Starting phenix.real_space_refine on Sun Mar 24 22:23:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cw4_27023/03_2024/8cw4_27023_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cw4_27023/03_2024/8cw4_27023.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cw4_27023/03_2024/8cw4_27023.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cw4_27023/03_2024/8cw4_27023.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cw4_27023/03_2024/8cw4_27023_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cw4_27023/03_2024/8cw4_27023_trim_updated.pdb" } resolution = 3.0 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= 0.006 sd= 0.094 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: 5 Type Number sf(0) Gaussians P 70 5.49 5 S 350 5.16 5 C 26110 2.51 5 N 5530 2.21 5 O 7210 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1A PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1B PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1C PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1D PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1E PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1F PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1G PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1H PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1I PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1J PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1K PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1L PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1M PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1N PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2A PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2B PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2C PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2D PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2E PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2F PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2G PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2H PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2I PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2J PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2K PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2L PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2M PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2N PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3A PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3B PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3C PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3D PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3E PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3F PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3G PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3H PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3I PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3J PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3K PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3L PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3M PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3N PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4A PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4B PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4C PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4D PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4E PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4F PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4G PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4H PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4I PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4J PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4K PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4L PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4M PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4N PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5C PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5D PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5E PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5F PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5G PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5H PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5I PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5J PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5K PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5L PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5M PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5N PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 39270 Number of models: 1 Model: "" Number of chains: 135 Chain: "1A" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "1B" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "1C" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "1D" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "1E" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "1F" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "1G" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "1H" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "1I" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "1J" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "1K" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "1L" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "1M" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "1N" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "2A" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "2B" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "2C" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "2D" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "2E" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "2F" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "2G" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "2H" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "2I" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "2J" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "2K" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "2L" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "2M" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "2N" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "3A" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "3B" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "3C" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "3D" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "3E" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "3F" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "3G" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "3H" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "3I" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "3J" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "3K" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "3L" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "3M" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "3N" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "4A" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "4B" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "4C" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "4D" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "4E" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "4F" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "4G" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "4H" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "4I" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "4J" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "4K" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "4L" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "4M" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "4N" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "5A" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "5B" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "5C" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "5D" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "5E" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "5F" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "5G" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "5H" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "5I" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "5J" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "5K" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "5L" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "5M" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "5N" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 510 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "1B" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'PGW': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "1C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "1D" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "1E" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "1F" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "1G" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "1H" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "1I" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "1J" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "1K" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "1L" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "1M" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "1N" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "2B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "2C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "2D" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'PGW': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "2E" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "2F" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "2G" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "2H" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "2I" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "2J" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "2K" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "2L" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "2M" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "2N" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "3B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "3C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "3D" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'PGW': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "3E" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "3F" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "3G" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "3H" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "3I" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "3J" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "3K" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "3L" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "3M" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "3N" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "4B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "4C" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'PGW': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4D" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "4E" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "4F" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "4G" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "4H" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "4I" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "4J" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "4K" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "4L" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "4M" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "4N" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "5B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "5C" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'PGW': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "5D" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "5E" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "5F" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "5G" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "5H" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "5I" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "5J" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "5K" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "5L" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "5M" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Chain: "5N" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGW': 1} Classifications: {'undetermined': 1} Time building chain proxies: 17.70, per 1000 atoms: 0.45 Number of scatterers: 39270 At special positions: 0 Unit cell: (92.65, 92.65, 262.69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 350 16.00 P 70 15.00 O 7210 8.00 N 5530 7.00 C 26110 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 13.32 Conformation dependent library (CDL) restraints added in 5.8 seconds 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8820 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 210 helices and 0 sheets defined 77.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.47 Creating SS restraints... Processing helix chain '1A' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR1A 46 " --> pdb=" O THR1A 42 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TRP1A 47 " --> pdb=" O TRP1A 43 " (cutoff:3.500A) Proline residue: 1A 49 - end of helix Processing helix chain '1A' and resid 70 through 84 Proline residue: 1A 74 - end of helix removed outlier: 3.501A pdb=" N ILE1A 83 " --> pdb=" O LEU1A 80 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY1A 84 " --> pdb=" O ILE1A 81 " (cutoff:3.500A) Processing helix chain '1A' and resid 86 through 93 removed outlier: 3.589A pdb=" N THR1A 93 " --> pdb=" O LEU1A 89 " (cutoff:3.500A) Processing helix chain '1B' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR1B 46 " --> pdb=" O THR1B 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP1B 47 " --> pdb=" O TRP1B 43 " (cutoff:3.500A) Proline residue: 1B 49 - end of helix Processing helix chain '1B' and resid 70 through 84 Proline residue: 1B 74 - end of helix removed outlier: 3.501A pdb=" N ILE1B 83 " --> pdb=" O LEU1B 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY1B 84 " --> pdb=" O ILE1B 81 " (cutoff:3.500A) Processing helix chain '1B' and resid 86 through 93 removed outlier: 3.589A pdb=" N THR1B 93 " --> pdb=" O LEU1B 89 " (cutoff:3.500A) Processing helix chain '1C' and resid 34 through 64 removed outlier: 3.644A pdb=" N THR1C 46 " --> pdb=" O THR1C 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP1C 47 " --> pdb=" O TRP1C 43 " (cutoff:3.500A) Proline residue: 1C 49 - end of helix Processing helix chain '1C' and resid 70 through 84 Proline residue: 1C 74 - end of helix removed outlier: 3.501A pdb=" N ILE1C 83 " --> pdb=" O LEU1C 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY1C 84 " --> pdb=" O ILE1C 81 " (cutoff:3.500A) Processing helix chain '1C' and resid 86 through 93 removed outlier: 3.590A pdb=" N THR1C 93 " --> pdb=" O LEU1C 89 " (cutoff:3.500A) Processing helix chain '1D' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR1D 46 " --> pdb=" O THR1D 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP1D 47 " --> pdb=" O TRP1D 43 " (cutoff:3.500A) Proline residue: 1D 49 - end of helix Processing helix chain '1D' and resid 70 through 84 Proline residue: 1D 74 - end of helix removed outlier: 3.502A pdb=" N ILE1D 83 " --> pdb=" O LEU1D 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY1D 84 " --> pdb=" O ILE1D 81 " (cutoff:3.500A) Processing helix chain '1D' and resid 86 through 93 removed outlier: 3.590A pdb=" N THR1D 93 " --> pdb=" O LEU1D 89 " (cutoff:3.500A) Processing helix chain '1E' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR1E 46 " --> pdb=" O THR1E 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP1E 