Starting phenix.real_space_refine on Sun Mar 10 14:28:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w38_32273/03_2024/7w38_32273_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w38_32273/03_2024/7w38_32273.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w38_32273/03_2024/7w38_32273.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w38_32273/03_2024/7w38_32273.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w38_32273/03_2024/7w38_32273_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w38_32273/03_2024/7w38_32273_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 16 5.49 5 Mg 6 5.21 5 S 615 5.16 5 C 67098 2.51 5 N 18271 2.21 5 O 20171 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.25s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 106178 Number of models: 1 Model: "" Number of chains: 55 Chain: "A" Number of atoms: 3240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3240 Classifications: {'peptide': 413} Link IDs: {'PTRANS': 23, 'TRANS': 389} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3042 Classifications: {'peptide': 388} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 367} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 2968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 2968 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 362} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 3039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3039 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 17, 'TRANS': 362} Chain: "E" Number of atoms: 2860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2860 Classifications: {'peptide': 375} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 18, 'TRANS': 356} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 7, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 67 Chain: "G" Number of atoms: 1889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1889 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 235} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1805 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 221} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "I" Number of atoms: 1958 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 250, 1955 Classifications: {'peptide': 250} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 244} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 250, 1955 Classifications: {'peptide': 250} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 244} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 1981 Chain: "J" Number of atoms: 1880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1880 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 232} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1777 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 225} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "L" Number of atoms: 1866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1866 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 227} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "M" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1876 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 234} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "N" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1514 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 6, 'TRANS': 195} Chain: "O" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1649 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 210} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "P" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1587 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "Q" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1588 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 190} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1559 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 2, 'TRANS': 198} Chain: "S" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1641 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 206} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "T" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1683 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'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: "U" Number of atoms: 5945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 764, 5945 Classifications: {'peptide': 764} Link IDs: {'PTRANS': 29, 'TRANS': 734} Chain breaks: 2 Chain: "V" Number of atoms: 3754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3754 Classifications: {'peptide': 472} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 16, 'TRANS': 455} Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 73 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: "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: "g" Number of atoms: 1880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1880 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 235} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "h" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1805 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 221} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "i" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1955 Classifications: {'peptide': 250} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 244} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "j" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1861 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 232} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "k" Number of atoms: 1782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1782 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 225} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "l" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1861 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 227} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "m" Number of atoms: 1881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1881 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 5, 'TRANS': 234} Chain: "n" Number of atoms: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1510 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 195} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "o" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1659 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 210} Chain: "p" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1591 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain: "q" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1588 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 190} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "r" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1559 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 2, 'TRANS': 198} Chain: "s" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1654 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 206} Chain: "t" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1687 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 7, 'TRANS': 208} Chain: "x" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 588 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 4, 'TRANS': 71} Chain: "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: "F" Number of atoms: 3251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3251 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 18, 'TRANS': 396} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "u" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "e" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 425 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 10 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 GLN X 380 " occ=0.89 ... (7 atoms not shown) pdb=" NE2 GLN X 380 " occ=0.89 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 Time building chain proxies: 41.10, per 1000 atoms: 0.39 Number of scatterers: 106178 At special positions: 0 Unit cell: (338.39, 215.09, 219.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 615 16.00 P 16 15.00 Mg 6 11.99 O 20171 8.00 N 18271 7.00 C 67098 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: 30.59 Conformation dependent library (CDL) restraints added in 15.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN c 401 " pdb="ZN ZN c 401 " - pdb=" NE2 HIS c 115 " pdb="ZN ZN c 401 " - pdb=" NE2 HIS c 113 " 26880 Ramachandran restraints generated. 13440 Oldfield, 0 Emsley, 13440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 25286 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: 497 helices and 84 sheets defined 55.3% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 50.71 Creating SS restraints... Processing helix chain 'A' and resid 26 through 36 removed outlier: 3.894A pdb=" N ILE A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 64 removed outlier: 4.105A pdb=" N ARG A 43 " --> pdb=" O SER A 39 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLN A 44 " --> pdb=" O THR A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 79 removed outlier: 3.905A pdb=" N TRP A 78 " --> pdb=" O PRO A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 91 removed outlier: 5.258A pdb=" N THR A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLN A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 165 removed outlier: 4.827A pdb=" N MET A 164 " --> pdb=" O THR A 160 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N GLN A 165 " --> pdb=" O VAL A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 178 removed outlier: 4.052A pdb=" N VAL A 177 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLY A 178 " --> pdb=" O TYR A 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 173 through 178' Processing helix chain 'A' and resid 180 through 197 removed outlier: 3.782A pdb=" N VAL A 190 " --> pdb=" O LYS A 186 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N THR A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Proline residue: A 194 - end of helix Processing helix chain 'A' and resid 198 through 205 removed outlier: 5.034A pdb=" N VAL A 202 " --> pdb=" O PRO A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 233 Processing helix chain 'A' and resid 241 through 246 removed outlier: 4.097A pdb=" N LEU A 245 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N VAL A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 241 through 246' Processing helix chain 'A' and resid 251 through 267 removed outlier: 3.699A pdb=" N THR A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LYS A 267 " --> pdb=" O MET A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 281 removed outlier: 4.238A pdb=" N ILE A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 308 removed outlier: 4.448A 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 360 removed outlier: 5.645A pdb=" N ARG A 351 " --> pdb=" O ASP A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 378 removed outlier: 4.140A pdb=" N LEU A 373 " --> pdb=" O ARG A 369 " (cutoff:3.500A) Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 381 through 400 removed outlier: 3.689A pdb=" N ALA A 399 " --> pdb=" O PHE A 395 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ARG A 400 " --> pdb=" O ALA A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 417 Processing helix chain 'A' and resid 425 through 430 removed outlier: 4.015A pdb=" N TYR A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 423 removed outlier: 4.359A pdb=" N LYS A 422 " --> pdb=" O SER A 419 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE A 423 " --> pdb=" O TYR A 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 87 removed outlier: 4.342A pdb=" N MET B 85 " --> pdb=" O ASN B 81 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LYS B 86 " --> pdb=" O GLN B 82 " (cutoff:3.500A) Proline residue: B 87 - end of helix Processing helix chain 'B' and resid 92 through 104 removed outlier: 4.501A pdb=" N ARG B 96 " --> pdb=" O GLN B 92 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY B 104 " --> pdb=" O ASP B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 175 removed outlier: 3.636A pdb=" N THR B 172 " --> pdb=" O ASP B 168 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL B 173 " --> pdb=" O PRO B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 188 removed outlier: 4.390A pdb=" N ILE B 187 " --> pdb=" O THR B 183 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLY B 188 " --> pdb=" O TYR B 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 183 through 188' Processing helix chain 'B' and resid 190 through 201 removed outlier: 5.794A pdb=" N ILE B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLN B 195 " --> pdb=" O ASP B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 207 Processing helix chain 'B' and resid 208 through 215 removed outlier: 5.130A pdb=" N GLU B 212 " --> pdb=" O PRO B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 243 Processing helix chain 'B' and resid 251 through 256 removed outlier: 4.260A pdb=" N LEU B 255 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ILE B 256 " --> pdb=" O GLY B 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 251 through 256' Processing helix chain 'B' and resid 261 through 278 removed outlier: 4.533A pdb=" N LYS B 265 " --> pdb=" O GLY B 261 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA B 278 " --> pdb=" O ALA B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 293 removed outlier: 4.801A pdb=" N ILE B 290 " --> pdb=" O GLU B 286 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N GLY B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 317 removed outlier: 3.893A pdb=" N ILE B 305 " --> pdb=" O GLY B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.864A pdb=" N ILE B 342 " --> pdb=" O ASP B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 370 Processing helix chain 'B' and resid 379 through 388 removed outlier: 3.899A pdb=" N LEU B 383 " --> pdb=" O THR B 379 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LYS B 387 " --> pdb=" O LEU B 383 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N ASP B 388 " --> pdb=" O ILE B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 410 Processing helix chain 'B' and resid 415 through 427 removed outlier: 3.691A pdb=" N PHE B 419 " --> pdb=" O THR B 415 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU B 424 " --> pdb=" O LYS B 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 65 removed outlier: 3.920A pdb=" N LEU C 33 " --> pdb=" O GLU C 29 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE C 34 " --> pdb=" O GLU C 30 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU C 63 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLN C 64 " --> pdb=" O ARG C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 109 removed outlier: 4.895A pdb=" N THR C 109 " --> pdb=" O ILE C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 142 Processing helix chain 'C' and resid 154 through 171 removed outlier: 4.748A pdb=" N LEU C 167 " --> pdb=" O GLU C 163 " (cutoff:3.500A) Proline residue: C 168 - end of helix Processing helix chain 'C' and resid 172 through 179 removed outlier: 3.887A pdb=" N LEU C 178 " --> pdb=" O LEU C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 208 Processing helix chain 'C' and resid 217 through 225 removed outlier: 3.711A pdb=" N GLN C 221 " --> pdb=" O SER C 217 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LYS C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N PHE C 223 " --> pdb=" O LEU C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 242 removed outlier: 4.589A pdb=" N VAL C 236 " --> pdb=" O ARG C 232 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N MET C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 258 removed outlier: 4.242A pdb=" N SER C 257 " --> pdb=" O SER C 253 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ARG C 258 " --> pdb=" O ILE C 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 253 through 258' Processing helix chain 'C' and resid 267 through 283 removed outlier: 5.211A pdb=" N GLY C 282 " --> pdb=" O ASN C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 302 removed outlier: 4.347A pdb=" N LEU C 301 " --> pdb=" O ARG C 297 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ASP C 302 " --> pdb=" O ILE C 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 297 through 302' Processing helix chain 'C' and resid 307 through 312 removed outlier: 4.073A pdb=" N ILE C 311 " --> pdb=" O ARG C 307 " (cutoff:3.500A) removed outlier: 5.882A 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: 4.110A pdb=" N ILE C 328 " --> pdb=" O ALA C 324 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG C 334 " --> pdb=" O LYS C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 352 removed outlier: 4.073A pdb=" N ILE C 347 " --> pdb=" O ASN C 343 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET C 351 " --> pdb=" O ILE C 347 " (cutoff:3.500A) Proline residue: C 352 - end of helix Processing helix chain 'C' and resid 355 through 374 removed outlier: 4.059A pdb=" N VAL C 359 " --> pdb=" O SER C 355 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LYS C 360 " --> pdb=" O GLY C 356 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU C 373 " --> pdb=" O TYR C 369 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG C 374 " --> pdb=" O ALA C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 397 removed outlier: 4.992A pdb=" N LYS C 397 " --> pdb=" O LYS C 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 76 removed outlier: 4.286A pdb=" N TYR D 44 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS D 45 " --> pdb=" O TYR D 41 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU D 47 " --> pdb=" O ARG D 43 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL D 56 " --> pdb=" O GLU D 52 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLN D 57 " --> pdb=" O PHE D 53 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU D 58 " --> pdb=" O LEU D 54 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU D 59 " --> pdb=" O GLU D 55 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS D 66 " --> pdb=" O LYS D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 168 removed outlier: 3.807A pdb=" N ILE D 167 " --> pdb=" O MET D 163 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N GLY D 168 " --> pdb=" O TYR D 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 163 through 168' Processing helix chain 'D' and resid 170 through 187 removed outlier: 3.582A pdb=" N GLU D 182 " --> pdb=" O ARG D 178 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N LEU D 183 " --> pdb=" O GLU D 179 " (cutoff:3.500A) Proline residue: D 184 - end of helix Processing helix chain 'D' and resid 188 through 195 Processing helix chain 'D' and resid 211 through 223 Processing helix chain 'D' and resid 231 through 236 removed outlier: 4.396A pdb=" N PHE D 235 " --> pdb=" O VAL D 231 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N VAL D 236 " --> pdb=" O GLY D 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 231 through 236' Processing helix chain 'D' and resid 241 through 258 removed outlier: 3.812A pdb=" N VAL D 250 " --> pdb=" O MET D 246 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE D 251 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA D 258 " --> pdb=" O ALA D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 271 removed outlier: 4.793A pdb=" N ILE D 270 " --> pdb=" O GLU D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 299 removed outlier: 6.259A pdb=" N ARG D 283 " --> pdb=" O THR D 279 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL D 285 " --> pdb=" O ALA D 281 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N PHE D 299 " --> pdb=" O GLN D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 323 removed outlier: 4.056A pdb=" N LEU D 322 " --> pdb=" O ASP D 318 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG D 323 " --> pdb=" O PRO D 319 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 318 through 323' Processing helix chain 'D' and resid 338 through 353 removed outlier: 4.548A pdb=" N LYS D 351 " --> pdb=" O THR D 347 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N MET D 352 " --> pdb=" O ILE D 348 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ASN D 353 " --> pdb=" O THR D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 367 removed outlier: 4.303A pdb=" N TYR D 363 " --> pdb=" O ASP D 359 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG D 366 " --> pdb=" O ASP D 362 " (cutoff:3.500A) Proline residue: D 367 - end of helix Processing helix chain 'D' and resid 371 through 390 removed outlier: 4.345A pdb=" N ILE D 375 " --> pdb=" O SER D 371 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN D 376 " --> pdb=" O GLY D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 408 removed outlier: 3.637A pdb=" N LYS D 404 " --> pdb=" O GLU D 400 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS D 408 " --> pdb=" O LYS D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 159 removed outlier: 6.792A pdb=" N LYS D 159 " --> pdb=" O LEU D 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 154 through 159' Processing helix chain 'E' and resid 17 through 49 removed outlier: 4.670A pdb=" N ARG E 25 " --> pdb=" O GLU E 21 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU E 26 " --> pdb=" O ILE E 22 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP E 46 " --> pdb=" O LYS E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 93 removed outlier: 4.044A pdb=" N LEU E 92 " --> pdb=" O ASP E 88 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N LYS E 93 " --> pdb=" O LYS E 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 88 through 93' Processing helix chain 'E' and resid 116 through 125 removed outlier: 3.992A pdb=" N TYR E 120 " --> pdb=" O ASP E 116 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N HIS E 124 " --> pdb=" O TYR E 120 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU E 125 " --> pdb=" O ASN E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 136 removed outlier: 3.773A pdb=" N ILE E 135 " --> pdb=" O SER E 131 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N GLY E 136 " --> pdb=" O TYR E 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 131 through 136' Processing helix chain 'E' and resid 138 through 155 removed outlier: 3.733A pdb=" N VAL E 148 " --> pdb=" O GLU E 144 " (cutoff:3.500A) removed outlier: 4.506A 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: 4.427A pdb=" N GLN E 190 " --> pdb=" O ALA E 186 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LEU E 191 " --> pdb=" O VAL E 187 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP E 192 " --> pdb=" O ALA E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 226 removed outlier: 3.748A pdb=" N GLN E 226 " --> pdb=" O ALA E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 265 removed outlier: 5.231A pdb=" N ARG E 251 " --> pdb=" O THR E 247 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N GLU E 252 " --> pdb=" O SER E 248 " (cutoff:3.500A) removed outlier: 4.404A 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: 3.703A pdb=" N GLY E 318 " --> pdb=" O LYS E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 336 removed outlier: 4.188A pdb=" N ILE E 331 " --> pdb=" O ASP E 327 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ASP E 336 " --> pdb=" O VAL E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 358 removed outlier: 4.473A pdb=" N LEU E 343 " --> pdb=" O ASN E 339 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ARG E 344 " --> pdb=" O GLY E 340 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ALA E 357 " --> pdb=" O PHE E 353 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ASP E 358 " --> pdb=" O ALA E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 380 removed outlier: 4.071A pdb=" N PHE E 367 " --> pdb=" O VAL E 363 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET E 368 " --> pdb=" O GLN E 364 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASP E 376 " --> pdb=" O ARG E 372 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LYS E 379 " --> pdb=" O ALA E 375 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LEU E 380 " --> pdb=" O ASP E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 204 removed outlier: 5.049A pdb=" N SER E 202 " --> pdb=" O VAL E 199 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N ILE E 203 " --> pdb=" O SER E 200 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VAL E 204 " --> pdb=" O SER E 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 199 through 204' Processing helix chain 'G' and resid 22 through 35 removed outlier: 3.737A pdb=" N ILE G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ASN G 33 " --> pdb=" O PHE G 29 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N GLN G 34 " --> pdb=" O LYS G 30 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N GLY G 35 " --> pdb=" O ALA G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 67 removed outlier: 4.217A pdb=" N VAL G 66 " --> pdb=" O ASP G 62 " (cutoff:3.500A) removed outlier: 5.200A 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 106 Processing helix chain 'G' and resid 110 through 129 removed outlier: 4.088A pdb=" N VAL G 124 " --> pdb=" O ASP G 120 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N TYR G 125 " --> pdb=" O ILE G 121 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR G 126 " --> pdb=" O SER G 122 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ALA G 129 " --> pdb=" O TYR G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 186 removed outlier: 4.428A pdb=" N LYS G 185 " --> pdb=" O LYS G 181 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N LYS G 186 " --> pdb=" O LYS G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 207 removed outlier: 3.706A pdb=" N LEU G 202 " --> pdb=" O ALA G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 216 removed outlier: 4.398A pdb=" N ILE G 215 " --> pdb=" O LYS G 211 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N GLU G 216 " --> pdb=" O PRO G 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 211 through 216' Processing helix chain 'G' and resid 231 through 245 removed outlier: 3.806A pdb=" N ARG G 245 " --> pdb=" O ALA G 241 " (cutoff:3.500A) Processing helix chain 'g' and resid 22 through 35 removed outlier: 3.808A pdb=" N ILE g 32 " --> pdb=" O ALA g 28 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ASN g 33 " --> pdb=" O PHE g 29 