.943A pdb=" N GLY Z 218 " --> pdb=" O LYS Z 214 " (cutoff:3.500A) Processing helix chain 'Z' and resid 226 through 238 removed outlier: 4.594A pdb=" N GLN Z 231 " --> pdb=" O ILE Z 227 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU Z 237 " --> pdb=" O VAL Z 233 " (cutoff:3.500A) Proline residue: Z 238 - end of helix Processing helix chain 'Z' and resid 242 through 290 removed outlier: 5.189A pdb=" N VAL Z 246 " --> pdb=" O LEU Z 242 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LYS Z 247 " --> pdb=" O GLN Z 243 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N PHE Z 249 " --> pdb=" O PHE Z 245 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N TYR Z 250 " --> pdb=" O VAL Z 246 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU Z 251 " --> pdb=" O LYS Z 247 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LYS Z 252 " --> pdb=" O ALA Z 248 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN Z 254 " --> pdb=" O TYR Z 250 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL Z 258 " --> pdb=" O ASN Z 254 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL Z 259 " --> pdb=" O ASP Z 255 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU Z 262 " --> pdb=" O VAL Z 258 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ALA Z 263 " --> pdb=" O VAL Z 259 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N SER Z 264 " --> pdb=" O VAL Z 260 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY Z 290 " --> pdb=" O GLU Z 286 " (cutoff:3.500A) Processing helix chain 'a' and resid 6 through 12 removed outlier: 5.078A pdb=" N GLN a 12 " --> pdb=" O LEU a 8 " (cutoff:3.500A) Processing helix chain 'a' and resid 19 through 32 removed outlier: 4.645A pdb=" N ARG a 24 " --> pdb=" O ALA a 20 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N GLU a 27 " --> pdb=" O HIS a 23 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LEU a 28 " --> pdb=" O ARG a 24 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N TYR a 29 " --> pdb=" O LEU a 25 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR a 30 " --> pdb=" O GLU a 26 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS a 31 " --> pdb=" O GLU a 27 " (cutoff:3.500A) Processing helix chain 'a' and resid 34 through 41 removed outlier: 4.530A pdb=" N THR a 38 " --> pdb=" O TRP a 34 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU a 39 " --> pdb=" O HIS a 35 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N VAL a 41 " --> pdb=" O LEU a 37 " (cutoff:3.500A) Processing helix chain 'a' and resid 51 through 68 removed outlier: 5.922A pdb=" N GLY a 55 " --> pdb=" O ALA a 51 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N LEU a 59 " --> pdb=" O GLY a 55 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N TYR a 60 " --> pdb=" O LEU a 56 " (cutoff:3.500A) Processing helix chain 'a' and resid 72 through 88 removed outlier: 4.512A pdb=" N LEU a 76 " --> pdb=" O ASN a 72 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N THR a 88 " --> pdb=" O VAL a 84 " (cutoff:3.500A) Processing helix chain 'a' and resid 90 through 105 removed outlier: 4.028A pdb=" N THR a 95 " --> pdb=" O ASN a 91 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYS a 105 " --> pdb=" O ARG a 101 " (cutoff:3.500A) Processing helix chain 'a' and resid 109 through 124 removed outlier: 4.289A pdb=" N LEU a 113 " --> pdb=" O GLU a 109 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU a 123 " --> pdb=" O GLY a 119 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ASN a 124 " --> pdb=" O ALA a 120 " (cutoff:3.500A) Processing helix chain 'a' and resid 130 through 143 removed outlier: 3.654A pdb=" N GLU a 139 " --> pdb=" O ILE a 135 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N MET a 141 " --> pdb=" O ASP a 137 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU a 142 " --> pdb=" O VAL a 138 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ASN a 143 " --> pdb=" O GLU a 139 " (cutoff:3.500A) Processing helix chain 'a' and resid 148 through 164 removed outlier: 6.248A pdb=" N HIS a 152 " --> pdb=" O VAL a 148 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER a 153 " --> pdb=" O THR a 149 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N TYR a 163 " --> pdb=" O SER a 159 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N GLN a 164 " --> pdb=" O SER a 160 " (cutoff:3.500A) Processing helix chain 'a' and resid 167 through 184 removed outlier: 4.066A pdb=" N SER a 171 " --> pdb=" O GLY a 167 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N TYR a 172 " --> pdb=" O ASN a 168 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ASP a 184 " --> pdb=" O LEU a 180 " (cutoff:3.500A) Processing helix chain 'a' and resid 189 through 207 removed outlier: 3.522A pdb=" N GLN a 193 " --> pdb=" O PRO a 189 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N GLU a 195 " --> pdb=" O SER a 191 " (cutoff:3.500A) Processing helix chain 'a' and resid 215 through 220 Proline residue: a 220 - end of helix Processing helix chain 'a' and resid 230 through 243 removed outlier: 4.382A pdb=" N ILE a 234 " --> pdb=" O ARG a 230 " (cutoff:3.500A) Processing helix chain 'a' and resid 246 through 258 removed outlier: 3.775A pdb=" N THR a 250 " --> pdb=" O GLU a 246 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ALA a 254 " --> pdb=" O THR a 250 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N TRP a 255 " --> pdb=" O LEU a 251 " (cutoff:3.500A) Processing helix chain 'a' and resid 260 through 285 removed outlier: 4.751A pdb=" N ASN a 264 " --> pdb=" O ASP a 260 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ALA a 266 " --> pdb=" O ALA a 262 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLN a 267 " --> pdb=" O ALA a 263 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS a 276 " --> pdb=" O ILE a 272 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU a 277 " --> pdb=" O GLN a 273 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N MET a 278 " --> pdb=" O LEU a 274 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N GLU a 279 " --> pdb=" O LEU a 275 " (cutoff:3.500A) removed outlier: 4.309A 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: 3.845A pdb=" N ILE a 296 " --> pdb=" O THR a 292 " (cutoff:3.500A) Processing helix chain 'a' and resid 303 through 318 removed outlier: 3.946A pdb=" N VAL a 307 " --> pdb=" O THR a 303 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLU a 308 " --> pdb=" O VAL a 304 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N LEU a 309 " --> pdb=" O ASN a 305 " (cutoff:3.500A) Processing helix chain 'a' and resid 344 through 376 removed outlier: 4.592A pdb=" N GLY a 348 " --> pdb=" O GLN a 344 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASP a 359 " --> pdb=" O PHE a 355 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ASP a 373 " --> pdb=" O HIS a 369 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ILE a 374 " --> pdb=" O GLN a 370 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR a 376 " --> pdb=" O HIS a 372 " (cutoff:3.500A) Processing helix chain 'a' and resid 221 through 227 removed outlier: 4.133A pdb=" N ARG a 226 " --> pdb=" O VAL a 221 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASN a 227 " --> pdb=" O LEU a 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 221 through 227' Processing helix chain 'b' and resid 24 through 45 removed outlier: 3.691A pdb=" N ASN b 44 " --> pdb=" O LYS b 40 " (cutoff:3.500A) Proline residue: b 45 - end of helix Processing helix chain 'b' and resid 67 through 76 removed outlier: 4.373A pdb=" N ILE b 71 " --> pdb=" O ASP b 67 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU b 75 " --> pdb=" O ILE b 71 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N HIS b 76 " --> pdb=" O LEU b 72 " (cutoff:3.500A) Processing helix chain 'b' and resid 85 through 100 removed outlier: 3.935A pdb=" N GLY b 89 " --> pdb=" O THR b 85 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ILE b 90 " --> pdb=" O PHE b 86 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ARG b 91 " --> pdb=" O CYS b 87 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N HIS b 99 " --> pdb=" O LEU b 95 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ARG b 100 " --> pdb=" O ALA b 96 " (cutoff:3.500A) Processing helix chain 'b' and resid 120 through 135 removed outlier: 3.730A pdb=" N LEU b 124 " --> pdb=" O ASN b 120 " (cutoff:3.500A) Processing helix chain 'b' and resid 150 through 162 removed outlier: 4.055A pdb=" N GLY b 162 " --> pdb=" O ASN b 158 " (cutoff:3.500A) Processing helix chain 'b' and resid 179 through 190 removed outlier: 3.552A pdb=" N LEU b 183 " --> pdb=" O LEU b 179 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER b 185 " --> pdb=" O ASP b 181 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N SER b 186 " --> pdb=" O ALA b 182 " (cutoff:3.500A) Proline residue: b 187 - end of helix removed outlier: 3.636A pdb=" N ALA b 190 " --> pdb=" O SER b 186 " (cutoff:3.500A) Processing helix chain 'b' and resid 13 through 19 removed outlier: 4.032A pdb=" N MET b 16 " --> pdb=" O SER b 13 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG b 17 " --> pdb=" O GLU b 14 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN b 18 " --> pdb=" O TYR b 15 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N GLY b 19 " --> pdb=" O MET b 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 13 through 19' Processing helix chain 'c' and resid 34 through 49 removed outlier: 3.921A pdb=" N GLY c 48 " --> pdb=" O HIS c 44 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL c 49 " --> pdb=" O GLY c 45 " (cutoff:3.500A) Processing helix chain 'c' and resid 83 through 103 removed outlier: 3.856A pdb=" N VAL c 87 " --> pdb=" O SER c 83 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ASP c 88 " --> pdb=" O VAL c 84 " (cutoff:3.500A) Proline residue: c 89 - end of helix removed outlier: 4.422A pdb=" N GLN c 101 " --> pdb=" O ASP c 97 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR c 102 " --> pdb=" O MET c 98 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLY c 103 " --> pdb=" O LEU c 99 " (cutoff:3.500A) Processing helix chain 'c' and resid 123 through 137 removed outlier: 3.603A pdb=" N SER c 132 " --> pdb=" O ASN c 128 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE c 133 " --> pdb=" O THR c 129 " (cutoff:3.500A) Processing helix chain 'c' and resid 146 through 151 removed outlier: 3.908A pdb=" N SER c 150 " --> pdb=" O ASP c 146 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N VAL c 151 " --> pdb=" O PRO c 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 146 through 151' Processing helix chain 'c' and resid 165 through 171 removed outlier: 5.000A pdb=" N VAL c 169 " --> pdb=" O ALA c 165 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N LEU c 170 " --> pdb=" O ASN c 166 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N GLY c 171 " --> pdb=" O MET c 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 165 through 171' Processing helix chain 'c' and resid 179 through 185 removed outlier: 4.544A pdb=" N HIS c 183 " --> pdb=" O SER c 179 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N LEU c 184 " --> pdb=" O ASN c 180 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ASN c 185 " --> pdb=" O LEU c 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 179 through 185' Processing helix chain 'c' and resid 188 through 195 removed outlier: 3.519A pdb=" N HIS c 194 " --> pdb=" O GLN c 190 " (cutoff:3.500A) Processing helix chain 'c' and resid 211 through 223 removed outlier: 6.132A pdb=" N LYS c 215 " --> pdb=" O GLU c 211 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N MET c 216 " --> pdb=" O LEU c 212 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS c 222 " --> pdb=" O LEU c 218 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N LYS c 223 " --> pdb=" O ASN c 219 " (cutoff:3.500A) Processing helix chain 'c' and resid 224 through 230 removed outlier: 5.180A pdb=" N GLY c 228 " --> pdb=" O SER c 224 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N LEU c 229 " --> pdb=" O TRP c 225 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR c 230 " --> pdb=" O MET c 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 224 through 230' Processing helix chain 'c' and resid 236 through 260 removed outlier: 4.134A pdb=" N GLU c 250 " --> pdb=" O LYS c 246 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU c 251 " --> pdb=" O GLU c 247 " (cutoff:3.500A) Processing helix chain 'c' and resid 266 through 275 removed outlier: 3.829A pdb=" N LEU c 270 " --> pdb=" O THR c 266 " (cutoff:3.500A) Processing helix chain 'c' and resid 285 through 309 removed outlier: 3.976A pdb=" N VAL c 307 " --> pdb=" O MET c 303 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N PHE c 309 " --> pdb=" O ASP c 305 " (cutoff:3.500A) Processing helix chain 'd' and resid 15 through 32 removed outlier: 3.951A pdb=" N CYS d 19 " --> pdb=" O ASN d 15 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU d 31 " --> pdb=" O LYS d 27 " (cutoff:3.500A) Processing helix chain 'd' and resid 43 through 66 removed outlier: 3.847A pdb=" N GLN d 47 " --> pdb=" O LEU d 43 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU d 48 " --> pdb=" O THR d 44 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ILE d 49 " --> pdb=" O LYS d 45 " (cutoff:3.500A) Processing helix chain 'd' and resid 67 through 84 removed outlier: 3.859A pdb=" N ARG d 73 " --> pdb=" O PRO d 69 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP d 84 " --> pdb=" O CYS d 80 " (cutoff:3.500A) Processing helix chain 'd' and resid 95 through 110 removed outlier: 4.382A pdb=" N LEU d 99 " --> pdb=" O MET d 95 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN d 110 " --> pdb=" O LEU d 106 " (cutoff:3.500A) Processing helix chain 'd' and resid 111 through 123 removed outlier: 3.691A pdb=" N LEU d 119 " --> pdb=" O PHE d 115 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU d 120 " --> pdb=" O HIS d 116 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ARG d 121 " --> pdb=" O THR d 117 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU d 122 " --> pdb=" O GLU d 118 " (cutoff:3.500A) Proline residue: d 123 - end of helix Processing helix chain 'd' and resid 124 through 129 removed outlier: 4.285A pdb=" N GLN d 128 " --> pdb=" O ALA d 124 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N THR d 129 " --> pdb=" O LYS d 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 124 through 129' Processing helix chain 'd' and resid 130 through 146 Proline residue: d 136 - end of helix removed outlier: 4.536A pdb=" N GLU d 145 " --> pdb=" O GLN d 141 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLY d 146 " --> pdb=" O TYR d 142 " (cutoff:3.500A) Processing helix chain 'd' and resid 147 through 158 removed outlier: 4.193A pdb=" N VAL d 151 " --> pdb=" O SER d 147 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLY d 156 " --> pdb=" O PHE d 152 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASN d 157 " --> pdb=" O LEU d 153 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ILE d 158 " --> pdb=" O ALA d 154 " (cutoff:3.500A) Processing helix chain 'd' and resid 163 through 185 removed outlier: 4.504A pdb=" N ILE d 169 " --> pdb=" O PHE d 165 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU d 177 " --> pdb=" O THR d 173 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS d 184 " --> pdb=" O GLY d 180 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ALA d 185 " --> pdb=" O CYS d 181 " (cutoff:3.500A) Processing helix chain 'd' and resid 190 through 199 removed outlier: 4.148A pdb=" N ALA d 194 " --> pdb=" O LEU d 190 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N THR d 195 " --> pdb=" O PHE d 191 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N LEU d 198 " --> pdb=" O ALA d 194 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N PHE d 199 " --> pdb=" O THR d 195 " (cutoff:3.500A) Processing helix chain 'd' and resid 203 through 213 removed outlier: 3.934A pdb=" N THR d 207 " --> pdb=" O PRO d 203 " (cutoff:3.500A) Processing helix chain 'd' and resid 236 through 256 removed outlier: 3.812A pdb=" N GLU d 241 " --> pdb=" O ILE d 237 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N MET d 255 " --> pdb=" O ARG d 251 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ILE d 256 " --> pdb=" O GLN d 252 " (cutoff:3.500A) Processing helix chain 'f' and resid 10 through 20 removed outlier: 5.138A pdb=" N GLN f 14 " --> pdb=" O PRO f 10 " (cutoff:3.500A) Proline residue: f 17 - end of helix Processing helix chain 'f' and resid 27 through 48 removed outlier: 3.975A pdb=" N ARG f 34 " --> pdb=" O GLY f 30 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ASP f 35 " --> pdb=" O LYS f 31 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLU f 48 " --> pdb=" O GLU f 44 " (cutoff:3.500A) Processing helix chain 'f' and resid 54 through 60 removed outlier: 3.709A pdb=" N MET f 58 " --> pdb=" O ASP f 54 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL f 60 " --> pdb=" O LEU f 56 " (cutoff:3.500A) Processing helix chain 'f' and resid 61 through 75 removed outlier: 3.802A 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 98 removed outlier: 4.527A pdb=" N SER f 85 " --> pdb=" O GLN f 81 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL f 92 " --> pdb=" O SER f 88 " (cutoff:3.500A) Proline residue: f 93 - end of helix removed outlier: 4.418A pdb=" N LEU f 96 " --> pdb=" O VAL f 92 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS f 97 " --> pdb=" O PRO f 93 " (cutoff:3.500A) Processing helix chain 'f' and resid 99 through 105 Processing helix chain 'f' and resid 106 through 111 Processing helix chain 'f' and resid 115 through 120 removed outlier: 6.324A pdb=" N LYS f 119 " --> pdb=" O PRO f 115 " (cutoff:3.500A) Processing helix chain 'f' and resid 129 through 148 Processing helix chain 'f' and resid 153 through 169 Processing helix chain 'f' and resid 193 through 209 removed outlier: 3.596A pdb=" N ALA f 197 " --> pdb=" O PRO f 193 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET f 209 " --> pdb=" O CYS f 205 " (cutoff:3.500A) Processing helix chain 'f' and resid 210 through 227 removed outlier: 5.460A pdb=" N VAL f 214 " --> pdb=" O GLU f 210 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ASP f 215 " --> pdb=" O ILE f 211 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N MET f 216 " --> pdb=" O GLU f 212 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N TYR f 226 " --> pdb=" O ASP f 222 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA f 227 " --> pdb=" O GLU f 223 " (cutoff:3.500A) Processing helix chain 'f' and resid 231 through 246 removed outlier: 4.923A pdb=" N SER f 235 " --> pdb=" O LEU f 231 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASN f 238 " --> pdb=" O THR f 234 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N TYR f 239 " --> pdb=" O SER f 235 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL f 240 " --> pdb=" O CYS f 236 " (cutoff:3.500A) Proline residue: f 241 - end of helix removed outlier: 4.975A pdb=" N GLU f 244 " --> pdb=" O VAL f 240 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASN f 245 " --> pdb=" O PRO f 241 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N SER f 246 " --> pdb=" O GLU f 242 " (cutoff:3.500A) Processing helix chain 'f' and resid 253 through 264 removed outlier: 4.194A pdb=" N ARG f 261 " --> pdb=" O ARG f 257 " (cutoff:3.500A) removed outlier: 5.118A 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 266 through 275 removed outlier: 4.270A pdb=" N LEU f 270 " --> pdb=" O LEU f 266 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N MET f 271 " --> pdb=" O ARG f 267 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N MET f 275 " --> pdb=" O MET f 271 " (cutoff:3.500A) Processing helix chain 'f' and resid 279 through 285 removed outlier: 3.705A pdb=" N CYS f 285 " --> pdb=" O ILE f 281 " (cutoff:3.500A) Processing