47 " --> pdb=" O TRP1E 43 " (cutoff:3.500A) Proline residue: 1E 49 - end of helix Processing helix chain '1E' and resid 70 through 84 Proline residue: 1E 74 - end of helix removed outlier: 3.501A pdb=" N ILE1E 83 " --> pdb=" O LEU1E 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY1E 84 " --> pdb=" O ILE1E 81 " (cutoff:3.500A) Processing helix chain '1E' and resid 86 through 93 removed outlier: 3.590A pdb=" N THR1E 93 " --> pdb=" O LEU1E 89 " (cutoff:3.500A) Processing helix chain '1F' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR1F 46 " --> pdb=" O THR1F 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP1F 47 " --> pdb=" O TRP1F 43 " (cutoff:3.500A) Proline residue: 1F 49 - end of helix Processing helix chain '1F' and resid 70 through 84 Proline residue: 1F 74 - end of helix removed outlier: 3.502A pdb=" N ILE1F 83 " --> pdb=" O LEU1F 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY1F 84 " --> pdb=" O ILE1F 81 " (cutoff:3.500A) Processing helix chain '1F' and resid 86 through 93 removed outlier: 3.590A pdb=" N THR1F 93 " --> pdb=" O LEU1F 89 " (cutoff:3.500A) Processing helix chain '1G' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR1G 46 " --> pdb=" O THR1G 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP1G 47 " --> pdb=" O TRP1G 43 " (cutoff:3.500A) Proline residue: 1G 49 - end of helix Processing helix chain '1G' and resid 70 through 84 Proline residue: 1G 74 - end of helix removed outlier: 3.502A pdb=" N ILE1G 83 " --> pdb=" O LEU1G 80 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY1G 84 " --> pdb=" O ILE1G 81 " (cutoff:3.500A) Processing helix chain '1G' and resid 86 through 93 removed outlier: 3.589A pdb=" N THR1G 93 " --> pdb=" O LEU1G 89 " (cutoff:3.500A) Processing helix chain '1H' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR1H 46 " --> pdb=" O THR1H 42 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TRP1H 47 " --> pdb=" O TRP1H 43 " (cutoff:3.500A) Proline residue: 1H 49 - end of helix Processing helix chain '1H' and resid 70 through 84 Proline residue: 1H 74 - end of helix removed outlier: 3.501A pdb=" N ILE1H 83 " --> pdb=" O LEU1H 80 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY1H 84 " --> pdb=" O ILE1H 81 " (cutoff:3.500A) Processing helix chain '1H' and resid 86 through 93 removed outlier: 3.590A pdb=" N THR1H 93 " --> pdb=" O LEU1H 89 " (cutoff:3.500A) Processing helix chain '1I' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR1I 46 " --> pdb=" O THR1I 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP1I 47 " --> pdb=" O TRP1I 43 " (cutoff:3.500A) Proline residue: 1I 49 - end of helix Processing helix chain '1I' and resid 70 through 84 Proline residue: 1I 74 - end of helix removed outlier: 3.501A pdb=" N ILE1I 83 " --> pdb=" O LEU1I 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY1I 84 " --> pdb=" O ILE1I 81 " (cutoff:3.500A) Processing helix chain '1I' and resid 86 through 93 removed outlier: 3.590A pdb=" N THR1I 93 " --> pdb=" O LEU1I 89 " (cutoff:3.500A) Processing helix chain '1J' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR1J 46 " --> pdb=" O THR1J 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP1J 47 " --> pdb=" O TRP1J 43 " (cutoff:3.500A) Proline residue: 1J 49 - end of helix Processing helix chain '1J' and resid 70 through 84 Proline residue: 1J 74 - end of helix removed outlier: 3.501A pdb=" N ILE1J 83 " --> pdb=" O LEU1J 80 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY1J 84 " --> pdb=" O ILE1J 81 " (cutoff:3.500A) Processing helix chain '1J' and resid 86 through 93 removed outlier: 3.590A pdb=" N THR1J 93 " --> pdb=" O LEU1J 89 " (cutoff:3.500A) Processing helix chain '1K' and resid 34 through 64 removed outlier: 3.644A pdb=" N THR1K 46 " --> pdb=" O THR1K 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP1K 47 " --> pdb=" O TRP1K 43 " (cutoff:3.500A) Proline residue: 1K 49 - end of helix Processing helix chain '1K' and resid 70 through 84 Proline residue: 1K 74 - end of helix removed outlier: 3.501A pdb=" N ILE1K 83 " --> pdb=" O LEU1K 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY1K 84 " --> pdb=" O ILE1K 81 " (cutoff:3.500A) Processing helix chain '1K' and resid 86 through 93 removed outlier: 3.589A pdb=" N THR1K 93 " --> pdb=" O LEU1K 89 " (cutoff:3.500A) Processing helix chain '1L' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR1L 46 " --> pdb=" O THR1L 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP1L 47 " --> pdb=" O TRP1L 43 " (cutoff:3.500A) Proline residue: 1L 49 - end of helix Processing helix chain '1L' and resid 70 through 84 Proline residue: 1L 74 - end of helix removed outlier: 3.501A pdb=" N ILE1L 83 " --> pdb=" O LEU1L 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY1L 84 " --> pdb=" O ILE1L 81 " (cutoff:3.500A) Processing helix chain '1L' and resid 86 through 93 removed outlier: 3.589A pdb=" N THR1L 93 " --> pdb=" O LEU1L 89 " (cutoff:3.500A) Processing helix chain '1M' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR1M 46 " --> pdb=" O THR1M 42 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TRP1M 47 " --> pdb=" O TRP1M 43 " (cutoff:3.500A) Proline residue: 1M 49 - end of helix Processing helix chain '1M' and resid 70 through 84 Proline residue: 1M 74 - end of helix removed outlier: 3.501A pdb=" N ILE1M 83 " --> pdb=" O LEU1M 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY1M 84 " --> pdb=" O