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLN g 34 " --> pdb=" O LYS g 30 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N GLY g 35 " --> pdb=" O ALA g 31 " (cutoff:3.500A) Processing helix chain 'g' and resid 62 through 67 removed outlier: 4.604A pdb=" N VAL g 66 " --> pdb=" O ASP g 62 " (cutoff:3.500A) removed outlier: 5.302A 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 106 Processing helix chain 'g' and resid 110 through 129 removed outlier: 4.074A pdb=" N VAL g 124 " --> pdb=" O ASP g 120 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N TYR g 125 " --> pdb=" O ILE g 121 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N THR g 126 " --> pdb=" O SER g 122 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ALA g 129 " --> pdb=" O TYR g 125 " (cutoff:3.500A) Processing helix chain 'g' and resid 171 through 186 removed outlier: 3.933A pdb=" N LYS g 185 " --> pdb=" O LYS g 181 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS g 186 " --> pdb=" O LYS g 182 " (cutoff:3.500A) Processing helix chain 'g' and resid 190 through 207 removed outlier: 3.702A pdb=" N LEU g 202 " --> pdb=" O ALA g 198 " (cutoff:3.500A) Processing helix chain 'g' and resid 211 through 216 removed outlier: 4.430A pdb=" N ILE g 215 " --> pdb=" O LYS g 211 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLU g 216 " --> pdb=" O PRO g 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 211 through 216' Processing helix chain 'g' and resid 231 through 244 removed outlier: 4.708A pdb=" N GLU g 244 " --> pdb=" O VAL g 240 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 33 removed outlier: 3.801A 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 58 through 63 removed outlier: 4.566A pdb=" N VAL H 62 " --> pdb=" O ASP H 58 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N HIS H 63 " --> pdb=" O GLU H 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 58 through 63' Processing helix chain 'H' and resid 79 through 102 Processing helix chain 'H' and resid 106 through 124 removed outlier: 3.696A pdb=" N THR H 122 " --> pdb=" O MET H 118 " (cutoff:3.500A) removed outlier: 3.530A 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: 4.113A pdb=" N SER H 198 " --> pdb=" O THR H 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 233 removed outlier: 4.947A pdb=" N ALA H 232 " --> pdb=" O ASP H 228 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ILE H 233 " --> pdb=" O TYR H 229 " (cutoff:3.500A) Processing helix chain 'h' and resid 19 through 33 removed outlier: 3.728A pdb=" N GLY h 32 " --> pdb=" O ALA h 28 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ALA h 33 " --> pdb=" O VAL h 29 " (cutoff:3.500A) Processing helix chain 'h' and resid 58 through 63 removed outlier: 4.739A pdb=" N VAL h 62 " --> pdb=" O ASP h 58 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N HIS h 63 " --> pdb=" O GLU h 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 58 through 63' Processing helix chain 'h' and resid 79 through 102 Processing helix chain 'h' and resid 106 through 124 Processing helix chain 'h' and resid 166 through 178 Processing helix chain 'h' and resid 183 through 199 removed outlier: 4.133A pdb=" N SER h 198 " --> pdb=" O THR h 194 " (cutoff:3.500A) Processing helix chain 'h' and resid 222 through 233 Processing helix chain 'I' and resid 2 through 7 removed outlier: 3.761A pdb=" N ASP I 6 " --> pdb=" O SER I 2 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N SER I 7 " --> pdb=" O ARG I 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 2 through 7' Processing helix chain 'I' and resid 18 through 32 removed outlier: 3.852A pdb=" N HIS I 30 " --> pdb=" O GLU I 26 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ALA I 31 " --> pdb=" O ALA I 27 " (cutoff:3.500A) removed outlier: 5.450A 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: 3.782A pdb=" N ILE I 117 " --> pdb=" O ALA I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 179 removed outlier: 3.629A pdb=" N ALA I 171 " --> pdb=" O ASN I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 185 through 201 Processing helix chain 'I' and resid 207 through 212 removed outlier: 3.969A pdb=" N VAL I 211 " --> pdb=" O SER I 207 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N GLU I 212 " --> pdb=" O ALA I 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 207 through 212' Processing helix chain 'I' and resid 229 through 251 Processing helix chain 'i' and resid 2 through 7 removed outlier: 4.383A pdb=" N ASP i 6 " --> pdb=" O SER i 2 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N SER i 7 " --> pdb=" O ARG i 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 2 through 7' Processing helix chain 'i' and resid 18 through 32 removed outlier: 3.830A pdb=" N HIS i 30 " --> pdb=" O GLU i 26 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA i 31 " --> pdb=" O ALA i 27 " (cutoff:3.500A) removed outlier: 5.466A 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: 3.780A pdb=" N ILE i 117 " --> pdb=" O ALA i 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 167 through 179 Processing helix chain 'i' and resid 185 through 201 Processing helix chain 'i' and resid 207 through 212 removed outlier: 4.302A pdb=" N VAL i 211 " --> pdb=" O SER i 207 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLU i 212 " --> pdb=" O ALA i 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 207 through 212' Processing helix chain 'i' and resid 229 through 251 Processing helix chain 'J' and resid 16 through 29 removed outlier: 3.661A pdb=" N LYS J 28 " --> pdb=" O GLU J 24 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLY J 29 " --> pdb=" O ALA J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 removed outlier: 4.376A pdb=" N VAL J 59 " --> pdb=" O ASP J 55 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ARG J 60 " --> pdb=" O GLU J 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 55 through 60' Processing helix chain 'J' and resid 76 through 99 Processing helix chain 'J' and resid 103 through 121 Processing helix chain 'J' and resid 164 through 176 removed outlier: 3.756A pdb=" N VAL J 168 " --> pdb=" O GLY J 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 177 through 182 Processing helix chain 'J' and resid 183 through 199 removed outlier: 4.184A pdb=" N VAL J 198 " --> pdb=" O ALA J 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 221 through 240 removed outlier: 3.661A pdb=" N ILE J 225 " --> pdb=" O ASN J 221 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU J 240 " --> pdb=" O LYS J 236 " (cutoff:3.500A) Processing helix chain 'j' and resid 16 through 29 removed outlier: 3.598A pdb=" N GLY j 29 " --> pdb=" O ALA j 25 " (cutoff:3.500A) Processing helix chain 'j' and resid 55 through 60 removed outlier: 4.488A pdb=" N VAL j 59 " --> pdb=" O ASP j 55 " (cutoff:3.500A) removed outlier: 4.407A 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: 3.771A pdb=" N TYR j 118 " --> pdb=" O LEU j 114 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR j 119 " --> pdb=" O LYS j 115 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN j 120 " --> pdb=" O GLN j 116 " (cutoff:3.500A) Processing helix chain 'j' and resid 164 through 176 removed outlier: 3.696A pdb=" N VAL j 168 " --> pdb=" O GLY j 164 " (cutoff:3.500A) Processing helix chain 'j' and resid 177 through 182 Processing helix chain 'j' and resid 183 through 199 removed outlier: 3.938A pdb=" N VAL j 198 " --> pdb=" O ALA j 194 " (cutoff:3.500A) Processing helix chain 'j' and resid 221 through 240 Processing helix chain 'K' and resid 21 through 34 removed outlier: 4.047A pdb=" N LYS K 32 " --> pdb=" O ILE K 28 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LEU K 33 " --> pdb=" O GLU K 29 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLY K 34 " --> pdb=" O ALA K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 103 removed outlier: 3.888A pdb=" N ALA K 85 " --> pdb=" O LEU K 81 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LYS K 86 " --> pdb=" O ILE K 82 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N THR K 87 " --> pdb=" O ALA K 83 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LEU K 88 " --> pdb=" O ASP K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 121 removed outlier: 4.078A pdb=" N LEU K 119 " --> pdb=" O ALA K 115 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA K 120 " --> pdb=" O VAL K 116 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N LEU K 121 " --> pdb=" O SER K 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 173 through 185 removed outlier: 3.675A pdb=" N GLU K 183 " --> pdb=" O SER K 179 " (cutoff:3.500A) Processing helix chain 'K' and resid 190 through 206 Processing helix chain 'K' and resid 230 through 241 removed outlier: 4.483A pdb=" N ASP K 240 " --> pdb=" O GLU K 236 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ILE K 241 " --> pdb=" O VAL K 237 " (cutoff:3.500A) Processing helix chain 'k' and resid 21 through 34 removed outlier: 4.157A pdb=" N LYS k 32 " --> pdb=" O ILE k 28 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU k 33 " --> pdb=" O GLU k 29 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLY k 34 " --> pdb=" O ALA k 30 " (cutoff:3.500A) Processing helix chain 'k' and resid 81 through 103 removed outlier: 3.802A pdb=" N ALA k 85 " --> pdb=" O LEU k 81 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LYS k 86 " --> pdb=" O ILE k 82 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N THR k 87 " --> pdb=" O ALA k 83 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU k 88 " --> pdb=" O ASP k 84 " (cutoff:3.500A) Processing helix chain 'k' and resid 108 through 121 removed outlier: 4.167A pdb=" N LEU k 119 " --> pdb=" O ALA k 115 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ALA k 120 " --> pdb=" O VAL k 116 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N LEU k 121 " --> pdb=" O SER k 117 " (cutoff:3.500A) Processing helix chain 'k' and resid 173 through 185 removed outlier: 3.691A pdb=" N ALA k 177 " --> pdb=" O ALA k 173 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N SER k 179 " --> pdb=" O GLU k 175 " (cutoff:3.500A) Processing helix chain 'k' and resid 190 through 206 Processing helix chain 'k' and resid 230 through 241 removed outlier: 3.833A pdb=" N GLU k 236 " --> pdb=" O GLU k 232 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL k 237 " --> pdb=" O GLU k 233 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 32 removed outlier: 3.676A pdb=" N VAL L 29 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS L 30 " --> pdb=" O MET L 26 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLN L 31 " --> pdb=" O GLU L 27 " (cutoff:3.500A) removed outlier: 4.446A 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: 4.017A pdb=" N ILE L 118 " --> pdb=" O SER L 114 " (cutoff:3.500A) Proline residue: L 119 - end of helix removed outlier: 3.859A pdb=" N ARG L 122 " --> pdb=" O ILE L 118 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N TYR L 123 " --> pdb=" O PRO L 119 " (cutoff:3.500A) Processing helix chain 'L' and resid 164 through 180 removed outlier: 4.488A pdb=" N ALA L 168 " --> pdb=" O ARG L 164 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N SER L 177 " --> pdb=" O GLU L 173 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLU L 178 " --> pdb=" O ARG L 174 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE L 179 " --> pdb=" O HIS L 175 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N MET L 180 " --> pdb=" O MET L 176 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 200 removed outlier: 3.811A pdb=" N GLU L 197 " --> pdb=" O ARG L 193 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N THR L 198 " --> pdb=" O ALA L 194 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU L 199 " --> pdb=" O LEU L 195 " (cutoff:3.500A) Proline residue: L 200 - end of helix Processing helix chain 'L' and resid 225 through 236 removed outlier: 4.132A pdb=" N SER L 230 " --> pdb=" O ASP L 226 " (cutoff:3.500A) Proline residue: L 231 - end of helix removed outlier: 4.029A pdb=" N GLY L 235 " --> pdb=" O PRO L 231 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU L 236 " --> pdb=" O PHE L 232 " (cutoff:3.500A) Processing helix chain 'l' and resid 19 through 32 removed outlier: 3.568A pdb=" N GLU l 23 " --> pdb=" O ILE l 19 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS l 30 " --> pdb=" O MET l 26 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLN l 31 " --> pdb=" O GLU l 27 " (cutoff:3.500A) removed outlier: 4.701A 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: 4.113A pdb=" N ILE l 118 " --> pdb=" O SER l 114 " (cutoff:3.500A) Proline residue: l 119 - end of helix removed outlier: 3.749A pdb=" N ARG l 122 " --> pdb=" O ILE l 118 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N TYR l 123 " --> pdb=" O PRO l 119 " (cutoff:3.500A) Processing helix chain 'l' and resid 164 through 180 removed outlier: 4.526A pdb=" N ALA l 168 " --> pdb=" O ARG l 164 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N SER l 177 " --> pdb=" O GLU l 173 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLU l 178 " --> pdb=" O ARG l 174 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N PHE l 179 " --> pdb=" O HIS l 175 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N MET l 180 " --> pdb=" O MET l 176 " (cutoff:3.500A) Processing helix chain 'l' and resid 183 through 200 removed outlier: 3.659A pdb=" N GLU l 197 " --> pdb=" O ARG l 193 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N THR l 198 " --> pdb=" O ALA l 194 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LEU l 199 " --> pdb=" O LEU l 195 " (cutoff:3.500A) Proline residue: l 200 - end of helix Processing helix chain 'l' and resid 225 through 236 removed outlier: 4.047A pdb=" N SER l 230 " --> pdb=" O ASP l 226 " (cutoff:3.500A) Proline residue: l 231 - end of helix removed outlier: 5.905A pdb=" N GLY l 235 " --> pdb=" O PRO l 231 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N LEU l 236 " --> pdb=" O PHE l 232 " (cutoff:3.500A) Processing helix chain 'M' and resid 20 through 33 removed outlier: 3.765A pdb=" N GLU M 24 " --> pdb=" O VAL M 20 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN M 32 " --> pdb=" O LYS M 28 " (cutoff:3.500A) removed outlier: 4.596A 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: 4.137A pdb=" N TYR M 122 " --> pdb=" O TYR M 118 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR M 123 " --> pdb=" O VAL M 119 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LEU M 124 " --> pdb=" O HIS M 120 " (cutoff:3.500A) Processing helix chain 'M' and resid 168 through 179 removed outlier: 4.830A pdb=" N LYS M 178 " --> pdb=" O THR M 174 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N LEU M 179 " --> pdb=" O GLU M 175 " (cutoff:3.500A) Processing helix chain 'M' and resid 185 through 201 removed outlier: 3.854A pdb=" N LYS M 191 " --> pdb=" O ARG M 187 " (cutoff:3.500A) Processing helix chain 'M' and resid 228 through 244 Processing helix chain 'm' and resid 20 through 33 removed outlier: 3.716A pdb=" N GLU m 24 " --> pdb=" O VAL m 20 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN m 32 " --> pdb=" O LYS m 28 " (cutoff:3.500A) removed outlier: 4.716A 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: 4.050A pdb=" N TYR m 122 " --> pdb=" O TYR m 118 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N THR m 123 " --> pdb=" O VAL m 119 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU m 124 " --> pdb=" O HIS m 120 " (cutoff:3.500A) Processing helix chain 'm' and resid 168 through 179 removed outlier: 3.962A pdb=" N LYS m 178 " --> pdb=" O THR m 174 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU m 179 " --> pdb=" O GLU m 175 " (cutoff:3.500A) Processing helix chain 'm' and resid 185 through 201 removed outlier: 3.806A pdb=" N LYS m 191 " --> pdb=" O ARG m 187 " (cutoff:3.500A) Processing helix chain 'm' and resid 228 through 244 Processing helix chain 'N' and resid 48 through 71 Processing helix chain 'N' and resid 75 through 91 Processing helix chain 'N' and resid 131 through 143 removed outlier: 4.039A pdb=" N ILE N 135 " --> pdb=" O GLY N 131 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N GLY N 137 " --> pdb=" O SER N 133 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N TYR N 138 " --> pdb=" O TYR N 134 " (cutoff:3.500A) Processing helix chain 'N' and resid 148 through 167 Processing helix chain 'n' and resid 48 through 71 Processing helix chain 'n' and resid 75 through 91 removed outlier: 3.642A pdb=" N TYR n 90 " --> pdb=" O MET n 86 " (cutoff:3.500A) Processing helix chain 'n' and resid 131 through 143 removed outlier: 4.030A pdb=" N ILE n 135 " --> pdb=" O GLY n 131 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N GLY n 137 " --> pdb=" O SER n 133 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N TYR n 138 " --> pdb=" O TYR n 134 " (cutoff:3.500A) Processing helix chain 'n' and resid 148 through 167 Processing helix chain 'O' and resid 48 through 71 Processing helix chain 'O' and resid 75 through 91 removed outlier: 3.868A pdb=" N ARG O 89 " --> pdb=" O GLN O 85 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N TYR O 90 " --> pdb=" O MET O 86 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLN O 91 " --> pdb=" O LEU O 87 " (cutoff:3.500A) Processing helix chain 'O' and resid 130 through 142 removed outlier: 3.885A pdb=" N ALA O 134 " --> pdb=" O GLY O 130 " (cutoff:3.500A) Processing helix chain 'O' and resid 147 through 166 Processing helix chain 'o' and resid 48 through 71 Processing helix chain 'o' and resid 75 through 91 removed outlier: 3.614A pdb=" N ALA o 79 " --> pdb=" O ARG o 75 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR o 90 " --> pdb=" O MET o 86 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN o 91 " --> pdb=" O LEU o 87 " (cutoff:3.500A) Processing helix chain 'o' and resid 130 through 142 removed outlier: 3.715A pdb=" N ALA o 134 " --> pdb=" O GLY o 130 " (cutoff:3.500A) Processing helix chain 'o' and resid 147 through 166 Processing helix chain 'P' and resid 2 through 8 removed outlier: 3.538A pdb=" N TYR P 6 " --> pdb=" O SER P 2 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ASN P 7 " --> pdb=" O ILE P 3 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLY P 8 " --> pdb=" O MET P 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 2 through 8' Processing helix chain 'P' and resid 56 through 79 Processing helix chain 'P' and resid 83 through 99 removed outlier: 4.257A pdb=" N LYS P 98 " --> pdb=" O LEU P 94 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ARG P 99 " --> pdb=" O LEU P 95 " (cutoff:3.500A) Processing helix chain 'P' and resid 142 through 154 removed outlier: 3.869A pdb=" N SER P 152 " --> pdb=" O GLY P 148 " (cutoff:3.500A) Processing helix chain 'P' and resid 159 through 179 removed outlier: 4.077A pdb=" N ARG P 177 " --> pdb=" O ASN P 173 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP P 178 " --> pdb=" O ALA P 174 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ALA P 179 " --> pdb=" O VAL P 175 " (cutoff:3.500A) Processing helix chain 'p' and resid 2 through 8 removed outlier: 3.598A pdb=" N TYR p 6 " --> pdb=" O SER p 2 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ASN p 7 " --> pdb=" O ILE p 3 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLY p 8 " --> pdb=" O MET p 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 2 through 8' Processing helix chain 'p' and resid 56 through 79 Processing helix chain 'p' and resid 83 through 99 removed outlier: 4.056A pdb=" N LYS p 98 " --> pdb=" O LEU p 94 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARG p 99 " --> pdb=" O LEU p 95 " (cutoff:3.500A) Processing helix chain 'p' and resid 142 through 154 removed outlier: 3.878A pdb=" N SER p 152 " --> pdb=" O GLY p 148 " (cutoff:3.500A) Processing helix chain 'p' and resid 159 through 179 removed outlier: 4.116A pdb=" N ARG p 177 " --> pdb=" O ASN p 173 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASP p 178 " --> pdb=" O ALA p 174 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ALA p 179 " --> pdb=" O VAL p 175 " (cutoff:3.500A) Processing helix chain 'Q' and resid 50 through 72 removed outlier: 6.461A pdb=" N VAL Q 54 " --> pdb=" O ALA Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 95 removed outlier: 4.163A pdb=" N ARG Q 93 " --> pdb=" O ALA Q 89 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N SER Q 94 " --> pdb=" O ASP Q 90 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ARG Q 95 " --> pdb=" O CYS Q 91 " (cutoff:3.500A) Processing helix chain 'Q' and resid 133 through 147 removed outlier: 4.665A pdb=" N PHE Q 137 " --> pdb=" O GLY Q 133 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU Q 138 " --> pdb=" O TYR Q 134 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N SER Q 141 " --> pdb=" O PHE Q 137 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ILE Q 142 " --> pdb=" O LEU Q 138 " (cutoff:3.500A) Processing helix chain 'Q' and resid 152 through 170 Processing helix chain 'q' and resid 50 through 72 removed outlier: 6.582A pdb=" N VAL q 54 " --> pdb=" O ALA q 50 " (cutoff:3.500A) Processing helix chain 'q' and resid 76 through 95 removed outlier: 4.289A pdb=" N ARG q 93 " --> pdb=" O ALA q 89 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N SER q 94 " --> pdb=" O ASP q 90 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ARG q 95 " --> pdb=" O CYS q 91 " (cutoff:3.500A) Processing helix chain 'q' and resid 133 through 147 removed outlier: 4.564A pdb=" N PHE q 137 " --> pdb=" O GLY q 133 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LEU q 138 " --> pdb=" O TYR q 134 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N SER q 141 " --> pdb=" O PHE q 137 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ILE q 142 " --> pdb=" O LEU q 138 " (cutoff:3.500A) Processing helix chain 'q' and resid 152 through 170 Processing helix chain 'R' and resid 48 through 71 Processing helix chain 'R' and resid 75 through 91 removed outlier: 3.962A pdb=" N GLN R 89 " --> pdb=" O ASN R 85 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N TYR R 90 " --> pdb=" O MET R 86 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LYS R 91 " --> pdb=" O VAL R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 143 removed outlier: 3.758A pdb=" N VAL R 138 " --> pdb=" O TYR R 134 " (cutoff:3.500A) Processing helix chain 'R' and resid 148 through 167 Processing helix chain 'R' and resid 191 through 201 Processing helix chain 'r' and resid 48 through 71 Processing helix chain 'r' and resid 75 through 91 removed outlier: 4.086A pdb=" N GLN r 89 " --> pdb=" O ASN r 85 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N TYR r 90 " --> pdb=" O MET r 86 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LYS r 91 " --> pdb=" O VAL r 87 " (cutoff:3.500A) Processing helix chain 'r' and resid 131 through 143 removed outlier: 3.812A pdb=" N VAL r 138 " --> pdb=" O TYR r 134 " (cutoff:3.500A) Processing helix chain 'r' and resid 148 through 167 Processing helix chain 'r' and resid 191 through 201 Processing helix chain 'S' and resid 57 through 80 Processing helix chain 'S' and resid 84 through 100 removed outlier: 3.964A pdb=" N ARG S 99 " --> pdb=" O ILE S 95 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ARG S 100 " --> pdb=" O LEU S 96 " (cutoff:3.500A) Processing helix chain 'S' and resid 141 through 153 Proline residue: S 147 - end of helix Processing helix chain 'S' and resid 167 through 186 Processing helix chain 's' and resid 57 through 80 Processing helix chain 's' and resid 84 through 100 removed outlier: 3.886A pdb=" N ARG s 99 " --> pdb=" O ILE s 95 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ARG s 100 " --> pdb=" O LEU s 96 " (cutoff:3.500A) Processing helix chain 's' and resid 141 through 153 Proline residue: s 147 - end of helix Processing helix chain 's' and resid 167 through 186 Processing helix chain 'T' and resid 56 through 78 removed outlier: 4.033A pdb=" N LEU T 77 " --> pdb=" O ASP T 73 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLY T 78 " --> pdb=" O GLU T 74 " (cutoff:3.500A) Processing helix chain 'T' and resid 84 through 103 removed outlier: 3.712A pdb=" N LYS T 102 " --> pdb=" O SER T 98 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N MET T 103 " --> pdb=" O ARG T 99 " (cutoff:3.500A) Processing helix chain 'T' and resid 140 through 157 removed outlier: 4.210A pdb=" N TYR T 144 " --> pdb=" O GLY T 140 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLN T 147 " --> pdb=" O ALA T 143 " (cutoff:3.500A) Proline residue: T 148 - end of helix removed outlier: 3.781A 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: 4.871A pdb=" N HIS T 213 " --> pdb=" O TRP T 209 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N MET T 214 " --> pdb=" O ASP T 210 " (cutoff:3.500A) removed outlier: 4.475A 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: 3.990A pdb=" N LEU t 77 " --> pdb=" O ASP t 73 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLY t 78 " --> pdb=" O GLU t 74 " (cutoff:3.500A) Processing helix chain 't' and resid 84 through 103 removed outlier: 3.657A pdb=" N LYS t 102 " --> pdb=" O SER t 98 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N MET t 103 " --> pdb=" O ARG t 99 " (cutoff:3.500A) Processing helix chain 't' and resid 140 through 157 removed outlier: 4.338A pdb=" N TYR t 144 " --> pdb=" O GLY t 140 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N GLN t 147 " --> pdb=" O ALA t 143 " (cutoff:3.500A) Proline residue: t 148 - end of helix Processing helix chain 't' and resid 161 through 180 Processing helix chain 't' and resid 209 through 215 removed outlier: 4.783A pdb=" N HIS t 213 " --> pdb=" O TRP t 209 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N MET t 214 " --> pdb=" O ASP t 210 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE t 215 " --> pdb=" O ILE t 211 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 209 through 215' Processing helix chain 'U' and resid 58 through 72 removed outlier: 4.701A pdb=" N LEU U 62 " --> pdb=" O GLN U 58 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N HIS U 70 " --> pdb=" O LYS U 66 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU U 71 " --> pdb=" O VAL U 67 " (cutoff:3.500A) Processing helix chain 'U' and resid 73 through 85 Processing helix chain 'U' and resid 94 through 117 removed outlier: 4.978A