helix chain 'f' and resid 287 through 293 Processing helix chain 'f' and resid 313 through 318 removed outlier: 4.386A pdb=" N LEU f 317 " --> pdb=" O GLU f 313 " (cutoff:3.500A) Processing helix chain 'f' and resid 325 through 336 Processing helix chain 'f' and resid 347 through 354 removed outlier: 3.535A pdb=" N LEU f 353 " --> pdb=" O TYR f 349 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N GLU f 354 " --> pdb=" O LYS f 350 " (cutoff:3.500A) Processing helix chain 'f' and resid 355 through 360 removed outlier: 4.995A pdb=" N GLY f 359 " --> pdb=" O ASN f 355 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLY f 360 " --> pdb=" O ASN f 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 355 through 360' Processing helix chain 'f' and resid 367 through 383 Processing helix chain 'f' and resid 395 through 402 removed outlier: 4.444A pdb=" N ASN f 402 " --> pdb=" O TRP f 398 " (cutoff:3.500A) Processing helix chain 'f' and resid 405 through 419 removed outlier: 3.757A pdb=" N SER f 409 " --> pdb=" O HIS f 405 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU f 418 " --> pdb=" O LEU f 414 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU f 419 " --> pdb=" O GLY f 415 " (cutoff:3.500A) Processing helix chain 'f' and resid 422 through 433 removed outlier: 5.618A pdb=" N LEU f 426 " --> pdb=" O VAL f 422 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N THR f 427 " --> pdb=" O ASP f 423 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N GLN f 428 " --> pdb=" O GLY f 424 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE f 429 " --> pdb=" O GLY f 425 " (cutoff:3.500A) Processing helix chain 'f' and resid 437 through 456 removed outlier: 3.653A pdb=" N SER f 453 " --> pdb=" O GLY f 449 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLY f 454 " --> pdb=" O ILE f 450 " (cutoff:3.500A) Processing helix chain 'f' and resid 460 through 473 removed outlier: 4.566A pdb=" N ALA f 464 " --> pdb=" O ASP f 460 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LEU f 465 " --> pdb=" O PRO f 461 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N LEU f 471 " --> pdb=" O SER f 467 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N HIS f 472 " --> pdb=" O ASP f 468 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ASN f 473 " --> pdb=" O TYR f 469 " (cutoff:3.500A) Processing helix chain 'f' and resid 474 through 490 removed outlier: 3.611A pdb=" N GLY f 484 " --> pdb=" O GLY f 480 " (cutoff:3.500A) Processing helix chain 'f' and resid 494 through 507 removed outlier: 4.105A pdb=" N LEU f 498 " --> pdb=" O ARG f 494 " (cutoff:3.500A) Proline residue: f 503 - end of helix Processing helix chain 'f' and resid 511 through 527 removed outlier: 3.708A pdb=" N ALA f 526 " --> pdb=" O CYS f 522 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N VAL f 527 " --> pdb=" O GLY f 523 " (cutoff:3.500A) Processing helix chain 'f' and resid 530 through 544 removed outlier: 4.073A pdb=" N VAL f 534 " --> pdb=" O CYS f 530 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR f 535 " --> pdb=" O ASN f 531 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER f 536 " --> pdb=" O GLY f 532 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU f 544 " --> pdb=" O GLN f 540 " (cutoff:3.500A) Processing helix chain 'f' and resid 545 through 551 removed outlier: 4.098A pdb=" N GLU f 549 " --> pdb=" O LYS f 545 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU f 550 " --> pdb=" O SER f 546 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS f 551 " --> pdb=" O GLU f 547 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 545 through 551' Processing helix chain 'f' and resid 555 through 567 Proline residue: f 559 - end of helix removed outlier: 3.991A pdb=" N LEU f 562 " --> pdb=" O LEU f 558 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASN f 565 " --> pdb=" O GLY f 561 " (cutoff:3.500A) Processing helix chain 'f' and resid 572 through 582 removed outlier: 5.531A pdb=" N ILE f 576 " --> pdb=" O ALA f 572 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU f 577 " --> pdb=" O ILE f 573 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL f 582 " --> pdb=" O ALA f 578 " (cutoff:3.500A) Processing helix chain 'f' and resid 588 through 599 removed outlier: 3.878A pdb=" N THR f 593 " --> pdb=" O SER f 589 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA f 599 " --> pdb=" O VAL f 595 " (cutoff:3.500A) Processing helix chain 'f' and resid 605 through 615 removed outlier: 3.744A pdb=" N VAL f 609 " --> pdb=" O ASN f 605 " (cutoff:3.500A) Processing helix chain 'f' and resid 618 through 623 removed outlier: 4.665A pdb=" N SER f 622 " --> pdb=" O GLU f 618 " (cutoff:3.500A) Processing helix chain 'f' and resid 645 through 658 removed outlier: 6.386A pdb=" N HIS f 649 " --> pdb=" O ASP f 645 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLN f 650 " --> pdb=" O MET f 646 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ILE f 657 " --> pdb=" O ALA f 653 " (cutoff:3.500A) Processing helix chain 'f' and resid 671 through 680 removed outlier: 5.240A pdb=" N PHE f 675 " --> pdb=" O ALA f 671 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY f 676 " --> pdb=" O LEU f 672 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N LEU f 679 " --> pdb=" O PHE f 675 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ARG f 680 " --> pdb=" O GLY f 676 " (cutoff:3.500A) Processing helix chain 'f' and resid 687 through 698 Proline residue: f 691 - end of helix removed outlier: 3.749A pdb=" N LEU f 694 " --> pdb=" O VAL f 690 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N LEU f 696 " --> pdb=" O LEU f 692 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ILE f 697 " --> pdb=" O ALA f 693 " (cutoff:3.500A) Processing helix chain 'f' and resid 701 through 715 removed outlier: 3.870A pdb=" N ASN f 705 " --> pdb=" O ASN f 701 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE f 713 " --> pdb=" O THR f 709 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER f 714 " --> pdb=" O LEU f 710 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N HIS f 715 " --> pdb=" O SER f 711 " (cutoff:3.500A) Processing helix chain 'f' and resid 721 through 732 removed outlier: 3.541A pdb=" N SER f 725 " --> pdb=" O VAL f 721 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ILE f 726 " --> pdb=" O SER f 722 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE f 727 " --> pdb=" O TYR f 723 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA f 728 " --> pdb=" O ASN f 724 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N MET f 729 " --> pdb=" O SER f 725 " (cutoff:3.500A) Processing helix chain 'f' and resid 739 through 753 removed outlier: 3.550A pdb=" N MET f 744 " --> pdb=" O ARG f 740 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LEU f 745 " --> pdb=" O LEU f 741 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ARG f 746 " --> pdb=" O ALA f 742 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN f 750 " --> pdb=" O ARG f 746 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N TYR f 751 " --> pdb=" O GLN f 747 " (cutoff:3.500A) Processing helix chain 'f' and resid 773 through 787 removed outlier: 4.516A pdb=" N THR f 777 " --> pdb=" O LYS f 773 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU f 778 " --> pdb=" O GLY f 774 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N CYS f 779 " --> pdb=" O THR f 775 " (cutoff:3.500A) Proline residue: f 780 - end of helix removed outlier: 5.157A pdb=" N ASP f 784 " --> pdb=" O PRO f 780 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ARG f 785 " --> pdb=" O TYR f 781 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLN f 786 " --> pdb=" O HIS f 782 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LEU f 787 " --> pdb=" O SER f 783 " (cutoff:3.500A) Processing helix chain 'f' and resid 798 through 803 removed outlier: 4.598A pdb=" N SER f 802 " --> pdb=" O THR f 798 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N PHE f 803 " --> pdb=" O VAL f 799 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 798 through 803' Processing helix chain 'f' and resid 176 through 181 Processing helix chain 'f' and resid 294 through 299 removed outlier: 4.643A pdb=" N MET f 297 " --> pdb=" O MET f 294 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LEU f 298 " --> pdb=" O ALA f 295 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY f 299 " --> pdb=" O PHE f 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 294 through 299' Processing helix chain 'f' and resid 629 through 634 removed outlier: 3.738A pdb=" N LYS f 632 " --> pdb=" O LYS f 629 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU f 633 " --> pdb=" O ASP f 630 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS f 634 " --> pdb=" O LYS f 631 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 629 through 634' Processing helix chain 'f' and resid 170 through 175 Processing helix chain 'V' and resid 54 through 89 Processing helix chain 'V' and resid 91 through 108 Proline residue: V 102 - end of helix removed outlier: 4.156A pdb=" N ARG V 106 " --> pdb=" O PRO V 102 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ARG V 107 " --> pdb=" O SER V 103 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LEU V 108 " --> pdb=" O THR V 104 " (cutoff:3.500A) Processing helix chain 'V' and resid 109 through 121 Processing helix chain 'V' and resid 125 through 135 removed outlier: 4.021A pdb=" N ASP V 129 " --> pdb=" O ASN V 125 " (cutoff:3.500A) Proline residue: V 133 - end of helix Processing helix chain 'V' and resid 152 through 158 Proline residue: V 158 - end of helix Processing helix chain 'V' and resid 160 through 179 Processing helix chain 'V' and resid 180 through 199 removed outlier: 3.842A pdb=" N GLN V 198 " --> pdb=" O LYS V 194 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ASN V 199 " --> pdb=" O ILE V 195 " (cutoff:3.500A) Processing helix chain 'V' and resid 202 through 222 removed outlier: 4.507A pdb=" N VAL V 206 " --> pdb=" O ALA V 202 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS V 209 " --> pdb=" O LEU V 205 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE V 220 " --> pdb=" O ARG V 216 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU V 221 " --> pdb=" O VAL V 217 " (cutoff:3.500A) Processing helix chain 'V' and resid 225 through 242 removed outlier: 4.401A pdb=" N SER V 229 " --> pdb=" O ASP V 225 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N PHE V 230 " --> pdb=" O VAL V 226 " (cutoff:3.500A) Processing helix chain 'V' and resid 243 through 262 removed outlier: 3.511A pdb=" N GLN V 247 " --> pdb=" O ASP V 243 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR V 261 " --> pdb=" O ASN V 257 " (cutoff:3.500A) Processing helix chain 'V' and resid 263 through 274 removed outlier: 3.738A pdb=" N ALA V 267 " --> pdb=" O LEU V 263 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS V 273 " --> pdb=" O LYS V 269 " (cutoff:3.500A) Processing helix chain 'V' and resid 281 through 300 removed outlier: 3.835A pdb=" N LEU V 300 " --> pdb=" O LYS V 296 " (cutoff:3.500A) Processing helix chain 'V' and resid 301 through 316 removed outlier: 3.684A pdb=" N ALA V 305 " --> pdb=" O GLU V 301 " (cutoff:3.500A) Processing helix chain 'V' and resid 321 through 340 Processing helix chain 'V' and resid 344 through 350 removed outlier: 4.523A pdb=" N PHE V 348 " --> pdb=" O ASP V 344 " (cutoff:3.500A) Processing helix chain 'V' and resid 353 through 370 Proline residue: V 359 - end of helix removed outlier: 3.546A pdb=" N GLY V 370 " --> pdb=" O ALA V 366 " (cutoff:3.500A) Processing helix chain 'V' and resid 371 through 383 Processing helix chain 'V' and resid 384 through 390 Processing helix chain 'V' and resid 391 through 415 removed outlier: 3.518A pdb=" N ILE V 395 " --> pdb=" O THR V 391 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N HIS V 400 " --> pdb=" O ILE V 396 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ILE V 403 " --> pdb=" O ARG V 399 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N LYS V 404 " --> pdb=" O HIS V 400 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR V 405 " --> pdb=" O ASN V 401 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N SER V 415 " --> pdb=" O SER V 411 " (cutoff:3.500A) Processing helix chain 'V' and resid 418 through 427 removed outlier: 3.814A pdb=" N ILE V 422 " --> pdb=" O SER V 418 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ALA V 423 " --> pdb=" O LEU V 419 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN V 424 " --> pdb=" O ALA V 420 " (cutoff:3.500A) Processing helix chain 'V' and resid 430 through 445 removed outlier: 3.658A pdb=" N ALA V 434 " --> pdb=" O SER V 430 " (cutoff:3.500A) Processing helix chain 'V' and resid 465 through 494 removed outlier: 4.900A pdb=" N THR V 469 " --> pdb=" O ASP V 465 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ARG V 470 " --> pdb=" O ILE V 466 " (cutoff:3.500A) Proline residue: V 472 - end of helix removed outlier: 5.402A pdb=" N GLN V 478 " --> pdb=" O LEU V 474 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ARG V 479 " --> pdb=" O ALA V 475 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ILE V 480 " --> pdb=" O PHE V 476 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N SER V 481 " --> pdb=" O HIS V 477 " (cutoff:3.500A) Processing helix chain 'e' and resid 42 through 47 removed outlier: 4.286A pdb=" N ASP e 46 " --> pdb=" O ASN e 42 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ASN e 47 " --> pdb=" O TRP e 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 42 through 47' Processing helix chain 'e' and resid 51 through 64 removed outlier: 4.911A pdb=" N GLN e 55 " --> pdb=" O ASP e 51 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'E' and resid 55 through 58 removed outlier: 4.118A pdb=" N ARG E 97 " --> pdb=" O LEU E 111 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG E 109 " --> pdb=" O ALA E 99 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'E' and resid 69 through 72 Processing sheet with id= 3, first strand: chain 'E' and resid 194 through 198 removed outlier: 3.638A pdb=" N LYS E 274 " --> pdb=" O CYS E 228 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA E 278 " --> pdb=" O MET E 232 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N MET E 275 " --> pdb=" O LYS E 168 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY E 174 " --> pdb=" O THR E 279 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR E 173 " --> pdb=" O ILE E 299 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'F' and resid 95 through 98 removed outlier: 3.545A pdb=" N GLU F 95 " --> pdb=" O VAL F 123 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL F 123 " --> pdb=" O ILE F 94 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL F 93 " --> pdb=" O ASP F 149 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ASP F 149 " --> pdb=" O VAL F 93 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'F' and resid 246 through 252 removed outlier: 4.006A pdb=" N LYS F 327 " --> pdb=" O SER F 281 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY F 227 " --> pdb=" O THR F 332 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'F' and resid 121 through 126 removed outlier: 3.611A pdb=" N ALA F 122 " --> pdb=" O LEU F 134 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN F 130 " --> pdb=" O THR F 126 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'G' and resid 68 through 72 removed outlier: 6.432A pdb=" N HIS G 68 " --> pdb=" O MET G 80 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE G 76 " --> pdb=" O ILE G 72 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY G 77 " --> pdb=" O ILE G 141 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N MET G 138 " --> pdb=" O CYS G 154 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'G' and resid 164 through 169 removed outlier: 6.897A pdb=" N LYS G 164 " --> pdb=" O ARG G 43 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N THR G 38 " --> pdb=" O GLN G 53 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN G 53 " --> pdb=" O THR G 38 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N GLU G 214 " --> pdb=" O LYS G 54 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N VAL G 217 " --> pdb=" O LEU G 230 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'H' and resid 65 through 68 removed outlier: 6.512A pdb=" N ILE H 72 " --> pdb=" O ILE H 68 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N HIS H 71 " --> pdb=" O TRP H 139 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP H 139 " --> pdb=" O HIS H 71 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY H 138 " --> pdb=" O TYR H 145 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N LEU H 146 " --> pdb=" O TRP H 158 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'H' and resid 160 through 164 removed outlier: 5.393A pdb=" N VAL H 210 " --> pdb=" O LEU H 221 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'h' and resid 65 through 68 removed outlier: 6.549A pdb=" N ILE h 72 " --> pdb=" O ILE h 68 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER h 133 " --> pdb=" O SER h 77 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LEU h 146 " --> pdb=" O TRP h 158 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'h' and resid 160 through 164 removed outlier: 3.523A pdb=" N GLU h 49 " --> pdb=" O PRO h 34 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ASN h 207 " --> pdb=" O LYS h 50 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N VAL h 210 " --> pdb=" O LEU h 221 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'I' and resid 65 through 68 removed outlier: 6.613A pdb=" N MET I 72 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU I 134 " --> pdb=" O SER I 150 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY I 138 " --> pdb=" O GLN I 146 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU I 147 " --> pdb=" O TRP I 159 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASN I 155 " --> pdb=" O ASP I 151 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'I' and resid 161 through 165 removed outlier: 5.367A pdb=" N THR I 33 " --> pdb=" O GLU I 48 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N ILE I 213 " --> pdb=" O LEU I 228 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'J' and resid 62 through 65 removed outlier: 6.473A pdb=" N VAL J 69 " --> pdb=" O LEU J 65 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER J 130 " --> pdb=" O ALA J 74 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU J 144 " --> pdb=" O TRP J 156 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'J' and resid 158 through 162 removed outlier: 4.797A pdb=" N THR J 31 " --> pdb=" O GLU J 46 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N ASN J 205 " --> pdb=" O LYS J 47 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'j' and resid 62 through 65 removed outlier: 6.243A pdb=" N VAL j 69 " --> pdb=" O LEU j 65 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ASN j 68 " --> pdb=" O PHE j 136 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE j 136 " --> pdb=" O ASN j 68 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER j 130 " --> pdb=" O ALA j 74 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N LEU j 144 " --> pdb=" O TRP j 156 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'j' and resid 158 through 162 removed outlier: 4.776A pdb=" N THR j 31 " --> pdb=" O GLU j 46 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ASN j 205 " --> pdb=" O LYS j 47 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'K' and resid 66 through 70 removed outlier: 6.680A pdb=" N LYS K 66 " --> pdb=" O MET K 78 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE K 74 " --> pdb=" O ILE K 70 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'K' and resid 167 through 171 removed outlier: 5.992A pdb=" N THR K 36 " --> pdb=" O GLU K 51 