ILE1M 81 " (cutoff:3.500A) Processing helix chain '1M' and resid 86 through 93 removed outlier: 3.589A pdb=" N THR1M 93 " --> pdb=" O LEU1M 89 " (cutoff:3.500A) Processing helix chain '1N' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR1N 46 " --> pdb=" O THR1N 42 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TRP1N 47 " --> pdb=" O TRP1N 43 " (cutoff:3.500A) Proline residue: 1N 49 - end of helix Processing helix chain '1N' and resid 70 through 84 Proline residue: 1N 74 - end of helix removed outlier: 3.501A pdb=" N ILE1N 83 " --> pdb=" O LEU1N 80 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY1N 84 " --> pdb=" O ILE1N 81 " (cutoff:3.500A) Processing helix chain '1N' and resid 86 through 93 removed outlier: 3.590A pdb=" N THR1N 93 " --> pdb=" O LEU1N 89 " (cutoff:3.500A) Processing helix chain '2A' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR2A 46 " --> pdb=" O THR2A 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP2A 47 " --> pdb=" O TRP2A 43 " (cutoff:3.500A) Proline residue: 2A 49 - end of helix Processing helix chain '2A' and resid 70 through 84 Proline residue: 2A 74 - end of helix removed outlier: 3.501A pdb=" N ILE2A 83 " --> pdb=" O LEU2A 80 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY2A 84 " --> pdb=" O ILE2A 81 " (cutoff:3.500A) Processing helix chain '2A' and resid 86 through 93 removed outlier: 3.590A pdb=" N THR2A 93 " --> pdb=" O LEU2A 89 " (cutoff:3.500A) Processing helix chain '2B' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR2B 46 " --> pdb=" O THR2B 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP2B 47 " --> pdb=" O TRP2B 43 " (cutoff:3.500A) Proline residue: 2B 49 - end of helix Processing helix chain '2B' and resid 70 through 84 Proline residue: 2B 74 - end of helix removed outlier: 3.501A pdb=" N ILE2B 83 " --> pdb=" O LEU2B 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY2B 84 " --> pdb=" O ILE2B 81 " (cutoff:3.500A) Processing helix chain '2B' and resid 86 through 93 removed outlier: 3.590A pdb=" N THR2B 93 " --> pdb=" O LEU2B 89 " (cutoff:3.500A) Processing helix chain '2C' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR2C 46 " --> pdb=" O THR2C 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP2C 47 " --> pdb=" O TRP2C 43 " (cutoff:3.500A) Proline residue: 2C 49 - end of helix Processing helix chain '2C' and resid 70 through 84 Proline residue: 2C 74 - end of helix removed outlier: 3.502A pdb=" N ILE2C 83 " --> pdb=" O LEU2C 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY2C 84 " --> pdb=" O ILE2C 81 " (cutoff:3.500A) Processing helix chain '2C' and resid 86 through 93 removed outlier: 3.589A pdb=" N THR2C 93 " --> pdb=" O LEU2C 89 " (cutoff:3.500A) Processing helix chain '2D' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR2D 46 " --> pdb=" O THR2D 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP2D 47 " --> pdb=" O TRP2D 43 " (cutoff:3.500A) Proline residue: 2D 49 - end of helix Processing helix chain '2D' and resid 70 through 84 Proline residue: 2D 74 - end of helix removed outlier: 3.502A pdb=" N ILE2D 83 " --> pdb=" O LEU2D 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY2D 84 " --> pdb=" O ILE2D 81 " (cutoff:3.500A) Processing helix chain '2D' and resid 86 through 93 removed outlier: 3.589A pdb=" N THR2D 93 " --> pdb=" O LEU2D 89 " (cutoff:3.500A) Processing helix chain '2E' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR2E 46 " --> pdb=" O THR2E 42 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TRP2E 47 " --> pdb=" O TRP2E 43 " (cutoff:3.500A) Proline residue: 2E 49 - end of helix Processing helix chain '2E' and resid 70 through 84 Proline residue: 2E 74 - end of helix removed outlier: 3.501A pdb=" N ILE2E 83 " --> pdb=" O LEU2E 80 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY2E 84 " --> pdb=" O ILE2E 81 " (cutoff:3.500A) Processing helix chain '2E' and resid 86 through 93 removed outlier: 3.590A pdb=" N THR2E 93 " --> pdb=" O LEU2E 89 " (cutoff:3.500A) Processing helix chain '2F' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR2F 46 " --> pdb=" O THR2F 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP2F 47 " --> pdb=" O TRP2F 43 " (cutoff:3.500A) Proline residue: 2F 49 - end of helix Processing helix chain '2F' and resid 70 through 84 Proline residue: 2F 74 - end of helix removed outlier: 3.502A pdb=" N ILE2F 83 " --> pdb=" O LEU2F 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY2F 84 " --> pdb=" O ILE2F 81 " (cutoff:3.500A) Processing helix chain '2F' and resid 86 through 93 removed outlier: 3.589A pdb=" N THR2F 93 " --> pdb=" O LEU2F 89 " (cutoff:3.500A) Processing helix chain '2G' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR2G 46 " --> pdb=" O THR2G 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP2G 47 " --> pdb=" O TRP2G 43 " (cutoff:3.500A) Proline residue: 2G 49 - end of helix Processing helix chain '2G' and resid 70 through 84 Proline residue: 2G 74 - end of helix removed outlier: 3.501A pdb=" N ILE2G 83 " --> pdb=" O LEU2G 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY2G 84 " --> pdb=" O ILE2G 81 " (cutoff:3.500A) Processing helix chain '2G' and resid 86 through 93 removed outlier: 3.589A pdb=" N THR2G 93 " --> pdb=" O LEU2G 89 " (cutoff:3.500A) Processing helix chain '2H' and resid 34 through 64 removed outlier: 3.644A pdb=" N THR2H 46 " --> pdb=" O THR2H 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP2H 