pdb=" N GLU U 98 " --> pdb=" O SER U 94 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N THR U 99 " --> pdb=" O GLU U 95 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASP U 117 " --> pdb=" O VAL U 113 " (cutoff:3.500A) Processing helix chain 'U' and resid 127 through 145 removed outlier: 3.800A pdb=" N VAL U 134 " --> pdb=" O LEU U 130 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN U 135 " --> pdb=" O GLU U 131 " (cutoff:3.500A) Processing helix chain 'U' and resid 146 through 158 removed outlier: 4.385A pdb=" N ALA U 150 " --> pdb=" O LYS U 146 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLY U 152 " --> pdb=" O LYS U 148 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU U 155 " --> pdb=" O ILE U 151 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG U 158 " --> pdb=" O ALA U 154 " (cutoff:3.500A) Processing helix chain 'U' and resid 159 through 169 removed outlier: 4.068A pdb=" N PHE U 163 " --> pdb=" O ARG U 159 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU U 169 " --> pdb=" O LYS U 165 " (cutoff:3.500A) Processing helix chain 'U' and resid 177 through 189 removed outlier: 4.837A pdb=" N GLN U 189 " --> pdb=" O MET U 185 " (cutoff:3.500A) Processing helix chain 'U' and resid 191 through 206 removed outlier: 4.292A pdb=" N LYS U 196 " --> pdb=" O GLN U 192 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL U 197 " --> pdb=" O PHE U 193 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N VAL U 202 " --> pdb=" O LEU U 198 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LYS U 203 " --> pdb=" O ARG U 199 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ILE U 204 " --> pdb=" O VAL U 200 " (cutoff:3.500A) Processing helix chain 'U' and resid 212 through 224 removed outlier: 4.406A pdb=" N VAL U 216 " --> pdb=" O ASP U 212 " (cutoff:3.500A) Processing helix chain 'U' and resid 225 through 240 removed outlier: 3.824A pdb=" N VAL U 229 " --> pdb=" O ASP U 225 " (cutoff:3.500A) Processing helix chain 'U' and resid 241 through 256 removed outlier: 3.562A pdb=" N TYR U 246 " --> pdb=" O LEU U 242 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLN U 247 " --> pdb=" O LEU U 243 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ILE U 248 " --> pdb=" O MET U 244 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N CYS U 249 " --> pdb=" O ALA U 245 " (cutoff:3.500A) Processing helix chain 'U' and resid 257 through 269 removed outlier: 4.863A pdb=" N GLN U 266 " --> pdb=" O SER U 262 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ASN U 267 " --> pdb=" O SER U 263 " (cutoff:3.500A) Processing helix chain 'U' and resid 320 through 329 removed outlier: 3.673A pdb=" N ILE U 326 " --> pdb=" O THR U 322 " (cutoff:3.500A) Processing helix chain 'U' and resid 331 through 346 removed outlier: 4.604A pdb=" N LEU U 337 " --> pdb=" O MET U 333 " (cutoff:3.500A) Processing helix chain 'U' and resid 349 through 358 removed outlier: 4.654A pdb=" N LEU U 353 " --> pdb=" O ASP U 349 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ASP U 358 " --> pdb=" O LYS U 354 " (cutoff:3.500A) Processing helix chain 'U' and resid 364 through 378 removed outlier: 4.189A pdb=" N SER U 374 " --> pdb=" O VAL U 370 " (cutoff:3.500A) Processing helix chain 'U' and resid 383 through 390 removed outlier: 4.168A pdb=" N ARG U 387 " --> pdb=" O ASP U 383 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ASN U 389 " --> pdb=" O PHE U 385 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LEU U 390 " --> pdb=" O LEU U 386 " (cutoff:3.500A) Processing helix chain 'U' and resid 391 through 396 removed outlier: 4.703A pdb=" N ALA U 396 " --> pdb=" O TRP U 392 " (cutoff:3.500A) Processing helix chain 'U' and resid 397 through 413 removed outlier: 5.747A pdb=" N LYS U 401 " --> pdb=" O THR U 397 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N PHE U 402 " --> pdb=" O ASN U 398 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLY U 409 " --> pdb=" O THR U 405 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL U 410 " --> pdb=" O ALA U 406 " (cutoff:3.500A) Processing helix chain 'U' and resid 419 through 424 removed outlier: 4.525A pdb=" N MET U 423 " --> pdb=" O ALA U 419 " (cutoff:3.500A) Processing helix chain 'U' and resid 435 through 451 removed outlier: 3.666A pdb=" N GLU U 439 " --> pdb=" O SER U 435 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY U 442 " --> pdb=" O GLN U 438 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N LEU U 443 " --> pdb=" O GLU U 439 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N TYR U 444 " --> pdb=" O GLY U 440 " (cutoff:3.500A) Processing helix chain 'U' and resid 455 through 468 removed outlier: 3.961A pdb=" N ASP U 459 " --> pdb=" O GLY U 455 " (cutoff:3.500A) Processing helix chain 'U' and resid 471 through 486 removed outlier: 5.734A pdb=" N HIS U 475 " --> pdb=" O ASP U 471 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N GLY U 476 " --> pdb=" O ILE U 472 " (cutoff:3.500A) Processing helix chain 'U' and resid 490 through 504 removed outlier: 3.918A pdb=" N LEU U 496 " --> pdb=" O ASP U 492 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR U 499 " --> pdb=" O ASP U 495 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ASP U 504 " --> pdb=" O ASN U 500 " (cutoff:3.500A) Processing helix chain 'U' and resid 505 through 521 removed outlier: 4.248A pdb=" N GLU U 510 " --> pdb=" O ALA U 506 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ALA U 511 " --> pdb=" O VAL U 507 " (cutoff:3.500A) Processing helix chain 'U' and resid 525 through 539 removed outlier: 3.704A pdb=" N GLN U 537 " --> pdb=" O VAL U 533 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU U 538 " --> pdb=" O GLY U 534 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR U 539 " --> pdb=" O TYR U 535 " (cutoff:3.500A) Processing helix chain 'U' and resid 541 through 556 removed outlier: 4.381A pdb=" N LEU U 545 " --> pdb=" O HIS U 541 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL U 550 " --> pdb=" O ARG U 546 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N MET U 556 " --> pdb=" O ILE U 552 " (cutoff:3.500A) Processing helix chain 'U' and resid 563 through 573 Processing helix chain 'U' and resid 575 through 591 Processing helix chain 'U' and resid 595 through 609 removed outlier: 3.585A pdb=" N ARG U 601 " --> pdb=" O LYS U 597 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA U 606 " --> pdb=" O LEU U 602 " (cutoff:3.500A) Processing helix chain 'U' and resid 611 through 627 removed outlier: 3.906A pdb=" N LEU U 622 " --> pdb=" O ALA U 618 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N GLY U 623 " --> pdb=" O VAL U 619 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N PHE U 624 " --> pdb=" O GLU U 620 " (cutoff:3.500A) Processing helix chain 'U' and resid 630 through 643 Proline residue: U 634 - end of helix removed outlier: 4.064A pdb=" N SER U 638 " --> pdb=" O PRO U 634 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N LEU U 639 " --> pdb=" O SER U 635 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU U 640 " --> pdb=" O VAL U 636 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU U 642 " --> pdb=" O SER U 638 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N SER U 643 " --> pdb=" O LEU U 639 " (cutoff:3.500A) Processing helix chain 'U' and resid 645 through 661 Processing helix chain 'U' and resid 665 through 677 Proline residue: U 674 - end of helix removed outlier: 4.559A pdb=" N ASN U 677 " --> pdb=" O GLU U 673 " (cutoff:3.500A) Processing helix chain 'U' and resid 680 through 696 removed outlier: 3.972A pdb=" N ILE U 696 " --> pdb=" O ALA U 692 " (cutoff:3.500A) Processing helix chain 'U' and resid 704 through 719 removed outlier: 4.296A pdb=" N GLN U 708 " --> pdb=" O PRO U 704 " (cutoff:3.500A) Processing helix chain 'U' and resid 723 through 739 Processing helix chain 'U' and resid 756 through 769 removed outlier: 3.967A pdb=" N GLN U 768 " --> pdb=" O LEU U 764 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N PHE U 769 " --> pdb=" O VAL U 765 " (cutoff:3.500A) Processing helix chain 'U' and resid 772 through 784 removed outlier: 3.827A pdb=" N SER U 776 " --> pdb=" O TRP U 772 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N HIS U 777 " --> pdb=" O PHE U 773 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N PHE U 778 " --> pdb=" O PRO U 774 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LEU U 779 " --> pdb=" O LEU U 775 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N SER U 780 " --> pdb=" O SER U 776 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU U 781 " --> pdb=" O HIS U 777 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ALA U 782 " --> pdb=" O PHE U 778 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N THR U 784 " --> pdb=" O SER U 780 " (cutoff:3.500A) Processing helix chain 'U' and resid 807 through 812 removed outlier: 4.981A pdb=" N PHE U 811 " --> pdb=" O LYS U 807 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ALA U 812 " --> pdb=" O PRO U 808 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 807 through 812' Processing helix chain 'U' and resid 885 through 890 removed outlier: 4.041A pdb=" N LEU U 889 " --> pdb=" O MET U 885 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N LYS U 890 " --> pdb=" O PRO U 886 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 885 through 890' Processing helix chain 'V' and resid 54 through 89 Processing helix chain 'V' and resid 91 through 105 Proline residue: V 102 - end of helix Processing helix chain 'V' and resid 109 through 120 removed outlier: 3.764A pdb=" N LEU V 113 " --> pdb=" O ASN V 109 " (cutoff:3.500A) Processing helix chain 'V' and resid 125 through 136 Proline residue: V 133 - end of helix removed outlier: 5.536A pdb=" N GLU V 136 " --> pdb=" O LEU V 132 " (cutoff:3.500A) Processing helix chain 'V' and resid 152 through 158 Proline residue: V 158 - end of helix Processing helix chain 'V' and resid 160 through 179 removed outlier: 3.607A pdb=" N LYS V 179 " --> pdb=" O MET V 175 " (cutoff:3.500A) Processing helix chain 'V' and resid 180 through 199 removed outlier: 3.681A pdb=" N GLN V 198 " --> pdb=" O LYS V 194 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ASN V 199 " --> pdb=" O ILE V 195 " (cutoff:3.500A) Processing helix chain 'V' and resid 202 through 222 removed outlier: 4.493A pdb=" N VAL V 206 " --> pdb=" O ALA V 202 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS V 209 " --> pdb=" O LEU V 205 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE V 220 " --> pdb=" O ARG V 216 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU V 221 " --> pdb=" O VAL V 217 " (cutoff:3.500A) Processing helix chain 'V' and resid 225 through 242 removed outlier: 3.819A pdb=" N SER V 229 " --> pdb=" O ASP V 225 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N PHE V 230 " --> pdb=" O VAL V 226 " (cutoff:3.500A) Processing helix chain 'V' and resid 244 through 262 removed outlier: 6.593A pdb=" N ALA V 248 " --> pdb=" O ALA V 244 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N THR V 249 " --> pdb=" O ASP V 245 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU V 251 " --> pdb=" O GLN V 247 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR V 261 " --> pdb=" O ASN V 257 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N SER V 262 " --> pdb=" O TYR V 258 " (cutoff:3.500A) Processing helix chain 'V' and resid 265 through 272 Processing helix chain 'V' and resid 282 through 300 removed outlier: 5.696A pdb=" N ALA V 286 " --> pdb=" O ASN V 282 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG V 287 " --> pdb=" O ASN V 283 " (cutoff:3.500A) Processing helix chain 'V' and resid 301 through 316 Processing helix chain 'V' and resid 321 through 340 removed outlier: 4.161A pdb=" N LYS V 325 " --> pdb=" O ALA V 321 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N THR V 327 " --> pdb=" O GLY V 323 " (cutoff:3.500A) Processing helix chain 'V' and resid 344 through 350 removed outlier: 4.228A pdb=" N PHE V 348 " --> pdb=" O ASP V 344 " (cutoff:3.500A) Processing helix chain 'V' and resid 351 through 358 removed outlier: 5.480A pdb=" N ARG V 355 " --> pdb=" O PRO V 351 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N SER V 356 " --> pdb=" O SER V 352 " (cutoff:3.500A) Processing helix chain 'V' and resid 359 through 370 removed outlier: 3.690A pdb=" N THR V 369 " --> pdb=" O GLN V 365 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N GLY V 370 " --> pdb=" O ALA V 366 " (cutoff:3.500A) Processing helix chain 'V' and resid 371 through 383 removed outlier: 4.075A pdb=" N PHE V 375 " --> pdb=" O ASN V 371 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN V 381 " --> pdb=" O GLN V 377 " (cutoff:3.500A) Processing helix chain 'V' and resid 384 through 390 Processing helix chain 'V' and resid 391 through 414 removed outlier: 4.436A pdb=" N ARG V 397 " --> pdb=" O THR V 393 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LEU V 398 " --> pdb=" O LEU V 394 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ARG V 399 " --> pdb=" O ILE V 395 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N HIS V 400 " --> pdb=" O ILE V 396 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ASN V 401 " --> pdb=" O ARG V 397 " (cutoff:3.500A) Processing helix chain 'V' and resid 418 through 427 Processing helix chain 'V' and resid 430 through 445 removed outlier: 4.290A pdb=" N ALA V 434 " --> pdb=" O SER V 430 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU V 435 " --> pdb=" O PRO V 431 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE V 436 " --> pdb=" O GLU V 432 " (cutoff:3.500A) Processing helix chain 'V' and resid 465 through 495 removed outlier: 4.704A pdb=" N ARG V 470 " --> pdb=" O ILE V 466 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLU V 471 " --> pdb=" O TYR V 467 " (cutoff:3.500A) Proline residue: V 472 - end of helix removed outlier: 4.159A pdb=" N ARG V 495 " --> pdb=" O VAL V 491 " (cutoff:3.500A) Processing helix chain 'V' and resid 508 through 525 Processing helix chain 'W' and resid 21 through 38 Proline residue: W 29 - end of helix Processing helix chain 'W' and resid 39 through 58 Processing helix chain 'W' and resid 59 through 78 Processing helix chain 'W' and resid 79 through 95 removed outlier: 3.742A pdb=" N GLU W 85 " --> pdb=" O ASP W 81 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ARG W 94 " --> pdb=" O LEU W 90 " (cutoff:3.500A) Processing helix chain 'W' and resid 97 through 115 Processing helix chain 'W' and resid 118 through 132 removed outlier: 4.199A pdb=" N LEU W 122 " --> pdb=" O LEU W 118 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N MET W 130 " --> pdb=" O ASP W 126 " (cutoff:3.500A) Processing helix chain 'W' and resid 140 through 156 removed outlier: 4.787A pdb=" N ARG W 144 " --> pdb=" O ILE W 140 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLN W 155 " --> pdb=" O THR W 151 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASN W 156 " --> pdb=" O ILE W 152 " (cutoff:3.500A) Processing helix chain 'W' and resid 158 through 169 removed outlier: 3.859A pdb=" N GLN W 167 " --> pdb=" O ALA W 163 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLU W 168 " --> pdb=" O SER W 164 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU W 169 " --> pdb=" O ILE W 165 " (cutoff:3.500A) Processing helix chain 'W' and resid 172 through 177 removed outlier: 4.854A pdb=" N SER W 176 " --> pdb=" O GLU W 172 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N MET W 177 " --> pdb=" O THR W 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 172 through 177' Processing helix chain 'W' and resid 180 through 197 removed outlier: 4.173A pdb=" N GLN W 189 " --> pdb=" O PHE W 185 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N MET W 190 " --> pdb=" O ILE W 186 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ARG W 191 " --> pdb=" O LEU W 187 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU W 192 " --> pdb=" O GLU W 188 " (cutoff:3.500A) Processing helix chain 'W' and resid 199 through 213 removed outlier: 3.634A pdb=" N ILE W 204 " --> pdb=" O ILE W 200 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYS W 212 " --> pdb=" O LYS W 208 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N PHE W 213 " --> pdb=" O ILE W 209 " (cutoff:3.500A) Processing helix chain 'W' and resid 215 through 220 removed outlier: 4.342A pdb=" N THR W 219 " --> pdb=" O GLN W 215 " (cutoff:3.500A) removed outlier: 6.319A 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 222 through 238 removed outlier: 4.486A pdb=" N TYR W 226 " --> pdb=" O LEU W 222 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ASN W 228 " --> pdb=" O LEU W 224 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU W 229 " --> pdb=" O LYS W 225 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N MET W 230 " --> pdb=" O TYR W 226 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE W 231 " --> pdb=" O TYR W 227 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN W 232 " --> pdb=" O ASN W 228 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU W 237 " --> pdb=" O LEU W 233 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLY W 238 " --> pdb=" O ASP W 234 " (cutoff:3.500A) Processing helix chain 'W' and resid 239 through 258 removed outlier: 5.440A pdb=" N ILE W 243 " --> pdb=" O SER W 239 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASP W 252 " --> pdb=" O ARG W 248 " (cutoff:3.500A) removed outlier: 4.992A 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: 4.475A pdb=" N TYR W 273 " --> pdb=" O SER W 269 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N VAL W 274 " --> pdb=" O VAL W 270 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ILE W 275 " --> pdb=" O VAL W 271 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LEU W 276 " --> pdb=" O LEU W 272 " (cutoff:3.500A) Proline residue: W 278 - end of helix Processing helix chain 'W' and resid 280 through 292 removed outlier: 4.995A pdb=" N GLY W 292 " --> pdb=" O HIS W 288 " (cutoff:3.500A) Processing helix chain 'W' and resid 299 through 310 removed outlier: 4.415A pdb=" N LYS W 303 " --> pdb=" O ILE W 299 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU W 308 " --> pdb=" O ASP W 304 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE W 309 " --> pdb=" O LEU W 305 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N THR W 310 " --> pdb=" O LEU W 306 " (cutoff:3.500A) Processing helix chain 'W' and resid 316 through 325 removed outlier: 4.094A pdb=" N GLU W 322 " --> pdb=" O SER W 318 " (cutoff:3.500A) Processing helix chain 'W' and resid 334 through 341 Processing helix chain 'W' and resid 344 through 370 removed outlier: 3.722A pdb=" N TYR W 369 " --> pdb=" O ILE W 365 " (cutoff:3.500A) Processing helix chain 'W' and resid 374 through 383 Processing helix chain 'W' and resid 385 through 400 Processing helix chain 'W' and resid 420 through 456 Processing helix chain 'W' and resid 293 through 298 removed outlier: 3.693A pdb=" N LEU W 296 " --> pdb=" O ASP W 293 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N GLU W 297 " --> pdb=" O LYS W 294 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU W 298 " --> pdb=" O LYS W 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 293 through 298' Processing helix chain 'X' and resid 43 through 61 Processing helix chain 'X' and resid 62 through 77 removed outlier: 4.645A pdb=" N LEU X 66 " --> pdb=" O GLN X 62 " (cutoff:3.500A) Proline residue: X 75 - end of helix Processing helix chain 'X' and resid 81 through 99 removed outlier: 3.688A pdb=" N ASP X 98 " --> pdb=" O ASP X 94 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N MET X 99 " --> pdb=" O LEU X 95 " (cutoff:3.500A) Processing helix chain 'X' and resid 102 through 121 removed outlier: 4.398A pdb=" N GLU X 106 " --> pdb=" O ALA X 102 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL X 107 " --> pdb=" O THR X 103 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N GLU X 108 " --> pdb=" O GLY X 104 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LEU X 109 " --> pdb=" O GLN X 105 " (cutoff:3.500A) Processing helix chain 'X' and resid 122 through 141 removed outlier: 3.874A pdb=" N PHE X 138 " --> pdb=" O VAL X 134 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASP X 139 " --> pdb=" O SER X 135 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR X 140 " --> pdb=" O LEU X 136 " (cutoff:3.500A) Processing helix chain 'X' and resid 143 through 161 removed outlier: 4.197A pdb=" N LEU X 147 " --> pdb=" O TYR X 143 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG X 155 " --> pdb=" O SER X 151 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU X 156 " --> pdb=" O GLN X 152 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N MET X 160 " --> pdb=" O GLU X 156 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ASP X 161 " --> pdb=" O LEU X 157 " (cutoff:3.500A) Processing helix chain 'X' and resid 162 through 181 removed outlier: 3.939A pdb=" N LEU X 166 " --> pdb=" O ASP X 162 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL X 167 " --> pdb=" O LYS X 163 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N GLU X 168 " --> pdb=" O ALA X 164 " (cutoff:3.500A) Processing helix chain 'X' and resid 182 through 201 removed outlier: 4.760A pdb=" N ALA X 199 " --> pdb=" O THR X 195 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ILE X 200 " --> pdb=" O THR X 196 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N TYR X 201 " --> pdb=" O ALA X 197 " (cutoff:3.500A) Processing helix chain 'X' and resid 204 through 222 removed outlier: 5.455A pdb=" N ALA X 208 " --> pdb=" O PRO X 204 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR X 209 " --> pdb=" O LYS X 205 " (cutoff:3.500A) Processing helix chain 'X' and resid 224 through 240 Processing helix chain 'X' and resid 243 through 262 removed outlier: 4.042A pdb=" N THR X 249 " --> pdb=" O PRO X 245 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN X 262 " --> pdb=" O LYS X 258 " (cutoff:3.500A) Processing helix chain 'X' and resid 263 through 273 removed outlier: 4.207A pdb=" N VAL X 267 " --> pdb=" O THR X 263 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN X 268 " --> pdb=" O PRO X 264 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLY X 273 " --> pdb=" O ALA X 269 " (cutoff:3.500A) Processing helix chain 'X' and resid 274 through 280 Processing helix chain 'X' and resid 281 through 297 Processing helix chain 'X' and resid 298 through 310 Processing helix chain 'X' and resid 316 through 341 removed outlier: 3.983A pdb=" N HIS X 322 " --> pdb=" O ILE X 318 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU X 323 " --> pdb=" O ILE X 319 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ALA X 324 " --> pdb=" O SER X 320 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N LYS X 325 " --> pdb=" O THR X 321 " (cutoff:3.500A) Proline residue: X 341 - end of helix Processing helix chain 'X' and resid 346 through 355 removed outlier: 3.549A pdb=" N ILE X 350 " --> pdb=" O GLN X 346 " (cutoff:3.500A) Processing helix chain 'X' and resid 357 through 372 removed outlier: 4.060A pdb=" N VAL X 361 " --> pdb=" O SER X 357 " (cutoff:3.500A) Processing helix chain 'X' and resid 394 through 418 removed outlier: 6.091A pdb=" N GLU X 398 " --> pdb=" O ASP X 394 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA X 399 " --> pdb=" O LYS X 395 " (cutoff:3.500A) Processing helix chain 'Y' and resid 15 through 28 removed outlier: 4.613A pdb=" N ILE Y 19 " --> pdb=" O PRO Y 15 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA Y 20 " --> pdb=" O ASP Y 16 " (cutoff:3.500A) Processing helix chain 'Y' and resid 33 through 48 removed outlier: 5.159A pdb=" N VAL Y 37 " --> pdb=" O GLY Y 33 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ARG Y 38 " --> pdb=" O ASP Y 34 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU Y 41 " --> pdb=" O VAL Y 37 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ASP Y 47 " --> pdb=" O ALA Y 43 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ASN Y 48 " --> pdb=" O ALA Y 44 " (cutoff:3.500A) Processing helix chain 'Y' and resid 51 through 60 removed outlier: 4.397A pdb=" N GLU Y 55 " --> pdb=" O ALA Y 51 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ALA Y 56 " --> pdb=" O PRO Y 52 " (cutoff:3.500A) Processing helix chain 'Y' and resid 66 through 95 removed outlier: 4.087A pdb=" N GLU Y 89 " --> pdb=" O ASP Y 85 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASN Y 94 " --> pdb=" O ASP Y 90 " (cutoff:3.500A) Processing helix chain 'Y' and resid 98 through 115 removed outlier: 3.747A pdb=" N GLU Y 109 " --> pdb=" O MET Y 105 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N TYR Y 110 " --> pdb=" O ALA Y 106 " (cutoff:3.500A) Processing helix chain 'Y' and resid 116 through 131 removed outlier: 4.213A pdb=" N ASP Y 129 " --> pdb=" O ARG Y 125 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LYS Y 130 " --> pdb=" O LYS Y 126 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR Y 131 " --> pdb=" O THR Y 127 " (cutoff:3.500A) Processing helix chain 'Y' and resid 133 through 152 Processing helix chain 'Y' and resid 153 through 172 removed outlier: 3.949A pdb=" N GLU Y 162 " --> pdb=" O THR Y 158 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU Y 169 " --> pdb=" O LYS Y 165 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N GLU Y 170 " --> pdb=" O SER Y 166 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N GLY Y 171 " --> pdb=" O LEU Y 167 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLY Y 172 " --> pdb=" O ILE Y 168 " (cutoff:3.500A) Processing helix chain 'Y' and resid 173 through 192 removed outlier: 4.539A pdb=" N ARG Y 192 " --> pdb=" O CYS Y 188 " (cutoff:3.500A) Processing helix chain 'Y' and resid 193 through 202 Processing helix chain 'Y' and resid 203 through 208 removed outlier: 6.365A pdb=" N THR Y 207 " --> pdb=" O ASP Y 203 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N PHE Y 208 " --> pdb=" O THR Y 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 203 through 208' Processing helix chain 'Y' and resid 215 through 231 removed outlier: 3.870A pdb=" N ILE Y 229 " --> pdb=" O TYR Y 225 " (cutoff:3.500A) Processing helix chain 'Y' and resid 232 through 239 removed outlier: 3.640A pdb=" N GLU Y 238 " --> pdb=" O PRO Y 234 " (cutoff:3.500A) Processing helix chain 'Y' and resid 243 through 254 