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N LEU K 217 " --> pdb=" O PHE K 229 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'L' and resid 63 through 66 removed outlier: 6.733A pdb=" N ILE L 70 " --> pdb=" O VAL L 66 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N HIS L 69 " --> pdb=" O TYR L 137 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ILE L 144 " --> pdb=" O CYS L 156 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASN L 152 " --> pdb=" O CYS L 148 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'L' and resid 158 through 162 removed outlier: 3.703A pdb=" N ILE L 212 " --> pdb=" O TYR L 224 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLY L 216 " --> pdb=" O GLU L 220 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N GLU L 220 " --> pdb=" O GLY L 216 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'M' and resid 65 through 69 removed outlier: 6.842A pdb=" N ARG M 65 " --> pdb=" O VAL M 77 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL M 73 " --> pdb=" O VAL M 69 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY M 138 " --> pdb=" O GLY M 74 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LEU M 148 " --> pdb=" O TYR M 160 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL M 156 " --> pdb=" O ASP M 152 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'M' and resid 162 through 166 removed outlier: 4.710A pdb=" N THR M 35 " --> pdb=" O GLU M 50 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'N' and resid 34 through 37 removed outlier: 6.477A pdb=" N ILE N 41 " --> pdb=" O ILE N 37 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ARG N 40 " --> pdb=" O TRP N 103 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'N' and resid 125 through 129 removed outlier: 6.489A pdb=" N THR N 2 " --> pdb=" O ASP N 17 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER N 18 " --> pdb=" O VAL N 173 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N VAL N 173 " --> pdb=" O SER N 18 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'O' and resid 34 through 37 removed outlier: 6.499A pdb=" N ILE O 41 " --> pdb=" O ILE O 37 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ASN O 40 " --> pdb=" O VAL O 103 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER O 118 " --> pdb=" O TYR O 114 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'O' and resid 124 through 128 removed outlier: 6.146A pdb=" N THR O 2 " --> pdb=" O ASP O 17 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N THR O 18 " --> pdb=" O ASN O 172 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ASN O 172 " --> pdb=" O THR O 18 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LYS O 182 " --> pdb=" O SER O 179 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'o' and resid 34 through 37 removed outlier: 6.508A pdb=" N ILE o 41 " --> pdb=" O ILE o 37 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ASN o 40 " --> pdb=" O VAL o 103 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER o 118 " --> pdb=" O TYR o 114 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'o' and resid 124 through 128 removed outlier: 6.511A pdb=" N THR o 2 " --> pdb=" O ASP o 17 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR o 18 " --> pdb=" O ASN o 172 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ASN o 172 " --> pdb=" O THR o 18 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS o 182 " --> pdb=" O SER o 179 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'P' and resid 42 through 45 removed outlier: 6.147A pdb=" N LEU P 49 " --> pdb=" O MET P 45 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ARG P 48 " --> pdb=" O LEU P 112 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA P 54 " --> pdb=" O GLU P 106 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'P' and resid 136 through 140 removed outlier: 6.193A pdb=" N ALA P 10 " --> pdb=" O ASP P 25 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLY P 184 " --> pdb=" O ARG P 26 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL P 185 " --> pdb=" O LEU P 200 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LYS P 194 " --> pdb=" O GLU P 191 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'p' and resid 42 through 45 removed outlier: 5.056A pdb=" N LEU p 49 " --> pdb=" O MET p 45 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ARG p 48 " --> pdb=" O LEU p 112 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ALA p 54 " --> pdb=" O GLU p 106 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'p' and resid 136 through 140 removed outlier: 5.927A pdb=" N ALA p 10 " --> pdb=" O ASP p 25 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N GLY p 184 " --> pdb=" O ARG p 26 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N VAL p 185 " --> pdb=" O LEU p 200 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS p 194 " --> pdb=" O GLU p 191 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'Q' and resid 41 through 48 removed outlier: 6.016A pdb=" N LYS Q 41 " --> pdb=" O TYR Q 107 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LEU Q 115 " --> pdb=" O ALA Q 127 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'Q' and resid 129 through 133 removed outlier: 6.485A pdb=" N TYR Q 3 " --> pdb=" O ASP Q 18 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP Q 18 " --> pdb=" O TYR Q 3 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'q' and resid 41 through 48 removed outlier: 5.868A pdb=" N LYS q 41 " --> pdb=" O TYR q 107 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N LEU q 115 " --> pdb=" O ALA q 127 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'q' and resid 129 through 133 removed outlier: 6.552A pdb=" N TYR q 3 " --> pdb=" O ASP q 18 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP q 18 " --> pdb=" O TYR q 3 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'R' and resid 34 through 37 removed outlier: 3.796A pdb=" N ILE R 37 " --> pdb=" O LEU R 41 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU R 41 " --> pdb=" O ILE R 37 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR R 44 " --> pdb=" O MET R 100 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N MET R 100 " --> pdb=" O THR R 44 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ASN R 119 " --> pdb=" O ASP R 115 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'R' and resid 125 through 129 removed outlier: 6.379A pdb=" N THR R 2 " --> pdb=" O ASP R 17 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER R 18 " --> pdb=" O ALA R 173 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ALA R 173 " --> pdb=" O SER R 18 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N VAL R 174 " --> pdb=" O SER R 189 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N SER R 189 " --> pdb=" O VAL R 174 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LEU R 176 " --> pdb=" O VAL R 187 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'r' and resid 34 through 37 removed outlier: 3.517A pdb=" N ILE r 37 " --> pdb=" O LEU r 41 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU r 41 " --> pdb=" O ILE r 37 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR r 44 " --> pdb=" O MET r 100 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N MET r 100 " --> pdb=" O THR r 44 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ASN r 119 " --> pdb=" O ASP r 115 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'r' and resid 125 through 129 removed outlier: 6.508A pdb=" N THR r 2 " --> pdb=" O ASP r 17 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL r 12 " --> pdb=" O VAL r 179 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER r 18 " --> pdb=" O ALA r 173 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ALA r 173 " --> pdb=" O SER r 18 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL r 174 " --> pdb=" O SER r 189 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N SER r 189 " --> pdb=" O VAL r 174 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU r 176 " --> pdb=" O VAL r 187 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY r 183 " --> pdb=" O ARG r 180 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'S' and resid 43 through 46 removed outlier: 6.684A pdb=" N THR S 50 " --> pdb=" O LEU S 46 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LYS S 49 " --> pdb=" O LEU S 113 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'S' and resid 135 through 139 removed outlier: 5.637A pdb=" N THR S 11 " --> pdb=" O ASP S 26 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR S 27 " --> pdb=" O ALA S 192 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA S 192 " --> pdb=" O THR S 27 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 's' and resid 43 through 46 removed outlier: 6.617A pdb=" N THR s 50 " --> pdb=" O LEU s 46 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LYS s 49 " --> pdb=" O LEU s 113 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 's' and resid 135 through 139 removed outlier: 6.328A pdb=" N THR s 11 " --> pdb=" O ASP s 26 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP s 26 " --> pdb=" O THR s 11 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR s 27 " --> pdb=" O ALA s 192 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ALA s 192 " --> pdb=" O THR s 27 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'T' and resid 42 through 45 removed outlier: 6.635A pdb=" N THR T 49 " --> pdb=" O VAL T 45 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N SER T 48 " --> pdb=" O TYR T 115 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'T' and resid 136 through 139 removed outlier: 4.377A pdb=" N VAL T 11 " --> pdb=" O THR T 139 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL T 6 " --> pdb=" O SER T 29 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N SER T 29 " --> pdb=" O VAL T 6 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLY T 8 " --> pdb=" O LEU T 27 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N LEU T 27 " --> pdb=" O GLY T 8 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N SER T 10 " --> pdb=" O ASP T 25 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ASP T 25 " --> pdb=" O SER T 10 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ARG T 186 " --> pdb=" O MET T 26 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ILE T 189 " --> pdb=" O GLU T 200 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 't' and resid 42 through 45 removed outlier: 6.704A pdb=" N THR t 49 " --> pdb=" O VAL t 45 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N SER t 48 " --> pdb=" O TYR t 115 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY t 113 " --> pdb=" O MET t 50 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR t 109 " --> pdb=" O SER t 54 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 't' and resid 136 through 139 removed outlier: 4.414A pdb=" N VAL t 11 " --> pdb=" O THR t 139 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL t 6 " --> pdb=" O SER t 29 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N SER t 29 " --> pdb=" O VAL t 6 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N GLY t 8 " --> pdb=" O LEU t 27 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N LEU t 27 " --> pdb=" O GLY t 8 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N SER t 10 " --> pdb=" O ASP t 25 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ASP t 25 " --> pdb=" O SER t 10 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA t 23 " --> pdb=" O LEU t 12 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ARG t 186 " --> pdb=" O MET t 26 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE t 189 " --> pdb=" O GLU t 200 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'g' and resid 68 through 72 removed outlier: 6.297A pdb=" N HIS g 68 " --> pdb=" O MET g 80 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE g 76 " --> pdb=" O ILE g 72 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N MET g 138 " --> pdb=" O CYS g 154 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'g' and resid 165 through 169 removed outlier: 6.369A pdb=" N THR g 38 " --> pdb=" O GLN g 53 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN g 53 " --> pdb=" O THR g 38 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N GLU g 214 " --> pdb=" O LYS g 54 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N VAL g 217 " --> pdb=" O LEU g 230 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'i' and resid 65 through 68 removed outlier: 6.609A pdb=" N MET i 72 " --> pdb=" O LEU i 68 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU i 134 " --> pdb=" O SER i 150 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY i 138 " --> pdb=" O GLN i 146 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU i 147 " --> pdb=" O TRP i 159 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'i' and resid 161 through 165 removed outlier: 5.066A pdb=" N THR i 33 " --> pdb=" O GLU i 48 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLY i 42 " --> pdb=" O ALA i 39 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ILE i 213 " --> pdb=" O LEU i 228 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'k' and resid 67 through 70 removed outlier: 6.615A pdb=" N ILE k 74 " --> pdb=" O ILE k 70 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N HIS k 73 " --> pdb=" O VAL k 146 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU k 153 " --> pdb=" O CYS k 165 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'k' and resid 167 through 171 removed outlier: 6.415A pdb=" N THR k 36 " --> pdb=" O GLU k 51 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N LEU k 217 " --> pdb=" O PHE k 229 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'l' and resid 63 through 66 removed outlier: 6.643A pdb=" N ILE l 70 " --> pdb=" O VAL l 66 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N HIS l 69 " --> pdb=" O TYR l 137 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE l 144 " --> pdb=" O CYS l 156 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASN l 152 " --> pdb=" O CYS l 148 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'l' and resid 158 through 162 removed outlier: 5.070A pdb=" N ALA l 34 " --> pdb=" O LEU l 49 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ASN l 209 " --> pdb=" O LYS l 50 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'm' and resid 65 through 69 removed outlier: 6.647A pdb=" N ARG m 65 " --> pdb=" O VAL m 77 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL m 73 " --> pdb=" O VAL m 69 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'm' and resid 162 through 166 removed outlier: 4.786A pdb=" N THR m 35 " --> pdb=" O GLU m 50 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU m 50 " --> pdb=" O THR m 35 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'n' and resid 34 through 37 removed outlier: 6.557A pdb=" N ILE n 41 " --> pdb=" O ILE n 37 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ARG n 40 " --> pdb=" O TRP n 103 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'n' and resid 125 through 129 removed outlier: 6.401A pdb=" N THR n 2 " --> pdb=" O ASP n 17 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER n 18 " --> pdb=" O VAL n 173 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N VAL n 173 " --> pdb=" O SER n 18 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY n 183 " --> pdb=" O ALA n 180 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'x' and resid 6 through 9 removed outlier: 3.789A pdb=" N LEU x 70 " --> pdb=" O MET x 47 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET x 72 " --> pdb=" O LYS x 45 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'x' and resid 265 through 273 removed outlier: 7.381A pdb=" N LEU x 310 " --> pdb=" O THR x 258 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'x' and resid 274 through 278 removed outlier: 6.035A pdb=" N ARG x 330 " --> pdb=" O VAL x 343 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'x' and resid 352 through 355 removed outlier: 3.730A pdb=" N MET x 355 " --> pdb=" O GLY x 416 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLY x 416 " --> pdb=" O MET x 355 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'x' and resid 454 through 458 removed outlier: 6.422A pdb=" N GLU x 446 " --> pdb=" O ARG x 442 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG x 442 " --> pdb=" O GLU x 446 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER x 438 " --> pdb=" O PHE x 450 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU x 424 " --> pdb=" O TYR x 476 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'x' and resid 248 through 251 removed outlier: 7.126A pdb=" N GLY x 248 " --> pdb=" O PRO x 321 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU x 250 " --> pdb=" O ARG x 319 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'x' and resid 322 through 327 removed outlier: 8.991A pdb=" N ALA x 322 " --> pdb=" O PRO x 482 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'y' and resid 11 through 17 removed outlier: 5.148A pdb=" N LYS y 11 " --> pdb=" O THR y 7 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N SER y 65 " --> pdb=" O GLN y 2 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU y 69 " --> pdb=" O LYS y 6 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'A' and resid 120 through 123 removed outlier: 6.910A pdb=" N ILE A 112 " --> pdb=" O ILE A 102 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'A' and resid 236 through 241 removed outlier: 3.694A pdb=" N CYS A 236 " --> pdb=" O ALA A 269 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N CYS A 270 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS A 316 " --> pdb=" O CYS A 270 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL A 212 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU A 214 " --> pdb=" O MET A 319 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLY A 216 " --> pdb=" O THR A 321 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'B' and resid 106 through 111 removed outlier: 4.832A pdb=" N HIS B 154 " --> pdb=" O PRO B 106 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'B' and resid 120 through 125 removed outlier: 4.298A pdb=" N SER B 129 " --> pdb=" O THR B 125 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'B' and resid 245 through 251 removed outlier: 5.470A pdb=" N THR B 246 " --> pdb=" O PRO B 279 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE B 281 " --> pdb=" O THR B 246 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N SER B 280 " --> pdb=" O ASP B 324 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA B 330 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL B 222 " --> pdb=" O VAL B 327 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY B 226 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR B 225 " --> pdb=" O ILE B 351 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'C' and resid 71 through 75 Processing sheet with id= 77, first strand: chain 'C' and resid 83 through 88 removed outlier: 7.777A pdb=" N LYS C 83 " --> pdb=" O VAL C 99 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL C 99 " --> pdb=" O LYS C 83 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL C 97 " --> pdb=" O VAL C 85 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'C' and resid 209 through 214 removed outlier: 3.693A pdb=" N VAL C 214 " --> pdb=" O PHE C 247 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N SER C 244 " --> pdb=" O ASN C 288 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N MET C 248 " --> pdb=" O ILE C 292 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA C 294 " --> pdb=" O MET C 248 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY C 190 " --> pdb=" O THR C 295 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ARG C 313 " --> pdb=" O GLY C 185 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'D' and resid 102 through 105 removed outlier: 6.934A pdb=" N ILE D 102 " --> pdb=" O LEU D 93 