47 " --> pdb=" O TRP2H 43 " (cutoff:3.500A) Proline residue: 2H 49 - end of helix Processing helix chain '2H' and resid 70 through 84 Proline residue: 2H 74 - end of helix removed outlier: 3.501A pdb=" N ILE2H 83 " --> pdb=" O LEU2H 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY2H 84 " --> pdb=" O ILE2H 81 " (cutoff:3.500A) Processing helix chain '2H' and resid 86 through 93 removed outlier: 3.590A pdb=" N THR2H 93 " --> pdb=" O LEU2H 89 " (cutoff:3.500A) Processing helix chain '2I' and resid 34 through 64 removed outlier: 3.646A pdb=" N THR2I 46 " --> pdb=" O THR2I 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP2I 47 " --> pdb=" O TRP2I 43 " (cutoff:3.500A) Proline residue: 2I 49 - end of helix Processing helix chain '2I' and resid 70 through 84 Proline residue: 2I 74 - end of helix removed outlier: 3.502A pdb=" N ILE2I 83 " --> pdb=" O LEU2I 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY2I 84 " --> pdb=" O ILE2I 81 " (cutoff:3.500A) Processing helix chain '2I' and resid 86 through 93 removed outlier: 3.589A pdb=" N THR2I 93 " --> pdb=" O LEU2I 89 " (cutoff:3.500A) Processing helix chain '2J' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR2J 46 " --> pdb=" O THR2J 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP2J 47 " --> pdb=" O TRP2J 43 " (cutoff:3.500A) Proline residue: 2J 49 - end of helix Processing helix chain '2J' and resid 70 through 84 Proline residue: 2J 74 - end of helix removed outlier: 3.501A pdb=" N ILE2J 83 " --> pdb=" O LEU2J 80 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY2J 84 " --> pdb=" O ILE2J 81 " (cutoff:3.500A) Processing helix chain '2J' and resid 86 through 93 removed outlier: 3.590A pdb=" N THR2J 93 " --> pdb=" O LEU2J 89 " (cutoff:3.500A) Processing helix chain '2K' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR2K 46 " --> pdb=" O THR2K 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP2K 47 " --> pdb=" O TRP2K 43 " (cutoff:3.500A) Proline residue: 2K 49 - end of helix Processing helix chain '2K' and resid 70 through 84 Proline residue: 2K 74 - end of helix removed outlier: 3.501A pdb=" N ILE2K 83 " --> pdb=" O LEU2K 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY2K 84 " --> pdb=" O ILE2K 81 " (cutoff:3.500A) Processing helix chain '2K' and resid 86 through 93 removed outlier: 3.590A pdb=" N THR2K 93 " --> pdb=" O LEU2K 89 " (cutoff:3.500A) Processing helix chain '2L' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR2L 46 " --> pdb=" O THR2L 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP2L 47 " --> pdb=" O TRP2L 43 " (cutoff:3.500A) Proline residue: 2L 49 - end of helix Processing helix chain '2L' and resid 70 through 84 Proline residue: 2L 74 - end of helix removed outlier: 3.501A pdb=" N ILE2L 83 " --> pdb=" O LEU2L 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY2L 84 " --> pdb=" O ILE2L 81 " (cutoff:3.500A) Processing helix chain '2L' and resid 86 through 93 removed outlier: 3.589A pdb=" N THR2L 93 " --> pdb=" O LEU2L 89 " (cutoff:3.500A) Processing helix chain '2M' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR2M 46 " --> pdb=" O THR2M 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP2M 47 " --> pdb=" O TRP2M 43 " (cutoff:3.500A) Proline residue: 2M 49 - end of helix Processing helix chain '2M' and resid 70 through 84 Proline residue: 2M 74 - end of helix removed outlier: 3.501A pdb=" N ILE2M 83 " --> pdb=" O LEU2M 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY2M 84 " --> pdb=" O ILE2M 81 " (cutoff:3.500A) Processing helix chain '2M' and resid 86 through 93 removed outlier: 3.590A pdb=" N THR2M 93 " --> pdb=" O LEU2M 89 " (cutoff:3.500A) Processing helix chain '2N' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR2N 46 " --> pdb=" O THR2N 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP2N 47 " --> pdb=" O TRP2N 43 " (cutoff:3.500A) Proline residue: 2N 49 - end of helix Processing helix chain '2N' and resid 70 through 84 Proline residue: 2N 74 - end of helix removed outlier: 3.501A pdb=" N ILE2N 83 " --> pdb=" O LEU2N 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY2N 84 " --> pdb=" O ILE2N 81 " (cutoff:3.500A) Processing helix chain '2N' and resid 86 through 93 removed outlier: 3.589A pdb=" N THR2N 93 " --> pdb=" O LEU2N 89 " (cutoff:3.500A) Processing helix chain '3A' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR3A 46 " --> pdb=" O THR3A 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP3A 47 " --> pdb=" O TRP3A 43 " (cutoff:3.500A) Proline residue: 3A 49 - end of helix Processing helix chain '3A' and resid 70 through 84 Proline residue: 3A 74 - end of helix removed outlier: 3.502A pdb=" N ILE3A 83 " --> pdb=" O LEU3A 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY3A 84 " --> pdb=" O ILE3A 81 " (cutoff:3.500A) Processing helix chain '3A' and resid 86 through 93 removed outlier: 3.589A pdb=" N THR3A 93 " --> pdb=" O LEU3A 89 " (cutoff:3.500A) Processing helix chain '3B' and resid 34 through 64 removed outlier: 3.646A pdb=" N THR3B 46 " --> pdb=" O THR3B 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP3B 47 " --> pdb=" O TRP3B 43 " (cutoff:3.500A) Proline residue: 3B 49 - end of helix Processing helix chain '3B' and resid 70 through 84 Proline residue: 3B 74 - end of helix removed outlier: 3.501A pdb=" N ILE3B 83 " --> pdb=" O LEU3B 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY3B 84 " --> pdb=" O ILE3B 81 " (cutoff:3.500A) Processing helix chain '3B' and resid 86 through 93 removed outlier: 3.589A pdb=" N THR3B 93 " --> pdb=" O LEU3B 89 " (cutoff:3.500A) Processing helix chain '3C' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR3C 46 " --> pdb=" O THR3C 42 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TRP3C 47 " --> pdb=" O TRP3C 43 " (cutoff:3.500A) Proline residue: 3C 49 - end of helix Processing helix chain '3C' and resid 70 through 84 Proline residue: 3C 74 - end of helix removed outlier: 3.502A pdb=" N ILE3C 83 " --> pdb=" O LEU3C 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY3C 84 " --> pdb=" O ILE3C 81 " (cutoff:3.500A) Processing helix chain '3C' and resid 86 through 93 removed outlier: 3.589A pdb=" N THR3C 93 " --> pdb=" O LEU3C 89 " (cutoff:3.500A) Processing helix chain '3D' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR3D 46 " --> pdb=" O THR3D 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP3D 47 " --> pdb=" O TRP3D 43 " (cutoff:3.500A) Proline residue: 3D 49 - end of helix Processing helix chain '3D' and resid 70 through 84 Proline residue: 3D 74 - end of helix removed outlier: 3.502A pdb=" N ILE3D 83 " --> pdb=" O LEU3D 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY3D 84 " --> pdb=" O ILE3D 81 " (cutoff:3.500A) Processing helix chain '3D' and resid 86 through 93 removed outlier: 3.590A pdb=" N THR3D 93 " --> pdb=" O LEU3D 89 " (cutoff:3.500A) Processing helix chain '3E' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR3E 46 " --> pdb=" O THR3E 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP3E 47 " --> pdb=" O TRP3E 43 " (cutoff:3.500A) Proline residue: 3E 49 - end of helix Processing helix chain '3E' and resid 70 through 84 Proline residue: 3E 74 - end of helix removed outlier: 3.502A pdb=" N ILE3E 83 " --> pdb=" O LEU3E 80 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY3E 84 " --> pdb=" O ILE3E 81 " (cutoff:3.500A) Processing helix chain '3E' and resid 86 through 93 removed outlier: 3.589A pdb=" N THR3E 93 " --> pdb=" O LEU3E 89 " (cutoff:3.500A) Processing helix chain '3F' and resid 34 through 64 removed outlier: 3.644A pdb=" N THR3F 46 " --> pdb=" O THR3F 42 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TRP3F 47 " --> pdb=" O TRP3F 43 " (cutoff:3.500A) Proline residue: 3F 49 - end of helix Processing helix chain '3F' and resid 70 through 84 Proline residue: 3F 74 - end of helix removed outlier: 3.502A pdb=" N ILE3F 83 " --> pdb=" O LEU3F 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY3F 84 " --> pdb=" O ILE3F 81 " (cutoff:3.500A) Processing helix chain '3F' and resid 86 through 93 removed outlier: 3.590A pdb=" N THR3F 93 " --> pdb=" O LEU3F 89 " (cutoff:3.500A) Processing helix chain '3G' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR3G 46 " --> pdb=" O THR3G 42 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TRP3G 47 " --> pdb=" O TRP3G 43 " (cutoff:3.500A) Proline residue: 3G 49 - end of helix Processing helix chain '3G' and resid 70 through 84 Proline residue: 3G 74 - end of helix removed outlier: 3.502A pdb=" N ILE3G 83 " --> pdb=" O LEU3G 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY3G 84 " --> pdb=" O ILE3G 81 " (cutoff:3.500A) Processing helix chain '3G' and resid 86 through 93 removed outlier: 3.589A pdb=" N THR3G 93 " --> pdb=" O LEU3G 89 " (cutoff:3.500A) Processing helix chain '3H' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR3H 46 " --> pdb=" O THR3H 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP3H 47 " --> pdb=" O TRP3H 43 " (cutoff:3.500A) Proline residue: 3H 49 - end of helix Processing helix chain '3H' and resid 70 through 84 Proline residue: 3H 74 - end of helix removed outlier: 3.501A pdb=" N ILE3H 83 " --> pdb=" O LEU3H 80 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY3H 84 " --> pdb=" O ILE3H 81 " (cutoff:3.500A) Processing helix chain '3H' and resid 86 through 93 removed outlier: 3.590A pdb=" N THR3H 93 " --> pdb=" O LEU3H 89 " (cutoff:3.500A) Processing helix chain '3I' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR3I 46 " --> pdb=" O THR3I 42 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TRP3I 47 " --> pdb=" O TRP3I 43 " (cutoff:3.500A) Proline residue: 3I 49 - end of helix Processing helix chain '3I' and resid 70 through 84 Proline residue: 3I 74 - end of helix removed outlier: 3.501A pdb=" N ILE3I 83 " --> pdb=" O LEU3I 80 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY3I 84 " --> pdb=" O ILE3I 81 " (cutoff:3.500A) Processing helix chain '3I' and resid 86 through 93 removed outlier: 3.590A pdb=" N THR3I 93 " --> pdb=" O LEU3I 89 " (cutoff:3.500A) Processing helix chain '3J' and resid 34 through 64 removed outlier: 3.644A pdb=" N THR3J 46 " --> pdb=" O THR3J 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP3J 47 " --> pdb=" O TRP3J 43 " (cutoff:3.500A) Proline residue: 3J 49 - end of helix Processing helix chain '3J' and resid 70 through 84 Proline residue: 3J 74 - end of helix removed outlier: 3.502A pdb=" N ILE3J 83 " --> pdb=" O LEU3J 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY3J 84 " --> pdb=" O ILE3J 81 " (cutoff:3.500A) Processing helix chain '3J' and resid 86 through 93 removed outlier: 3.590A pdb=" N THR3J 93 " --> pdb=" O LEU3J 89 " (cutoff:3.500A) Processing helix chain '3K' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR3K 46 " --> pdb=" O THR3K 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP3K 