removed outlier: 4.102A pdb=" N VAL Y 249 " --> pdb=" O GLU Y 245 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU Y 250 " --> pdb=" O ILE Y 246 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N SER Y 252 " --> pdb=" O GLU Y 248 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU Y 253 " --> pdb=" O VAL Y 249 " (cutoff:3.500A) Proline residue: Y 254 - end of helix Processing helix chain 'Y' and resid 255 through 266 removed outlier: 4.297A pdb=" N LEU Y 263 " --> pdb=" O TYR Y 259 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR Y 264 " --> pdb=" O LEU Y 260 " (cutoff:3.500A) Processing helix chain 'Y' and resid 268 through 286 removed outlier: 3.821A pdb=" N PHE Y 272 " --> pdb=" O TYR Y 268 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLN Y 273 " --> pdb=" O SER Y 269 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL Y 277 " --> pdb=" O GLN Y 273 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N TRP Y 286 " --> pdb=" O MET Y 282 " (cutoff:3.500A) Processing helix chain 'Y' and resid 291 through 312 removed outlier: 3.992A pdb=" N TYR Y 295 " --> pdb=" O HIS Y 291 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL Y 296 " --> pdb=" O TYR Y 292 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE Y 301 " --> pdb=" O ARG Y 297 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N SER Y 310 " --> pdb=" O GLN Y 306 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N TYR Y 311 " --> pdb=" O LEU Y 307 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ARG Y 312 " --> pdb=" O LEU Y 308 " (cutoff:3.500A) Processing helix chain 'Y' and resid 315 through 323 removed outlier: 3.834A pdb=" N GLU Y 321 " --> pdb=" O GLY Y 317 " (cutoff:3.500A) Processing helix chain 'Y' and resid 326 through 341 removed outlier: 3.692A pdb=" N GLY Y 341 " --> pdb=" O PHE Y 337 " (cutoff:3.500A) Processing helix chain 'Y' and resid 361 through 388 removed outlier: 5.012A pdb=" N GLN Y 365 " --> pdb=" O SER Y 361 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ASN Y 388 " --> pdb=" O SER Y 384 " (cutoff:3.500A) Processing helix chain 'Z' and resid 12 through 28 removed outlier: 4.240A pdb=" N VAL Z 20 " --> pdb=" O LEU Z 16 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LYS Z 28 " --> pdb=" O ASN Z 24 " (cutoff:3.500A) Processing helix chain 'Z' and resid 71 through 86 Processing helix chain 'Z' and resid 102 through 117 removed outlier: 4.951A pdb=" N ILE Z 106 " --> pdb=" O HIS Z 102 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ALA Z 107 " --> pdb=" O LYS Z 103 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ASN Z 109 " --> pdb=" O ASP Z 105 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLU Z 110 " --> pdb=" O ILE Z 106 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ARG Z 114 " --> pdb=" O GLU Z 110 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N TYR Z 115 " --> pdb=" O LEU Z 111 " (cutoff:3.500A) removed outlier: 4.045A 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: 3.851A pdb=" N VAL Z 170 " --> pdb=" O GLU Z 166 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY Z 171 " --> pdb=" O ALA Z 167 " (cutoff:3.500A) Processing helix chain 'Z' and resid 185 through 214 removed outlier: 3.816A pdb=" N ARG Z 190 " --> pdb=" O THR Z 186 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN Z 194 " --> pdb=" O ARG Z 190 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL Z 195 " --> pdb=" O ILE Z 191 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N HIS Z 196 " --> pdb=" O THR Z 192 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N LYS Z 214 " --> pdb=" O SER Z 210 " (cutoff:3.500A) Processing helix chain 'Z' and resid 225 through 237 removed outlier: 5.556A pdb=" N GLN Z 229 " --> pdb=" O GLN Z 225 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LEU Z 230 " --> pdb=" O ILE Z 226 " (cutoff:3.500A) Processing helix chain 'Z' and resid 242 through 290 removed outlier: 3.776A pdb=" N VAL Z 259 " --> pdb=" O ASP Z 255 " (cutoff:3.500A) Processing helix chain 'a' and resid 4 through 12 Processing helix chain 'a' and resid 17 through 32 removed outlier: 3.738A pdb=" N GLU a 27 " --> pdb=" O HIS a 23 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS a 32 " --> pdb=" O LEU a 28 " (cutoff:3.500A) Processing helix chain 'a' and resid 33 through 48 removed outlier: 4.521A pdb=" N LEU a 37 " --> pdb=" O LEU a 33 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LEU a 39 " --> pdb=" O HIS a 35 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N GLN a 40 " --> pdb=" O GLN a 36 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL a 41 " --> pdb=" O LEU a 37 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LEU a 42 " --> pdb=" O THR a 38 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASP a 43 " --> pdb=" O LEU a 39 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL a 45 " --> pdb=" O VAL a 41 " (cutoff:3.500A) Proline residue: a 48 - end of helix Processing helix chain 'a' and resid 55 through 68 removed outlier: 5.737A pdb=" N LEU a 59 " --> pdb=" O GLY a 55 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N TYR a 60 " --> pdb=" O LEU a 56 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE a 67 " --> pdb=" O PHE a 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 73 through 88 Processing helix chain 'a' and resid 89 through 105 removed outlier: 5.282A pdb=" N LYS a 105 " --> pdb=" O ARG a 101 " (cutoff:3.500A) Processing helix chain 'a' and resid 109 through 123 removed outlier: 4.517A pdb=" N LEU a 113 " --> pdb=" O GLU a 109 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR a 116 " --> pdb=" O ILE a 112 " (cutoff:3.500A) Processing helix chain 'a' and resid 130 through 139 removed outlier: 4.811A pdb=" N GLU a 139 " --> pdb=" O ILE a 135 " (cutoff:3.500A) Processing helix chain 'a' and resid 149 through 166 removed outlier: 3.582A pdb=" N SER a 153 " --> pdb=" O THR a 149 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ARG a 154 " --> pdb=" O SER a 150 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE a 166 " --> pdb=" O TYR a 162 " (cutoff:3.500A) Processing helix chain 'a' and resid 169 through 184 removed outlier: 3.679A pdb=" N LEU a 177 " --> pdb=" O TYR a 173 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG a 178 " --> pdb=" O LYS a 174 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL a 183 " --> pdb=" O PHE a 179 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ASP a 184 " --> pdb=" O LEU a 180 " (cutoff:3.500A) Processing helix chain 'a' and resid 189 through 207 Processing helix chain 'a' and resid 213 through 219 removed outlier: 4.866A pdb=" N LEU a 217 " --> pdb=" O PHE a 213 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N MET a 218 " --> pdb=" O GLY a 214 " (cutoff:3.500A) Processing helix chain 'a' and resid 220 through 227 removed outlier: 5.837A pdb=" N SER a 224 " --> pdb=" O PRO a 220 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N LEU a 225 " --> pdb=" O VAL a 221 " (cutoff:3.500A) Processing helix chain 'a' and resid 230 through 243 removed outlier: 4.081A pdb=" N ILE a 234 " --> pdb=" O ARG a 230 " (cutoff:3.500A) Processing helix chain 'a' and resid 244 through 255 removed outlier: 4.297A pdb=" N PHE a 248 " --> pdb=" O ASN a 244 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N THR a 253 " --> pdb=" O GLN a 249 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ALA a 254 " --> pdb=" O THR a 250 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TRP a 255 " --> pdb=" O LEU a 251 " (cutoff:3.500A) Processing helix chain 'a' and resid 257 through 265 removed outlier: 4.391A pdb=" N LEU a 261 " --> pdb=" O GLN a 257 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ALA a 263 " --> pdb=" O PRO a 259 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ASN a 264 " --> pdb=" O ASP a 260 " (cutoff:3.500A) Processing helix chain 'a' and resid 266 through 285 removed outlier: 4.168A pdb=" N LEU a 277 " --> pdb=" O GLN a 273 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N MET a 278 " --> pdb=" O LEU a 274 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU a 279 " --> pdb=" O LEU a 275 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET a 280 " --> pdb=" O CYS a 276 " (cutoff:3.500A) Proline residue: a 285 - end of helix Processing helix chain 'a' and resid 292 through 301 Processing helix chain 'a' and resid 303 through 318 removed outlier: 3.759A pdb=" N VAL a 307 " --> pdb=" O THR a 303 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLU a 308 " --> pdb=" O VAL a 304 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N LEU a 309 " --> pdb=" O ASN a 305 " (cutoff:3.500A) Processing helix chain 'a' and resid 342 through 376 removed outlier: 4.085A pdb=" N ILE a 346 " --> pdb=" O ASP a 342 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LYS a 347 " --> pdb=" O LEU a 343 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR a 358 " --> pdb=" O GLU a 354 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ASP a 359 " --> pdb=" O PHE a 355 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL a 360 " --> pdb=" O TRP a 356 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ASP a 373 " --> pdb=" O HIS a 369 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ILE a 374 " --> pdb=" O GLN a 370 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR a 376 " --> pdb=" O HIS a 372 " (cutoff:3.500A) Processing helix chain 'b' and resid 13 through 18 removed outlier: 4.759A pdb=" N ARG b 17 " --> pdb=" O SER b 13 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ASN b 18 " --> pdb=" O GLU b 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 13 through 18' Processing helix chain 'b' and resid 24 through 44 Processing helix chain 'b' and resid 67 through 78 removed outlier: 5.029A pdb=" N ILE b 71 " --> pdb=" O ASP b 67 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N THR b 77 " --> pdb=" O SER b 73 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N VAL b 78 " --> pdb=" O LYS b 74 " (cutoff:3.500A) Processing helix chain 'b' and resid 85 through 100 removed outlier: 3.785A pdb=" N ILE b 90 " --> pdb=" O PHE b 86 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ARG b 91 " --> pdb=" O CYS b 87 " (cutoff:3.500A) Processing helix chain 'b' and resid 120 through 135 removed outlier: 3.679A pdb=" N LYS b 133 " --> pdb=" O LYS b 129 " (cutoff:3.500A) Processing helix chain 'b' and resid 152 through 162 Processing helix chain 'b' and resid 179 through 190 removed outlier: 4.527A pdb=" N LEU b 183 " --> pdb=" O LEU b 179 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N SER b 186 " --> pdb=" O ALA b 182 " (cutoff:3.500A) Proline residue: b 187 - end of helix Processing helix chain 'd' and resid 17 through 33 removed outlier: 5.072A pdb=" N GLU d 21 " --> pdb=" O SER d 17 " (cutoff:3.500A) Processing helix chain 'd' and resid 44 through 66 removed outlier: 5.353A pdb=" N LEU d 48 " --> pdb=" O THR d 44 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA d 51 " --> pdb=" O GLN d 47 " (cutoff:3.500A) Processing helix chain 'd' and resid 67 through 85 removed outlier: 3.579A pdb=" N PHE d 71 " --> pdb=" O ASP d 67 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N TYR d 74 " --> pdb=" O SER d 70 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N MET d 75 " --> pdb=" O PHE d 71 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N TYR d 85 " --> pdb=" O TYR d 81 " (cutoff:3.500A) Processing helix chain 'd' and resid 93 through 110 removed outlier: 5.474A pdb=" N GLN d 97 " --> pdb=" O ALA d 93 " (cutoff:3.500A) Processing helix chain 'd' and resid 111 through 123 removed outlier: 4.183A pdb=" N GLU d 120 " --> pdb=" O HIS d 116 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ARG d 121 " --> pdb=" O THR d 117 " (cutoff:3.500A) removed outlier: 4.494A 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 130 through 146 Proline residue: d 136 - end of helix removed outlier: 3.632A pdb=" N GLU d 145 " --> pdb=" O GLN d 141 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLY d 146 " --> pdb=" O TYR d 142 " (cutoff:3.500A) Processing helix chain 'd' and resid 147 through 158 removed outlier: 4.472A pdb=" N VAL d 151 " --> pdb=" O SER d 147 " (cutoff:3.500A) Processing helix chain 'd' and resid 163 through 184 removed outlier: 3.920A pdb=" N ILE d 169 " --> pdb=" O PHE d 165 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU d 177 " --> pdb=" O THR d 173 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU d 183 " --> pdb=" O ALA d 179 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N LYS d 184 " --> pdb=" O GLY d 180 " (cutoff:3.500A) Processing helix chain 'd' and resid 191 through 198 removed outlier: 5.079A pdb=" N THR d 195 " --> pdb=" O PHE d 191 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N LEU d 198 " --> pdb=" O ALA d 194 " (cutoff:3.500A) Processing helix chain 'd' and resid 203 through 213 removed outlier: 5.000A pdb=" N THR d 207 " --> pdb=" O PRO d 203 " (cutoff:3.500A) Processing helix chain 'd' and resid 234 through 254 Proline residue: d 238 - end of helix removed outlier: 3.607A pdb=" N ALA d 243 " --> pdb=" O SER d 239 " (cutoff:3.500A) Processing helix chain 'd' and resid 3 through 8 removed outlier: 5.672A pdb=" N LYS d 6 " --> pdb=" O GLU d 3 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N GLY d 7 " --> pdb=" O GLN d 4 " (cutoff:3.500A) Processing helix chain 'f' and resid 6 through 23 Proline residue: f 10 - end of helix Proline residue: f 13 - end of helix Proline residue: f 17 - end of helix Proline residue: f 21 - end of helix Processing helix chain 'f' and resid 27 through 48 removed outlier: 3.787A pdb=" N GLU f 32 " --> pdb=" O PRO f 28 " (cutoff:3.500A) Processing helix chain 'f' and resid 54 through 64 removed outlier: 4.110A pdb=" N ARG f 62 " --> pdb=" O MET f 58 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N LEU f 63 " --> pdb=" O LEU f 59 " (cutoff:3.500A) Processing helix chain 'f' and resid 65 through 76 Proline residue: f 73 - end of helix removed outlier: 4.230A pdb=" N GLU f 76 " --> pdb=" O ARG f 72 " (cutoff:3.500A) Processing helix chain 'f' and resid 81 through 91 Processing helix chain 'f' and resid 102 through 111 removed outlier: 4.114A pdb=" N LYS f 107 " --> pdb=" O TYR f 103 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLU f 108 " --> pdb=" O GLY f 104 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ILE f 109 " --> pdb=" O LYS f 105 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TYR f 110 " --> pdb=" O LEU f 106 " (cutoff:3.500A) Processing helix chain 'f' and resid 117 through 126 removed outlier: 4.741A pdb=" N PHE f 121 " --> pdb=" O GLU f 117 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ASP f 124 " --> pdb=" O ARG f 120 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ILE f 125 " --> pdb=" O PHE f 121 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ILE f 126 " --> pdb=" O ALA f 122 " (cutoff:3.500A) Processing helix chain 'f' and resid 130 through 149 removed outlier: 3.768A pdb=" N TYR f 142 " --> pdb=" O GLU f 138 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG f 143 " --> pdb=" O CYS f 139 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLN f 148 " --> pdb=" O LEU f 144 " (cutoff:3.500A) Processing helix chain 'f' and resid 153 through 175 removed outlier: 4.434A pdb=" N VAL f 159 " --> pdb=" O GLY f 155 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLN f 171 " --> pdb=" O ALA f 167 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N GLU f 172 " --> pdb=" O LYS f 168 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ASP f 174 " --> pdb=" O TRP f 170 " (cutoff:3.500A) Processing helix chain 'f' and resid 176 through 189 removed outlier: 4.302A pdb=" N GLN f 180 " --> pdb=" O ALA f 176 " (cutoff:3.500A) Proline residue: f 183 - end of helix Processing helix chain 'f' and resid 193 through 209 removed outlier: 4.169A pdb=" N LEU f 207 " --> pdb=" O GLU f 203 " (cutoff:3.500A) Processing helix chain 'f' and resid 212 through 227 removed outlier: 4.415A pdb=" N MET f 216 " --> pdb=" O GLU f 212 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA f 227 " --> pdb=" O GLU f 223 " (cutoff:3.500A) Processing helix chain 'f' and resid 230 through 247 removed outlier: 4.397A pdb=" N THR f 234 " --> pdb=" O CYS f 230 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N SER f 235 " --> pdb=" O LEU f 231 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N CYS f 236 " --> pdb=" O TYR f 232 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N VAL f 237 " --> pdb=" O LEU f 233 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN f 238 " --> pdb=" O THR f 234 " (cutoff:3.500A) Proline residue: f 241 - end of helix removed outlier: 4.812A pdb=" N GLU f 244 " --> pdb=" O VAL f 240 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ALA f 247 " --> pdb=" O PRO f 243 " (cutoff:3.500A) Processing helix chain 'f' and resid 253 through 263 removed outlier: 3.633A 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 272 through 278 removed outlier: 5.948A pdb=" N GLU f 276 " --> pdb=" O LEU f 272 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N LEU f 277 " --> pdb=" O ASN f 273 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N VAL f 278 " --> pdb=" O ASP f 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 272 through 278' Processing helix chain 'f' and resid 284 through 294 removed outlier: 4.450A pdb=" N VAL f 288 " --> pdb=" O SER f 284 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N MET f 294 " --> pdb=" O VAL f 290 " (cutoff:3.500A) Processing helix chain 'f' and resid 296 through 308 removed outlier: 3.933A pdb=" N VAL f 303 " --> pdb=" O GLY f 299 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLU f 306 " --> pdb=" O GLY f 302 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER f 308 " --> pdb=" O PHE f 304 " (cutoff:3.500A) Processing helix chain 'f' and resid 314 through 322 Processing helix chain 'f' and resid 325 through 335 Processing helix chain 'f' and resid 345 through 351 removed outlier: 4.456A pdb=" N TYR f 349 " --> pdb=" O PRO f 345 " (cutoff:3.500A) Processing helix chain 'f' and resid 354 through 361 removed outlier: 3.656A pdb=" N PHE f 358 " --> pdb=" O GLU f 354 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N GLY f 359 " --> pdb=" O ASN f 355 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLY f 360 " --> pdb=" O ASN f 356 " (cutoff:3.500A) Processing helix chain 'f' and resid 367 through 383 Processing helix chain 'f' and resid 395 through 402 removed outlier: 4.427A pdb=" N ASN f 402 " --> pdb=" O TRP f 398 " (cutoff:3.500A) Processing helix chain 'f' and resid 403 through 419 removed outlier: 4.125A pdb=" N GLY f 415 " --> pdb=" O ALA f 411 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET f 416 " --> pdb=" O ALA f 412 " (cutoff:3.500A) Processing helix chain 'f' and resid 423 through 436 removed outlier: 4.678A pdb=" N THR f 427 " --> pdb=" O ASP f 423 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLN f 428 " --> pdb=" O GLY f 424 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR f 432 " --> pdb=" O GLN f 428 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N SER f 435 " --> pdb=" O LYS f 431 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N SER f 436 " --> pdb=" O TYR f 432 " (cutoff:3.500A) Processing helix chain 'f' and resid 437 through 453 removed outlier: 3.776A pdb=" N ASN f 452 " --> pdb=" O CYS f 448 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER f 453 " --> pdb=" O GLY f 449 " (cutoff:3.500A) Processing helix chain 'f' and resid 460 through 472 removed outlier: 5.428A pdb=" N ASP f 468 " --> pdb=" O ALA f 464 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N TYR f 469 " --> pdb=" O LEU f 465 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LEU f 471 " --> pdb=" O SER f 467 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N HIS f 472 " --> pdb=" O ASP f 468 " (cutoff:3.500A) Processing helix chain 'f' and resid 474 through 490 Processing helix chain 'f' and resid 494 through 507 Proline residue: f 503 - end of helix removed outlier: 3.950A pdb=" N GLY f 506 " --> pdb=" O LEU f 502 " (cutoff:3.500A) Processing helix chain 'f' and resid 511 through 527 removed outlier: 4.574A pdb=" N VAL f 527 " --> pdb=" O GLY f 523 " (cutoff:3.500A) Processing helix chain 'f' and resid 530 through 544 removed outlier: 4.313A pdb=" N GLU f 544 " --> pdb=" O GLN f 540 " (cutoff:3.500A) Processing helix chain 'f' and resid 545 through 552 Processing helix chain 'f' and resid 554 through 567 removed outlier: 4.647A pdb=" N LEU f 558 " --> pdb=" O TYR f 554 " (cutoff:3.500A) Proline residue: f 559 - end of helix removed outlier: 4.268A pdb=" N LEU f 562 " --> pdb=" O LEU f 558 " (cutoff:3.500A) Processing helix chain 'f' and resid 572 through 582 removed outlier: 4.937A pdb=" N ILE f 576 " --> pdb=" O ALA f 572 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU f 577 " --> pdb=" O ILE f 573 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL f 582 " --> pdb=" O ALA f 578 " (cutoff:3.500A) Processing helix chain 'f' and resid 585 through 601 removed outlier: 4.282A pdb=" N SER f 589 " --> pdb=" O GLU f 585 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR f 600 " --> pdb=" O ASP f 596 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ALA f 601 " --> pdb=" O VAL f 597 " (cutoff:3.500A) Processing helix chain 'f' and resid 605 through 624 removed outlier: 5.264A pdb=" N VAL f 609 " --> pdb=" O ASN f 605 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N CYS f 616 " --> pdb=" O LEU f 612 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N SER f 617 " --> pdb=" O LEU f 613 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N SER f 622 " --> pdb=" O GLU f 618 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LYS f 623 " --> pdb=" O HIS f 619 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N GLU f 624 " --> pdb=" O PHE f 620 " (cutoff:3.500A) Processing helix chain 'f' and resid 626 through 641 removed outlier: 6.238A pdb=" N ASP f 630 " --> pdb=" O GLU f 626 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LYS f 631 " --> pdb=" O GLU f 627 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLU f 633 " --> pdb=" O LYS f 629 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP f 636 " --> pdb=" O LYS f 632 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N LYS f 637 " --> pdb=" O GLU f 633 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ASP f 638 " --> pdb=" O LYS f 634 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N LYS f 639 " --> pdb=" O LYS f 635 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N LYS f 640 " --> pdb=" O ASP f 636 " (cutoff:3.500A) Processing helix chain 'f' and resid 645 through 658 removed outlier: 5.036A pdb=" N HIS f 649 " --> pdb=" O ASP f 645 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA f 653 " --> pdb=" O HIS f 649 " (cutoff:3.500A) Processing helix chain 'f' and resid 666 through 680 removed outlier: 3.837A pdb=" N MET f 670 " --> pdb=" O ILE f 666 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ALA f 671 " --> pdb=" O GLY f 667 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N LEU f 672 " --> pdb=" O ALA f 668 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N ARG f 673 " --> pdb=" O GLU f 669 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N THR f 674 " --> pdb=" O MET f 670 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N PHE f 675 " --> pdb=" O ALA f 671 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY f 676 " --> pdb=" O LEU f 672 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG f 680 " --> pdb=" O GLY f 676 " (cutoff:3.500A) Processing helix chain 'f' and resid 691 through 699 removed outlier: 4.399A pdb=" N ALA f 695 " --> pdb=" O PRO f 691 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ILE f 697 " --> pdb=" O ALA f 693 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N SER f 698 " --> pdb=" O LEU f 694 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N VAL f 699 " --> pdb=" O ALA f 695 " (cutoff:3.500A) Processing helix chain 'f' and resid 701 through 717 removed outlier: 3.841A pdb=" N PHE f 713 " --> pdb=" O THR f 709 " (cutoff:3.500A) Processing helix chain 'f' and resid 721 through 734 removed outlier: 4.489A pdb=" N SER f 725 " --> pdb=" O VAL f 721 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ILE f 726 " --> pdb=" O SER f 722 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N PHE f 727 " --> pdb=" O TYR f 723 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N GLY f 733 " --> pdb=" O MET f 729 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N SER f 734 " --> pdb=" O GLY f 730 " (cutoff:3.500A) Processing helix chain 'f' and resid 739 through 754 removed outlier: 3.689A pdb=" N TYR f 751 " --> pdb=" O GLN f 747 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N LYS f 754 " --> pdb=" O GLN f 750 " (cutoff:3.500A) Processing helix chain 'f' and resid 771 through 776 removed outlier: 4.612A pdb=" N LEU f 776 " --> pdb=" O GLY f 772 " (cutoff:3.500A) Processing helix chain 'f' and resid 778 through 787 removed outlier: 4.474A pdb=" N ASP f 784 " --> pdb=" O PRO f 780 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLN f 786 " --> pdb=" O HIS f 782 " (cutoff:3.500A) Processing helix chain 'f' and resid 797 through 804 removed outlier: 4.402A pdb=" N VAL f 801 " --> pdb=" O LEU f 797 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N LEU f 804 " --> pdb=" O LEU f 800 " (cutoff:3.500A) Processing helix chain 'f' and resid 93 through 98 removed outlier: 3.667A pdb=" N PHE f 98 " --> pdb=" O PRO f 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 93 through 98' Processing helix chain 'x' and resid 25 through 37 Processing helix chain 'c' and resid 34 through 49 Processing helix chain 'c' and resid 88 through 103 removed outlier: 4.417A pdb=" N GLN c 92 " --> pdb=" O ASP c 88 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLY c 103 " --> pdb=" O LEU c 99 " (cutoff:3.500A) Processing helix chain 'c' and resid 123 through 137 removed outlier: 3.681A pdb=" N ASN c 128 " --> pdb=" O GLY c 124 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N THR c 129 " --> pdb=" O VAL c 125 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLN c 130 " --> pdb=" O ASP c 126 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN c 131 " --> pdb=" O ILE c 127 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N