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'D' and resid 226 through 230 removed outlier: 5.336A pdb=" N ALA D 226 " --> pdb=" O PRO D 259 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE D 261 " --> pdb=" O ALA D 226 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET D 204 " --> pdb=" O MET D 309 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY D 206 " --> pdb=" O THR D 311 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'U' and resid 800 through 804 No H-bonds generated for sheet with id= 81 Processing sheet with id= 82, first strand: chain 'W' and resid 404 through 408 Processing sheet with id= 83, first strand: chain 'X' and resid 376 through 380 Processing sheet with id= 84, first strand: chain 'Y' and resid 345 through 349 removed outlier: 3.927A pdb=" N ILE Y 353 " --> pdb=" O ASP Y 348 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'Z' and resid 46 through 50 removed outlier: 8.000A pdb=" N GLN Z 7 " --> pdb=" O HIS Z 157 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N THR Z 159 " --> pdb=" O GLN Z 7 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N SER Z 140 " --> pdb=" O SER Z 119 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N SER Z 119 " --> pdb=" O SER Z 140 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N VAL Z 35 " --> pdb=" O THR Z 97 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N VAL Z 36 " --> pdb=" O VAL Z 56 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL Z 56 " --> pdb=" O VAL Z 36 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ASN Z 52 " --> pdb=" O LEU Z 40 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'a' and resid 320 through 326 removed outlier: 3.843A pdb=" N THR a 334 " --> pdb=" O LYS a 321 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'b' and resid 4 through 10 Processing sheet with id= 88, first strand: chain 'b' and resid 107 through 114 removed outlier: 3.602A pdb=" N ASN b 137 " --> pdb=" O MET b 107 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA b 111 " --> pdb=" O ASP b 139 " (cutoff:3.500A) Processing sheet with id= 89, first strand: chain 'c' and resid 52 through 56 removed outlier: 4.987A pdb=" N VAL c 53 " --> pdb=" O SER c 114 " (cutoff:3.500A) Processing sheet with id= 90, first strand: chain 'c' and resid 66 through 69 Processing sheet with id= 91, first strand: chain 'c' and resid 141 through 145 removed outlier: 3.694A pdb=" N ASP c 158 " --> pdb=" O VAL c 144 " (cutoff:3.500A) Processing sheet with id= 92, first strand: chain 'f' and resid 757 through 760 No H-bonds generated for sheet with id= 92 Processing sheet with id= 93, first strand: chain 'f' and resid 825 through 829 removed outlier: 4.012A pdb=" N THR f 863 " --> pdb=" O GLN f 826 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG f 828 " --> pdb=" O THR f 861 " (cutoff:3.500A) Processing sheet with id= 94, first strand: chain 'f' and resid 868 through 871 removed outlier: 6.099A pdb=" N HIS f 868 " --> pdb=" O GLU f 885 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N GLU f 885 " --> pdb=" O HIS f 868 " (cutoff:3.500A) 5517 hydrogen bonds defined for protein. 16455 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 47.47 Time building geometry restraints manager: 34.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 26093 1.33 - 1.46: 27919 1.46 - 1.58: 57377 1.58 - 1.71: 11 1.71 - 1.84: 1069 Bond restraints: 112469 Sorted by residual: bond pdb=" C VAL f 240 " pdb=" N PRO f 241 " ideal model delta sigma weight residual 1.334 1.415 -0.081 2.34e-02 1.83e+03 1.19e+01 bond pdb=" CA LEU f 502 " pdb=" C LEU f 502 " ideal model delta sigma weight residual 1.523 1.557 -0.034 1.00e-02 1.00e+04 1.13e+01 bond pdb=" C GLU f 585 " pdb=" N PRO f 586 " ideal model delta sigma weight residual 1.336 1.370 -0.034 1.08e-02 8.57e+03 1.01e+01 bond pdb=" CA LEU d 36 " pdb=" C LEU d 36 " ideal model delta sigma weight residual 1.524 1.558 -0.034 1.26e-02 6.30e+03 7.16e+00 bond pdb=" C GLY I 158 " pdb=" O GLY I 158 " ideal model delta sigma weight residual 1.231 1.202 0.029 1.11e-02 8.12e+03 6.96e+00 ... (remaining 112464 not shown) Histogram of bond angle deviations from ideal: 94.48 - 103.52: 1321 103.52 - 112.56: 58418 112.56 - 121.60: 67084 121.60 - 130.64: 24663 130.64 - 139.68: 445 Bond angle restraints: 151931 Sorted by residual: angle pdb=" C PRO C 318 " pdb=" N PRO C 319 " pdb=" CA PRO C 319 " ideal model delta sigma weight residual 120.38 111.75 8.63 1.03e+00 9.43e-01 7.03e+01 angle pdb=" C ASN g 224 " pdb=" N PRO g 225 " pdb=" CA PRO g 225 " ideal model delta sigma weight residual 120.83 113.97 6.86 1.02e+00 9.61e-01 4.52e+01 angle pdb=" N PRO A 74 " pdb=" CA PRO A 74 " pdb=" C PRO A 74 " ideal model delta sigma weight residual 110.70 116.75 -6.05 1.22e+00 6.72e-01 2.46e+01 angle pdb=" C LEU B 73 " pdb=" N MET B 74 " pdb=" CA MET B 74 " ideal model delta sigma weight residual 121.58 112.13 9.45 1.95e+00 2.63e-01 2.35e+01 angle pdb=" C GLU E 217 " pdb=" N MET E 218 " pdb=" CA MET E 218 " ideal model delta sigma weight residual 121.14 112.70 8.44 1.75e+00 3.27e-01 2.32e+01 ... (remaining 151926 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.60: 64806 25.60 - 51.20: 3590 51.20 - 76.79: 328 76.79 - 102.39: 48 102.39 - 127.99: 4 Dihedral angle restraints: 68776 sinusoidal: 27913 harmonic: 40863 Sorted by residual: dihedral pdb=" O1B ADP C 501 " pdb=" O3A ADP C 501 " pdb=" PB ADP C 501 " pdb=" PA ADP C 501 " ideal model delta sinusoidal sigma weight residual -60.00 67.99 -127.99 1 2.00e+01 2.50e-03 3.88e+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 65.78 -125.78 1 2.00e+01 2.50e-03 3.80e+01 dihedral pdb=" CA GLY p 101 " pdb=" C GLY p 101 " pdb=" N PRO p 102 " pdb=" CA PRO p 102 " ideal model delta harmonic sigma weight residual -180.00 -150.05 -29.95 0 5.00e+00 4.00e-02 3.59e+01 ... (remaining 68773 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 15679 0.091 - 0.183: 1458 0.183 - 0.274: 44 0.274 - 0.366: 10 0.366 - 0.457: 1 Chirality restraints: 17192 Sorted by residual: chirality pdb=" CB ILE U 911 " pdb=" CA ILE U 911 " pdb=" CG1 ILE U 911 " pdb=" CG2 ILE U 911 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.46 2.00e-01 2.50e+01 5.22e+00 chirality pdb=" CB ILE D 308 " pdb=" CA ILE D 308 " pdb=" CG1 ILE D 308 " pdb=" CG2 ILE D 308 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" CB ILE Y 65 " pdb=" CA ILE Y 65 " pdb=" CG1 ILE Y 65 " pdb=" CG2 ILE Y 65 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.10e+00 ... (remaining 17189 not shown) Planarity restraints: 19582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL c 49 " -0.069 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO c 50 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO c 50 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO c 50 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP m 215 " 0.024 2.00e-02 2.50e+03 2.41e-02 1.46e+01 pdb=" CG TRP m 215 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP m 215 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP m 215 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP m 215 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP m 215 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP m 215 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP m 215 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP m 215 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP m 215 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP M 215 " 0.020 2.00e-02 2.50e+03 2.20e-02 1.21e+01 pdb=" CG TRP M 215 " -0.057 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 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP M 215 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP M 215 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 215 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 215 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP M 215 " 0.003 2.00e-02 2.50e+03 ... (remaining 19579 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 159 2.37 - 3.00: 55735 3.00 - 3.64: 170954 3.64 - 4.27: 244741 4.27 - 4.90: 410369 Nonbonded interactions: 881958 Sorted by model distance: nonbonded pdb=" OD2 ASP c 126 " pdb="ZN ZN c 401 " model vdw 1.739 2.230 nonbonded pdb=" CG ASP c 126 " pdb="ZN ZN c 401 " model vdw 1.989 2.460 nonbonded pdb=" OD1 ASP c 126 " pdb="ZN ZN c 401 " model vdw 2.204 2.230 nonbonded pdb=" OG SER J 11 " pdb=" OD1 ASP J 13 " model vdw 2.207 2.440 nonbonded pdb=" O PHE D 345 " pdb=" OG1 THR D 349 " model vdw 2.211 2.440 ... (remaining 881953 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'G' and (resid 6 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 through 195 or (resid 196 and (n \ ame N or name CA or name C or name O or name CB )) or resid 197 through 222 or ( \ resid 223 and (name N or name CA or name C or name O or name CB )) or resid 224 \ through 245)) selection = (chain 'g' and resid 6 through 245) } ncs_group { reference = (chain 'H' and (resid 3 through 140 or (resid 141 and (name N or name CA or name \ C or name O or name CB )) or resid 142 through 199 or (resid 200 and (name N or \ name CA or name C or name O or name CB )) or resid 201 through 234)) selection = (chain 'h' and (resid 3 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 69 or (resid 70 and (name N or name \ CA or name C or name O or name CB )) or resid 71 through 175 or (resid 176 and \ (name N or name CA or name C or name O or name CB )) or resid 177 through 234)) } ncs_group { reference = (chain 'I' and (resid 4 through 198 or (resid 199 and (name N or name CA or name \ C or name O or name CB )) or resid 200 through 204 or (resid 205 and (name N or \ name CA or name C or name O or name CB )) or resid 206 through 251)) selection = (chain 'i' and (resid 4 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 228 or (resid 229 and (name N or na \ me CA or name C or name O or name CB )) or resid 230 or (resid 231 and (name N o \ r name CA or name C or name O or name CB )) or resid 232 through 238 or (resid 2 \ 39 and (name N or name CA or name C or name O or name CB )) or resid 240 through \ 251)) } ncs_group { reference = (chain 'J' and (resid 2 through 169 or (resid 170 and (name N or name CA or name \ C or name O or name CB )) or resid 171 through 206 or (resid 207 and (name N or \ name CA or name C or name O or name CB )) or resid 208 through 223 or (resid 22 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 225 through \ 231 or (resid 232 and (name N or name CA or name C or name O or name CB )) or re \ sid 233 through 238 or (resid 239 through 240 and (name N or name CA or name C o \ r name O or name CB )))) selection = (chain 'j' and (resid 2 through 37 or (resid 38 and (name N or name CA or name C \ or name O or name CB )) or resid 39 through 173 or (resid 174 and (name N or na \ me CA or name C or name O or name CB )) or resid 175 through 181 or (resid 182 a \ nd (name N or name CA or name C or name O or name CB )) or resid 183 through 188 \ or (resid 189 and (name N or name CA or name C or name O or name CB )) or resid \ 190 through 217 or (resid 218 and (name N or name CA or name C or name O or nam \ e CB )) or resid 219 through 240)) } ncs_group { reference = (chain 'K' and ((resid 8 and (name N or name CA or name C or name O or name CB ) \ ) or resid 9 through 240 or (resid 241 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2 or name CD1)))) selection = (chain 'k' and (resid 8 through 126 or (resid 127 through 129 and (name N or nam \ e CA or name C or name O or name CB )) or resid 130 through 207 or (resid 208 an \ d (name N or name CA or name C or name O or name CB )) or resid 209 through 241) \ ) } ncs_group { reference = (chain 'L' and (resid 4 through 207 or (resid 208 and (name N or name CA or name \ C or name O or name CB )) or resid 209 through 237 or (resid 238 and (name N or \ name CA or name C or name O or name CB )) or resid 239 through 241)) selection = (chain 'l' and (resid 4 through 217 or (resid 218 and (name N or name CA or name \ C or name O or name CB )) or resid 219 through 241)) } ncs_group { reference = (chain 'M' and resid 5 through 244) selection = (chain 'm' and (resid 5 through 187 or (resid 188 and (name N or name CA or name \ C or name O or name CB )) or resid 189 through 244)) } ncs_group { reference = (chain 'N' and (resid 1 through 149 or (resid 150 and (name N or name CA or name \ C or name O or name CB )) or resid 151 through 202)) selection = chain 'n' } ncs_group { reference = chain 'O' selection = (chain 'o' and (resid 1 through 179 or (resid 180 and (name N or name CA or name \ C or name O or name CB )) or resid 181 through 193 or (resid 194 and (name N or \ name CA or name C or name O or name CB )) or resid 195 through 202 or (resid 20 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 204 through \ 220)) } ncs_group { reference = chain 'P' selection = (chain 'p' and (resid 2 through 191 or (resid 192 and (name N or name CA or name \ C or name O or name CB )) or resid 193 through 205)) } ncs_group { reference = (chain 'Q' and (resid 1 through 94 or (resid 95 and (name N or name CA or name C \ or name O or name CB )) or resid 96 through 108 or (resid 109 and (name N or na \ me CA or name C or name O or name CB )) or resid 110 through 199)) selection = chain 'q' } ncs_group { reference = (chain 'R' and (resid 1 through 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 88 or (resid 89 and (name N or name C \ A or name C or name O or name CB )) or resid 90 through 201)) selection = chain 'r' } ncs_group { reference = (chain 'S' and (resid 1 through 199 or (resid 200 and (name N or name CA or name \ C or name O or name CB )) or resid 201 through 213)) selection = (chain 's' and ((resid 1 and (name N or name CA or name C or name O or name CB ) \ ) or resid 2 through 161 or (resid 162 and (name N or name CA or name C or name \ O or name CB )) or resid 163 through 168 or (resid 169 and (name N or name CA or \ name C or name O or name CB )) or resid 170 through 213)) } ncs_group { reference = chain 'T' selection = (chain 't' and (resid 1 through 205 or (resid 206 and (name N or name CA or name \ C or name O or name CB )) or resid 207 through 216)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.940 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.090 Extract box with map and model: 47.220 Check model and map are aligned: 1.070 Set scattering table: 0.740 Process input model: 275.690 Find NCS groups from input model: 7.240 Set up NCS constraints: 0.510 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:2.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 343.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 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 0.081 112469 Z= 0.333 Angle : 0.844 13.632 151931 Z= 0.434 Chirality : 0.052 0.457 17192 Planarity : 0.006 0.104 19582 Dihedral : 14.849 127.991 42468 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.91 % Favored : 93.04 % Rotamer: Outliers : 0.55 % Allowed : 0.58 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.20 % 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: -1.22 (0.07), residues: 13971 helix: -0.01 (0.06), residues: 6134 sheet: -0.20 (0.11), residues: 2107 loop : -1.89 (0.08), residues: 5730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP m 215 HIS 0.016 0.001 HIS c 115 PHE 0.025 0.002 PHE a 67 TYR 0.038 0.002 TYR E 386 ARG 0.008 0.001 ARG f 763 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27942 Ramachandran restraints generated. 13971 Oldfield, 0 Emsley, 13971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27942 Ramachandran restraints generated. 13971 Oldfield, 0 Emsley, 13971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 12025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 478 time to evaluate : 9.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 225 MET cc_start: 0.7391 (tpt) cc_final: 0.7028 (tpt) REVERT: x 71 MET cc_start: 0.6942 (tpp) cc_final: 0.5405 (tpp) REVERT: x 93 THR cc_start: 0.5897 (OUTLIER) cc_final: 0.5480 (m) REVERT: x 163 MET cc_start: 0.4788 (ptm) cc_final: 0.4435 (tmm) REVERT: x 334 LYS cc_start: 0.7489 (OUTLIER) cc_final: 0.6887 (pttp) REVERT: x 340 ASN cc_start: 0.6927 (OUTLIER) cc_final: 0.6534 (p0) REVERT: A 299 MET cc_start: 0.8831 (tpp) cc_final: 0.8325 (mmt) REVERT: B 329 MET cc_start: 0.9228 (mmm) cc_final: 0.8992 (tpp) REVERT: D 163 MET cc_start: 0.8357 (mmp) cc_final: 0.7942 (mmm) REVERT: D 204 MET cc_start: 0.7553 (ppp) cc_final: 0.7233 (ppp) REVERT: U 695 MET cc_start: 0.8465 (mmt) cc_final: 0.8228 (mmm) REVERT: U 797 MET cc_start: 0.6960 (tpt) cc_final: 0.6659 (tpt) REVERT: W 73 MET cc_start: 0.7964 (ppp) cc_final: 0.7606 (ppp) REVERT: W 190 MET cc_start: 0.8830 (mpp) cc_final: 0.8242 (mtt) REVERT: X 212 MET cc_start: 0.8785 (tpp) cc_final: 0.8250 (tpp) REVERT: X 254 MET cc_start: 0.8356 (mmt) cc_final: 0.7926 (mmp) REVERT: Y 214 MET cc_start: 0.5443 (mmt) cc_final: 0.4988 (mmt) REVERT: a 87 MET cc_start: 0.7460 (ppp) cc_final: 0.6751 (ppp) REVERT: a 218 MET cc_start: 0.8271 (mtt) cc_final: 0.8030 (mtt) REVERT: b 7 MET cc_start: 0.8637 (mmm) cc_final: 0.8381 (mmm) REVERT: c 167 MET cc_start: 0.8408 (mmp) cc_final: 0.7999 (tmm) REVERT: c 265 MET cc_start: 0.7715 (pmm) cc_final: 0.7379 (ppp) REVERT: d 206 MET cc_start: 0.8373 (mtm) cc_final: 0.8159 (mtt) REVERT: d 208 ASP cc_start: 0.9059 (t0) cc_final: 0.8736 (p0) REVERT: f 58 MET cc_start: 0.8149 (pmm) cc_final: 0.7625 (pmm) REVERT: f 306 GLU cc_start: 0.6576 (tp30) cc_final: 0.6320 (mm-30) REVERT: f 407 MET cc_start: 0.6275 (mpp) cc_final: 0.5319 (mpp) REVERT: f 477 MET cc_start: 0.6179 (tpt) cc_final: 0.5767 (tpp) REVERT: f 524 MET cc_start: 0.8518 (ptt) cc_final: 0.7967 (ppp) REVERT: f 729 MET cc_start: 0.7053 (mmp) cc_final: 0.6443 (mmm) REVERT: V 175 MET cc_start: 0.8042 (tmm) cc_final: 0.7733 (tmm) REVERT: V 176 MET cc_start: 0.8032 (tpt) cc_final: 0.7534 (ttt) outliers start: 66 outliers final: 11 residues processed: 539 average time/residue: 0.8904 time to fit residues: 861.0757 Evaluate side-chains 463 residues out of total 12025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 449 time to evaluate : 9.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 91 LYS Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain x residue 93 THR Chi-restraints excluded: chain x residue 334 LYS Chi-restraints excluded: chain x residue 340 ASN 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 D residue 329 ARG Chi-restraints excluded: chain W residue 26 GLN Chi-restraints excluded: chain Z residue 176 LEU Chi-restraints excluded: chain Z residue 260 VAL Chi-restraints excluded: chain a residue 340 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1388 random chunks: chunk 1172 optimal weight: 2.9990 chunk 1052 optimal weight: 9.9990 chunk 583 optimal weight: 8.9990 chunk 359 optimal weight: 8.9990 chunk 709 optimal weight: 40.0000 chunk 562 optimal weight: 20.0000 chunk 1087 optimal weight: 40.0000 chunk 420 optimal weight: 10.0000 chunk 661 optimal weight: 9.9990 chunk 809 optimal weight: 10.0000 chunk 1260 optimal weight: 7.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 86 GLN H 169 ASN ** J 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 GLN O 80 ASN S 157 ASN T 147 GLN i 146 GLN p 169 GLN ** x 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 112 ASN x 421 GLN x 494 GLN ** y 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 79 ASN U 697 GLN ** U 707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 711 GLN W 155 GLN W 170 GLN W 362 ASN W 444 HIS X 48 GLN X 375 HIS ** Z 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 231 GLN ** Z 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 258 GLN ** c 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 493 ASN ** f 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 848 GLN V 214 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 112469 Z= 0.266 Angle : 0.615 12.153 151931 Z= 0.320 Chirality : 0.042 0.206 17192 Planarity : 0.004 0.056 19582 Dihedral : 6.428 122.387 15508 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.33 % Favored : 93.64 % Rotamer: Outliers : 0.45 % Allowed : 7.23 % Favored : 92.