SER c 132 " --> pdb=" O ASN c 128 " (cutoff:3.500A) Processing helix chain 'c' and resid 146 through 151 removed outlier: 3.691A pdb=" N SER c 150 " --> pdb=" O ASP c 146 " (cutoff:3.500A) removed outlier: 6.842A 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 188 through 195 removed outlier: 3.864A pdb=" N HIS c 194 " --> pdb=" O GLN c 190 " (cutoff:3.500A) Processing helix chain 'c' and resid 210 through 220 removed outlier: 4.035A pdb=" N ASN c 219 " --> pdb=" O LYS c 215 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N LEU c 220 " --> pdb=" O MET c 216 " (cutoff:3.500A) Processing helix chain 'c' and resid 224 through 230 removed outlier: 4.175A pdb=" N GLY c 228 " --> pdb=" O SER c 224 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU c 229 " --> pdb=" O TRP c 225 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR c 230 " --> pdb=" O MET c 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 224 through 230' Processing helix chain 'c' and resid 234 through 259 removed outlier: 4.216A pdb=" N CYS c 238 " --> pdb=" O TYR c 234 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU c 250 " --> pdb=" O LYS c 246 " (cutoff:3.500A) Processing helix chain 'c' and resid 266 through 275 removed outlier: 4.231A pdb=" N VAL c 275 " --> pdb=" O ALA c 271 " (cutoff:3.500A) Processing helix chain 'c' and resid 280 through 310 removed outlier: 5.468A pdb=" N LEU c 284 " --> pdb=" O PRO c 280 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU c 285 " --> pdb=" O LYS c 281 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N HIS c 287 " --> pdb=" O HIS c 283 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N VAL c 288 " --> pdb=" O LEU c 284 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASP c 289 " --> pdb=" O GLU c 285 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL c 290 " --> pdb=" O GLU c 286 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LYS c 310 " --> pdb=" O THR c 306 " (cutoff:3.500A) Processing helix chain 'c' and resid 165 through 170 removed outlier: 3.654A pdb=" N MET c 168 " --> pdb=" O ALA c 165 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL c 169 " --> pdb=" O ASN c 166 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU c 170 " --> pdb=" O MET c 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 165 through 170' Processing helix chain 'F' and resid 25 through 36 removed outlier: 5.170A pdb=" N MET F 36 " --> pdb=" O GLU F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 84 removed outlier: 3.893A pdb=" N LEU F 48 " --> pdb=" O ARG F 44 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU F 60 " --> pdb=" O LYS F 56 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR F 63 " --> pdb=" O VAL F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 116 removed outlier: 5.276A pdb=" N SER F 115 " --> pdb=" O ILE F 111 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLN F 116 " --> pdb=" O ASP F 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 111 through 116' Processing helix chain 'F' and resid 141 through 146 removed outlier: 4.787A pdb=" N LEU F 145 " --> pdb=" O ASP F 141 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N LYS F 146 " --> pdb=" O ALA F 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 141 through 146' Processing helix chain 'F' and resid 169 through 177 removed outlier: 5.974A pdb=" N VAL F 177 " --> pdb=" O LYS F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 189 removed outlier: 4.172A pdb=" N ILE F 188 " --> pdb=" O GLN F 184 " (cutoff:3.500A) removed outlier: 5.344A 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: 4.765A pdb=" N LEU F 204 " --> pdb=" O GLU F 200 " (cutoff:3.500A) Proline residue: F 205 - end of helix Processing helix chain 'F' and resid 209 through 216 removed outlier: 4.144A pdb=" N LEU F 215 " --> pdb=" O LYS F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 232 through 244 removed outlier: 4.769A pdb=" N LEU F 236 " --> pdb=" O GLY F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 279 removed outlier: 4.506A pdb=" N ALA F 279 " --> pdb=" O ALA F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 293 removed outlier: 3.802A pdb=" N THR F 293 " --> pdb=" O ASP F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 318 removed outlier: 5.369A pdb=" N GLN F 307 " --> pdb=" O ASP F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 339 removed outlier: 4.657A pdb=" N LEU F 338 " --> pdb=" O ARG F 334 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ASP F 339 " --> pdb=" O VAL F 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 334 through 339' Processing helix chain 'F' and resid 358 through 371 removed outlier: 6.065A pdb=" N ARG F 362 " --> pdb=" O ASN F 358 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA F 363 " --> pdb=" O GLU F 359 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG F 371 " --> pdb=" O GLN F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 389 removed outlier: 4.520A pdb=" N ASP F 389 " --> pdb=" O ALA F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 411 removed outlier: 4.022A pdb=" N CYS F 400 " --> pdb=" O CYS F 396 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL F 401 " --> pdb=" O LYS F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 429 Processing helix chain 'u' and resid 22 through 34 Processing helix chain 'u' and resid 37 through 42 removed outlier: 3.701A pdb=" N GLN u 41 " --> pdb=" O PRO u 37 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N ARG u 42 " --> pdb=" O PRO u 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 37 through 42' Processing helix chain 'u' and resid 55 through 60 removed outlier: 3.588A pdb=" N TYR u 59 " --> pdb=" O THR u 55 " (cutoff:3.500A) Processing helix chain 'e' and resid 51 through 64 removed outlier: 5.155A pdb=" N GLN e 55 " --> pdb=" O ASP e 51 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY e 64 " --> pdb=" O LEU e 60 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 118 through 123 removed outlier: 4.852A pdb=" N ALA A 119 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ILE A 112 " --> pdb=" O ILE A 102 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N LYS A 116 " --> pdb=" O CYS A 98 " (cutoff:3.500A) removed outlier: 11.703A pdb=" N CYS A 98 " --> pdb=" O LYS A 116 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N MET A 138 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ARG A 139 " --> pdb=" O LEU A 153 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE A 151 " --> pdb=" O GLY A 141 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 211 through 216 removed outlier: 3.538A pdb=" N PHE A 215 " --> pdb=" O ILE A 341 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 236 through 240 Processing sheet with id= 4, first strand: chain 'B' and resid 107 through 113 removed outlier: 4.301A pdb=" N CYS B 148 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N SER B 149 " --> pdb=" O LEU B 163 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'B' and resid 114 through 117 No H-bonds generated for sheet with id= 5 Processing sheet with id= 6, first strand: chain 'B' and resid 245 through 250 removed outlier: 3.543A pdb=" N THR B 246 " --> pdb=" O PRO B 279 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY B 226 " --> pdb=" O THR B 331 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'C' and resid 78 through 81 removed outlier: 3.793A pdb=" N ARG C 78 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LYS C 84 " --> pdb=" O MET C 80 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LEU C 86 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N CYS C 112 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ARG C 113 " --> pdb=" O LEU C 127 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LYS C 125 " --> pdb=" O ALA C 115 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'C' and resid 186 through 190 Processing sheet with id= 9, first strand: chain 'C' and resid 209 through 214 removed outlier: 4.897A pdb=" N ASP C 249 " --> pdb=" O VAL C 214 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER C 244 " --> pdb=" O ASN C 288 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'C' and resid 84 through 89 removed outlier: 3.582A pdb=" N VAL C 89 " --> pdb=" O GLY C 93 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY C 93 " --> pdb=" O VAL C 89 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'D' and resid 109 through 112 removed outlier: 3.986A pdb=" N SER D 109 " --> pdb=" O SER D 105 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE D 102 " --> pdb=" O LEU D 93 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N SER D 129 " --> pdb=" O LEU D 143 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASP D 141 " --> pdb=" O ALA D 131 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'D' and resid 226 through 230 removed outlier: 6.520A pdb=" N ARG D 200 " --> pdb=" O VAL D 305 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL D 307 " --> pdb=" O ARG D 200 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLY D 206 " --> pdb=" O THR D 311 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG D 329 " --> pdb=" O GLY D 201 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'E' and resid 78 through 83 removed outlier: 3.754A pdb=" N CYS E 83 " --> pdb=" O GLU E 67 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLU E 67 " --> pdb=" O CYS E 83 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ILE E 70 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE E 56 " --> pdb=" O LEU E 100 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR E 96 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG E 97 " --> pdb=" O LEU E 111 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG E 109 " --> pdb=" O ALA E 99 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'E' and resid 194 through 198 removed outlier: 5.716A pdb=" N ASN E 194 " --> pdb=" O PRO E 227 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA E 278 " --> pdb=" O MET E 232 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LYS E 168 " --> pdb=" O VAL E 273 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N MET E 275 " --> pdb=" O LYS E 168 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY E 174 " --> pdb=" O THR E 279 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'G' and resid 68 through 72 removed outlier: 6.446A pdb=" N HIS G 68 " --> pdb=" O MET G 80 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE G 76 " --> pdb=" O ILE G 72 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY G 77 " --> pdb=" O ILE G 141 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL G 151 " --> pdb=" O PHE G 163 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N CYS G 161 " --> pdb=" O LYS G 153 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N TYR G 159 " --> pdb=" O ASP G 155 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'G' and resid 164 through 169 removed outlier: 6.540A pdb=" N LYS G 164 " --> pdb=" O ARG G 43 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N VAL G 217 " --> pdb=" O LEU G 230 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'g' and resid 68 through 72 removed outlier: 6.322A pdb=" N HIS g 68 " --> pdb=" O MET g 80 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE g 76 " --> pdb=" O ILE g 72 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VAL g 151 " --> pdb=" O PHE g 163 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N CYS g 161 " --> pdb=" O LYS g 153 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP g 155 " --> pdb=" O TYR g 159 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N TYR g 159 " --> pdb=" O ASP g 155 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'g' and resid 165 through 169 Processing sheet with id= 19, first strand: chain 'H' and resid 65 through 68 removed outlier: 6.489A pdb=" N ILE H 72 " --> pdb=" O ILE H 68 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'H' and resid 160 through 164 removed outlier: 3.719A pdb=" N GLU H 49 " --> pdb=" O PRO H 34 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ASN H 207 " --> pdb=" O LYS H 50 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N VAL H 210 " --> pdb=" O LEU H 221 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASN H 214 " --> pdb=" O GLY H 217 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'h' and resid 65 through 68 removed outlier: 6.524A pdb=" N ILE h 72 " --> pdb=" O ILE h 68 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'h' and resid 160 through 164 removed outlier: 4.904A pdb=" N ASN h 207 " --> pdb=" O LYS h 50 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N VAL h 210 " --> pdb=" O LEU h 221 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'I' and resid 65 through 68 removed outlier: 6.571A pdb=" N MET I 72 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ASP I 71 " --> pdb=" O TRP I 139 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU I 147 " --> pdb=" O TRP I 159 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'I' and resid 161 through 165 removed outlier: 5.082A pdb=" N THR I 33 " --> pdb=" O GLU I 48 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ILE I 213 " --> pdb=" O LEU I 228 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'i' and resid 65 through 68 removed outlier: 6.649A pdb=" N MET i 72 " --> pdb=" O LEU i 68 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ASP i 71 " --> pdb=" O TRP i 139 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU i 147 " --> pdb=" O TRP i 159 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'i' and resid 161 through 165 removed outlier: 5.253A pdb=" N THR i 33 " --> pdb=" O GLU i 48 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE i 213 " --> pdb=" O LEU i 228 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'J' and resid 69 through 75 removed outlier: 4.466A pdb=" N THR J 152 " --> pdb=" O ASP J 148 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'J' and resid 158 through 162 removed outlier: 5.387A pdb=" N THR J 31 " --> pdb=" O GLU J 46 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N ASN J 205 " --> pdb=" O LYS J 47 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'j' and resid 69 through 75 removed outlier: 3.612A pdb=" N GLY j 135 " --> pdb=" O ARG j 143 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N THR j 152 " --> pdb=" O ASP j 148 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'j' and resid 158 through 162 removed outlier: 5.658A pdb=" N THR j 31 " --> pdb=" O GLU j 46 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ASN j 205 " --> pdb=" O LYS j 47 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'K' and resid 67 through 70 removed outlier: 6.510A pdb=" N ILE K 74 " --> pdb=" O ILE K 70 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N HIS K 73 " --> pdb=" O VAL K 146 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'K' and resid 167 through 171 removed outlier: 5.631A pdb=" N THR K 36 " --> pdb=" O GLU K 51 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ASN K 214 " --> pdb=" O LYS K 52 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N LEU K 217 " --> pdb=" O PHE K 229 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'k' and resid 67 through 70 removed outlier: 6.475A pdb=" N ILE k 74 " --> pdb=" O ILE k 70 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N HIS k 73 " --> pdb=" O VAL k 146 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'k' and resid 167 through 171 removed outlier: 5.557A pdb=" N THR k 36 " --> pdb=" O GLU k 51 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N ASN k 214 " --> pdb=" O LYS k 52 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LEU k 217 " --> pdb=" O PHE k 229 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'L' and resid 63 through 66 removed outlier: 6.474A pdb=" N ILE L 70 " --> pdb=" O VAL L 66 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N HIS L 69 " --> pdb=" O TYR L 137 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ILE L 144 " --> pdb=" O CYS L 156 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASN L 152 " --> pdb=" O CYS L 148 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'L' and resid 158 through 162 removed outlier: 4.723A pdb=" N ALA L 34 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ASN L 209 " --> pdb=" O LYS L 50 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'l' and resid 63 through 66 removed outlier: 6.470A pdb=" N ILE l 70 " --> pdb=" O VAL l 66 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N HIS l 69 " --> pdb=" O TYR l 137 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU l 132 " --> pdb=" O THR l 147 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ILE l 144 " --> pdb=" O CYS l 156 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASN l 152 " --> pdb=" O CYS l 148 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'l' and resid 158 through 162 removed outlier: 5.138A pdb=" N ALA l 34 " --> pdb=" O LEU l 49 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ASN l 209 " --> pdb=" O LYS l 50 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'M' and resid 66 through 69 removed outlier: 3.615A pdb=" N VAL M 69 " --> pdb=" O VAL M 73 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL M 73 " --> pdb=" O VAL M 69 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LEU M 148 " --> pdb=" O TYR M 160 " (cutoff:3.500A) Processing sheet with id= 40, 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= 41, first strand: chain 'm' and resid 66 through 69 removed outlier: 6.702A pdb=" N VAL m 73 " --> pdb=" O VAL m 69 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU m 148 " --> pdb=" O TYR m 160 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'm' and resid 162 through 166 removed outlier: 4.700A pdb=" N THR m 35 " --> pdb=" O GLU m 50 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'N' and resid 34 through 37 removed outlier: 6.534A pdb=" N ILE N 41 " --> pdb=" O ILE N 37 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N ARG N 40 " --> pdb=" O TRP N 103 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'N' and resid 125 through 129 removed outlier: 6.439A pdb=" N THR N 2 " --> pdb=" O ASP N 17 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N VAL N 173 " --> pdb=" O SER N 18 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY N 183 " --> pdb=" O ALA N 180 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'n' and resid 34 through 37 removed outlier: 6.523A pdb=" N ILE n 41 " --> pdb=" O ILE n 37 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ARG n 40 " --> pdb=" O TRP n 103 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP n 104 " --> pdb=" O GLY n 108 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'n' and resid 125 through 129 removed outlier: 6.342A pdb=" N THR n 2 " --> pdb=" O ASP n 17 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER n 18 " --> pdb=" O VAL n 173 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N VAL n 173 " --> pdb=" O SER n 18 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY n 183 " --> pdb=" O ALA n 180 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'O' and resid 34 through 37 removed outlier: 6.501A pdb=" N ILE O 41 " --> pdb=" O ILE O 37 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ASN O 40 " --> pdb=" O VAL O 103 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N SER O 118 " --> pdb=" O TYR O 114 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'O' and resid 124 through 128 removed outlier: 6.097A pdb=" N THR O 2 " --> pdb=" O ASP O 17 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N THR O 18 " --> pdb=" O ASN O 172 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N ASN O 172 " --> pdb=" O THR O 18 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS O 182 " --> pdb=" O SER O 179 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'o' and resid 34 through 37 removed outlier: 6.431A pdb=" N ILE o 41 " --> pdb=" O ILE o 37 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N ASN o 40 " --> pdb=" O VAL o 103 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER o 118 " --> pdb=" O TYR o 114 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'o' and resid 124 through 128 removed outlier: 6.332A pdb=" N THR o 2 " --> pdb=" O ASP o 17 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR o 18 " --> pdb=" O ASN o 172 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ASN o 172 " --> pdb=" O THR o 18 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LYS o 182 " --> pdb=" O SER o 179 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'P' and resid 42 through 45 removed outlier: 5.711A pdb=" N LEU P 49 " --> pdb=" O MET P 45 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ARG P 48 " --> pdb=" O LEU P 112 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA P 54 " --> pdb=" O GLU P 106 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'P' and resid 136 through 140 removed outlier: 6.221A pdb=" N ALA P 10 " --> pdb=" O ASP P 25 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLY P 184 " --> pdb=" O ARG P 26 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N VAL P 185 " --> pdb=" O LEU P 200 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LYS P 194 " --> pdb=" O GLU P 191 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'p' and resid 42 through 45 removed outlier: 5.881A pdb=" N LEU p 49 " --> pdb=" O MET p 45 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ARG p 48 " --> pdb=" O LEU p 112 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA p 54 " --> pdb=" O GLU p 106 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'p' and resid 136 through 140 removed outlier: 5.996A pdb=" N ALA p 10 " --> pdb=" O ASP p 25 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N GLY p 184 " --> pdb=" O ARG p 26 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N VAL p 185 " --> pdb=" O LEU p 200 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS p 194 " --> pdb=" O GLU p 191 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'Q' and resid 35 through 38 removed outlier: 6.543A pdb=" N ILE Q 42 " --> pdb=" O MET Q 38 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LYS Q 41 " --> pdb=" O TYR Q 107 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'Q' and resid 129 through 132 removed outlier: 3.623A pdb=" N LEU Q 4 " --> pdb=" O HIS Q 132 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N TYR Q 3 " --> pdb=" O ASP Q 18 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'q' and resid 35 through 38 removed outlier: 6.310A pdb=" N ILE q 42 " --> pdb=" O MET q 38 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N LYS q 41 " --> pdb=" O TYR q 107 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'q' and resid 129 through 132 removed outlier: 6.416A pdb=" N TYR q 3 " --> pdb=" O ASP q 18 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'R' and resid 34 through 37 removed outlier: 6.606A pdb=" N LEU R 41 " --> pdb=" O ILE R 37 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N MET R 100 " --> pdb=" O THR R 44 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'R' and resid 125 through 129 removed outlier: 6.088A pdb=" N THR R 2 " --> pdb=" O ASP R 17 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY R 11 " --> pdb=" O PHE R 8 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ALA R 173 " --> pdb=" O SER R 18 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LEU R 176 " --> pdb=" O VAL R 187 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'r' and resid 34 through 37 removed outlier: 3.572A pdb=" N ILE r 37 " --> pdb=" O LEU r 41 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU r 41 " --> pdb=" O ILE r 37 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR r 44 " --> pdb=" O MET r 100 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N MET r 100 " --> pdb=" O THR r 44 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'r' and resid 125 through 129 removed outlier: 6.130A pdb=" N THR r 2 " --> pdb=" O ASP r 17 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY r 11 " --> pdb=" O PHE r 8 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL r 12 " --> pdb=" O VAL r 179 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ALA r 173 " --> pdb=" O SER r 18 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N LEU r 176 " --> pdb=" O VAL r 187 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY r 183 " --> pdb=" O ARG r 180 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'S' and resid 43 through 46 removed outlier: 6.625A pdb=" N THR S 50 " --> pdb=" O LEU S 46 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LYS S 49 " --> pdb=" O LEU S 113 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'S' and resid 135 through 139 removed outlier: 5.570A pdb=" N THR S 11 " --> pdb=" O ASP S 26 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N THR S 27 " --> pdb=" O ALA S 192 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ALA S 192 " --> pdb=" O THR S 27 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 's' and resid 43 through 46 removed outlier: 6.700A pdb=" N THR s 50 " --> pdb=" O LEU s 46 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LYS s 49 " --> pdb=" O LEU s 113 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 's' and resid 135 through 139 removed outlier: 5.544A pdb=" N THR s 11 " --> pdb=" O ASP s 26 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR s 27 " --> pdb=" O ALA s 192 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ALA s 192 " --> pdb=" O THR s 27 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY s 202 " --> pdb=" O THR s 199 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'T' and resid 42 through 45 removed outlier: 6.643A pdb=" N THR T 49 " --> pdb=" O VAL T 45 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N SER T 48 " --> pdb=" O TYR T 115 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'T' and resid 136 through 139 removed outlier: 4.267A pdb=" N VAL T 11 " --> pdb=" O THR T 139 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL T 6 " --> pdb=" O SER T 29 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N SER T 29 " --> pdb=" O VAL T 6 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLY T 8 " --> pdb=" O LEU T 27 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N LEU T 27 " --> pdb=" O GLY T 8 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N SER T 10 " --> pdb=" O ASP T 25 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ASP T 25 " --> pdb=" O SER T 10 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ARG T 186 " --> pdb=" O MET T 26 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE T 189 " --> pdb=" O GLU T 200 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 't' and resid 42 through 45 removed outlier: 6.691A pdb=" N THR t 49 " --> pdb=" O VAL t 45 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N SER t 48 " --> pdb=" O TYR t 115 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 't' and resid 136 through 139 removed outlier: 4.283A pdb=" N VAL t 11 " --> pdb=" O THR t 139 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL t 6 " --> pdb=" O SER t 29 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N SER t 29 " --> pdb=" O VAL t 6 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N GLY t 8 " --> pdb=" O LEU t 27 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N LEU t 27 " --> pdb=" O GLY t 8 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N SER t 10 " --> pdb=" O ASP t 25 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ASP t 25 " --> pdb=" O SER t 10 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ARG t 186 " --> pdb=" O MET t 26 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ILE t 189 " --> pdb=" O GLU t 200 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'V' and resid 449 through 453 removed outlier: 4.162A pdb=" N SER V 450 " --> pdb=" O GLN V 459 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN V 459 " --> pdb=" O SER V 450 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR V 457 " --> pdb=" O ASN V 452 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'W' and resid 404 through 408 Processing sheet with id= 73, first strand: chain 'X' and resid 376 through 379 No H-bonds generated for sheet with id= 73 Processing sheet with id= 74, first strand: chain 'Y' and resid 345 through 348 Processing sheet with id= 75, first strand: chain 'Z' and resid 47 through 50 removed outlier: 3.902A pdb=" N ALA Z 137 " --> pdb=" O VAL Z 158 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N SER Z 160 " --> pdb=" O THR Z 135 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N THR Z 135 " --> pdb=" O SER Z 160 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP Z 125 " --> pdb=" O PRO Z 134 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL Z 120 " --> pdb=" O VAL Z 92 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE Z 124 " --> pdb=" O HIS Z 96 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN Z 52 " --> pdb=" O LEU Z 40 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'a' and resid 321 through 326 removed outlier: 6.936A pdb=" N LYS a 321 " --> pdb=" O THR a 334 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'b' and resid 47 through 54 removed outlier: 3.927A pdb=" N ASN b 48 " --> pdb=" O GLU b 4 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU b 54 " --> pdb=" O VAL b 10 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ARG b 108 " --> pdb=" O SER b 5 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET b 7 " --> pdb=" O ARG b 108 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASP b 11 " --> pdb=" O PHE b 112 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N GLY b 114 " --> pdb=" O ASP b 11 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N GLY b 167 " --> pdb=" O VAL b 136 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N VAL b 138 " --> pdb=" O GLY b 167 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N HIS b 169 " --> pdb=" O VAL b 138 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE b 140 " --> pdb=" O HIS b 169 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N VAL b 173 " --> pdb=" O ASN b 142 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'f' and resid 811 through 815 removed outlier: 3.590A pdb=" N ALA f 880 " --> pdb=" O GLY f 812 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER f 814 " --> pdb=" O ALA f 880 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU f 882 " --> pdb=" O SER f 814 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'x' and resid 44 through 47 removed outlier: 3.786A pdb=" N LYS x 45 " --> pdb=" O MET x 72 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N MET x 72 " --> pdb=" O LYS x 45 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU x 70 " --> pdb=" O MET x 47 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'c' and resid 52 through 58 removed outlier: 4.434A pdb=" N VAL c 53 " --> pdb=" O SER c 114 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLY c 110 " --> pdb=" O MET c 57 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TRP c 111 " --> pdb=" O VAL c 141 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL c 145 " --> pdb=" O HIS c 113 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N ALA c 140 " --> pdb=" O LEU c 162 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N LEU c 162 " --> pdb=" O ALA c 140 " (cutoff:3.500A) removed outlier: 9.182A pdb=" N ILE c 157 " --> pdb=" O ILE c 205 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE c 205 " --> pdb=" O ILE c 157 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ALA c 159 " --> pdb=" O ILE c 203 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N HIS c 199 " --> pdb=" O ILE c 163 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N GLU c 29 " --> pdb=" O SER c 202 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR c 204 " --> pdb=" O GLU c 29 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE c 33 " --> pdb=" O ASN c 206 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'F' and resid 95 through 98 removed outlier: 3.725A pdb=" N CYS F 121 " --> pdb=" O LEU F 97 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL F 123 " --> pdb=" O ILE F 94 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL F 151 " --> pdb=" O SER F 91 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ASP F 149 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLY F 152 " --> pdb=" O LEU F 161 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LEU F 159 " --> pdb=" O ASN F 154 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'F' and resid 246 through 252 removed outlier: 3.770A pdb=" N GLY F 227 " --> pdb=" O THR F 332 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'F' and resid 121 through 126 removed outlier: 3.771A pdb=" N GLN F 130 " --> pdb=" O THR F 126 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'u' and resid 11 through 17 removed outlier: 4.675A pdb=" N LYS u 11 " --> pdb=" O THR u 7 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N MET u 1 " --> pdb=" O VAL u 17 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER u 65 " --> pdb=" O GLN u 2 " (cutoff:3.500A) 5690 hydrogen bonds defined for protein. 16998 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: 49.90 Time building geometry restraints manager: 33.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 27757 1.33 - 1.46: 22207 1.46 - 1.58: 56991 1.58 - 1.71: 21 1.71 - 1.83: 1029 Bond restraints: 108005 Sorted by residual: bond pdb=" C4 ATP B 501 " pdb=" C5 ATP B 501 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.62e+01 bond pdb=" C4 ATP A 501 " pdb=" C5 ATP A 501 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.46e+01 bond pdb=" C5 ATP B 501 " pdb=" C6 ATP B 501 " ideal model delta sigma weight residual 1.409 1.477 -0.068 1.00e-02 1.00e+04 4.64e+01 bond pdb=" C5 ATP A 501 " pdb=" C6 ATP A 501 " ideal model delta sigma weight residual 1.409 1.472 -0.063 1.00e-02 1.00e+04 4.03e+01 bond pdb=" C5 ATP A 501 " pdb=" N7 ATP A 501 " ideal model delta sigma weight residual 1.387 1.335 0.052 1.00e-02 1.00e+04 2.66e+01 ... (remaining 108000 not shown) Histogram of bond angle deviations from ideal: 95.20 - 104.12: 1463 104.12 - 113.04: 58799 113.04 - 121.96: 64273 121.96 - 130.88: 20983 130.88 - 139.80: 424 Bond angle restraints: 145942 Sorted by residual: angle pdb=" PB ATP B 501 " pdb=" O3B ATP B 501 " pdb=" PG ATP B 501 " ideal model delta sigma weight residual 139.87 122.28 17.59 1.00e+00 1.00e+00 3.10e+02 angle pdb=" PB ATP A 501 " pdb=" O3B ATP A 501 " pdb=" PG ATP A 501 " ideal model delta sigma weight residual 139.87 124.62 15.25 1.00e+00 1.00e+00 2.32e+02 angle pdb=" PA ATP A 501 " pdb=" O3A ATP A 501 " pdb=" PB ATP A 501 " ideal model delta sigma weight residual 136.83 123.14 13.69 1.00e+00 1.00e+00 1.87e+02 angle pdb=" PA ATP B 501 " pdb=" O3A ATP B 501 " pdb=" PB ATP B 501 " ideal model delta sigma weight residual 136.83 123.96 12.87 1.00e+00 1.00e+00 1.66e+02 angle pdb=" C5 ATP A 501 " pdb=" C4 ATP A 501 " pdb=" N3 ATP A 501 " ideal model delta sigma weight residual 126.80 117.90 8.90 1.00e+00 1.00e+00 7.92e+01 ... (remaining 145937 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.80: 63951 30.80 - 61.60: 1891 61.60 - 92.39: 134 92.39 - 123.19: 2 123.19 - 153.99: 1 Dihedral angle restraints: 65979 sinusoidal: 26680 harmonic: 39299 Sorted by residual: dihedral pdb=" CB CYS A 236 " pdb=" SG CYS A 236 " pdb=" SG CYS A 270 " pdb=" CB CYS A 270 " ideal model delta sinusoidal sigma weight residual -86.00 -152.38 66.38 1 1.00e+01 1.00e-02 5.75e+01 dihedral pdb=" C5' ADP C 501 " pdb=" O5' ADP C 501 " pdb=" PA ADP C 501 " pdb=" O2A ADP C 501 " ideal model delta sinusoidal sigma weight residual -60.00 93.99 -153.99 1 2.00e+01 2.50e-03 4.56e+01 dihedral pdb=" CA PHE d 199 " pdb=" C PHE d 199 " pdb=" N PHE d 200 " pdb=" CA PHE d 200 " ideal model delta harmonic sigma weight residual -180.00 -151.06 -28.94 0 5.00e+00 4.00e-02 3.35e+01 ... (remaining 65976 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 13811 0.066 - 0.132: 2503 0.132 - 0.198: 197 0.198 - 0.264: 26 0.264 - 0.330: 5 Chirality restraints: 16542 Sorted by residual: 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 2.31 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CB VAL c 151 " pdb=" CA VAL c 151 " pdb=" CG1 VAL c 151 " pdb=" CG2 VAL c 151 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CB THR x 68 " pdb=" CA THR x 68 " pdb=" OG1 THR x 68 " pdb=" CG2 THR x 68 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 16539 not shown) Planarity restraints: 18814 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA V 286 " 0.021 2.00e-02 2.50e+03 4.36e-02 1.90e+01 pdb=" C ALA V 286 " -0.075 2.00e-02 2.50e+03 pdb=" O ALA V 286 " 0.029 2.00e-02 2.50e+03 pdb=" N ARG V 287 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG V 287 " -0.018 2.00e-02 2.50e+03 3.71e-02 1.38e+01 pdb=" C ARG V 287 " 0.064 2.00e-02 2.50e+03 pdb=" O ARG V 287 " -0.024 2.00e-02 2.50e+03 pdb=" N TYR V 288 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO V 497 " -0.057 5.00e-02 4.00e+02 8.69e-02 1.21e+01 pdb=" N PRO V 498 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO V 498 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO V 498 " -0.049 5.00e-02 4.00e+02 ... (remaining 18811 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 121 2.38 - 3.01: 53049 3.01 - 3.64: 162404 3.64 - 4.27: 232959 4.27 - 4.90: 396703 Nonbonded interactions: 845236 Sorted by model distance: nonbonded pdb=" O1G ATP A 501 " pdb="MG MG A 502 " model vdw 1.750 2.170 nonbonded pdb=" OG1 THR A 223 " pdb="MG MG A 502 " model vdw 1.796 2.170 nonbonded pdb=" OG1 THR D 213 " pdb="MG MG D 502 " model vdw 1.943 2.170 nonbonded pdb=" OG1 THR F 234 " pdb="MG MG F 502 " model vdw 1.996 2.170 nonbonded pdb=" O3B ADP F 501 " pdb="MG MG F 502 " model vdw 1.999 2.170 ... (remaining 845231 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'G' and (resid 2 through 44 or (resid 45 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 through 195 or (resid 196 and (n \ ame N or name CA or name C or name O or name CB )) or resid 197 through 222 or ( \ resid 223 and (name N or name CA or name C or name O or name CB )) or resid 224 \ through 245)) selection = (chain 'g' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB )) or resid 4 through 245)) } ncs_group { reference = (chain 'H' and (resid 3 through 140 or (resid 141 and (name N or name CA or name \ C or name O or name CB )) or resid 142 through 199 or (resid 200 and (name N or \ name CA or name C or name O or name CB )) or resid 201 through 234)) selection = (chain 'h' and (resid 3 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB )) or resid 71 through 175 or (resid 176 and (name N or na \ me CA or name C or name O or name CB )) or resid 177 through 234)) } ncs_group { reference = (chain 'I' and (resid 2 through 6 or resid 8 through 198 or (resid 199 and (name \ N or name CA or name C or name O or name CB )) or resid 200 through 204 or (res \ id 205 and (name N or name CA or name C or name O or name CB )) or resid 206 thr \ ough 251)) selection = (chain 'i' and (resid 2 through 6 or resid 8 through 228 or (resid 229 and (name \ N or name CA or name C or name O or name CB )) or resid 230 or (resid 231 and ( \ name N or name CA or name C or name O or name CB )) or resid 232 through 251)) } ncs_group { reference = (chain 'J' and (resid 2 through 169 or (resid 170 and (name N or name CA or name \ C or name O or name CB )) or resid 171 through 206 or (resid 207 and (name N or \ name CA or name C or name O or name CB )) or resid 208 through 223 or (resid 22 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 225 through \ 231 or (resid 232 and (name N or name CA or name C or name O or name CB )) or re \ sid 233 through 238 or (resid 239 through 240 and (name N or name CA or name C o \ r name O or name CB )))) selection = (chain 'j' and (resid 2 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 240)) } ncs_group { reference = (chain 'K' and (resid 8 through 240 or (resid 241 and (name N or name CA or name \ C or name O or name CB or name CG1 or name CG2 or name CD1)))) selection = (chain 'k' and (resid 8 through 126 or (resid 127 through 129 and (name N or nam \ e CA or name C or name O or name CB )) or resid 130 through 241)) } ncs_group { reference = (chain 'L' and (resid 4 through 207 or (resid 208 and (name N or name CA or name \ C or name O or name CB )) or resid 209 through 237 or (resid 238 and (name N or \ name CA or name C or name O or name CB )) or resid 239 through 241)) selection = (chain 'l' and (resid 4 through 217 or (resid 218 and (name N or name CA or name \ C or name O or name CB )) or resid 219 through 241)) } ncs_group { reference = chain 'M' selection = (chain 'm' and ((resid 5 and (name N or name CA or name C or name O or name CB ) \ ) or resid 6 through 187 or (resid 188 and (name N or name CA or name C or name \ O or name CB )) or resid 189 through 244)) } ncs_group { reference = (chain 'N' and (resid 1 through 149 or (resid 150 and (name N or name CA or name \ C or name O or name CB )) or resid 151 through 202)) selection = chain 'n' } ncs_group { reference = chain 'O' selection = (chain 'o' and (resid 1 through 193 or (resid 194 and (name N or name CA or name \ C or name O or name CB )) or resid 195 through 202 or (resid 203 and (name N or \ name CA or name C or name O or name CB )) or resid 204 through 220)) } ncs_group { reference = chain 'P' selection = (chain 'p' and (resid 2 through 191 or (resid 192 and (name N or name CA or name \ C or name O or name CB )) or resid 193 through 205)) } ncs_group { reference = chain 'Q' selection = chain 'q' } ncs_group { reference = chain 'R' selection = chain 'r' } ncs_group { reference = chain 'S' selection = (chain 's' and ((resid 1 and (name N or name CA or name C or name O or name CB ) \ ) or resid 2 through 161 or (resid 162 and (name N or name CA or name C or name \ O or name CB )) or resid 163 through 168 or (resid 169 and (name N or name CA or \ name C or name O or name CB )) or resid 170 through 213)) } ncs_group { reference = chain 'T' selection = (chain 't' and (resid 1 through 205 or (resid 206 and (name N or name CA or name \ C or name O or name CB )) or resid 207 through 216)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 51.240 Check model and map are aligned: 1.220 Set scattering table: 0.710 Process input model: 275.900 Find NCS groups from input model: 6.570 Set up NCS constraints: 0.710 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: 0.030 Load rotamer database and sin/cos tables:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 348.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 108005 Z= 0.258 Angle : 0.800 17.595 145942 Z= 0.427 Chirality : 0.049 0.330 16542 Planarity : 0.006 0.087 18814 Dihedral : 14.034 153.991 40687 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.69 % Favored : 94.23 % Rotamer: Outliers : 0.18 % Allowed : 0.51 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.07), residues: 13440 helix: 0.37 (0.06), residues: 6378 sheet: 0.54 (0.12), residues: 2010 loop : -1.75 (0.08), residues: 5052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP M 215 HIS 0.016 0.001 HIS f 715 PHE 0.033 0.002 PHE B 365 TYR 0.027 0.001 TYR m 198 ARG 0.016 0.000 ARG b 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26880 Ramachandran restraints generated. 13440 Oldfield, 0 Emsley, 13440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26880 Ramachandran restraints generated. 13440 Oldfield, 0 Emsley, 13440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 11548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 456 time to evaluate : 9.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 188 MET cc_start: 0.2280 (tmm) cc_final: 0.2047 (ttp) REVERT: U 725 MET cc_start: 0.8469 (mmm) cc_final: 0.8068 (mmt) REVERT: W 88 MET cc_start: 0.9138 (tpt) cc_final: 0.8890 (tpp) REVERT: W 117 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7551 (m-30) REVERT: Y 48 ASN cc_start: 0.7516 (OUTLIER) cc_final: 0.6711 (t0) REVERT: a 124 ASN cc_start: 0.8171 (OUTLIER) cc_final: 0.7780 (p0) REVERT: b 16 MET cc_start: 0.5750 (mmm) cc_final: 0.5382 (mmm) REVERT: f 297 MET cc_start: 0.2513 (mmt) cc_final: 0.1941 (ttm) REVERT: f 321 MET cc_start: 0.4952 (ppp) cc_final: 0.3845 (ppp) REVERT: f 662 MET cc_start: 0.4573 (ppp) cc_final: 0.4268 (ppp) REVERT: p 4 MET cc_start: 0.8663 (mmm) cc_final: 0.8366 (mmt) REVERT: c 107 MET cc_start: 0.7501 (mmm) cc_final: 0.7133 (mmp) REVERT: c 292 MET cc_start: 0.9362 (mmp) cc_final: 0.9085 (mmt) REVERT: F 36 MET cc_start: 0.7303 (tpt) cc_final: 0.6046 (tmm) outliers start: 20 outliers final: 6 residues processed: 476 average time/residue: 0.8811 time to fit residues: 751.1096 Evaluate side-chains 441 residues out of total 11548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 432 time to evaluate : 9.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain W residue 117 ASP Chi-restraints excluded: chain Y residue 48 ASN Chi-restraints excluded: chain a residue 122 LYS Chi-restraints excluded: chain a residue 124 ASN Chi-restraints excluded: chain F residue 416 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1334 random chunks: chunk 1126 optimal weight: 20.0000 chunk 1011 optimal weight: 9.9990 chunk 561 optimal weight: 20.0000 chunk 345 optimal weight: 10.0000 chunk 682 optimal weight: 9.9990 chunk 540 optimal weight: 20.0000 chunk 1045 optimal weight: 20.0000 chunk 404 optimal weight: 10.0000 chunk 635 optimal weight: 9.9990 chunk 778 optimal weight: 5.9990 chunk 1211 optimal weight: 7.9990 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 36 ASN C 124 HIS ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 GLN D 376 ASN E 220 ASN I 123 GLN ** J 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 203 GLN ** P 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 29 GLN ** V 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 78 ASN X 334 ASN Y 48 ASN Y 94 ASN ** b 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 457 ASN ** h 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 99 HIS k 221 GLN ** c 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 108005 Z= 0.348 Angle : 0.606 10.442 145942 Z= 0.319 Chirality : 0.042 0.191 16542 Planarity : 0.004 0.069 18814 Dihedral : 6.136 160.856 14932 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.63 % Favored : 94.30 % Rotamer: Outliers : 0.26 % Allowed : 6.07 % Favored : 93.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.07), residues: 13440 helix: 1.37 (0.07), residues: 6398 sheet: 0.55 (0.12), residues: 1998 loop : -1.58 (0.08), residues: 5044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP M 215 HIS 0.009 0.001 HIS f 715 PHE 0.025 0.001 PHE a 355 TYR 0.019 0.001 TYR J 118 ARG 0.007 0.000 ARG V 180 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26880 Ramachandran restraints generated. 13440 Oldfield, 0 Emsley, 13440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26880 Ramachandran restraints generated. 13440 Oldfield, 0 Emsley, 13440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 11548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 433 time to evaluate : 9.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 336 MET cc_start: 0.8789 (mtt) cc_final: 0.8532 (mtt) REVERT: E 108 MET cc_start: 0.8883 (mmm) cc_final: 0.8404 (mmm) REVERT: L 26 MET cc_start: 0.8439 (tpt) cc_final: 0.8189 (tpt) REVERT: P 158 MET cc_start: 0.8733 (mtp) cc_final: 0.8449 (mtp) REVERT: U 188 MET cc_start: 0.2622 (tmm) cc_final: 0.2377 (ttt) REVERT: U 333 MET cc_start: 0.7252 (pmm) cc_final: 0.6893 (pmm) REVERT: U 423 MET cc_start: 0.5158 (ppp) cc_final: 0.4819 (ppp) REVERT: V 276 PHE cc_start: 0.8210 (t80) cc_final: 0.7914 (t80) REVERT: W 16 MET cc_start: 0.3663 (mmt) cc_final: 0.2833 (mmm) REVERT: W 88 MET cc_start: 0.9141 (tpt) cc_final: 0.8930 (tpp) REVERT: Y 389 MET cc_start: 0.8699 (mpp) cc_final: 0.8292 (mpp) REVERT: a 124 ASN cc_start: 0.8132 (OUTLIER) cc_final: 0.7580 (p0) REVERT: b 16 MET cc_start: 0.6126 (mmm) cc_final: 0.5826 (mmm) REVERT: d 75 MET cc_start: 0.7181 (mmp) cc_final: 0.6910 (mmt) REVERT: f 271 MET cc_start: 0.6835 (mpp) cc_final: 0.6423 (mpp) REVERT: f 294 MET cc_start: 0.6279 (OUTLIER) cc_final: 0.5814 (ptp) REVERT: f 297 MET cc_start: 0.2870 (mmt) cc_final: 0.2227 (ttm) REVERT: f 729 MET cc_start: 0.6250 (mmt) cc_final: 0.4908 (mtt) REVERT: f 761 MET cc_start: 0.6788 (mmm) cc_final: 0.6294 (mmm) REVERT: l 26 MET cc_start: 0.7360 (mmt) cc_final: 0.6918 (mmm) REVERT: p 4 MET cc_start: 0.8674 (mmm) cc_final: 0.8353 (mmt) REVERT: q 1 MET cc_start: 0.8594 (ppp) cc_final: 0.8122 (ppp) REVERT: c 107 MET cc_start: 0.7620 (mmm) cc_final: 0.7148 (mmp) REVERT: c 248 MET cc_start: 0.9366 (mtm) cc_final: 0.9139 (mtm) REVERT: c 292 MET cc_start: 0.9366 (mmp) cc_final: 0.9114 (mmt) REVERT: u 1 MET cc_start: 0.6398 (tpp) cc_final: 0.6016 (tpp) outliers start: 28 outliers final: 11 residues processed: 444 average time/residue: 0.8351 time to fit residues: 669.0656 Evaluate side-chains 442 residues out of total 11548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 429 time to evaluate : 9.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain V residue 139 MET Chi-restraints excluded: chain W residue 190 MET Chi-restraints excluded: chain a residue 122 LYS Chi-restraints excluded: chain a residue 124 ASN Chi-restraints excluded: chain a residue 165 THR Chi-restraints excluded: chain d residue 112 VAL Chi-restraints excluded: chain f residue 216 MET Chi-restraints excluded: chain f residue 294 MET Chi-restraints excluded: chain h residue 181 ASP Chi-restraints excluded: chain c residue 54 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1334 random chunks: chunk 673 optimal weight: 7.9990 chunk 375 optimal weight: 0.8980 chunk 1008 optimal weight: 5.9990 chunk 824 optimal weight: 1.9990 chunk 334 optimal weight: 5.9990 chunk 1213 optimal weight: 7.9990 chunk 1311 optimal weight: 8.9990 chunk 1080 optimal weight: 5.9990 chunk 1203 optimal weight: 10.0000 chunk 413 optimal weight: 10.0000 chunk 973 optimal weight: 7.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 124 HIS ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 29 GLN ** V 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 457 ASN ** h 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 44 GLN ** e 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 108005 Z= 0.191 Angle : 0.528 9.829 145942 Z= 0.276 Chirality : 0.041 0.185 16542 Planarity : 0.004 0.061 18814 Dihedral : 5.945 160.482 14925 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.30 % Favored : 94.63 % Rotamer: Outliers : 0.56 % Allowed : 8.45 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.07), residues: 13440 helix: 1.65 (0.07), residues: 6408 sheet: 0.55 (0.12), residues: 1998 loop : -1.50 (0.09), residues: 5034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP M 215 HIS 0.007 0.001 HIS f 202 PHE 0.026 0.001 PHE a 355 TYR 0.014 0.001 TYR J 118 ARG 0.004 0.000 ARG E 251 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26880 Ramachandran restraints generated. 13440 Oldfield, 0 Emsley, 13440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26880 Ramachandran restraints generated. 13440 Oldfield, 0 Emsley, 13440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 11548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 431 time to evaluate : 9.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 80 MET cc_start: 0.8605 (mtm) cc_final: 0.8104 (pmm) REVERT: C 336 MET cc_start: 0.8738 (mtt) cc_final: 0.8510 (mtt) REVERT: P 158 MET cc_start: 0.8692 (mtp) cc_final: 0.8426 (mtp) REVERT: U 188 MET cc_start: 0.2788 (tmm) cc_final: 0.2502 (ttt) REVERT: U 325 MET cc_start: 0.5198 (mmt) cc_final: 0.4835 (mmm) REVERT: U 333 MET cc_start: 0.7223 (pmm) cc_final: 0.6929 (pmm) REVERT: U 725 MET cc_start: 0.8439 (mmm) cc_final: 0.7802 (mmt) REVERT: U 885 MET cc_start: 0.7687 (mpp) cc_final: 0.7427 (mpp) REVERT: V 276 PHE cc_start: 0.8089 (t80) cc_final: 0.7802 (t80) REVERT: W 16 MET cc_start: 0.3899 (mmt) cc_final: 0.3043 (mmm) REVERT: W 88 MET cc_start: 0.9095 (tpt) cc_final: 0.8867 (tpp) REVERT: Y 389 MET cc_start: 0.8704 (mpp) cc_final: 0.8270 (mpp) REVERT: a 87 MET cc_start: 0.6242 (ppp) cc_final: 0.5934 (ppp) REVERT: a 124 ASN cc_start: 0.8120 (OUTLIER) cc_final: 0.7499 (p0) REVERT: b 16 MET cc_start: 0.6252 (mmm) cc_final: 0.5947 (mmm) REVERT: d 75 MET cc_start: 0.7223 (mmp) cc_final: 0.6795 (mmt) REVERT: f 271 MET cc_start: 0.6906 (mpp) cc_final: 0.6485 (mpp) REVERT: f 294 MET cc_start: 0.6253 (OUTLIER) cc_final: 0.5735 (ptp) REVERT: f 297 MET cc_start: 0.2921 (mmt) cc_final: 0.2118 (ttm) REVERT: f 321 MET cc_start: 0.4981 (ppp) cc_final: 0.3716 (ppp) REVERT: f 761 MET cc_start: 0.6915 (mmm) cc_final: 0.6405 (mmm) REVERT: l 26 MET cc_start: 0.7285 (mmt) cc_final: 0.6792 (mmm) REVERT: p 4 MET cc_start: 0.8665 (mmm) cc_final: 0.8335 (mmt) REVERT: q 1 MET cc_start: 0.8572 (ppp) cc_final: 0.8236 (ppp) REVERT: c 107 MET cc_start: 0.7630 (mmm) cc_final: 0.7161 (mmp) REVERT: c 248 MET cc_start: 0.9355 (mtm) cc_final: 0.9065 (mtm) REVERT: c 292 MET cc_start: 0.9350 (mmp) cc_final: 0.9038 (mmt) REVERT: u 1 MET cc_start: 0.6488 (tpp) cc_final: 0.6286 (tpp) outliers start: 62 outliers final: 26 residues processed: 471 average time/residue: 0.8384 time to fit residues: 713.4919 Evaluate side-chains 457 residues out of total 11548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 429 time to evaluate : 9.