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.20 % 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: -0.41 (0.07), residues: 13971 helix: 0.89 (0.07), residues: 6267 sheet: -0.05 (0.11), residues: 2078 loop : -1.72 (0.08), residues: 5626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP m 215 HIS 0.007 0.001 HIS Z 145 PHE 0.030 0.001 PHE W 309 TYR 0.017 0.001 TYR U 246 ARG 0.005 0.000 ARG f 828 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27942 Ramachandran restraints generated. 13971 Oldfield, 0 Emsley, 13971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27942 Ramachandran restraints generated. 13971 Oldfield, 0 Emsley, 13971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 12025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 451 time to evaluate : 9.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 218 MET cc_start: 0.9103 (pmm) cc_final: 0.8868 (pmm) REVERT: E 277 MET cc_start: 0.8858 (mmp) cc_final: 0.8510 (mmp) REVERT: E 386 TYR cc_start: 0.6898 (p90) cc_final: 0.6649 (p90) REVERT: F 366 MET cc_start: 0.9023 (mmp) cc_final: 0.8775 (mmp) REVERT: K 156 MET cc_start: 0.8455 (tpp) cc_final: 0.8208 (ttm) REVERT: i 174 MET cc_start: 0.8762 (ptm) cc_final: 0.8532 (ttt) REVERT: k 206 MET cc_start: 0.6725 (mmm) cc_final: 0.6107 (mmm) REVERT: x 71 MET cc_start: 0.7250 (tpp) cc_final: 0.6547 (tpp) REVERT: x 163 MET cc_start: 0.4906 (ptm) cc_final: 0.4410 (tpt) REVERT: x 334 LYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7606 (pttt) REVERT: A 299 MET cc_start: 0.8748 (tpp) cc_final: 0.8287 (mmt) REVERT: B 164 MET cc_start: 0.8789 (ppp) cc_final: 0.8524 (ppp) REVERT: B 329 MET cc_start: 0.9086 (mmm) cc_final: 0.8759 (mmp) REVERT: D 152 MET cc_start: 0.6868 (tmm) cc_final: 0.6548 (tmm) REVERT: D 204 MET cc_start: 0.7255 (ppp) cc_final: 0.6781 (ppp) REVERT: U 520 MET cc_start: 0.8450 (mmm) cc_final: 0.8233 (tpp) REVERT: U 797 MET cc_start: 0.7362 (tpt) cc_final: 0.7098 (tpt) REVERT: W 190 MET cc_start: 0.8816 (mpp) cc_final: 0.8525 (mtt) REVERT: X 212 MET cc_start: 0.8720 (tpp) cc_final: 0.8139 (tpp) REVERT: X 254 MET cc_start: 0.8363 (mmt) cc_final: 0.7896 (mmp) REVERT: Y 214 MET cc_start: 0.5652 (mmt) cc_final: 0.5109 (mmt) REVERT: a 312 MET cc_start: 0.8509 (mmm) cc_final: 0.8102 (mmm) REVERT: c 167 MET cc_start: 0.8502 (mmp) cc_final: 0.7925 (tmm) REVERT: c 265 MET cc_start: 0.7819 (pmm) cc_final: 0.6618 (ppp) REVERT: f 58 MET cc_start: 0.8288 (pmm) cc_final: 0.7800 (pmm) REVERT: f 306 GLU cc_start: 0.6639 (tp30) cc_final: 0.6389 (mm-30) REVERT: f 524 MET cc_start: 0.8446 (ptt) cc_final: 0.7943 (ppp) REVERT: f 729 MET cc_start: 0.7341 (mmp) cc_final: 0.6960 (mmp) REVERT: f 731 MET cc_start: 0.7303 (OUTLIER) cc_final: 0.6783 (tmm) REVERT: f 829 MET cc_start: 0.7550 (pmm) cc_final: 0.7252 (pmm) REVERT: V 176 MET cc_start: 0.7937 (tpt) cc_final: 0.7440 (ttt) outliers start: 54 outliers final: 27 residues processed: 484 average time/residue: 0.8807 time to fit residues: 765.6257 Evaluate side-chains 474 residues out of total 12025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 445 time to evaluate : 9.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 259 MET Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain K residue 189 MET Chi-restraints excluded: chain N residue 86 MET Chi-restraints excluded: chain l residue 61 LYS Chi-restraints excluded: chain n residue 145 GLU Chi-restraints excluded: chain x residue 90 GLU Chi-restraints excluded: chain x residue 334 LYS Chi-restraints excluded: chain x residue 336 LYS Chi-restraints excluded: chain y residue 20 SER Chi-restraints excluded: chain y residue 25 ASN Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain W residue 26 GLN Chi-restraints excluded: chain W residue 117 ASP Chi-restraints excluded: chain Y residue 72 LYS Chi-restraints excluded: chain Z residue 127 LYS Chi-restraints excluded: chain Z residue 176 LEU Chi-restraints excluded: chain Z residue 257 MET Chi-restraints excluded: chain Z residue 260 VAL Chi-restraints excluded: chain a residue 280 MET Chi-restraints excluded: chain a residue 340 VAL Chi-restraints excluded: chain b residue 54 LEU Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain d residue 189 ILE Chi-restraints excluded: chain f residue 731 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1388 random chunks: chunk 700 optimal weight: 30.0000 chunk 391 optimal weight: 5.9990 chunk 1049 optimal weight: 9.9990 chunk 858 optimal weight: 30.0000 chunk 347 optimal weight: 30.0000 chunk 1262 optimal weight: 0.0470 chunk 1364 optimal weight: 5.9990 chunk 1124 optimal weight: 8.9990 chunk 1252 optimal weight: 9.9990 chunk 430 optimal weight: 0.5980 chunk 1013 optimal weight: 8.9990 overall best weight: 4.3284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 45 ASN E 339 ASN H 169 ASN ** J 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 421 GLN ** y 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 697 GLN U 707 ASN U 711 GLN ** Z 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 34 ASN ** d 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 112469 Z= 0.172 Angle : 0.547 11.743 151931 Z= 0.282 Chirality : 0.041 0.239 17192 Planarity : 0.004 0.052 19582 Dihedral : 6.084 119.802 15497 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.15 % Favored : 93.84 % Rotamer: Outliers : 0.61 % Allowed : 10.66 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.20 % 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: 13971 helix: 1.31 (0.07), residues: 6268 sheet: 0.05 (0.11), residues: 2101 loop : -1.65 (0.08), residues: 5602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP f 154 HIS 0.008 0.001 HIS V 214 PHE 0.029 0.001 PHE W 309 TYR 0.019 0.001 TYR U 246 ARG 0.006 0.000 ARG f 120 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27942 Ramachandran restraints generated. 13971 Oldfield, 0 Emsley, 13971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27942 Ramachandran restraints generated. 13971 Oldfield, 0 Emsley, 13971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 12025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 448 time to evaluate : 9.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 366 MET cc_start: 0.8977 (mmp) cc_final: 0.8755 (mmp) REVERT: K 156 MET cc_start: 0.8446 (tpp) cc_final: 0.7919 (ttt) REVERT: x 71 MET cc_start: 0.7257 (tpp) cc_final: 0.6598 (tpp) REVERT: x 163 MET cc_start: 0.4885 (ptm) cc_final: 0.4608 (tmm) REVERT: x 334 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7567 (pttt) REVERT: x 342 LYS cc_start: 0.6572 (OUTLIER) cc_final: 0.5924 (mmtt) REVERT: A 299 MET cc_start: 0.8800 (tpp) cc_final: 0.8463 (mmt) REVERT: B 164 MET cc_start: 0.8744 (ppp) cc_final: 0.8368 (ppp) REVERT: B 329 MET cc_start: 0.9112 (mmm) cc_final: 0.8667 (mmp) REVERT: C 150 MET cc_start: 0.7703 (pmm) cc_final: 0.7479 (pmm) REVERT: C 230 MET cc_start: 0.8497 (mmm) cc_final: 0.8245 (mmp) REVERT: D 153 MET cc_start: 0.7455 (OUTLIER) cc_final: 0.7140 (tpp) REVERT: D 204 MET cc_start: 0.7232 (ppp) cc_final: 0.6357 (ppp) REVERT: U 556 MET cc_start: 0.8402 (tpt) cc_final: 0.8059 (tpt) REVERT: U 797 MET cc_start: 0.7556 (tpt) cc_final: 0.7303 (tpt) REVERT: X 254 MET cc_start: 0.8380 (mmt) cc_final: 0.7863 (mmt) REVERT: Y 214 MET cc_start: 0.5680 (mmt) cc_final: 0.5094 (mmt) REVERT: Y 389 MET cc_start: 0.7137 (pmm) cc_final: 0.6797 (pmm) REVERT: Z 176 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7278 (pp) REVERT: c 57 MET cc_start: 0.8812 (pmm) cc_final: 0.8557 (pmm) REVERT: c 167 MET cc_start: 0.8489 (mmp) cc_final: 0.7924 (tmm) REVERT: c 265 MET cc_start: 0.7841 (pmm) cc_final: 0.6595 (ppp) REVERT: f 58 MET cc_start: 0.8303 (pmm) cc_final: 0.7880 (pmm) REVERT: f 294 MET cc_start: 0.6780 (mpp) cc_final: 0.3166 (tpt) REVERT: f 340 MET cc_start: 0.7581 (OUTLIER) cc_final: 0.7224 (ppp) REVERT: f 524 MET cc_start: 0.8435 (ptt) cc_final: 0.7930 (ppp) REVERT: f 731 MET cc_start: 0.7310 (OUTLIER) cc_final: 0.6852 (tmm) REVERT: f 825 MET cc_start: 0.7655 (mmt) cc_final: 0.7419 (mmt) REVERT: f 829 MET cc_start: 0.7569 (pmm) cc_final: 0.7292 (pmm) REVERT: V 176 MET cc_start: 0.7944 (tpt) cc_final: 0.7540 (ttt) outliers start: 73 outliers final: 36 residues processed: 499 average time/residue: 0.8677 time to fit residues: 781.7532 Evaluate side-chains 485 residues out of total 12025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 443 time to evaluate : 9.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 259 MET Chi-restraints excluded: chain F residue 354 PHE Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain N residue 86 MET Chi-restraints excluded: chain g residue 138 MET Chi-restraints excluded: chain j residue 173 GLU Chi-restraints excluded: chain l residue 61 LYS Chi-restraints excluded: chain o residue 65 LEU Chi-restraints excluded: chain p residue 90 MET Chi-restraints excluded: chain t residue 127 MET Chi-restraints excluded: chain x residue 90 GLU Chi-restraints excluded: chain x residue 266 THR Chi-restraints excluded: chain x residue 334 LYS Chi-restraints excluded: chain x residue 336 LYS Chi-restraints excluded: chain x residue 342 LYS Chi-restraints excluded: chain y residue 20 SER Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain U residue 21 GLU Chi-restraints excluded: chain U residue 614 VAL Chi-restraints excluded: chain W residue 26 GLN Chi-restraints excluded: chain Z residue 127 LYS Chi-restraints excluded: chain Z residue 176 LEU Chi-restraints excluded: chain Z residue 257 MET Chi-restraints excluded: chain Z residue 260 VAL Chi-restraints excluded: chain a residue 280 MET Chi-restraints excluded: chain a residue 340 VAL Chi-restraints excluded: chain b residue 8 VAL Chi-restraints excluded: chain c residue 303 MET Chi-restraints excluded: chain d residue 189 ILE Chi-restraints excluded: chain d residue 237 ILE Chi-restraints excluded: chain f residue 340 MET Chi-restraints excluded: chain f residue 731 MET Chi-restraints excluded: chain V residue 139 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1388 random chunks: chunk 1247 optimal weight: 1.9990 chunk 949 optimal weight: 3.9990 chunk 655 optimal weight: 20.0000 chunk 139 optimal weight: 4.9990 chunk 602 optimal weight: 10.0000 chunk 847 optimal weight: 20.0000 chunk 1267 optimal weight: 30.0000 chunk 1341 optimal weight: 8.9990 chunk 662 optimal weight: 20.0000 chunk 1201 optimal weight: 20.0000 chunk 361 optimal weight: 0.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 169 ASN ** J 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 GLN ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 390 ASN U 697 GLN U 707 ASN U 711 GLN ** Z 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 243 GLN ** a 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 112469 Z= 0.168 Angle : 0.537 12.148 151931 Z= 0.275 Chirality : 0.040 0.233 17192 Planarity : 0.003 0.052 19582 Dihedral : 5.894 116.358 15497 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 0.94 % Allowed : 12.47 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.20 % 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: 0.15 (0.07), residues: 13971 helix: 1.50 (0.07), residues: 6285 sheet: 0.09 (0.11), residues: 2105 loop : -1.58 (0.08), residues: 5581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP f 154 HIS 0.005 0.001 HIS E 19 PHE 0.026 0.001 PHE W 309 TYR 0.017 0.001 TYR Y 259 ARG 0.006 0.000 ARG W 364 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27942 Ramachandran restraints generated. 13971 Oldfield, 0 Emsley, 13971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27942 Ramachandran restraints generated. 13971 Oldfield, 0 Emsley, 13971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 12025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 445 time to evaluate : 9.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 277 MET cc_start: 0.8839 (mmp) cc_final: 0.8320 (mmp) REVERT: F 206 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7890 (mmm) REVERT: K 156 MET cc_start: 0.8445 (tpp) cc_final: 0.7953 (ttt) REVERT: R 93 MET cc_start: 0.8242 (mpp) cc_final: 0.7775 (mtm) REVERT: x 71 MET cc_start: 0.7260 (tpp) cc_final: 0.6644 (tpp) REVERT: x 163 MET cc_start: 0.4937 (ptm) cc_final: 0.4686 (tmm) REVERT: x 342 LYS cc_start: 0.6662 (OUTLIER) cc_final: 0.6022 (mmtt) REVERT: A 394 MET cc_start: 0.8985 (mmm) cc_final: 0.8401 (mmp) REVERT: B 164 MET cc_start: 0.8748 (ppp) cc_final: 0.8375 (ppp) REVERT: D 153 MET cc_start: 0.7475 (OUTLIER) cc_final: 0.7222 (tpp) REVERT: D 204 MET cc_start: 0.7260 (ppp) cc_final: 0.6311 (ppp) REVERT: U 325 MET cc_start: 0.9030 (mmp) cc_final: 0.8795 (mmp) REVERT: U 520 MET cc_start: 0.8483 (mmm) cc_final: 0.8266 (mmm) REVERT: U 556 MET cc_start: 0.8437 (tpt) cc_final: 0.8144 (tpt) REVERT: U 797 MET cc_start: 0.7579 (tpt) cc_final: 0.7324 (tpt) REVERT: W 267 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8562 (mt) REVERT: X 254 MET cc_start: 0.8354 (mmt) cc_final: 0.7853 (mmt) REVERT: Y 50 MET cc_start: 0.7480 (mmm) cc_final: 0.6595 (mmm) REVERT: Y 53 TYR cc_start: 0.7522 (OUTLIER) cc_final: 0.6931 (p90) REVERT: Z 176 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7245 (pp) REVERT: Z 261 TYR cc_start: 0.6799 (OUTLIER) cc_final: 0.6499 (m-10) REVERT: c 95 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.8210 (tpp) REVERT: c 167 MET cc_start: 0.8496 (mmp) cc_final: 0.8047 (tmm) REVERT: c 200 TYR cc_start: 0.5865 (OUTLIER) cc_final: 0.5451 (p90) REVERT: c 265 MET cc_start: 0.7780 (pmm) cc_final: 0.6529 (ppp) REVERT: f 58 MET cc_start: 0.8301 (pmm) cc_final: 0.7945 (pmm) REVERT: f 131 MET cc_start: 0.8735 (ptt) cc_final: 0.8409 (ppp) REVERT: f 294 MET cc_start: 0.6683 (mpp) cc_final: 0.3029 (tpt) REVERT: f 340 MET cc_start: 0.7575 (ttt) cc_final: 0.7234 (ppp) REVERT: f 524 MET cc_start: 0.8433 (ptt) cc_final: 0.7923 (ppp) REVERT: f 825 MET cc_start: 0.7696 (mmt) cc_final: 0.7459 (mmt) REVERT: f 829 MET cc_start: 0.7567 (pmm) cc_final: 0.7331 (pmm) REVERT: V 175 MET cc_start: 0.8321 (ppp) cc_final: 0.8052 (tmm) REVERT: V 225 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.7930 (p0) outliers start: 112 outliers final: 49 residues processed: 533 average time/residue: 0.8521 time to fit residues: 822.6528 Evaluate side-chains 502 residues out of total 12025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 443 time to evaluate : 9.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain F residue 206 MET Chi-restraints excluded: chain F residue 259 MET Chi-restraints excluded: chain F residue 354 PHE Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 189 MET Chi-restraints excluded: chain L residue 26 MET Chi-restraints excluded: chain L residue 176 MET Chi-restraints excluded: chain N residue 86 MET Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain g residue 138 MET Chi-restraints excluded: chain j residue 173 GLU Chi-restraints excluded: chain l residue 61 LYS Chi-restraints excluded: chain o residue 65 LEU Chi-restraints excluded: chain p residue 90 MET Chi-restraints excluded: chain t residue 127 MET Chi-restraints excluded: chain x residue 90 GLU Chi-restraints excluded: chain x residue 334 LYS Chi-restraints excluded: chain x residue 336 LYS Chi-restraints excluded: chain x residue 342 LYS Chi-restraints excluded: chain y residue 56 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 153 MET Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain U residue 21 GLU Chi-restraints excluded: chain U residue 614 VAL Chi-restraints excluded: chain U residue 754 HIS Chi-restraints excluded: chain W residue 26 GLN Chi-restraints excluded: chain W residue 267 LEU Chi-restraints excluded: chain W residue 420 ASP Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain Y residue 53 TYR Chi-restraints excluded: chain Y residue 154 ASN Chi-restraints excluded: chain Z residue 102 HIS Chi-restraints excluded: chain Z residue 127 LYS Chi-restraints excluded: chain Z residue 176 LEU Chi-restraints excluded: chain Z residue 257 MET Chi-restraints excluded: chain Z residue 260 VAL Chi-restraints excluded: chain Z residue 261 TYR Chi-restraints excluded: chain a residue 280 MET Chi-restraints excluded: chain a residue 340 VAL Chi-restraints excluded: chain b residue 8 VAL Chi-restraints excluded: chain b residue 54 LEU Chi-restraints excluded: chain c residue 27 THR Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 95 MET Chi-restraints excluded: chain c residue 200 TYR Chi-restraints excluded: chain c residue 303 MET Chi-restraints excluded: chain d residue 189 ILE Chi-restraints excluded: chain d residue 237 ILE Chi-restraints excluded: chain V residue 225 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1388 random chunks: chunk 1117 optimal weight: 10.0000 chunk 761 optimal weight: 8.9990 chunk 19 optimal weight: 30.0000 chunk 998 optimal weight: 10.0000 chunk 553 optimal weight: 2.9990 chunk 1144 optimal weight: 20.0000 chunk 927 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 685 optimal weight: 10.0000 chunk 1204 optimal weight: 10.0000 chunk 338 optimal weight: 30.0000 overall best weight: 8.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 169 ASN ** J 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 123 GLN i 146 GLN t 147 GLN ** x 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 201 ASN x 327 GLN ** y 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 GLN A 247 GLN B 314 ASN ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 278 ASN C 392 GLN ** D 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 412 HIS U 421 GLN ** U 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 698 GLN W 155 GLN W 228 ASN W 362 ASN X 213 GLN ** Z 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 254 ASN ** a 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 172 HIS ** c 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 112469 Z= 0.280 Angle : 0.597 12.191 151931 Z= 0.308 Chirality : 0.042 0.230 17192 Planarity : 0.004 0.054 19582 Dihedral : 5.936 113.821 15495 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.91 % Favored : 93.08 % Rotamer: Outliers : 1.54 % Allowed : 14.17 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.20 % 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: 0.15 (0.07), residues: 13971 helix: 1.50 (0.07), residues: 6277 sheet: 0.02 (0.11), residues: 2088 loop : -1.53 (0.08), residues: 5606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP m 215 HIS 0.008 0.001 HIS V 214 PHE 0.034 0.001 PHE X 374 TYR 0.020 0.001 TYR W 75 ARG 0.007 0.000 ARG E 213 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27942 Ramachandran restraints generated. 13971 Oldfield, 0 Emsley, 13971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27942 Ramachandran restraints generated. 13971 Oldfield, 0 Emsley, 13971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 12025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 442 time to evaluate : 10.