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain B residue 277 HIS Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain R residue 29 GLN Chi-restraints excluded: chain S residue 27 THR Chi-restraints excluded: chain T residue 117 ASP Chi-restraints excluded: chain V residue 139 MET Chi-restraints excluded: chain W residue 190 MET Chi-restraints excluded: chain W residue 366 MET Chi-restraints excluded: chain W residue 406 VAL Chi-restraints excluded: chain X residue 212 MET Chi-restraints excluded: chain Y residue 315 THR Chi-restraints excluded: chain a residue 124 ASN Chi-restraints excluded: chain a residue 319 LEU Chi-restraints excluded: chain b residue 107 MET Chi-restraints excluded: chain d residue 112 VAL Chi-restraints excluded: chain f residue 294 MET Chi-restraints excluded: chain g residue 111 VAL Chi-restraints excluded: chain h residue 181 ASP Chi-restraints excluded: chain j residue 183 THR Chi-restraints excluded: chain l residue 228 ASP Chi-restraints excluded: chain c residue 54 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1334 random chunks: chunk 1199 optimal weight: 5.9990 chunk 912 optimal weight: 30.0000 chunk 629 optimal weight: 6.9990 chunk 134 optimal weight: 20.0000 chunk 579 optimal weight: 6.9990 chunk 814 optimal weight: 40.0000 chunk 1217 optimal weight: 30.0000 chunk 1289 optimal weight: 50.0000 chunk 636 optimal weight: 30.0000 chunk 1154 optimal weight: 9.9990 chunk 347 optimal weight: 0.3980 overall best weight: 6.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 277 HIS ** D 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 172 GLN ** J 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 184 GLN Z 77 ASN ** b 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 457 ASN ** h 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 108005 Z= 0.248 Angle : 0.538 10.795 145942 Z= 0.281 Chirality : 0.041 0.184 16542 Planarity : 0.004 0.057 18814 Dihedral : 5.860 160.662 14920 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.78 % Favored : 94.16 % Rotamer: Outliers : 0.87 % Allowed : 10.40 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.08), residues: 13440 helix: 1.80 (0.07), residues: 6405 sheet: 0.58 (0.12), residues: 1996 loop : -1.46 (0.09), residues: 5039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP M 215 HIS 0.006 0.001 HIS f 752 PHE 0.024 0.001 PHE a 355 TYR 0.016 0.001 TYR J 118 ARG 0.004 0.000 ARG W 408 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26880 Ramachandran restraints generated. 13440 Oldfield, 0 Emsley, 13440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26880 Ramachandran restraints generated. 13440 Oldfield, 0 Emsley, 13440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 11548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 429 time to evaluate : 9.691 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: C 336 MET cc_start: 0.8799 (mtt) cc_final: 0.8593 (mtt) REVERT: D 267 ILE cc_start: 0.9080 (OUTLIER) cc_final: 0.8802 (tp) REVERT: I 201 MET cc_start: 0.8348 (mmp) cc_final: 0.8069 (mmt) REVERT: P 158 MET cc_start: 0.8720 (mtp) cc_final: 0.8456 (mtp) REVERT: U 188 MET cc_start: 0.3183 (tmm) cc_final: 0.2876 (ttt) REVERT: U 325 MET cc_start: 0.5221 (mmt) cc_final: 0.4858 (mmm) REVERT: U 725 MET cc_start: 0.8392 (mmm) cc_final: 0.7679 (mmt) REVERT: U 885 MET cc_start: 0.7701 (mpp) cc_final: 0.7432 (mpp) REVERT: V 276 PHE cc_start: 0.8032 (t80) cc_final: 0.7685 (t80) REVERT: W 16 MET cc_start: 0.3914 (mmt) cc_final: 0.3101 (mmm) REVERT: W 88 MET cc_start: 0.9077 (tpt) cc_final: 0.8849 (tpp) REVERT: Y 389 MET cc_start: 0.8754 (mpp) cc_final: 0.8313 (mpp) REVERT: b 16 MET cc_start: 0.6325 (mmm) cc_final: 0.6020 (mmm) REVERT: f 271 MET cc_start: 0.7012 (mpp) cc_final: 0.6593 (mpp) REVERT: f 761 MET cc_start: 0.6927 (mmm) cc_final: 0.6487 (mmm) REVERT: h 203 MET cc_start: 0.8718 (ptp) cc_final: 0.8364 (mtm) REVERT: l 26 MET cc_start: 0.7330 (mmt) cc_final: 0.6834 (mmm) REVERT: n 116 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.8179 (mtm) REVERT: p 4 MET cc_start: 0.8663 (mmm) cc_final: 0.8306 (mmt) REVERT: q 1 MET cc_start: 0.8576 (ppp) cc_final: 0.8251 (ppp) REVERT: c 107 MET cc_start: 0.7653 (mmm) cc_final: 0.7091 (mmp) REVERT: c 292 MET cc_start: 0.9373 (mmp) cc_final: 0.9134 (mmt) outliers start: 97 outliers final: 45 residues processed: 505 average time/residue: 0.8351 time to fit residues: 763.0579 Evaluate side-chains 475 residues out of total 11548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 428 time to evaluate : 9.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain A residue 423 PHE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 277 HIS Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 374 ASP Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 196 GLU Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain L residue 228 ASP Chi-restraints excluded: chain R residue 86 MET Chi-restraints excluded: chain S residue 27 THR Chi-restraints excluded: chain T residue 117 ASP Chi-restraints excluded: chain V residue 139 MET Chi-restraints excluded: chain V residue 206 VAL Chi-restraints excluded: chain W residue 190 MET Chi-restraints excluded: chain W residue 366 MET Chi-restraints excluded: chain W residue 406 VAL Chi-restraints excluded: chain X residue 212 MET Chi-restraints excluded: chain Y residue 249 VAL Chi-restraints excluded: chain Y residue 315 THR Chi-restraints excluded: chain a residue 122 LYS Chi-restraints excluded: chain a residue 165 THR Chi-restraints excluded: chain d residue 112 VAL Chi-restraints excluded: chain f residue 216 MET Chi-restraints excluded: chain f residue 294 MET Chi-restraints excluded: chain g residue 111 VAL Chi-restraints excluded: chain h residue 181 ASP Chi-restraints excluded: chain i residue 243 GLU Chi-restraints excluded: chain j residue 20 GLU Chi-restraints excluded: chain j residue 183 THR Chi-restraints excluded: chain l residue 228 ASP Chi-restraints excluded: chain m residue 188 ASP Chi-restraints excluded: chain n residue 116 MET Chi-restraints excluded: chain r residue 12 VAL Chi-restraints excluded: chain r residue 187 VAL Chi-restraints excluded: chain c residue 54 MET Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain F residue 352 ILE Chi-restraints excluded: chain u residue 22 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1334 random chunks: chunk 1073 optimal weight: 20.0000 chunk 731 optimal weight: 8.9990 chunk 18 optimal weight: 0.0370 chunk 960 optimal weight: 0.0870 chunk 532 optimal weight: 8.9990 chunk 1100 optimal weight: 20.0000 chunk 891 optimal weight: 50.0000 chunk 1 optimal weight: 50.0000 chunk 658 optimal weight: 6.9990 chunk 1157 optimal weight: 6.9990 chunk 325 optimal weight: 4.9990 overall best weight: 3.8242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 277 HIS ** D 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN R 29 GLN ** V 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 457 ASN ** h 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 44 GLN c 92 GLN ** u 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 108005 Z= 0.176 Angle : 0.513 12.126 145942 Z= 0.266 Chirality : 0.040 0.197 16542 Planarity : 0.004 0.056 18814 Dihedral : 5.734 161.390 14916 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.42 % Favored : 94.53 % Rotamer: Outliers : 0.93 % Allowed : 11.72 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.08), residues: 13440 helix: 1.89 (0.07), residues: 6420 sheet: 0.61 (0.12), residues: 1997 loop : -1.42 (0.09), residues: 5023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP M 215 HIS 0.015 0.001 HIS B 277 PHE 0.024 0.001 PHE a 355 TYR 0.014 0.001 TYR W 273 ARG 0.003 0.000 ARG W 94 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26880 Ramachandran restraints generated. 13440 Oldfield, 0 Emsley, 13440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26880 Ramachandran restraints generated. 13440 Oldfield, 0 Emsley, 13440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 11548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 432 time to evaluate : 9.702 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: D 267 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8780 (tp) REVERT: P 131 MET cc_start: 0.7831 (mmm) cc_final: 0.7579 (mmm) REVERT: P 158 MET cc_start: 0.8723 (mtp) cc_final: 0.8455 (mtp) REVERT: U 188 MET cc_start: 0.3199 (tmm) cc_final: 0.2923 (ttp) REVERT: U 325 MET cc_start: 0.5305 (mmt) cc_final: 0.4965 (mmt) REVERT: U 423 MET cc_start: 0.5865 (ppp) cc_final: 0.5347 (ppp) REVERT: U 725 MET cc_start: 0.8313 (mmm) cc_final: 0.7540 (mmt) REVERT: U 797 MET cc_start: 0.6975 (mmm) cc_final: 0.6643 (mmm) REVERT: U 885 MET cc_start: 0.7693 (mpp) cc_final: 0.7405 (mpp) REVERT: V 276 PHE cc_start: 0.8085 (t80) cc_final: 0.7682 (t80) REVERT: W 16 MET cc_start: 0.4049 (mmt) cc_final: 0.3175 (mmm) REVERT: Y 389 MET cc_start: 0.8753 (mpp) cc_final: 0.8295 (mpp) REVERT: a 141 MET cc_start: 0.7990 (pmm) cc_final: 0.7268 (pmm) REVERT: b 16 MET cc_start: 0.6352 (mmm) cc_final: 0.6050 (mmm) REVERT: d 75 MET cc_start: 0.7092 (mmp) cc_final: 0.6696 (mmt) REVERT: f 271 MET cc_start: 0.7007 (mpp) cc_final: 0.6607 (mpp) REVERT: f 297 MET cc_start: 0.3403 (mmt) cc_final: 0.2413 (ttm) REVERT: f 662 MET cc_start: 0.5202 (ppp) cc_final: 0.4480 (ppp) REVERT: f 761 MET cc_start: 0.6949 (mmm) cc_final: 0.6483 (mmm) REVERT: h 203 MET cc_start: 0.8698 (ptp) cc_final: 0.8322 (mtm) REVERT: i 184 MET cc_start: 0.8280 (mmm) cc_final: 0.7847 (mmm) REVERT: l 26 MET cc_start: 0.7306 (mmt) cc_final: 0.6802 (mmm) REVERT: n 116 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.8050 (mtm) REVERT: p 4 MET cc_start: 0.8661 (mmm) cc_final: 0.8315 (mmt) REVERT: p 146 MET cc_start: 0.9161 (mtm) cc_final: 0.8880 (mtm) REVERT: q 1 MET cc_start: 0.8544 (ppp) cc_final: 0.7984 (ppp) REVERT: s 83 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8539 (mtp) REVERT: c 107 MET cc_start: 0.7645 (mmm) cc_final: 0.7107 (mmp) REVERT: c 292 MET cc_start: 0.9354 (mmp) cc_final: 0.9099 (mmt) outliers start: 104 outliers final: 52 residues processed: 515 average time/residue: 0.8359 time to fit residues: 780.7478 Evaluate side-chains 482 residues out of total 11548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 427 time to evaluate : 9.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain A residue 423 PHE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 277 HIS Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 374 ASP Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain J residue 170 GLU Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain K residue 206 MET Chi-restraints excluded: chain R residue 29 GLN Chi-restraints excluded: chain S residue 27 THR Chi-restraints excluded: chain T residue 117 ASP Chi-restraints excluded: chain V residue 139 MET Chi-restraints excluded: chain W residue 131 VAL Chi-restraints excluded: chain W residue 190 MET Chi-restraints excluded: chain W residue 366 MET Chi-restraints excluded: chain W residue 406 VAL Chi-restraints excluded: chain X residue 45 VAL Chi-restraints excluded: chain X residue 212 MET Chi-restraints excluded: chain Y residue 249 VAL Chi-restraints excluded: chain Y residue 315 THR Chi-restraints excluded: chain a residue 57 ILE Chi-restraints excluded: chain a residue 122 LYS Chi-restraints excluded: chain a residue 165 THR Chi-restraints excluded: chain a residue 211 PHE Chi-restraints excluded: chain d residue 112 VAL Chi-restraints excluded: chain f residue 148 GLN Chi-restraints excluded: chain f residue 216 MET Chi-restraints excluded: chain f residue 294 MET Chi-restraints excluded: chain f residue 731 MET Chi-restraints excluded: chain f residue 746 ARG Chi-restraints excluded: chain g residue 111 VAL Chi-restraints excluded: chain i residue 243 GLU Chi-restraints excluded: chain j residue 20 GLU Chi-restraints excluded: chain j residue 134 VAL Chi-restraints excluded: chain j residue 183 THR Chi-restraints excluded: chain l residue 228 ASP Chi-restraints excluded: chain m residue 188 ASP Chi-restraints excluded: chain n residue 116 MET Chi-restraints excluded: chain p residue 58 THR Chi-restraints excluded: chain r residue 12 VAL Chi-restraints excluded: chain s residue 83 MET Chi-restraints excluded: chain c residue 54 MET Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain F residue 352 ILE Chi-restraints excluded: chain u residue 22 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1334 random chunks: chunk 433 optimal weight: 4.9990 chunk 1161 optimal weight: 20.0000 chunk 254 optimal weight: 7.9990 chunk 757 optimal weight: 8.9990 chunk 318 optimal weight: 5.9990 chunk 1290 optimal weight: 40.0000 chunk 1071 optimal weight: 20.0000 chunk 597 optimal weight: 30.0000 chunk 107 optimal weight: 4.9990 chunk 426 optimal weight: 7.9990 chunk 677 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 277 HIS ** D 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 HIS ** J 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 29 GLN ** V 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 457 ASN ** h 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 108005 Z= 0.252 Angle : 0.536 10.700 145942 Z= 0.279 Chirality : 0.041 0.268 16542 Planarity : 0.004 0.056 18814 Dihedral : 5.741 160.198 14916 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.83 % Favored : 94.11 % Rotamer: Outliers : 1.06 % Allowed : 12.51 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.08), residues: 13440 helix: 1.91 (0.07), residues: 6424 sheet: 0.59 (0.12), residues: 2010 loop : -1.43 (0.09), residues: 5006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP M 215 HIS 0.014 0.001 HIS B 277 PHE 0.022 0.001 PHE a 355 TYR 0.018 0.001 TYR V 264 ARG 0.004 0.000 ARG W 408 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26880 Ramachandran restraints generated. 13440 Oldfield, 0 Emsley, 13440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26880 Ramachandran restraints generated. 13440 Oldfield, 0 Emsley, 13440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 11548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 429 time to evaluate : 9.622 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: D 267 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8696 (mt) REVERT: P 131 MET cc_start: 0.7813 (mmm) cc_final: 0.7604 (mmm) REVERT: P 158 MET cc_start: 0.8737 (mtp) cc_final: 0.8472 (mtp) REVERT: U 325 MET cc_start: 0.5300 (mmt) cc_final: 0.4981 (mmt) REVERT: U 333 MET cc_start: 0.6833 (pmm) cc_final: 0.6579 (pmm) REVERT: U 423 MET cc_start: 0.6020 (ppp) cc_final: 0.5482 (ppp) REVERT: U 695 MET cc_start: 0.6600 (mtt) cc_final: 0.6247 (mtp) REVERT: U 725 MET cc_start: 0.8352 (mmm) cc_final: 0.7570 (mmt) REVERT: U 885 MET cc_start: 0.7710 (mpp) cc_final: 0.7368 (mpp) REVERT: V 276 PHE cc_start: 0.8041 (t80) cc_final: 0.7683 (t80) REVERT: V 463 MET cc_start: 0.8264 (ppp) cc_final: 0.7698 (ppp) REVERT: W 16 MET cc_start: 0.3943 (mmt) cc_final: 0.3104 (mmm) REVERT: Y 389 MET cc_start: 0.8795 (mpp) cc_final: 0.8355 (mpp) REVERT: a 141 MET cc_start: 0.8104 (pmm) cc_final: 0.7398 (pmm) REVERT: b 16 MET cc_start: 0.6420 (mmm) cc_final: 0.6131 (mmm) REVERT: d 75 MET cc_start: 0.7141 (mmp) cc_final: 0.6720 (mmt) REVERT: f 271 MET cc_start: 0.7050 (mpp) cc_final: 0.6664 (mpp) REVERT: f 297 MET cc_start: 0.3555 (mmt) cc_final: 0.2468 (ttm) REVERT: f 662 MET cc_start: 0.5340 (ppp) cc_final: 0.4698 (ppp) REVERT: f 761 MET cc_start: 0.7075 (mmm) cc_final: 0.6643 (mmm) REVERT: f 825 MET cc_start: 0.7661 (mpp) cc_final: 0.7412 (mpp) REVERT: g 73 THR cc_start: 0.9225 (OUTLIER) cc_final: 0.8989 (p) REVERT: h 203 MET cc_start: 0.8753 (ptp) cc_final: 0.8323 (mtm) REVERT: i 201 MET cc_start: 0.7276 (mmp) cc_final: 0.6920 (mmm) REVERT: l 26 MET cc_start: 0.7414 (mmt) cc_final: 0.6817 (mmm) REVERT: l 29 VAL cc_start: 0.9102 (OUTLIER) cc_final: 0.8828 (p) REVERT: n 116 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.8131 (mtm) REVERT: p 4 MET cc_start: 0.8666 (mmm) cc_final: 0.8279 (mmt) REVERT: q 1 MET cc_start: 0.8552 (ppp) cc_final: 0.7889 (ppp) REVERT: c 107 MET cc_start: 0.7691 (mmm) cc_final: 0.7089 (mmp) REVERT: c 265 MET cc_start: 0.8307 (pmm) cc_final: 0.8024 (pmm) REVERT: c 292 MET cc_start: 0.9358 (mmp) cc_final: 0.9065 (mmt) outliers start: 119 outliers final: 73 residues processed: 525 average time/residue: 0.8376 time to fit residues: 797.1276 Evaluate side-chains 504 residues out of total 11548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 427 time to evaluate : 9.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain A residue 423 PHE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 277 HIS Chi-restraints excluded: chain B residue 382 ASP Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 374 ASP Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain G residue 33 ASN Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 196 GLU Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain K residue 206 MET Chi-restraints excluded: chain L residue 228 ASP Chi-restraints excluded: chain R residue 45 MET Chi-restraints excluded: chain R residue 86 MET Chi-restraints excluded: chain S residue 27 THR Chi-restraints excluded: chain T residue 117 ASP Chi-restraints excluded: chain U residue 177 LEU Chi-restraints excluded: chain V residue 139 MET Chi-restraints excluded: chain V residue 206 VAL Chi-restraints excluded: chain W residue 131 VAL Chi-restraints excluded: chain W residue 190 MET Chi-restraints excluded: chain W residue 299 ILE Chi-restraints excluded: chain W residue 366 MET Chi-restraints excluded: chain W residue 406 VAL Chi-restraints excluded: chain W residue 413 ILE Chi-restraints excluded: chain X residue 45 VAL Chi-restraints excluded: chain X residue 212 MET Chi-restraints excluded: chain Y residue 229 ILE Chi-restraints excluded: chain Y residue 249 VAL Chi-restraints excluded: chain Y residue 315 THR Chi-restraints excluded: chain Z residue 226 ILE Chi-restraints excluded: chain Z residue 257 MET Chi-restraints excluded: chain a residue 57 ILE Chi-restraints excluded: chain a residue 87 MET Chi-restraints excluded: chain a residue 122 LYS Chi-restraints excluded: chain a residue 165 THR Chi-restraints excluded: chain a residue 211 PHE Chi-restraints excluded: chain a residue 305 ASN Chi-restraints excluded: chain a residue 359 ASP Chi-restraints excluded: chain d residue 72 GLU Chi-restraints excluded: chain d residue 112 VAL Chi-restraints excluded: chain f residue 216 MET Chi-restraints excluded: chain f residue 294 MET Chi-restraints excluded: chain f residue 731 MET Chi-restraints excluded: chain f residue 745 LEU Chi-restraints excluded: chain f residue 746 ARG Chi-restraints excluded: chain g residue 73 THR Chi-restraints excluded: chain g residue 111 VAL Chi-restraints excluded: chain h residue 181 ASP Chi-restraints excluded: chain i residue 243 GLU Chi-restraints excluded: chain j residue 20 GLU Chi-restraints excluded: chain j residue 134 VAL Chi-restraints excluded: chain j residue 183 THR Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain l residue 228 ASP Chi-restraints excluded: chain m residue 188 ASP Chi-restraints excluded: chain n residue 116 MET Chi-restraints excluded: chain o residue 65 LEU Chi-restraints excluded: chain p residue 58 THR Chi-restraints excluded: chain r residue 12 VAL Chi-restraints excluded: chain s residue 48 ASP Chi-restraints excluded: chain c residue 54 MET Chi-restraints excluded: chain c residue 69 VAL Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain F residue 352 ILE Chi-restraints excluded: chain u residue 22 THR Chi-restraints excluded: chain e residue 46 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1334 random chunks: chunk 1244 optimal weight: 9.9990 chunk 145 optimal weight: 5.9990 chunk 735 optimal weight: 8.9990 chunk 942 optimal weight: 6.9990 chunk 730 optimal weight: 5.9990 chunk 1086 optimal weight: 30.0000 chunk 720 optimal weight: 7.9990 chunk 1285 optimal weight: 40.0000 chunk 804 optimal weight: 3.9990 chunk 783 optimal weight: 30.0000 chunk 593 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 266 GLN ** V 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 292 GLN ** Y 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 44 HIS ** u 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 108005 Z= 0.249 Angle : 0.543 15.213 145942 Z= 0.281 Chirality : 0.041 0.244 16542 Planarity : 0.004 0.056 18814 Dihedral : 5.761 160.713 14916 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.79 % Favored : 94.15 % Rotamer: Outliers : 1.20 % Allowed : 13.16 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.08), residues: 13440 helix: 1.92 (0.07), residues: 6416 sheet: 0.61 (0.12), residues: 2000 loop : -1.42 (0.09), residues: 5024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP m 215 HIS 0.021 0.001 HIS B 277 PHE 0.021 0.001 PHE a 355 TYR 0.015 0.001 TYR W 273 ARG 0.005 0.000 ARG V 180 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26880 Ramachandran restraints generated. 13440 Oldfield, 0 Emsley, 13440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26880 Ramachandran restraints generated. 13440 Oldfield, 0 Emsley, 13440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 11548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 429 time to evaluate : 9.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 THR cc_start: 0.9203 (OUTLIER) cc_final: 0.8891 (p) REVERT: D 267 ILE cc_start: 0.9091 (OUTLIER) cc_final: 0.8695 (mt) REVERT: I 201 MET cc_start: 0.8313 (mmp) cc_final: 0.7938 (mmt) REVERT: J 211 MET cc_start: 0.7908 (mtt) cc_final: 0.7275 (mtt) REVERT: L 26 MET cc_start: 0.8465 (tpt) cc_final: 0.7709 (tpt) REVERT: P 158 MET cc_start: 0.8742 (mtp) cc_final: 0.8507 (mtp) REVERT: U 325 MET cc_start: 0.5388 (mmt) cc_final: 0.5058 (mmt) REVERT: U 423 MET cc_start: 0.6229 (ppp) cc_final: 0.5762 (ppp) REVERT: U 695 MET cc_start: 0.6626 (mtt) cc_final: 0.6287 (mtp) REVERT: U 725 MET cc_start: 0.8344 (mmm) cc_final: 0.7603 (mmt) REVERT: U 885 MET cc_start: 0.7711 (mpp) cc_final: 0.7400 (mpp) REVERT: V 276 PHE cc_start: 0.8023 (t80) cc_final: 0.7702 (t80) REVERT: V 463 MET cc_start: 0.8259 (ppp) cc_final: 0.7716 (ppp) REVERT: W 16 MET cc_start: 0.3879 (mmt) cc_final: 0.2972 (mmm) REVERT: Y 48 ASN cc_start: 0.8036 (OUTLIER) cc_final: 0.7761 (t0) REVERT: Y 211 TYR cc_start: 0.7023 (OUTLIER) cc_final: 0.5507 (p90) REVERT: Y 343 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8322 (tt) REVERT: Y 389 MET cc_start: 0.8808 (mpp) cc_final: 0.8378 (mpp) REVERT: b 16 MET cc_start: 0.6447 (mmm) cc_final: 0.6158 (mmm) REVERT: d 75 MET cc_start: 0.7127 (mmp) cc_final: 0.6737 (mmt) REVERT: f 271 MET cc_start: 0.7101 (mpp) cc_final: 0.6675 (mpp) REVERT: f 662 MET cc_start: 0.5386 (ppp) cc_final: 0.4739 (ppp) REVERT: f 761 MET cc_start: 0.7047 (mmm) cc_final: 0.6661 (mmm) REVERT: f 825 MET cc_start: 0.7684 (mpp) cc_final: 0.7433 (mpp) REVERT: g 73 THR cc_start: 0.9260 (OUTLIER) cc_final: 0.9051 (p) REVERT: l 26 MET cc_start: 0.7388 (mmt) cc_final: 0.6785 (mmm) REVERT: l 29 VAL cc_start: 0.9111 (OUTLIER) cc_final: 0.8860 (p) REVERT: n 116 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.8250 (mtm) REVERT: p 4 MET cc_start: 0.8677 (mmm) cc_final: 0.8323 (mmt) REVERT: p 146 MET cc_start: 0.9159 (mtm) cc_final: 0.8911 (mtm) REVERT: q 1 MET cc_start: 0.8553 (ppp) cc_final: 0.7871 (ppp) REVERT: c 107 MET cc_start: 0.7636 (mmm) cc_final: 0.7005 (mmp) REVERT: c 265 MET cc_start: 0.8357 (pmm) cc_final: 0.7999 (pmm) REVERT: c 292 MET cc_start: 0.9363 (mmp) cc_final: 0.9065 (mmt) REVERT: u 1 MET cc_start: 0.6625 (tpt) cc_final: 0.6279 (tpt) outliers start: 135 outliers final: 81 residues processed: 542 average time/residue: 0.8428 time to fit residues: 829.2098 Evaluate side-chains 516 residues out of total 11548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 427 time to evaluate : 9.