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 232 MET cc_start: 0.8656 (ptp) cc_final: 0.8299 (ptp) REVERT: E 277 MET cc_start: 0.9105 (mmp) cc_final: 0.8594 (mmp) REVERT: F 310 MET cc_start: 0.8713 (ppp) cc_final: 0.8420 (ppp) REVERT: F 366 MET cc_start: 0.9054 (mmp) cc_final: 0.8788 (mmp) REVERT: I 119 GLN cc_start: 0.9372 (OUTLIER) cc_final: 0.9100 (tm-30) REVERT: R 93 MET cc_start: 0.8333 (mpp) cc_final: 0.7931 (mtm) REVERT: n 164 MET cc_start: 0.8780 (mtm) cc_final: 0.8557 (mtp) REVERT: o 86 MET cc_start: 0.8684 (tmm) cc_final: 0.8437 (ttt) REVERT: t 141 TYR cc_start: 0.8368 (OUTLIER) cc_final: 0.8050 (m-10) REVERT: x 71 MET cc_start: 0.7228 (tpp) cc_final: 0.6634 (tpp) REVERT: x 163 MET cc_start: 0.4936 (ptm) cc_final: 0.4423 (tpp) REVERT: x 342 LYS cc_start: 0.6975 (OUTLIER) cc_final: 0.6462 (mptt) REVERT: A 299 MET cc_start: 0.8812 (tpp) cc_final: 0.8321 (mmt) REVERT: A 394 MET cc_start: 0.9004 (mmm) cc_final: 0.8422 (mmp) REVERT: B 164 MET cc_start: 0.8855 (ppp) cc_final: 0.8465 (ppp) REVERT: B 295 TYR cc_start: 0.6398 (OUTLIER) cc_final: 0.5178 (m-10) REVERT: D 153 MET cc_start: 0.7608 (mmm) cc_final: 0.7141 (tpp) REVERT: D 204 MET cc_start: 0.7426 (ppp) cc_final: 0.6528 (ppp) REVERT: U 560 MET cc_start: 0.6394 (tpp) cc_final: 0.5660 (tpp) REVERT: U 797 MET cc_start: 0.7688 (tpt) cc_final: 0.7424 (tpt) REVERT: W 190 MET cc_start: 0.9082 (OUTLIER) cc_final: 0.8841 (mmt) REVERT: W 267 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8581 (mt) REVERT: X 99 MET cc_start: 0.6813 (ttt) cc_final: 0.5857 (ppp) REVERT: X 254 MET cc_start: 0.8459 (mmt) cc_final: 0.7910 (mmt) REVERT: Y 50 MET cc_start: 0.7506 (mmm) cc_final: 0.6307 (mmm) REVERT: Y 53 TYR cc_start: 0.7858 (OUTLIER) cc_final: 0.7145 (p90) REVERT: Y 389 MET cc_start: 0.7323 (OUTLIER) cc_final: 0.6907 (pmm) REVERT: Z 125 ASP cc_start: 0.7004 (OUTLIER) cc_final: 0.6414 (p0) REVERT: Z 176 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.7294 (pp) REVERT: Z 261 TYR cc_start: 0.7123 (OUTLIER) cc_final: 0.6788 (m-10) REVERT: c 95 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.8261 (tpp) REVERT: c 167 MET cc_start: 0.8526 (mmp) cc_final: 0.8015 (tmm) REVERT: c 200 TYR cc_start: 0.6024 (OUTLIER) cc_final: 0.5567 (p90) REVERT: c 265 MET cc_start: 0.7839 (pmm) cc_final: 0.6587 (ppp) REVERT: f 58 MET cc_start: 0.8356 (pmm) cc_final: 0.8038 (pmm) REVERT: f 131 MET cc_start: 0.8788 (ptt) cc_final: 0.8373 (ppp) REVERT: f 340 MET cc_start: 0.7599 (OUTLIER) cc_final: 0.7282 (ppp) REVERT: f 524 MET cc_start: 0.8477 (ptt) cc_final: 0.8000 (ppp) REVERT: f 825 MET cc_start: 0.7913 (mmt) cc_final: 0.7640 (mmt) REVERT: V 175 MET cc_start: 0.8270 (ppp) cc_final: 0.7959 (tmm) outliers start: 184 outliers final: 88 residues processed: 596 average time/residue: 0.8239 time to fit residues: 893.3857 Evaluate side-chains 544 residues out of total 12025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 442 time to evaluate : 11.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain F residue 259 MET Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain F residue 354 PHE Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain H residue 207 ASN Chi-restraints excluded: chain I residue 119 GLN Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 214 ASP Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 189 MET Chi-restraints excluded: chain K residue 225 ASN Chi-restraints excluded: chain L residue 4 ASN Chi-restraints excluded: chain L residue 176 MET Chi-restraints excluded: chain N residue 86 MET Chi-restraints excluded: chain O residue 146 MET Chi-restraints excluded: chain S residue 27 THR Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain T residue 70 MET Chi-restraints excluded: chain g residue 51 VAL Chi-restraints excluded: chain g residue 69 LEU Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain l residue 230 SER Chi-restraints excluded: chain n residue 145 GLU Chi-restraints excluded: chain o residue 65 LEU Chi-restraints excluded: chain p residue 90 MET Chi-restraints excluded: chain t residue 127 MET Chi-restraints excluded: chain t residue 141 TYR Chi-restraints excluded: chain t residue 178 TYR Chi-restraints excluded: chain x residue 90 GLU Chi-restraints excluded: chain x residue 334 LYS Chi-restraints excluded: chain x residue 336 LYS Chi-restraints excluded: chain x residue 342 LYS Chi-restraints excluded: chain y residue 20 SER Chi-restraints excluded: chain y residue 56 LEU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain D residue 410 ASP Chi-restraints excluded: chain U residue 216 VAL Chi-restraints excluded: chain U residue 585 THR Chi-restraints excluded: chain U residue 614 VAL Chi-restraints excluded: chain U residue 675 MET Chi-restraints excluded: chain U residue 754 HIS Chi-restraints excluded: chain U residue 856 VAL Chi-restraints excluded: chain W residue 190 MET Chi-restraints excluded: chain W residue 267 LEU Chi-restraints excluded: chain W residue 370 TYR Chi-restraints excluded: chain W residue 420 ASP Chi-restraints excluded: chain X residue 210 LEU Chi-restraints excluded: chain X residue 251 LEU Chi-restraints excluded: chain X residue 345 VAL Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain Y residue 34 ASP Chi-restraints excluded: chain Y residue 53 TYR Chi-restraints excluded: chain Y residue 72 LYS Chi-restraints excluded: chain Y residue 154 ASN Chi-restraints excluded: chain Y residue 389 MET Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain Z residue 62 ASP Chi-restraints excluded: chain Z residue 102 HIS Chi-restraints excluded: chain Z residue 125 ASP Chi-restraints excluded: chain Z residue 127 LYS Chi-restraints excluded: chain Z residue 176 LEU Chi-restraints excluded: chain Z residue 257 MET Chi-restraints excluded: chain Z residue 260 VAL Chi-restraints excluded: chain Z residue 261 TYR Chi-restraints excluded: chain a residue 280 MET Chi-restraints excluded: chain a residue 334 THR Chi-restraints excluded: chain a residue 340 VAL Chi-restraints excluded: chain b residue 8 VAL Chi-restraints excluded: chain b residue 54 LEU Chi-restraints excluded: chain c residue 27 THR Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 95 MET Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 200 TYR Chi-restraints excluded: chain c residue 303 MET Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 189 ILE Chi-restraints excluded: chain d residue 237 ILE Chi-restraints excluded: chain f residue 277 LEU Chi-restraints excluded: chain f residue 340 MET Chi-restraints excluded: chain V residue 104 THR Chi-restraints excluded: chain V residue 225 ASP Chi-restraints excluded: chain V residue 421 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1388 random chunks: chunk 451 optimal weight: 20.0000 chunk 1208 optimal weight: 10.0000 chunk 265 optimal weight: 5.9990 chunk 787 optimal weight: 30.0000 chunk 331 optimal weight: 0.8980 chunk 1342 optimal weight: 30.0000 chunk 1114 optimal weight: 6.9990 chunk 621 optimal weight: 20.0000 chunk 111 optimal weight: 6.9990 chunk 444 optimal weight: 6.9990 chunk 705 optimal weight: 30.0000 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 169 ASN ** J 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 93 ASN ** y 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 GLN ** D 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 71 ASN ** Z 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 129 GLN ** b 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 112469 Z= 0.198 Angle : 0.563 12.395 151931 Z= 0.286 Chirality : 0.041 0.233 17192 Planarity : 0.004 0.052 19582 Dihedral : 5.795 114.739 15492 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 1.33 % Allowed : 15.24 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.20 % 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: 0.26 (0.07), residues: 13971 helix: 1.60 (0.07), residues: 6291 sheet: 0.11 (0.11), residues: 2074 loop : -1.50 (0.08), residues: 5606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP m 215 HIS 0.005 0.001 HIS E 19 PHE 0.024 0.001 PHE W 309 TYR 0.018 0.001 TYR W 75 ARG 0.005 0.000 ARG f 369 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27942 Ramachandran restraints generated. 13971 Oldfield, 0 Emsley, 13971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27942 Ramachandran restraints generated. 13971 Oldfield, 0 Emsley, 13971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 12025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 442 time to evaluate : 9.266 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: E 232 MET cc_start: 0.8701 (ptp) cc_final: 0.8444 (mpp) REVERT: E 277 MET cc_start: 0.9079 (mmp) cc_final: 0.8483 (mmp) REVERT: F 310 MET cc_start: 0.8722 (ppp) cc_final: 0.8432 (ppp) REVERT: F 366 MET cc_start: 0.8995 (mmp) cc_final: 0.8708 (mmp) REVERT: I 119 GLN cc_start: 0.9354 (OUTLIER) cc_final: 0.9143 (tm-30) REVERT: R 93 MET cc_start: 0.8298 (mpp) cc_final: 0.7932 (mtm) REVERT: n 164 MET cc_start: 0.8708 (mtm) cc_final: 0.8477 (mtp) REVERT: o 86 MET cc_start: 0.8689 (tmm) cc_final: 0.8404 (ttt) REVERT: q 1 MET cc_start: 0.8252 (ppp) cc_final: 0.7560 (ppp) REVERT: t 141 TYR cc_start: 0.8324 (OUTLIER) cc_final: 0.7922 (m-10) REVERT: x 71 MET cc_start: 0.7222 (tpp) cc_final: 0.6913 (tpp) REVERT: x 163 MET cc_start: 0.4890 (ptm) cc_final: 0.4391 (tpp) REVERT: x 342 LYS cc_start: 0.7056 (OUTLIER) cc_final: 0.6360 (mmtt) REVERT: A 164 MET cc_start: 0.7877 (ppp) cc_final: 0.7539 (ppp) REVERT: A 299 MET cc_start: 0.8785 (tpp) cc_final: 0.8399 (mmt) REVERT: A 309 PHE cc_start: 0.7993 (OUTLIER) cc_final: 0.7779 (m-10) REVERT: B 164 MET cc_start: 0.8887 (ppp) cc_final: 0.8497 (ppp) REVERT: B 295 TYR cc_start: 0.6422 (OUTLIER) cc_final: 0.5247 (m-10) REVERT: D 153 MET cc_start: 0.7604 (mmm) cc_final: 0.7287 (tpp) REVERT: D 204 MET cc_start: 0.7522 (ppp) cc_final: 0.6652 (ppp) REVERT: U 797 MET cc_start: 0.7788 (tpt) cc_final: 0.7534 (tpt) REVERT: W 190 MET cc_start: 0.9064 (OUTLIER) cc_final: 0.8812 (mmt) REVERT: W 267 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8581 (mt) REVERT: X 99 MET cc_start: 0.6710 (ttt) cc_final: 0.5780 (ppp) REVERT: X 254 MET cc_start: 0.8497 (mmt) cc_final: 0.8286 (mmt) REVERT: Y 50 MET cc_start: 0.7505 (mmm) cc_final: 0.6269 (mmm) REVERT: Y 53 TYR cc_start: 0.7881 (OUTLIER) cc_final: 0.7162 (p90) REVERT: Z 125 ASP cc_start: 0.6930 (OUTLIER) cc_final: 0.6436 (p0) REVERT: Z 176 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.7252 (pp) REVERT: Z 261 TYR cc_start: 0.7068 (OUTLIER) cc_final: 0.6719 (m-10) REVERT: c 95 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.8150 (tpp) REVERT: c 167 MET cc_start: 0.8471 (mmp) cc_final: 0.7906 (tmm) REVERT: c 200 TYR cc_start: 0.6109 (OUTLIER) cc_final: 0.5833 (p90) REVERT: c 265 MET cc_start: 0.7809 (pmm) cc_final: 0.6525 (ppp) REVERT: f 58 MET cc_start: 0.8355 (pmm) cc_final: 0.8054 (pmm) REVERT: f 131 MET cc_start: 0.8830 (ptt) cc_final: 0.8438 (ppp) REVERT: f 340 MET cc_start: 0.7603 (OUTLIER) cc_final: 0.7272 (ppp) REVERT: f 524 MET cc_start: 0.8439 (ptt) cc_final: 0.7957 (ppp) REVERT: f 744 MET cc_start: 0.8276 (ttm) cc_final: 0.8075 (ttm) REVERT: f 825 MET cc_start: 0.7892 (mmt) cc_final: 0.7635 (mmt) REVERT: f 829 MET cc_start: 0.7312 (pmm) cc_final: 0.6860 (tpt) REVERT: V 175 MET cc_start: 0.8239 (ppp) cc_final: 0.7961 (tmm) REVERT: e 30 LEU cc_start: 0.4835 (OUTLIER) cc_final: 0.4512 (mp) outliers start: 159 outliers final: 95 residues processed: 580 average time/residue: 0.8922 time to fit residues: 942.9323 Evaluate side-chains 552 residues out of total 12025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 442 time to evaluate : 9.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain F residue 259 MET Chi-restraints excluded: chain F residue 263 ASP Chi-restraints excluded: chain F residue 354 PHE Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain H residue 228 ASP Chi-restraints excluded: chain I residue 119 GLN Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 214 ASP Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 189 MET Chi-restraints excluded: chain K residue 225 ASN Chi-restraints excluded: chain L residue 4 ASN Chi-restraints excluded: chain L residue 176 MET Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain N residue 86 MET Chi-restraints excluded: chain S residue 27 THR Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain T residue 70 MET Chi-restraints excluded: chain g residue 51 VAL Chi-restraints excluded: chain g residue 69 LEU Chi-restraints excluded: chain g residue 73 THR Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain j residue 173 GLU Chi-restraints excluded: chain k residue 13 ASN Chi-restraints excluded: chain l residue 230 SER Chi-restraints excluded: chain o residue 65 LEU Chi-restraints excluded: chain p residue 58 THR Chi-restraints excluded: chain p residue 90 MET Chi-restraints excluded: chain q residue 132 HIS Chi-restraints excluded: chain t residue 127 MET Chi-restraints excluded: chain t residue 141 TYR Chi-restraints excluded: chain t residue 178 TYR Chi-restraints excluded: chain x residue 90 GLU Chi-restraints excluded: chain x residue 334 LYS Chi-restraints excluded: chain x residue 336 LYS Chi-restraints excluded: chain x residue 342 LYS Chi-restraints excluded: chain y residue 56 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain D residue 410 ASP Chi-restraints excluded: chain U residue 216 VAL Chi-restraints excluded: chain U residue 614 VAL Chi-restraints excluded: chain U residue 675 MET Chi-restraints excluded: chain U residue 754 HIS Chi-restraints excluded: chain U residue 856 VAL Chi-restraints excluded: chain W residue 190 MET Chi-restraints excluded: chain W residue 267 LEU Chi-restraints excluded: chain W residue 370 TYR Chi-restraints excluded: chain W residue 420 ASP Chi-restraints excluded: chain W residue 442 THR Chi-restraints excluded: chain X residue 210 LEU Chi-restraints excluded: chain X residue 345 VAL Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain Y residue 34 ASP Chi-restraints excluded: chain Y residue 39 ASP Chi-restraints excluded: chain Y residue 53 TYR Chi-restraints excluded: chain Y residue 72 LYS Chi-restraints excluded: chain Y residue 154 ASN Chi-restraints excluded: chain Y residue 389 MET Chi-restraints excluded: chain Z residue 102 HIS Chi-restraints excluded: chain Z residue 125 ASP Chi-restraints excluded: chain Z residue 127 LYS Chi-restraints excluded: chain Z residue 176 LEU Chi-restraints excluded: chain Z residue 257 MET Chi-restraints excluded: chain Z residue 260 VAL Chi-restraints excluded: chain Z residue 261 TYR Chi-restraints excluded: chain a residue 114 CYS Chi-restraints excluded: chain a residue 280 MET Chi-restraints excluded: chain a residue 334 THR Chi-restraints excluded: chain a residue 340 VAL Chi-restraints excluded: chain b residue 8 VAL Chi-restraints excluded: chain b residue 54 LEU Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 95 MET Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 200 TYR Chi-restraints excluded: chain c residue 226 MET Chi-restraints excluded: chain c residue 251 LEU Chi-restraints excluded: chain c residue 303 MET Chi-restraints excluded: chain d residue 106 LEU Chi-restraints excluded: chain d residue 189 ILE Chi-restraints excluded: chain d residue 237 ILE Chi-restraints excluded: chain f residue 76 GLU Chi-restraints excluded: chain f residue 211 ILE Chi-restraints excluded: chain f residue 277 LEU Chi-restraints excluded: chain f residue 340 MET Chi-restraints excluded: chain f residue 538 ILE Chi-restraints excluded: chain V residue 104 THR Chi-restraints excluded: chain V residue 225 ASP Chi-restraints excluded: chain V residue 421 ASP Chi-restraints excluded: chain e residue 30 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1388 random chunks: chunk 1294 optimal weight: 50.0000 chunk 151 optimal weight: 20.0000 chunk 765 optimal weight: 30.0000 chunk 980 optimal weight: 0.0010 chunk 759 optimal weight: 20.0000 chunk 1130 optimal weight: 7.9990 chunk 749 optimal weight: 10.0000 chunk 1337 optimal weight: 50.0000 chunk 837 optimal weight: 20.0000 chunk 815 optimal weight: 5.9990 chunk 617 optimal weight: 20.0000 overall best weight: 8.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 316 GLN H 169 ASN ** J 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 7 ASN ** y 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 29 GLN ** b 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 112469 Z= 0.285 Angle : 0.606 13.067 151931 Z= 0.311 Chirality : 0.042 0.230 17192 Planarity : 0.004 0.054 19582 Dihedral : 5.861 115.501 15492 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.01 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 1.57 % Allowed : 15.80 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.20 % 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: 0.16 (0.07), residues: 13971 helix: 1.50 (0.07), residues: 6303 sheet: 0.03 (0.11), residues: 2101 loop : -1.53 (0.08), residues: 5567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP m 215 HIS 0.006 0.001 HIS U 70 PHE 0.025 0.001 PHE W 309 TYR 0.022 0.001 TYR W 75 ARG 0.005 0.000 ARG F 364 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27942 Ramachandran restraints generated. 13971 Oldfield, 0 Emsley, 13971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27942 Ramachandran restraints generated. 13971 Oldfield, 0 Emsley, 13971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 12025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 441 time to evaluate : 9.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 232 MET cc_start: 0.8661 (ptp) cc_final: 0.8374 (mpp) REVERT: E 277 MET cc_start: 0.8994 (mmp) cc_final: 0.8384 (mmp) REVERT: F 310 MET cc_start: 0.8732 (ppp) cc_final: 0.8439 (ppp) REVERT: I 119 GLN cc_start: 0.9390 (OUTLIER) cc_final: 0.9135 (tm-30) REVERT: R 93 MET cc_start: 0.8335 (mpp) cc_final: 0.7969 (mtm) REVERT: n 164 MET cc_start: 0.8774 (mtm) cc_final: 0.8538 (mtp) REVERT: o 86 MET cc_start: 0.8683 (tmm) cc_final: 0.8453 (ttt) REVERT: q 1 MET cc_start: 0.8039 (ppp) cc_final: 0.7427 (ppp) REVERT: t 141 TYR cc_start: 0.8348 (OUTLIER) cc_final: 0.8020 (m-10) REVERT: x 163 MET cc_start: 0.4869 (ptm) cc_final: 0.4360 (tpp) REVERT: x 342 LYS cc_start: 0.7274 (OUTLIER) cc_final: 0.6731 (tttt) REVERT: A 309 PHE cc_start: 0.8112 (OUTLIER) cc_final: 0.7849 (m-10) REVERT: B 164 MET cc_start: 0.8938 (ppp) cc_final: 0.8543 (ppp) REVERT: B 295 TYR cc_start: 0.6568 (OUTLIER) cc_final: 0.5367 (m-10) REVERT: B 309 MET cc_start: 0.8902 (ttp) cc_final: 0.8693 (tmm) REVERT: D 153 MET cc_start: 0.7642 (mmm) cc_final: 0.7426 (tpp) REVERT: D 204 MET cc_start: 0.7621 (ppp) cc_final: 0.6767 (ppp) REVERT: U 560 MET cc_start: 0.6386 (tpp) cc_final: 0.5626 (tpp) REVERT: U 797 MET cc_start: 0.7931 (tpt) cc_final: 0.7449 (tpt) REVERT: W 190 MET cc_start: 0.9085 (OUTLIER) cc_final: 0.8806 (mmt) REVERT: W 267 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8615 (mt) REVERT: W 451 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7535 (tmm) REVERT: X 99 MET cc_start: 0.6684 (ttt) cc_final: 0.5794 (ppp) REVERT: X 254 MET cc_start: 0.8529 (mmt) cc_final: 0.8298 (mmt) REVERT: Y 50 MET cc_start: 0.7508 (mmm) cc_final: 0.6183 (mmm) REVERT: Y 53 TYR cc_start: 0.8034 (OUTLIER) cc_final: 0.7247 (p90) REVERT: Z 125 ASP cc_start: 0.7041 (OUTLIER) cc_final: 0.6479 (p0) REVERT: Z 176 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7212 (pp) REVERT: Z 261 TYR cc_start: 0.7312 (OUTLIER) cc_final: 0.6862 (m-80) REVERT: b 7 MET cc_start: 0.8294 (mmm) cc_final: 0.7628 (mmm) REVERT: b 154 THR cc_start: 0.7755 (OUTLIER) cc_final: 0.7414 (t) REVERT: c 95 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.8122 (tpp) REVERT: c 167 MET cc_start: 0.8520 (mmp) cc_final: 0.7893 (tmm) REVERT: c 200 TYR cc_start: 0.6142 (OUTLIER) cc_final: 0.5873 (p90) REVERT: c 265 MET cc_start: 0.7855 (pmm) cc_final: 0.6524 (ppp) REVERT: f 58 MET cc_start: 0.8398 (pmm) cc_final: 0.8130 (pmm) REVERT: f 131 MET cc_start: 0.8900 (ptt) cc_final: 0.8502 (ppp) REVERT: f 191 ILE cc_start: 0.5271 (OUTLIER) cc_final: 0.4830 (tp) REVERT: f 196 MET cc_start: 0.7884 (tpt) cc_final: 0.7396 (tmm) REVERT: f 340 MET cc_start: 0.7708 (OUTLIER) cc_final: 0.7330 (ppp) REVERT: f 524 MET cc_start: 0.8369 (ptt) cc_final: 0.7939 (ppp) REVERT: f 779 CYS cc_start: 0.8366 (OUTLIER) cc_final: 0.7872 (t) REVERT: f 825 MET cc_start: 0.8019 (mmt) cc_final: 0.7730 (mmt) REVERT: V 175 MET cc_start: 0.8272 (ppp) cc_final: 0.7951 (tmm) REVERT: V 176 MET cc_start: 0.8428 (tpp) cc_final: 0.7716 (ttt) REVERT: e 30 LEU cc_start: 0.4789 (OUTLIER) cc_final: 0.4488 (mp) outliers start: 187 outliers final: 115 residues processed: 598 average time/residue: 0.8350 time to fit residues: 907.9146 Evaluate side-chains 575 residues out of total 12025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 441 time to evaluate : 9.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain F residue 263 ASP Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain F residue 354 PHE Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 228 ASP Chi-restraints excluded: chain H residue 233 ILE Chi-restraints excluded: chain I residue 119 GLN Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 214 ASP Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 189 MET Chi-restraints excluded: chain K residue 225 ASN Chi-restraints excluded: chain L residue 4 ASN Chi-restraints excluded: chain L residue 176 MET Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain N residue 86 MET Chi-restraints excluded: chain O residue 146 MET Chi-restraints excluded: chain S residue 27 THR Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain T residue 70 MET Chi-restraints excluded: chain T residue 178 TYR Chi-restraints excluded: chain g residue 51 VAL Chi-restraints excluded: chain g residue 69 LEU Chi-restraints excluded: chain g residue 73 THR Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain h residue 186 ASP Chi-restraints excluded: chain j residue 173 GLU Chi-restraints excluded: chain k residue 13 ASN Chi-restraints excluded: chain l residue 230 SER Chi-restraints excluded: chain o residue 65 LEU Chi-restraints excluded: chain p residue 58 THR Chi-restraints excluded: chain p residue 90 MET Chi-restraints excluded: chain t residue 127 MET Chi-restraints excluded: chain t residue 141 TYR Chi-restraints excluded: chain t residue 178 TYR Chi-restraints excluded: chain x residue 90 GLU Chi-restraints excluded: chain x residue 334 LYS Chi-restraints excluded: chain x residue 336 LYS Chi-restraints excluded: chain x residue 342 LYS Chi-restraints excluded: chain y residue 56 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain D residue 403 TYR Chi-restraints excluded: chain D residue 410 ASP Chi-restraints excluded: chain U residue 216 VAL Chi-restraints excluded: chain U residue 577 ILE Chi-restraints excluded: chain U residue 614 VAL Chi-restraints excluded: chain U residue 675 MET Chi-restraints excluded: chain U residue 754 HIS Chi-restraints excluded: chain U residue 770 TRP Chi-restraints excluded: chain U residue 856 VAL Chi-restraints excluded: chain W residue 117 ASP Chi-restraints excluded: chain W residue 190 MET Chi-restraints excluded: chain W residue 267 LEU Chi-restraints excluded: chain W residue 370 TYR Chi-restraints excluded: chain W residue 420 ASP Chi-restraints excluded: chain W residue 442 THR Chi-restraints excluded: chain W residue 451 MET Chi-restraints excluded: chain X residue 210 LEU Chi-restraints excluded: chain X residue 345 VAL Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain Y residue 34 ASP Chi-restraints excluded: chain Y residue 39 ASP Chi-restraints excluded: chain Y residue 53 TYR Chi-restraints excluded: chain Y residue 72 LYS Chi-restraints excluded: chain Y residue 154 ASN Chi-restraints excluded: chain Y residue 389 MET Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain Z residue 62 ASP Chi-restraints excluded: chain Z residue 70 LEU Chi-restraints excluded: chain Z residue 85 VAL Chi-restraints excluded: chain Z residue 102 HIS Chi-restraints excluded: chain Z residue 125 ASP Chi-restraints excluded: chain Z residue 127 LYS Chi-restraints excluded: chain Z residue 176 LEU Chi-restraints excluded: chain Z residue 257 MET Chi-restraints excluded: chain Z residue 260 VAL Chi-restraints excluded: chain Z residue 261 TYR Chi-restraints excluded: chain a residue 114 CYS Chi-restraints excluded: chain a residue 280 MET Chi-restraints excluded: chain a residue 334 THR Chi-restraints excluded: chain a residue 340 VAL Chi-restraints excluded: chain b residue 8 VAL Chi-restraints excluded: chain b residue 54 LEU Chi-restraints excluded: chain b residue 154 THR Chi-restraints excluded: chain c residue 27 THR Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 95 MET Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 200 TYR Chi-restraints excluded: chain c residue 226 MET Chi-restraints excluded: chain c residue 303 MET Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 78 LEU Chi-restraints excluded: chain d residue 106 LEU Chi-restraints excluded: chain d residue 189 ILE Chi-restraints excluded: chain d residue 237 ILE Chi-restraints excluded: chain f residue 76 GLU Chi-restraints excluded: chain f residue 191 ILE Chi-restraints excluded: chain f residue 277 LEU Chi-restraints excluded: chain f residue 340 MET Chi-restraints excluded: chain f residue 538 ILE Chi-restraints excluded: chain f residue 779 CYS Chi-restraints excluded: chain V residue 104 THR Chi-restraints excluded: chain V residue 225 ASP Chi-restraints excluded: chain V residue 309 MET Chi-restraints excluded: chain V residue 364 THR Chi-restraints excluded: chain V residue 419 LEU Chi-restraints excluded: chain V residue 421 ASP Chi-restraints excluded: chain V residue 463 MET Chi-restraints excluded: chain e residue 30 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1388 random chunks: chunk 827 optimal weight: 30.0000 chunk 534 optimal weight: 30.0000 chunk 799 optimal weight: 40.0000 chunk 402 optimal weight: 20.0000 chunk 262 optimal weight: 9.9990 chunk 259 optimal weight: 20.0000 chunk 850 optimal weight: 40.0000 chunk 911 optimal weight: 2.9990 chunk 661 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 1051 optimal weight: 0.0670 overall best weight: 6.6130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 345 ASN H 169 ASN ** J 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 93 ASN ** y 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 HIS ** U 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 193 ASN a 344 GLN ** b 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 214 HIS ** e 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 112469 Z= 0.224 Angle : 0.582 13.087 151931 Z= 0.295 Chirality : 0.041 0.231 17192 Planarity : 0.004 0.054 19582 Dihedral : 5.789 114.823 15491 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 1.55 % Allowed : 16.27 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.20 % 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: 0.22 (0.07), residues: 13971 helix: 1.57 (0.07), residues: 6322 sheet: 0.04 (0.11), residues: 2104 loop : -1.52 (0.08), residues: 5545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP m 215 HIS 0.020 0.001 HIS U 756 PHE 0.024 0.001 PHE W 309 TYR 0.021 0.001 TYR W 75 ARG 0.003 0.000 ARG B 411 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27942 Ramachandran restraints generated. 13971 Oldfield, 0 Emsley, 13971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27942 Ramachandran restraints generated. 13971 Oldfield, 0 Emsley, 13971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 12025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 443 time to evaluate : 10.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 218 MET cc_start: 0.9186 (pmm) cc_final: 0.8910 (pmm) REVERT: E 232 MET cc_start: 0.8688 (ptp) cc_final: 0.8396 (mpp) REVERT: E 277 MET cc_start: 0.9014 (mmp) cc_final: 0.8389 (mmp) REVERT: F 310 MET cc_start: 0.8734 (ppp) cc_final: 0.8433 (ppp) REVERT: I 28 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8805 (mt) REVERT: I 119 GLN cc_start: 0.9372 (OUTLIER) cc_final: 0.9153 (tm-30) REVERT: K 156 MET cc_start: 0.8305 (tpp) cc_final: 0.8100 (ttm) REVERT: R 93 MET cc_start: 0.8313 (mpp) cc_final: 0.7994 (mtm) REVERT: n 164 MET cc_start: 0.8712 (mtm) cc_final: 0.8472 (mtp) REVERT: o 86 MET cc_start: 0.8673 (tmm) cc_final: 0.8411 (ttt) REVERT: t 141 TYR cc_start: 0.8316 (OUTLIER) cc_final: 0.7988 (m-10) REVERT: x 71 MET cc_start: 0.6383 (tpp) cc_final: 0.5336 (tpp) REVERT: x 163 MET cc_start: 0.4804 (ptm) cc_final: 0.4317 (tpp) REVERT: x 342 LYS cc_start: 0.7331 (OUTLIER) cc_final: 0.6769 (tttt) REVERT: A 309 PHE cc_start: 0.8127 (OUTLIER) cc_final: 0.7846 (m-10) REVERT: B 164 MET cc_start: 0.8951 (ppp) cc_final: 0.8611 (ppp) REVERT: B 295 TYR cc_start: 0.6624 (OUTLIER) cc_final: 0.5507 (m-10) REVERT: D 153 MET cc_start: 0.7660 (mmm) cc_final: 0.7370 (tpp) REVERT: D 204 MET cc_start: 0.7627 (ppp) cc_final: 0.6803 (ppp) REVERT: U 797 MET cc_start: 0.7918 (tpt) cc_final: 0.7413 (tpt) REVERT: W 190 MET cc_start: 0.9068 (OUTLIER) cc_final: 0.8771 (mmt) REVERT: W 267 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8638 (mt) REVERT: W 451 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7584 (tmm) REVERT: X 99 MET cc_start: 0.6654 (ttt) cc_final: 0.5776 (ppp) REVERT: X 254 MET cc_start: 0.8565 (mmt) cc_final: 0.8328 (mmt) REVERT: Y 50 MET cc_start: 0.7515 (mmm) cc_final: 0.6135 (mmm) REVERT: Y 53 TYR cc_start: 0.8022 (OUTLIER) cc_final: 0.7250 (p90) REVERT: Z 125 ASP cc_start: 0.7033 (OUTLIER) cc_final: 0.6515 (p0) REVERT: Z 176 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.7169 (pp) REVERT: Z 261 TYR cc_start: 0.7261 (OUTLIER) cc_final: 0.6786 (m-80) REVERT: b 7 MET cc_start: 0.8388 (mmm) cc_final: 0.7744 (mmm) REVERT: b 154 THR cc_start: 0.7756 (OUTLIER) cc_final: 0.7411 (t) REVERT: c 95 MET cc_start: 0.8369 (OUTLIER) cc_final: 0.8096 (tpp) REVERT: c 167 MET cc_start: 0.8540 (mmp) cc_final: 0.7919 (tmm) REVERT: c 200 TYR cc_start: 0.6249 (OUTLIER) cc_final: 0.5958 (p90) REVERT: d 39 THR cc_start: 0.5125 (OUTLIER) cc_final: 0.4735 (p) REVERT: f 58 MET cc_start: 0.8406 (pmm) cc_final: 0.8151 (pmm) REVERT: f 131 MET cc_start: 0.8937 (ptt) cc_final: 0.8539 (ppp) REVERT: f 191 ILE cc_start: 0.5252 (OUTLIER) cc_final: 0.4814 (tp) REVERT: f 196 MET cc_start: 0.7868 (tpt) cc_final: 0.7380 (tmm) REVERT: f 340 MET cc_start: 0.7730 (OUTLIER) cc_final: 0.7345 (ppp) REVERT: f 524 MET cc_start: 0.8379 (ptt) cc_final: 0.7945 (ppp) REVERT: f 779 CYS cc_start: 0.8390 (OUTLIER) cc_final: 0.7883 (t) REVERT: f 825 MET cc_start: 0.7953 (mmt) cc_final: 0.7699 (mmt) REVERT: f 829 MET cc_start: 0.7395 (pmm) cc_final: 0.6931 (tpt) REVERT: V 175 MET cc_start: 0.8265 (ppp) cc_final: 0.7928 (tmm) REVERT: V 176 MET cc_start: 0.8387 (tpp) cc_final: 0.7696 (ttt) REVERT: e 30 LEU cc_start: 0.4865 (OUTLIER) cc_final: 0.4589 (mp) outliers start: 185 outliers final: 114 residues processed: 602 average time/residue: 0.8554 time to fit residues: 935.4137 Evaluate side-chains 578 residues out of total 12025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 443 time to evaluate : 9.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain F residue 263 ASP Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 354 PHE Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 207 ASN Chi-restraints excluded: chain H residue 228 ASP Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 119 GLN Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 214 ASP Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 189 MET Chi-restraints excluded: chain K residue 225 ASN Chi-restraints excluded: chain L residue 4 ASN Chi-restraints excluded: chain L residue 176 MET Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain N residue 86 MET Chi-restraints excluded: chain S residue 27 THR Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain T residue 70 MET Chi-restraints excluded: chain T residue 178 TYR Chi-restraints excluded: chain g residue 51 VAL Chi-restraints excluded: chain g residue 69 LEU Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain j residue 173 GLU Chi-restraints excluded: chain k residue 13 ASN Chi-restraints excluded: chain l residue 230 SER Chi-restraints excluded: chain o residue 65 LEU Chi-restraints excluded: chain p residue 58 THR Chi-restraints excluded: chain p residue 90 MET Chi-restraints excluded: chain q residue 132 HIS Chi-restraints excluded: chain t residue 127 MET Chi-restraints excluded: chain t residue 141 TYR Chi-restraints excluded: chain t residue 178 TYR Chi-restraints excluded: chain x residue 90 GLU Chi-restraints excluded: chain x residue 334 LYS Chi-restraints excluded: chain x residue 336 LYS Chi-restraints excluded: chain x residue 342 LYS Chi-restraints excluded: chain y residue 20 SER Chi-restraints excluded: chain y residue 56 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 192 ASN Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 403 TYR Chi-restraints excluded: chain D residue 410 ASP Chi-restraints excluded: chain U residue 216 VAL Chi-restraints excluded: chain U residue 570 LEU Chi-restraints excluded: chain U residue 577 ILE Chi-restraints excluded: chain U residue 585 THR Chi-restraints excluded: chain U residue 614 VAL Chi-restraints excluded: chain U residue 675 MET Chi-restraints excluded: chain U residue 754 HIS Chi-restraints excluded: chain U residue 856 VAL Chi-restraints excluded: chain W residue 117 ASP Chi-restraints excluded: chain W residue 190 MET Chi-restraints excluded: chain W residue 267 LEU Chi-restraints excluded: chain W residue 370 TYR Chi-restraints excluded: chain W residue 420 ASP Chi-restraints excluded: chain W residue 442 THR Chi-restraints excluded: chain W residue 451 MET Chi-restraints excluded: chain X residue 210 LEU Chi-restraints excluded: chain X residue 345 VAL Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain Y residue 34 ASP Chi-restraints excluded: chain Y residue 39 ASP Chi-restraints excluded: chain Y residue 53 TYR Chi-restraints excluded: chain Y residue 72 LYS Chi-restraints excluded: chain Y residue 154 ASN Chi-restraints excluded: chain Y residue 389 MET Chi-restraints excluded: chain Z residue 62 ASP Chi-restraints excluded: chain Z residue 102 HIS Chi-restraints excluded: chain Z residue 125 ASP Chi-restraints excluded: chain Z residue 176 LEU Chi-restraints excluded: chain Z residue 257 MET Chi-restraints excluded: chain Z residue 260 VAL Chi-restraints excluded: chain Z residue 261 TYR Chi-restraints excluded: chain a residue 85 ARG Chi-restraints excluded: chain a residue 114 CYS Chi-restraints excluded: chain a residue 280 MET Chi-restraints excluded: chain a residue 334 THR Chi-restraints excluded: chain a residue 340 VAL Chi-restraints excluded: chain b residue 8 VAL Chi-restraints excluded: chain b residue 54 LEU Chi-restraints excluded: chain b residue 154 THR Chi-restraints excluded: chain c residue 27 THR Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 95 MET Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 200 TYR Chi-restraints excluded: chain c residue 226 MET Chi-restraints excluded: chain c residue 251 LEU Chi-restraints excluded: chain c residue 303 MET Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain d residue 78 LEU Chi-restraints excluded: chain d residue 106 LEU Chi-restraints excluded: chain d residue 120 GLU Chi-restraints excluded: chain d residue 189 ILE Chi-restraints excluded: chain d residue 237 ILE Chi-restraints excluded: chain f residue 76 GLU Chi-restraints excluded: chain f residue 191 ILE Chi-restraints excluded: chain f residue 277 LEU Chi-restraints excluded: chain f residue 340 MET Chi-restraints excluded: chain f residue 538 ILE Chi-restraints excluded: chain f residue 779 CYS Chi-restraints excluded: chain V residue 104 THR Chi-restraints excluded: chain V residue 225 ASP Chi-restraints excluded: chain V residue 309 MET Chi-restraints excluded: chain V residue 364 THR Chi-restraints excluded: chain V residue 421 ASP Chi-restraints excluded: chain V residue 474 LEU Chi-restraints excluded: chain e residue 30 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1388 random chunks: chunk 1216 optimal weight: 10.0000 chunk 1281 optimal weight: 40.0000 chunk 1169 optimal weight: 5.9990 chunk 1246 optimal weight: 8.9990 chunk 750 optimal weight: 50.0000 chunk 543 optimal weight: 30.0000 chunk 978 optimal weight: 20.0000 chunk 382 optimal weight: 5.9990 chunk 1126 optimal weight: 10.0000 chunk 1179 optimal weight: 50.0000 chunk 1242 optimal weight: 30.0000 overall best weight: 8.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 345 ASN F 417 HIS H 169 ASN ** J 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 93 ASN k 23 GLN x 281 GLN ** x 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 155 GLN ** Z 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 164 GLN ** b 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 758 ASN ** f 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 112469 Z= 0.271 Angle : 0.610 13.692 151931 Z= 0.311 Chirality : 0.042 0.239 17192 Planarity : 0.004 0.056 19582 Dihedral : 5.838 116.554 15491 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.01 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 1.55 % Allowed : 16.60 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.20 % 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: 0.16 (0.07), residues: 13971 helix: 1.51 (0.07), residues: 6293 sheet: 0.01 (0.11), residues: 2104 loop : -1.54 (0.08), residues: 5574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP m 215 HIS 0.007 0.001 HIS U 70 PHE 0.024 0.001 PHE W 309 TYR 0.023 0.001 TYR W 75 ARG 0.004 0.000 ARG B 411 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27942 Ramachandran restraints generated. 13971 Oldfield, 0 Emsley, 13971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27942 Ramachandran restraints generated. 13971 Oldfield, 0 Emsley, 13971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 12025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 442 time to evaluate : 9.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 232 MET cc_start: 0.8694 (ptp) cc_final: 0.8372 (mpp) REVERT: E 277 MET cc_start: 0.8979 (mmp) cc_final: 0.8358 (mmp) REVERT: F 310 MET cc_start: 0.8740 (ppp) cc_final: 0.8442 (ppp) REVERT: I 28 ILE cc_start: 0.9069 (OUTLIER) cc_final: 0.8829 (mt) REVERT: I 119 GLN cc_start: 0.9388 (OUTLIER) cc_final: 0.9145 (tm-30) REVERT: R 93 MET cc_start: 0.8338 (mpp) cc_final: 0.7994 (mtm) REVERT: T 50 MET cc_start: 0.8447 (ptt) cc_final: 0.8125 (ptt) REVERT: n 40 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7440 (mtm-85) REVERT: n 164 MET cc_start: 0.8751 (mtm) cc_final: 0.8511 (mtp) REVERT: o 86 MET cc_start: 0.8680 (tmm) cc_final: 0.8436 (ttt) REVERT: t 141 TYR cc_start: 0.8331 (OUTLIER) cc_final: 0.8001 (m-10) REVERT: x 71 MET cc_start: 0.6283 (tpp) cc_final: 0.5325 (tpp) REVERT: x 163 MET cc_start: 0.4769 (ptm) cc_final: 0.4318 (tpp) REVERT: x 342 LYS cc_start: 0.7536 (OUTLIER) cc_final: 0.7057 (tttt) REVERT: A 299 MET cc_start: 0.8782 (tpp) cc_final: 0.8423 (mmt) REVERT: A 309 PHE cc_start: 0.8205 (OUTLIER) cc_final: 0.7935 (m-10) REVERT: B 164 MET cc_start: 0.8992 (ppp) cc_final: 0.8625 (ppp) REVERT: B 295 TYR cc_start: 0.6676 (OUTLIER) cc_final: 0.5520 (m-10) REVERT: D 204 MET cc_start: 0.7677 (ppp) cc_final: 0.6871 (ppp) REVERT: U 520 MET cc_start: 0.8558 (mmm) cc_final: 0.8311 (mmm) REVERT: U 560 MET cc_start: 0.6306 (tpp) cc_final: 0.5539 (tpp) REVERT: U 797 MET cc_start: 0.7930 (tpt) cc_final: 0.7698 (tpt) REVERT: W 190 MET cc_start: 0.9073 (OUTLIER) cc_final: 0.8779 (mmt) REVERT: W 267 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8610 (mt) REVERT: W 451 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7552 (tmm) REVERT: X 99 MET cc_start: 0.6630 (ttt) cc_final: 0.5764 (ppp) REVERT: X 254 MET cc_start: 0.8575 (mmt) cc_final: 0.8325 (mmt) REVERT: Y 50 MET cc_start: 0.7529 (mmm) cc_final: 0.6159 (mmm) REVERT: Y 53 TYR cc_start: 0.8103 (OUTLIER) cc_final: 0.7313 (p90) REVERT: Z 125 ASP cc_start: 0.7085 (OUTLIER) cc_final: 0.6478 (p0) REVERT: Z 261 TYR cc_start: 0.7515 (OUTLIER) cc_final: 0.6977 (m-80) REVERT: a 357 CYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8792 (p) REVERT: b 7 MET cc_start: 0.8403 (mmm) cc_final: 0.7744 (mmm) REVERT: b 154 THR cc_start: 0.7816 (OUTLIER) cc_final: 0.7463 (t) REVERT: c 95 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.8126 (tpp) REVERT: c 167 MET cc_start: 0.8514 (mmp) cc_final: 0.7922 (tmm) REVERT: c 200 TYR cc_start: 0.6265 (OUTLIER) cc_final: 0.6005 (p90) REVERT: c 265 MET cc_start: 0.7825 (pmm) cc_final: 0.7373 (pmm) REVERT: d 39 THR cc_start: 0.5200 (OUTLIER) cc_final: 0.4827 (p) REVERT: f 58 MET cc_start: 0.8445 (pmm) cc_final: 0.8211 (pmm) REVERT: f 131 MET cc_start: 0.8984 (ptt) cc_final: 0.8594 (ppp) REVERT: f 191 ILE cc_start: 0.5284 (OUTLIER) cc_final: 0.4898 (pt) REVERT: f 340 MET cc_start: 0.7681 (OUTLIER) cc_final: 0.7328 (ppp) REVERT: f 524 MET cc_start: 0.8330 (ptt) cc_final: 0.7896 (ppp) REVERT: V 175 MET cc_start: 0.8266 (ppp) cc_final: 0.7895 (tmm) REVERT: V 176 MET cc_start: 0.8384 (tpp) cc_final: 0.7713 (ttt) REVERT: e 30 LEU cc_start: 0.4854 (OUTLIER) cc_final: 0.4613 (mp) outliers start: 185 outliers final: 125 residues processed: 597 average time/residue: 0.8756 time to fit residues: 950.6732 Evaluate side-chains 587 residues out of total 12025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 441 time to evaluate : 9.