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain A residue 423 PHE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 277 HIS Chi-restraints excluded: chain B residue 382 ASP Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 374 ASP Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 236 ASP Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 196 GLU Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain K residue 206 MET Chi-restraints excluded: chain L residue 228 ASP Chi-restraints excluded: chain R residue 86 MET Chi-restraints excluded: chain S residue 27 THR Chi-restraints excluded: chain U residue 177 LEU Chi-restraints excluded: chain V residue 139 MET Chi-restraints excluded: chain V residue 176 MET Chi-restraints excluded: chain V residue 206 VAL Chi-restraints excluded: chain V residue 451 ILE Chi-restraints excluded: chain W residue 131 VAL Chi-restraints excluded: chain W residue 190 MET Chi-restraints excluded: chain W residue 243 ILE Chi-restraints excluded: chain W residue 299 ILE Chi-restraints excluded: chain W residue 366 MET Chi-restraints excluded: chain W residue 406 VAL Chi-restraints excluded: chain W residue 413 ILE Chi-restraints excluded: chain X residue 45 VAL Chi-restraints excluded: chain X residue 212 MET Chi-restraints excluded: chain X residue 374 PHE Chi-restraints excluded: chain Y residue 48 ASN Chi-restraints excluded: chain Y residue 92 GLU Chi-restraints excluded: chain Y residue 186 LEU Chi-restraints excluded: chain Y residue 211 TYR Chi-restraints excluded: chain Y residue 241 ILE Chi-restraints excluded: chain Y residue 249 VAL Chi-restraints excluded: chain Y residue 291 HIS Chi-restraints excluded: chain Y residue 315 THR Chi-restraints excluded: chain Y residue 343 LEU Chi-restraints excluded: chain Z residue 226 ILE Chi-restraints excluded: chain Z residue 257 MET Chi-restraints excluded: chain a residue 57 ILE Chi-restraints excluded: chain a residue 87 MET Chi-restraints excluded: chain a residue 122 LYS Chi-restraints excluded: chain a residue 165 THR Chi-restraints excluded: chain a residue 211 PHE Chi-restraints excluded: chain a residue 359 ASP Chi-restraints excluded: chain d residue 72 GLU Chi-restraints excluded: chain d residue 112 VAL Chi-restraints excluded: chain f residue 216 MET Chi-restraints excluded: chain f residue 294 MET Chi-restraints excluded: chain f residue 731 MET Chi-restraints excluded: chain f residue 746 ARG Chi-restraints excluded: chain f residue 818 LEU Chi-restraints excluded: chain g residue 73 THR Chi-restraints excluded: chain g residue 111 VAL Chi-restraints excluded: chain g residue 175 SER Chi-restraints excluded: chain h residue 181 ASP Chi-restraints excluded: chain i residue 21 VAL Chi-restraints excluded: chain i residue 243 GLU Chi-restraints excluded: chain j residue 20 GLU Chi-restraints excluded: chain j residue 134 VAL Chi-restraints excluded: chain j residue 183 THR Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain l residue 228 ASP Chi-restraints excluded: chain m residue 188 ASP Chi-restraints excluded: chain n residue 116 MET Chi-restraints excluded: chain o residue 65 LEU Chi-restraints excluded: chain p residue 58 THR Chi-restraints excluded: chain r residue 12 VAL Chi-restraints excluded: chain s residue 48 ASP Chi-restraints excluded: chain t residue 70 MET Chi-restraints excluded: chain c residue 54 MET Chi-restraints excluded: chain c residue 69 VAL Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain F residue 352 ILE Chi-restraints excluded: chain u residue 22 THR Chi-restraints excluded: chain e residue 46 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1334 random chunks: chunk 795 optimal weight: 20.0000 chunk 513 optimal weight: 7.9990 chunk 767 optimal weight: 6.9990 chunk 387 optimal weight: 0.0020 chunk 252 optimal weight: 7.9990 chunk 249 optimal weight: 5.9990 chunk 817 optimal weight: 20.0000 chunk 875 optimal weight: 30.0000 chunk 635 optimal weight: 20.0000 chunk 119 optimal weight: 6.9990 chunk 1010 optimal weight: 0.2980 overall best weight: 4.0594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 108005 Z= 0.184 Angle : 0.528 15.429 145942 Z= 0.271 Chirality : 0.040 0.191 16542 Planarity : 0.004 0.056 18814 Dihedral : 5.695 161.074 14916 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.66 % Favored : 94.29 % Rotamer: Outliers : 0.98 % Allowed : 13.72 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.08), residues: 13440 helix: 1.96 (0.07), residues: 6418 sheet: 0.63 (0.12), residues: 1996 loop : -1.39 (0.09), residues: 5026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP m 215 HIS 0.007 0.001 HIS B 277 PHE 0.020 0.001 PHE a 355 TYR 0.014 0.001 TYR W 273 ARG 0.003 0.000 ARG d 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26880 Ramachandran restraints generated. 13440 Oldfield, 0 Emsley, 13440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26880 Ramachandran restraints generated. 13440 Oldfield, 0 Emsley, 13440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 11548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 432 time to evaluate : 9.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 THR cc_start: 0.9193 (OUTLIER) cc_final: 0.8891 (p) REVERT: D 267 ILE cc_start: 0.9077 (OUTLIER) cc_final: 0.8686 (mt) REVERT: I 201 MET cc_start: 0.8254 (mmp) cc_final: 0.8047 (mmt) REVERT: J 211 MET cc_start: 0.7803 (mtt) cc_final: 0.7162 (mtt) REVERT: L 26 MET cc_start: 0.8468 (tpt) cc_final: 0.7800 (tpt) REVERT: L 184 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8161 (tp) REVERT: P 158 MET cc_start: 0.8731 (mtp) cc_final: 0.8466 (mtp) REVERT: U 188 MET cc_start: 0.3773 (ttt) cc_final: 0.3555 (ttt) REVERT: U 325 MET cc_start: 0.5387 (mmt) cc_final: 0.5013 (mmt) REVERT: U 423 MET cc_start: 0.6287 (ppp) cc_final: 0.5830 (ppp) REVERT: U 695 MET cc_start: 0.6620 (mtt) cc_final: 0.6279 (mtp) REVERT: U 725 MET cc_start: 0.8304 (mmm) cc_final: 0.7537 (mmt) REVERT: U 885 MET cc_start: 0.7711 (mpp) cc_final: 0.7441 (mpp) REVERT: V 276 PHE cc_start: 0.8008 (t80) cc_final: 0.7653 (t80) REVERT: V 463 MET cc_start: 0.8223 (ppp) cc_final: 0.7672 (ppp) REVERT: Y 211 TYR cc_start: 0.6999 (OUTLIER) cc_final: 0.5478 (p90) REVERT: Y 343 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8314 (tt) REVERT: Y 389 MET cc_start: 0.8808 (mpp) cc_final: 0.8379 (mpp) REVERT: b 16 MET cc_start: 0.6442 (mmm) cc_final: 0.6143 (mmm) REVERT: d 75 MET cc_start: 0.7155 (mmp) cc_final: 0.6784 (mmt) REVERT: f 271 MET cc_start: 0.7102 (mpp) cc_final: 0.6661 (mpp) REVERT: f 662 MET cc_start: 0.5413 (ppp) cc_final: 0.4761 (ppp) REVERT: f 761 MET cc_start: 0.7130 (mmm) cc_final: 0.6697 (mmm) REVERT: f 825 MET cc_start: 0.7586 (mpp) cc_final: 0.7339 (mpp) REVERT: g 73 THR cc_start: 0.9235 (OUTLIER) cc_final: 0.9016 (p) REVERT: k 206 MET cc_start: 0.9053 (ttp) cc_final: 0.8829 (ttm) REVERT: l 26 MET cc_start: 0.7342 (mmt) cc_final: 0.6788 (mmm) REVERT: l 29 VAL cc_start: 0.9079 (OUTLIER) cc_final: 0.8827 (p) REVERT: l 180 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.8420 (tpp) REVERT: n 116 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.8223 (mtm) REVERT: p 146 MET cc_start: 0.9147 (mtm) cc_final: 0.8941 (mtm) REVERT: q 1 MET cc_start: 0.8533 (ppp) cc_final: 0.7824 (ppp) REVERT: c 107 MET cc_start: 0.7619 (mmm) cc_final: 0.6934 (mmp) REVERT: c 265 MET cc_start: 0.8343 (pmm) cc_final: 0.7964 (pmm) REVERT: c 292 MET cc_start: 0.9322 (mmp) cc_final: 0.9075 (mmt) REVERT: u 1 MET cc_start: 0.6602 (tpt) cc_final: 0.6176 (tpt) outliers start: 110 outliers final: 81 residues processed: 523 average time/residue: 0.8238 time to fit residues: 780.6009 Evaluate side-chains 519 residues out of total 11548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 429 time to evaluate : 8.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain A residue 423 PHE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 277 HIS Chi-restraints excluded: chain B residue 382 ASP Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 374 ASP Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain G residue 33 ASN Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 196 GLU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain K residue 206 MET Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain R residue 45 MET Chi-restraints excluded: chain S residue 27 THR Chi-restraints excluded: chain V residue 139 MET Chi-restraints excluded: chain V residue 206 VAL Chi-restraints excluded: chain V residue 451 ILE Chi-restraints excluded: chain W residue 131 VAL Chi-restraints excluded: chain W residue 190 MET Chi-restraints excluded: chain W residue 243 ILE Chi-restraints excluded: chain W residue 366 MET Chi-restraints excluded: chain W residue 406 VAL Chi-restraints excluded: chain W residue 413 ILE Chi-restraints excluded: chain X residue 45 VAL Chi-restraints excluded: chain X residue 212 MET Chi-restraints excluded: chain Y residue 186 LEU Chi-restraints excluded: chain Y residue 211 TYR Chi-restraints excluded: chain Y residue 229 ILE Chi-restraints excluded: chain Y residue 241 ILE Chi-restraints excluded: chain Y residue 249 VAL Chi-restraints excluded: chain Y residue 291 HIS Chi-restraints excluded: chain Y residue 315 THR Chi-restraints excluded: chain Y residue 343 LEU Chi-restraints excluded: chain Z residue 257 MET Chi-restraints excluded: chain a residue 57 ILE Chi-restraints excluded: chain a residue 87 MET Chi-restraints excluded: chain a residue 122 LYS Chi-restraints excluded: chain a residue 165 THR Chi-restraints excluded: chain a residue 211 PHE Chi-restraints excluded: chain a residue 305 ASN Chi-restraints excluded: chain a residue 359 ASP Chi-restraints excluded: chain d residue 72 GLU Chi-restraints excluded: chain d residue 112 VAL Chi-restraints excluded: chain f residue 216 MET Chi-restraints excluded: chain f residue 294 MET Chi-restraints excluded: chain f residue 731 MET Chi-restraints excluded: chain f residue 745 LEU Chi-restraints excluded: chain f residue 746 ARG Chi-restraints excluded: chain g residue 73 THR Chi-restraints excluded: chain g residue 111 VAL Chi-restraints excluded: chain g residue 175 SER Chi-restraints excluded: chain h residue 181 ASP Chi-restraints excluded: chain i residue 21 VAL Chi-restraints excluded: chain i residue 243 GLU Chi-restraints excluded: chain j residue 20 GLU Chi-restraints excluded: chain j residue 134 VAL Chi-restraints excluded: chain j residue 183 THR Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain l residue 180 MET Chi-restraints excluded: chain l residue 228 ASP Chi-restraints excluded: chain m residue 41 CYS Chi-restraints excluded: chain m residue 188 ASP Chi-restraints excluded: chain n residue 116 MET Chi-restraints excluded: chain o residue 65 LEU Chi-restraints excluded: chain p residue 58 THR Chi-restraints excluded: chain r residue 12 VAL Chi-restraints excluded: chain s residue 13 LEU Chi-restraints excluded: chain t residue 70 MET Chi-restraints excluded: chain c residue 54 MET Chi-restraints excluded: chain c residue 69 VAL Chi-restraints excluded: chain c residue 126 ASP Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain F residue 352 ILE Chi-restraints excluded: chain u residue 22 THR Chi-restraints excluded: chain e residue 46 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1334 random chunks: chunk 1169 optimal weight: 8.9990 chunk 1231 optimal weight: 7.9990 chunk 1123 optimal weight: 10.0000 chunk 1198 optimal weight: 10.0000 chunk 721 optimal weight: 8.9990 chunk 521 optimal weight: 6.9990 chunk 940 optimal weight: 5.9990 chunk 367 optimal weight: 9.9990 chunk 1082 optimal weight: 7.9990 chunk 1133 optimal weight: 5.9990 chunk 1193 optimal weight: 20.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 277 HIS ** D 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 170 GLN ** Y 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 108005 Z= 0.285 Angle : 0.568 12.670 145942 Z= 0.293 Chirality : 0.041 0.264 16542 Planarity : 0.004 0.055 18814 Dihedral : 5.785 157.961 14916 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.12 % Favored : 93.81 % Rotamer: Outliers : 1.08 % Allowed : 13.87 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.08), residues: 13440 helix: 1.92 (0.07), residues: 6416 sheet: 0.63 (0.12), residues: 1986 loop : -1.44 (0.09), residues: 5038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP m 215 HIS 0.006 0.001 HIS f 752 PHE 0.021 0.001 PHE P 69 TYR 0.015 0.001 TYR W 273 ARG 0.005 0.000 ARG W 408 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26880 Ramachandran restraints generated. 13440 Oldfield, 0 Emsley, 13440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26880 Ramachandran restraints generated. 13440 Oldfield, 0 Emsley, 13440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 11548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 429 time to evaluate : 9.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8444 (pp30) REVERT: A 173 THR cc_start: 0.9220 (OUTLIER) cc_final: 0.8905 (p) REVERT: C 336 MET cc_start: 0.8859 (mtt) cc_final: 0.8654 (mtt) REVERT: D 153 MET cc_start: 0.8154 (tpp) cc_final: 0.7903 (mmm) REVERT: D 267 ILE cc_start: 0.9122 (OUTLIER) cc_final: 0.8734 (mt) REVERT: J 211 MET cc_start: 0.7917 (mtt) cc_final: 0.7328 (mtt) REVERT: L 26 MET cc_start: 0.8559 (tpt) cc_final: 0.7946 (tpt) REVERT: U 188 MET cc_start: 0.3801 (ttt) cc_final: 0.3561 (ttt) REVERT: U 244 MET cc_start: 0.5534 (ppp) cc_final: 0.5242 (ppp) REVERT: U 325 MET cc_start: 0.5484 (mmt) cc_final: 0.5118 (mmt) REVERT: U 423 MET cc_start: 0.6427 (ppp) cc_final: 0.5978 (ppp) REVERT: U 695 MET cc_start: 0.6742 (mtt) cc_final: 0.6432 (mtp) REVERT: U 725 MET cc_start: 0.8367 (mmm) cc_final: 0.7645 (mmt) REVERT: U 885 MET cc_start: 0.7744 (mpp) cc_final: 0.7391 (mpp) REVERT: V 276 PHE cc_start: 0.7999 (t80) cc_final: 0.7646 (t80) REVERT: V 463 MET cc_start: 0.8271 (ppp) cc_final: 0.7707 (ppp) REVERT: W 456 GLN cc_start: 0.6025 (pp30) cc_final: 0.5059 (pm20) REVERT: Y 211 TYR cc_start: 0.7018 (OUTLIER) cc_final: 0.5461 (p90) REVERT: Y 389 MET cc_start: 0.8866 (mpp) cc_final: 0.8448 (mpp) REVERT: Z 226 ILE cc_start: 0.7086 (OUTLIER) cc_final: 0.6484 (mp) REVERT: b 16 MET cc_start: 0.6481 (mmm) cc_final: 0.6186 (mmm) REVERT: d 75 MET cc_start: 0.7153 (mmp) cc_final: 0.6791 (mmt) REVERT: f 271 MET cc_start: 0.7235 (mpp) cc_final: 0.6967 (mpp) REVERT: f 662 MET cc_start: 0.5597 (ppp) cc_final: 0.4941 (ppp) REVERT: g 73 THR cc_start: 0.9284 (OUTLIER) cc_final: 0.9063 (p) REVERT: k 206 MET cc_start: 0.9054 (ttp) cc_final: 0.8843 (ttm) REVERT: l 29 VAL cc_start: 0.9106 (OUTLIER) cc_final: 0.8874 (p) REVERT: p 4 MET cc_start: 0.8774 (mmm) cc_final: 0.8225 (mmt) REVERT: q 1 MET cc_start: 0.8546 (ppp) cc_final: 0.7865 (ppp) REVERT: c 107 MET cc_start: 0.7658 (mmm) cc_final: 0.6936 (mmp) REVERT: c 265 MET cc_start: 0.8421 (pmm) cc_final: 0.8016 (pmm) REVERT: c 292 MET cc_start: 0.9348 (mmp) cc_final: 0.9115 (mmt) REVERT: u 1 MET cc_start: 0.6639 (tpt) cc_final: 0.6252 (tpt) outliers start: 122 outliers final: 87 residues processed: 531 average time/residue: 0.8211 time to fit residues: 791.3985 Evaluate side-chains 520 residues out of total 11548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 426 time to evaluate : 9.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain A residue 423 PHE Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 277 HIS Chi-restraints excluded: chain B residue 382 ASP Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 374 ASP Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 236 ASP Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 196 GLU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain K residue 206 MET Chi-restraints excluded: chain L residue 228 ASP Chi-restraints excluded: chain R residue 45 MET Chi-restraints excluded: chain S residue 27 THR Chi-restraints excluded: chain V residue 139 MET Chi-restraints excluded: chain V residue 206 VAL Chi-restraints excluded: chain V residue 451 ILE Chi-restraints excluded: chain V residue 469 THR Chi-restraints excluded: chain W residue 190 MET Chi-restraints excluded: chain W residue 243 ILE Chi-restraints excluded: chain W residue 299 ILE Chi-restraints excluded: chain W residue 366 MET Chi-restraints excluded: chain W residue 406 VAL Chi-restraints excluded: chain W residue 413 ILE Chi-restraints excluded: chain X residue 45 VAL Chi-restraints excluded: chain X residue 212 MET Chi-restraints excluded: chain X residue 374 PHE Chi-restraints excluded: chain Y residue 73 MET Chi-restraints excluded: chain Y residue 92 GLU Chi-restraints excluded: chain Y residue 186 LEU Chi-restraints excluded: chain Y residue 211 TYR Chi-restraints excluded: chain Y residue 229 ILE Chi-restraints excluded: chain Y residue 241 ILE Chi-restraints excluded: chain Y residue 249 VAL Chi-restraints excluded: chain Y residue 291 HIS Chi-restraints excluded: chain Y residue 315 THR Chi-restraints excluded: chain Z residue 226 ILE Chi-restraints excluded: chain Z residue 257 MET Chi-restraints excluded: chain a residue 57 ILE Chi-restraints excluded: chain a residue 87 MET Chi-restraints excluded: chain a residue 122 LYS Chi-restraints excluded: chain a residue 165 THR Chi-restraints excluded: chain a residue 211 PHE Chi-restraints excluded: chain a residue 305 ASN Chi-restraints excluded: chain a residue 341 LEU Chi-restraints excluded: chain a residue 359 ASP Chi-restraints excluded: chain d residue 72 GLU Chi-restraints excluded: chain d residue 112 VAL Chi-restraints excluded: chain d residue 253 LEU Chi-restraints excluded: chain f residue 294 MET Chi-restraints excluded: chain f residue 731 MET Chi-restraints excluded: chain f residue 745 LEU Chi-restraints excluded: chain f residue 746 ARG Chi-restraints excluded: chain f residue 818 LEU Chi-restraints excluded: chain g residue 73 THR Chi-restraints excluded: chain g residue 111 VAL Chi-restraints excluded: chain h residue 181 ASP Chi-restraints excluded: chain i residue 21 VAL Chi-restraints excluded: chain i residue 243 GLU Chi-restraints excluded: chain j residue 20 GLU Chi-restraints excluded: chain j residue 134 VAL Chi-restraints excluded: chain j residue 183 THR Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain l residue 228 ASP Chi-restraints excluded: chain m residue 41 CYS Chi-restraints excluded: chain m residue 188 ASP Chi-restraints excluded: chain o residue 65 LEU Chi-restraints excluded: chain p residue 58 THR Chi-restraints excluded: chain r residue 12 VAL Chi-restraints excluded: chain s residue 13 LEU Chi-restraints excluded: chain s residue 48 ASP Chi-restraints excluded: chain c residue 54 MET Chi-restraints excluded: chain c residue 69 VAL Chi-restraints excluded: chain c residue 126 ASP Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain F residue 352 ILE Chi-restraints excluded: chain u residue 22 THR Chi-restraints excluded: chain e residue 46 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1334 random chunks: chunk 786 optimal weight: 7.9990 chunk 1266 optimal weight: 10.0000 chunk 773 optimal weight: 4.9990 chunk 601 optimal weight: 7.9990 chunk 880 optimal weight: 50.0000 chunk 1329 optimal weight: 20.0000 chunk 1223 optimal weight: 6.9990 chunk 1058 optimal weight: 20.0000 chunk 109 optimal weight: 10.0000 chunk 817 optimal weight: 8.9990 chunk 648 optimal weight: 4.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 HIS ** D 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 27 GLN ** V 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 108005 Z= 0.263 Angle : 0.560 12.913 145942 Z= 0.289 Chirality : 0.041 0.356 16542 Planarity : 0.004 0.055 18814 Dihedral : 5.795 157.541 14916 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.91 % Favored : 94.03 % Rotamer: Outliers : 0.94 % Allowed : 14.12 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.08), residues: 13440 helix: 1.91 (0.07), residues: 6418 sheet: 0.62 (0.12), residues: 1972 loop : -1.44 (0.09), residues: 5050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP m 215 HIS 0.007 0.001 HIS B 277 PHE 0.020 0.001 PHE P 69 TYR 0.015 0.001 TYR W 273 ARG 0.008 0.000 ARG U 559 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26880 Ramachandran restraints generated. 13440 Oldfield, 0 Emsley, 13440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26880 Ramachandran restraints generated. 13440 Oldfield, 0 Emsley, 13440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 11548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 427 time to evaluate : 9.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8443 (pp30) REVERT: A 173 THR cc_start: 0.9218 (OUTLIER) cc_final: 0.8909 (p) REVERT: D 153 MET cc_start: 0.8149 (tpp) cc_final: 0.7911 (mmm) REVERT: D 267 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8728 (mt) REVERT: J 211 MET cc_start: 0.7882 (mtt) cc_final: 0.7287 (mtt) REVERT: L 26 MET cc_start: 0.8560 (tpt) cc_final: 0.7951 (tpt) REVERT: U 188 MET cc_start: 0.3727 (ttt) cc_final: 0.3490 (ttt) REVERT: U 244 MET cc_start: 0.5496 (ppp) cc_final: 0.5215 (ppp) REVERT: U 325 MET cc_start: 0.5484 (mmt) cc_final: 0.5122 (mmt) REVERT: U 423 MET cc_start: 0.6520 (ppp) cc_final: 0.6129 (ppp) REVERT: U 695 MET cc_start: 0.6734 (mtt) cc_final: 0.6420 (mtp) REVERT: U 725 MET cc_start: 0.8355 (mmm) cc_final: 0.7621 (mmt) REVERT: U 885 MET cc_start: 0.7739 (mpp) cc_final: 0.7308 (mpp) REVERT: V 276 PHE cc_start: 0.7985 (t80) cc_final: 0.7656 (t80) REVERT: V 463 MET cc_start: 0.8289 (ppp) cc_final: 0.7730 (ppp) REVERT: Y 211 TYR cc_start: 0.6980 (OUTLIER) cc_final: 0.5429 (p90) REVERT: Y 343 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8334 (tt) REVERT: Y 389 MET cc_start: 0.8867 (mpp) cc_final: 0.8455 (mpp) REVERT: b 16 MET cc_start: 0.6518 (mmm) cc_final: 0.6224 (mmm) REVERT: d 75 MET cc_start: 0.7169 (mmp) cc_final: 0.6802 (mmt) REVERT: f 271 MET cc_start: 0.7190 (mpp) cc_final: 0.6933 (mpp) REVERT: f 662 MET cc_start: 0.5642 (ppp) cc_final: 0.4961 (ppp) REVERT: g 73 THR cc_start: 0.9292 (OUTLIER) cc_final: 0.9080 (p) REVERT: k 206 MET cc_start: 0.9062 (ttp) cc_final: 0.8833 (ttm) REVERT: l 29 VAL cc_start: 0.9099 (OUTLIER) cc_final: 0.8879 (p) REVERT: p 4 MET cc_start: 0.8761 (mmm) cc_final: 0.8199 (mmt) REVERT: q 1 MET cc_start: 0.8549 (ppp) cc_final: 0.7844 (ppp) REVERT: c 107 MET cc_start: 0.7661 (mmm) cc_final: 0.6898 (mmp) REVERT: c 265 MET cc_start: 0.8461 (pmm) cc_final: 0.8070 (pmm) REVERT: c 292 MET cc_start: 0.9348 (mmp) cc_final: 0.9112 (mmt) REVERT: u 1 MET cc_start: 0.6670 (tpt) cc_final: 0.6311 (tpt) outliers start: 106 outliers final: 87 residues processed: 513 average time/residue: 0.8565 time to fit residues: 795.8688 Evaluate side-chains 520 residues out of total 11548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 426 time to evaluate : 9.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain A residue 423 PHE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain B residue 199 GLU Chi-restraints excluded: chain B residue 277 HIS Chi-restraints excluded: chain B residue 382 ASP Chi-restraints excluded: chain C residue 106 ASN Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 374 ASP Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 236 ASP Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 196 GLU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain J residue 144 LEU Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain K residue 206 MET Chi-restraints excluded: chain L residue 228 ASP Chi-restraints excluded: chain R residue 45 MET Chi-restraints excluded: chain R residue 86 MET Chi-restraints excluded: chain S residue 27 THR Chi-restraints excluded: chain V residue 139 MET Chi-restraints excluded: chain V residue 206 VAL Chi-restraints excluded: chain V residue 451 ILE Chi-restraints excluded: chain V residue 469 THR Chi-restraints excluded: chain W residue 190 MET Chi-restraints excluded: chain W residue 243 ILE Chi-restraints excluded: chain W residue 366 MET Chi-restraints excluded: chain W residue 406 VAL Chi-restraints excluded: chain W residue 413 ILE Chi-restraints excluded: chain X residue 45 VAL Chi-restraints excluded: chain X residue 212 MET Chi-restraints excluded: chain X residue 218 HIS Chi-restraints excluded: chain X residue 374 PHE Chi-restraints excluded: chain Y residue 73 MET Chi-restraints excluded: chain Y residue 92 GLU Chi-restraints excluded: chain Y residue 186 LEU Chi-restraints excluded: chain Y residue 211 TYR Chi-restraints excluded: chain Y residue 229 ILE Chi-restraints excluded: chain Y residue 241 ILE Chi-restraints excluded: chain Y residue 249 VAL Chi-restraints excluded: chain Y residue 291 HIS Chi-restraints excluded: chain Y residue 315 THR Chi-restraints excluded: chain Y residue 343 LEU Chi-restraints excluded: chain a residue 57 ILE Chi-restraints excluded: chain a residue 87 MET Chi-restraints excluded: chain a residue 122 LYS Chi-restraints excluded: chain a residue 165 THR Chi-restraints excluded: chain a residue 211 PHE Chi-restraints excluded: chain a residue 305 ASN Chi-restraints excluded: chain a residue 341 LEU Chi-restraints excluded: chain a residue 359 ASP Chi-restraints excluded: chain d residue 112 VAL Chi-restraints excluded: chain d residue 253 LEU Chi-restraints excluded: chain f residue 216 MET Chi-restraints excluded: chain f residue 294 MET Chi-restraints excluded: chain f residue 731 MET Chi-restraints excluded: chain f residue 745 LEU Chi-restraints excluded: chain f residue 746 ARG Chi-restraints excluded: chain f residue 818 LEU Chi-restraints excluded: chain g residue 73 THR Chi-restraints excluded: chain g residue 111 VAL Chi-restraints excluded: chain h residue 181 ASP Chi-restraints excluded: chain i residue 21 VAL Chi-restraints excluded: chain i residue 243 GLU Chi-restraints excluded: chain j residue 20 GLU Chi-restraints excluded: chain j residue 134 VAL Chi-restraints excluded: chain j residue 183 THR Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain l residue 228 ASP Chi-restraints excluded: chain m residue 41 CYS Chi-restraints excluded: chain m residue 188 ASP Chi-restraints excluded: chain o residue 65 LEU Chi-restraints excluded: chain p residue 58 THR Chi-restraints excluded: chain r residue 12 VAL Chi-restraints excluded: chain s residue 169 ASP Chi-restraints excluded: chain c residue 54 MET Chi-restraints excluded: chain c residue 69 VAL Chi-restraints excluded: chain c residue 126 ASP Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain F residue 352 ILE Chi-restraints excluded: chain u residue 22 THR Chi-restraints excluded: chain e residue 46 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1334 random chunks: chunk 840 optimal weight: 20.0000 chunk 1127 optimal weight: 10.0000 chunk 324 optimal weight: 7.9990 chunk 975 optimal weight: 20.0000 chunk 156 optimal weight: 40.0000 chunk 294 optimal weight: 1.9990 chunk 1059 optimal weight: 20.0000 chunk 443 optimal weight: 6.9990 chunk 1088 optimal weight: 6.9990 chunk 134 optimal weight: 10.0000 chunk 195 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 HIS ** D 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 27 GLN ** U 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.052477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.027423 restraints weight = 990466.437| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 5.93 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.025 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.025 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3152 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 108005 Z= 0.247 Angle : 0.558 12.921 145942 Z= 0.287 Chirality : 0.041 0.324 16542 Planarity : 0.004 0.055 18814 Dihedral : 5.787 156.658 14916 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.98 % Favored : 93.97 % Rotamer: Outliers : 0.94 % Allowed : 14.18 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.08), residues: 13440 helix: 1.91 (0.07), residues: 6420 sheet: 0.63 (0.12), residues: 1971 loop : -1.44 (0.09), residues: 5049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP m 215 HIS 0.013 0.001 HIS B 277 PHE 0.020 0.001 PHE p 69 TYR 0.015 0.001 TYR W 273 ARG 0.003 0.000 ARG W 408 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20643.40 seconds wall clock time: 364 minutes 34.94 seconds (21874.94 seconds total)