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain E residue 345 ASN Chi-restraints excluded: chain F residue 263 ASP Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain F residue 354 PHE Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 207 ASN Chi-restraints excluded: chain H residue 228 ASP Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 119 GLN Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 214 ASP Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 189 MET Chi-restraints excluded: chain K residue 225 ASN Chi-restraints excluded: chain L residue 4 ASN Chi-restraints excluded: chain L residue 176 MET Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain N residue 86 MET Chi-restraints excluded: chain O residue 146 MET Chi-restraints excluded: chain S residue 27 THR Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain T residue 70 MET Chi-restraints excluded: chain T residue 178 TYR Chi-restraints excluded: chain g residue 51 VAL Chi-restraints excluded: chain g residue 69 LEU Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain j residue 173 GLU Chi-restraints excluded: chain k residue 13 ASN Chi-restraints excluded: chain l residue 230 SER Chi-restraints excluded: chain n residue 40 ARG Chi-restraints excluded: chain o residue 65 LEU Chi-restraints excluded: chain p residue 58 THR Chi-restraints excluded: chain p residue 90 MET Chi-restraints excluded: chain q residue 132 HIS Chi-restraints excluded: chain t residue 127 MET Chi-restraints excluded: chain t residue 141 TYR Chi-restraints excluded: chain t residue 178 TYR Chi-restraints excluded: chain x residue 90 GLU Chi-restraints excluded: chain x residue 334 LYS Chi-restraints excluded: chain x residue 336 LYS Chi-restraints excluded: chain x residue 342 LYS Chi-restraints excluded: chain y residue 20 SER Chi-restraints excluded: chain y residue 56 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 384 GLU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 368 ASP Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain D residue 403 TYR Chi-restraints excluded: chain D residue 410 ASP Chi-restraints excluded: chain U residue 216 VAL Chi-restraints excluded: chain U residue 570 LEU Chi-restraints excluded: chain U residue 577 ILE Chi-restraints excluded: chain U residue 585 THR Chi-restraints excluded: chain U residue 614 VAL Chi-restraints excluded: chain U residue 675 MET Chi-restraints excluded: chain U residue 754 HIS Chi-restraints excluded: chain U residue 770 TRP Chi-restraints excluded: chain U residue 819 VAL Chi-restraints excluded: chain U residue 856 VAL Chi-restraints excluded: chain W residue 117 ASP Chi-restraints excluded: chain W residue 190 MET Chi-restraints excluded: chain W residue 267 LEU Chi-restraints excluded: chain W residue 338 THR Chi-restraints excluded: chain W residue 370 TYR Chi-restraints excluded: chain W residue 420 ASP Chi-restraints excluded: chain W residue 442 THR Chi-restraints excluded: chain W residue 451 MET Chi-restraints excluded: chain X residue 210 LEU Chi-restraints excluded: chain X residue 345 VAL Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain Y residue 34 ASP Chi-restraints excluded: chain Y residue 39 ASP Chi-restraints excluded: chain Y residue 53 TYR Chi-restraints excluded: chain Y residue 72 LYS Chi-restraints excluded: chain Y residue 154 ASN Chi-restraints excluded: chain Y residue 389 MET Chi-restraints excluded: chain Z residue 62 ASP Chi-restraints excluded: chain Z residue 85 VAL Chi-restraints excluded: chain Z residue 102 HIS Chi-restraints excluded: chain Z residue 125 ASP Chi-restraints excluded: chain Z residue 257 MET Chi-restraints excluded: chain Z residue 260 VAL Chi-restraints excluded: chain Z residue 261 TYR Chi-restraints excluded: chain a residue 85 ARG Chi-restraints excluded: chain a residue 114 CYS Chi-restraints excluded: chain a residue 280 MET Chi-restraints excluded: chain a residue 334 THR Chi-restraints excluded: chain a residue 340 VAL Chi-restraints excluded: chain a residue 357 CYS Chi-restraints excluded: chain b residue 8 VAL Chi-restraints excluded: chain b residue 21 PHE Chi-restraints excluded: chain b residue 54 LEU Chi-restraints excluded: chain b residue 154 THR Chi-restraints excluded: chain c residue 27 THR Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 95 MET Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 200 TYR Chi-restraints excluded: chain c residue 226 MET Chi-restraints excluded: chain c residue 251 LEU Chi-restraints excluded: chain c residue 303 MET Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain d residue 78 LEU Chi-restraints excluded: chain d residue 120 GLU Chi-restraints excluded: chain d residue 189 ILE Chi-restraints excluded: chain d residue 237 ILE Chi-restraints excluded: chain f residue 76 GLU Chi-restraints excluded: chain f residue 191 ILE Chi-restraints excluded: chain f residue 277 LEU Chi-restraints excluded: chain f residue 340 MET Chi-restraints excluded: chain f residue 538 ILE Chi-restraints excluded: chain V residue 104 THR Chi-restraints excluded: chain V residue 225 ASP Chi-restraints excluded: chain V residue 309 MET Chi-restraints excluded: chain V residue 364 THR Chi-restraints excluded: chain V residue 421 ASP Chi-restraints excluded: chain V residue 463 MET Chi-restraints excluded: chain V residue 474 LEU Chi-restraints excluded: chain e residue 30 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1388 random chunks: chunk 818 optimal weight: 20.0000 chunk 1318 optimal weight: 9.9990 chunk 804 optimal weight: 3.9990 chunk 625 optimal weight: 7.9990 chunk 916 optimal weight: 10.0000 chunk 1382 optimal weight: 9.9990 chunk 1272 optimal weight: 8.9990 chunk 1101 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 chunk 850 optimal weight: 30.0000 chunk 675 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 345 ASN H 169 ASN ** J 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 93 ASN p 81 GLN ** x 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 281 GLN ** x 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 116 HIS ** f 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 112469 Z= 0.232 Angle : 0.599 14.605 151931 Z= 0.303 Chirality : 0.042 0.230 17192 Planarity : 0.004 0.055 19582 Dihedral : 5.783 115.941 15489 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.77 % Favored : 93.22 % Rotamer: Outliers : 1.38 % Allowed : 16.81 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.20 % 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: 13971 helix: 1.56 (0.07), residues: 6301 sheet: 0.02 (0.11), residues: 2114 loop : -1.54 (0.08), residues: 5556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP m 215 HIS 0.007 0.001 HIS U 70 PHE 0.024 0.001 PHE W 309 TYR 0.021 0.001 TYR W 75 ARG 0.007 0.000 ARG E 344 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 27942 Ramachandran restraints generated. 13971 Oldfield, 0 Emsley, 13971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 27942 Ramachandran restraints generated. 13971 Oldfield, 0 Emsley, 13971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 12025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 443 time to evaluate : 9.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 1 MET cc_start: 0.3230 (OUTLIER) cc_final: 0.2955 (tpt) REVERT: E 232 MET cc_start: 0.8732 (ptp) cc_final: 0.8419 (mpp) REVERT: E 277 MET cc_start: 0.9004 (mmp) cc_final: 0.8360 (mmp) REVERT: F 310 MET cc_start: 0.8738 (ppp) cc_final: 0.8426 (ppp) REVERT: I 28 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8802 (mt) REVERT: I 119 GLN cc_start: 0.9377 (OUTLIER) cc_final: 0.9159 (tm-30) REVERT: R 93 MET cc_start: 0.8320 (mpp) cc_final: 0.7985 (mtm) REVERT: T 50 MET cc_start: 0.8451 (ptt) cc_final: 0.8117 (ptt) REVERT: n 40 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7537 (mtm-85) REVERT: n 164 MET cc_start: 0.8709 (mtm) cc_final: 0.8462 (mtp) REVERT: o 86 MET cc_start: 0.8670 (tmm) cc_final: 0.8407 (ttt) REVERT: t 141 TYR cc_start: 0.8298 (OUTLIER) cc_final: 0.7959 (m-10) REVERT: x 71 MET cc_start: 0.6311 (tpp) cc_final: 0.5370 (tpp) REVERT: x 163 MET cc_start: 0.4777 (ptm) cc_final: 0.4366 (tpt) REVERT: x 342 LYS cc_start: 0.7595 (OUTLIER) cc_final: 0.7129 (tttt) REVERT: A 299 MET cc_start: 0.8785 (tpp) cc_final: 0.8438 (mmt) REVERT: A 309 PHE cc_start: 0.8205 (OUTLIER) cc_final: 0.7928 (m-10) REVERT: B 74 MET cc_start: 0.7175 (pmm) cc_final: 0.6388 (pmm) REVERT: B 164 MET cc_start: 0.8996 (ppp) cc_final: 0.8662 (ppp) REVERT: B 295 TYR cc_start: 0.6739 (OUTLIER) cc_final: 0.5556 (m-10) REVERT: B 309 MET cc_start: 0.8932 (ttp) cc_final: 0.8649 (tmm) REVERT: D 204 MET cc_start: 0.7645 (ppp) cc_final: 0.6859 (ppp) REVERT: U 520 MET cc_start: 0.8457 (mmm) cc_final: 0.8202 (mmm) REVERT: U 560 MET cc_start: 0.6293 (tpp) cc_final: 0.5480 (tpp) REVERT: U 675 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.8549 (mmt) REVERT: U 797 MET cc_start: 0.7912 (tpt) cc_final: 0.7684 (tpt) REVERT: W 190 MET cc_start: 0.9054 (OUTLIER) cc_final: 0.8745 (mmt) REVERT: W 267 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8628 (mt) REVERT: W 451 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7592 (tmm) REVERT: X 99 MET cc_start: 0.6622 (ttt) cc_final: 0.5749 (ppp) REVERT: X 254 MET cc_start: 0.8594 (mmt) cc_final: 0.8353 (mmt) REVERT: Y 50 MET cc_start: 0.7511 (mmm) cc_final: 0.6079 (mmm) REVERT: Y 53 TYR cc_start: 0.8100 (OUTLIER) cc_final: 0.7315 (p90) REVERT: Z 125 ASP cc_start: 0.7062 (OUTLIER) cc_final: 0.6429 (p0) REVERT: Z 261 TYR cc_start: 0.7505 (OUTLIER) cc_final: 0.6964 (m-80) REVERT: b 7 MET cc_start: 0.8393 (mmm) cc_final: 0.7718 (mmm) REVERT: b 154 THR cc_start: 0.7871 (OUTLIER) cc_final: 0.7519 (t) REVERT: c 95 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.8155 (tpp) REVERT: c 167 MET cc_start: 0.8501 (mmp) cc_final: 0.7934 (tmm) REVERT: c 200 TYR cc_start: 0.6294 (OUTLIER) cc_final: 0.5926 (p90) REVERT: c 265 MET cc_start: 0.7795 (pmm) cc_final: 0.7309 (pmm) REVERT: d 39 THR cc_start: 0.5156 (OUTLIER) cc_final: 0.4800 (p) REVERT: f 58 MET cc_start: 0.8453 (pmm) cc_final: 0.8224 (pmm) REVERT: f 131 MET cc_start: 0.9012 (ptt) cc_final: 0.8630 (ppp) REVERT: f 191 ILE cc_start: 0.5272 (OUTLIER) cc_final: 0.4890 (pt) REVERT: f 340 MET cc_start: 0.7743 (OUTLIER) cc_final: 0.7387 (ppp) REVERT: f 524 MET cc_start: 0.8324 (ptt) cc_final: 0.7876 (ppp) REVERT: f 829 MET cc_start: 0.7365 (pmm) cc_final: 0.6923 (tpt) REVERT: V 175 MET cc_start: 0.8278 (ppp) cc_final: 0.7917 (tmm) REVERT: V 176 MET cc_start: 0.8385 (tpp) cc_final: 0.7742 (ttt) REVERT: e 30 LEU cc_start: 0.4843 (OUTLIER) cc_final: 0.4610 (mp) outliers start: 165 outliers final: 127 residues processed: 580 average time/residue: 0.8740 time to fit residues: 921.4267 Evaluate side-chains 591 residues out of total 12025 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 442 time to evaluate : 9.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain E residue 345 ASN Chi-restraints excluded: chain F residue 263 ASP Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain F residue 354 PHE Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain G residue 86 ASP Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 207 ASN Chi-restraints excluded: chain H residue 228 ASP Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 119 GLN Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 214 ASP Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 189 MET Chi-restraints excluded: chain K residue 225 ASN Chi-restraints excluded: chain L residue 4 ASN Chi-restraints excluded: chain L residue 176 MET Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain N residue 86 MET Chi-restraints excluded: chain O residue 80 ASN Chi-restraints excluded: chain O residue 146 MET Chi-restraints excluded: chain S residue 27 THR Chi-restraints excluded: chain S residue 166 LEU Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain T residue 70 MET Chi-restraints excluded: chain T residue 127 MET Chi-restraints excluded: chain T residue 178 TYR Chi-restraints excluded: chain g residue 51 VAL Chi-restraints excluded: chain g residue 69 LEU Chi-restraints excluded: chain g residue 84 THR Chi-restraints excluded: chain i residue 59 VAL Chi-restraints excluded: chain j residue 173 GLU Chi-restraints excluded: chain k residue 13 ASN Chi-restraints excluded: chain l residue 230 SER Chi-restraints excluded: chain m residue 197 ILE Chi-restraints excluded: chain n residue 40 ARG Chi-restraints excluded: chain o residue 65 LEU Chi-restraints excluded: chain p residue 58 THR Chi-restraints excluded: chain p residue 90 MET Chi-restraints excluded: chain q residue 132 HIS Chi-restraints excluded: chain t residue 127 MET Chi-restraints excluded: chain t residue 141 TYR Chi-restraints excluded: chain t residue 178 TYR Chi-restraints excluded: chain x residue 90 GLU Chi-restraints excluded: chain x residue 334 LYS Chi-restraints excluded: chain x residue 336 LYS Chi-restraints excluded: chain x residue 342 LYS Chi-restraints excluded: chain y residue 20 SER Chi-restraints excluded: chain y residue 56 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 295 TYR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 143 LEU Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain D residue 403 TYR Chi-restraints excluded: chain D residue 410 ASP Chi-restraints excluded: chain U residue 216 VAL Chi-restraints excluded: chain U residue 570 LEU Chi-restraints excluded: chain U residue 577 ILE Chi-restraints excluded: chain U residue 585 THR Chi-restraints excluded: chain U residue 614 VAL Chi-restraints excluded: chain U residue 675 MET Chi-restraints excluded: chain U residue 754 HIS Chi-restraints excluded: chain U residue 770 TRP Chi-restraints excluded: chain U residue 819 VAL Chi-restraints excluded: chain U residue 856 VAL Chi-restraints excluded: chain W residue 117 ASP Chi-restraints excluded: chain W residue 190 MET Chi-restraints excluded: chain W residue 267 LEU Chi-restraints excluded: chain W residue 338 THR Chi-restraints excluded: chain W residue 370 TYR Chi-restraints excluded: chain W residue 420 ASP Chi-restraints excluded: chain W residue 442 THR Chi-restraints excluded: chain W residue 451 MET Chi-restraints excluded: chain X residue 210 LEU Chi-restraints excluded: chain X residue 345 VAL Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain Y residue 34 ASP Chi-restraints excluded: chain Y residue 39 ASP Chi-restraints excluded: chain Y residue 53 TYR Chi-restraints excluded: chain Y residue 72 LYS Chi-restraints excluded: chain Y residue 154 ASN Chi-restraints excluded: chain Y residue 389 MET Chi-restraints excluded: chain Z residue 62 ASP Chi-restraints excluded: chain Z residue 85 VAL Chi-restraints excluded: chain Z residue 102 HIS Chi-restraints excluded: chain Z residue 125 ASP Chi-restraints excluded: chain Z residue 257 MET Chi-restraints excluded: chain Z residue 260 VAL Chi-restraints excluded: chain Z residue 261 TYR Chi-restraints excluded: chain a residue 85 ARG Chi-restraints excluded: chain a residue 114 CYS Chi-restraints excluded: chain a residue 280 MET Chi-restraints excluded: chain a residue 334 THR Chi-restraints excluded: chain a residue 340 VAL Chi-restraints excluded: chain b residue 8 VAL Chi-restraints excluded: chain b residue 21 PHE Chi-restraints excluded: chain b residue 54 LEU Chi-restraints excluded: chain b residue 154 THR Chi-restraints excluded: chain c residue 27 THR Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 95 MET Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 200 TYR Chi-restraints excluded: chain c residue 226 MET Chi-restraints excluded: chain c residue 251 LEU Chi-restraints excluded: chain c residue 303 MET Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain d residue 78 LEU Chi-restraints excluded: chain d residue 106 LEU Chi-restraints excluded: chain d residue 120 GLU Chi-restraints excluded: chain d residue 189 ILE Chi-restraints excluded: chain d residue 237 ILE Chi-restraints excluded: chain f residue 76 GLU Chi-restraints excluded: chain f residue 191 ILE Chi-restraints excluded: chain f residue 340 MET Chi-restraints excluded: chain f residue 538 ILE Chi-restraints excluded: chain f residue 799 VAL Chi-restraints excluded: chain V residue 104 THR Chi-restraints excluded: chain V residue 192 MET Chi-restraints excluded: chain V residue 225 ASP Chi-restraints excluded: chain V residue 309 MET Chi-restraints excluded: chain V residue 364 THR Chi-restraints excluded: chain V residue 419 LEU Chi-restraints excluded: chain V residue 421 ASP Chi-restraints excluded: chain V residue 463 MET Chi-restraints excluded: chain V residue 474 LEU Chi-restraints excluded: chain e residue 30 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1388 random chunks: chunk 874 optimal weight: 4.9990 chunk 1172 optimal weight: 5.9990 chunk 337 optimal weight: 10.0000 chunk 1015 optimal weight: 0.0070 chunk 162 optimal weight: 8.9990 chunk 305 optimal weight: 4.9990 chunk 1102 optimal weight: 10.0000 chunk 461 optimal weight: 40.0000 chunk 1132 optimal weight: 3.9990 chunk 139 optimal weight: 0.3980 chunk 203 optimal weight: 7.9990 overall best weight: 2.8804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 GLN ** E 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 169 ASN ** J 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 23 GLN ** x 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 281 GLN ** x 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 366 HIS ** U 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 365 GLN ** Z 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 193 ASN a 143 ASN ** a 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 105 HIS ** b 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.040758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.023894 restraints weight = 1190631.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.024530 restraints weight = 896894.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.024546 restraints weight = 602099.756| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.023 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.022 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3147 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 112469 Z= 0.147 Angle : 0.570 14.266 151931 Z= 0.285 Chirality : 0.041 0.268 17192 Planarity : 0.004 0.054 19582 Dihedral : 5.604 114.790 15489 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.45 % Favored : 93.54 % Rotamer: Outliers : 1.02 % Allowed : 17.31 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.20 % 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: 13971 helix: 1.69 (0.07), residues: 6292 sheet: 0.15 (0.11), residues: 2086 loop : -1.49 (0.08), residues: 5593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP m 215 HIS 0.006 0.001 HIS U 70 PHE 0.022 0.001 PHE W 309 TYR 0.019 0.001 TYR c 201 ARG 0.003 0.000 ARG x 293 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19579.76 seconds wall clock time: 347 minutes 53.18 seconds (20873.18 seconds total)