47 " --> pdb=" O TRP3K 43 " (cutoff:3.500A) Proline residue: 3K 49 - end of helix Processing helix chain '3K' and resid 70 through 84 Proline residue: 3K 74 - end of helix removed outlier: 3.501A pdb=" N ILE3K 83 " --> pdb=" O LEU3K 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY3K 84 " --> pdb=" O ILE3K 81 " (cutoff:3.500A) Processing helix chain '3K' and resid 86 through 93 removed outlier: 3.590A pdb=" N THR3K 93 " --> pdb=" O LEU3K 89 " (cutoff:3.500A) Processing helix chain '3L' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR3L 46 " --> pdb=" O THR3L 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP3L 47 " --> pdb=" O TRP3L 43 " (cutoff:3.500A) Proline residue: 3L 49 - end of helix Processing helix chain '3L' and resid 70 through 84 Proline residue: 3L 74 - end of helix removed outlier: 3.502A pdb=" N ILE3L 83 " --> pdb=" O LEU3L 80 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY3L 84 " --> pdb=" O ILE3L 81 " (cutoff:3.500A) Processing helix chain '3L' and resid 86 through 93 removed outlier: 3.590A pdb=" N THR3L 93 " --> pdb=" O LEU3L 89 " (cutoff:3.500A) Processing helix chain '3M' and resid 34 through 64 removed outlier: 3.644A pdb=" N THR3M 46 " --> pdb=" O THR3M 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP3M 47 " --> pdb=" O TRP3M 43 " (cutoff:3.500A) Proline residue: 3M 49 - end of helix Processing helix chain '3M' and resid 70 through 84 Proline residue: 3M 74 - end of helix removed outlier: 3.501A pdb=" N ILE3M 83 " --> pdb=" O LEU3M 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY3M 84 " --> pdb=" O ILE3M 81 " (cutoff:3.500A) Processing helix chain '3M' and resid 86 through 93 removed outlier: 3.589A pdb=" N THR3M 93 " --> pdb=" O LEU3M 89 " (cutoff:3.500A) Processing helix chain '3N' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR3N 46 " --> pdb=" O THR3N 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP3N 47 " --> pdb=" O TRP3N 43 " (cutoff:3.500A) Proline residue: 3N 49 - end of helix Processing helix chain '3N' and resid 70 through 84 Proline residue: 3N 74 - end of helix removed outlier: 3.501A pdb=" N ILE3N 83 " --> pdb=" O LEU3N 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY3N 84 " --> pdb=" O ILE3N 81 " (cutoff:3.500A) Processing helix chain '3N' and resid 86 through 93 removed outlier: 3.590A pdb=" N THR3N 93 " --> pdb=" O LEU3N 89 " (cutoff:3.500A) Processing helix chain '4A' and resid 34 through 64 removed outlier: 3.644A pdb=" N THR4A 46 " --> pdb=" O THR4A 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP4A 47 " --> pdb=" O TRP4A 43 " (cutoff:3.500A) Proline residue: 4A 49 - end of helix Processing helix chain '4A' and resid 70 through 84 Proline residue: 4A 74 - end of helix removed outlier: 3.502A pdb=" N ILE4A 83 " --> pdb=" O LEU4A 80 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY4A 84 " --> pdb=" O ILE4A 81 " (cutoff:3.500A) Processing helix chain '4A' and resid 86 through 93 removed outlier: 3.590A pdb=" N THR4A 93 " --> pdb=" O LEU4A 89 " (cutoff:3.500A) Processing helix chain '4B' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR4B 46 " --> pdb=" O THR4B 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP4B 47 " --> pdb=" O TRP4B 43 " (cutoff:3.500A) Proline residue: 4B 49 - end of helix Processing helix chain '4B' and resid 70 through 84 Proline residue: 4B 74 - end of helix removed outlier: 3.501A pdb=" N ILE4B 83 " --> pdb=" O LEU4B 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY4B 84 " --> pdb=" O ILE4B 81 " (cutoff:3.500A) Processing helix chain '4B' and resid 86 through 93 removed outlier: 3.589A pdb=" N THR4B 93 " --> pdb=" O LEU4B 89 " (cutoff:3.500A) Processing helix chain '4C' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR4C 46 " --> pdb=" O THR4C 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP4C 47 " --> pdb=" O TRP4C 43 " (cutoff:3.500A) Proline residue: 4C 49 - end of helix Processing helix chain '4C' and resid 70 through 84 Proline residue: 4C 74 - end of helix removed outlier: 3.501A pdb=" N ILE4C 83 " --> pdb=" O LEU4C 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY4C 84 " --> pdb=" O ILE4C 81 " (cutoff:3.500A) Processing helix chain '4C' and resid 86 through 93 removed outlier: 3.589A pdb=" N THR4C 93 " --> pdb=" O LEU4C 89 " (cutoff:3.500A) Processing helix chain '4D' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR4D 46 " --> pdb=" O THR4D 42 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TRP4D 47 " --> pdb=" O TRP4D 43 " (cutoff:3.500A) Proline residue: 4D 49 - end of helix Processing helix chain '4D' and resid 70 through 84 Proline residue: 4D 74 - end of helix removed outlier: 3.501A pdb=" N ILE4D 83 " --> pdb=" O LEU4D 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY4D 84 " --> pdb=" O ILE4D 81 " (cutoff:3.500A) Processing helix chain '4D' and resid 86 through 93 removed outlier: 3.590A pdb=" N THR4D 93 " --> pdb=" O LEU4D 89 " (cutoff:3.500A) Processing helix chain '4E' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR4E 46 " --> pdb=" O THR4E 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP4E 47 " --> pdb=" O TRP4E 43 " (cutoff:3.500A) Proline residue: 4E 49 - end of helix Processing helix chain '4E' and resid 70 through 84 Proline residue: 4E 74 - end of helix removed outlier: 3.502A pdb=" N ILE4E 83 " --> pdb=" O LEU4E 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY4E 84 " --> pdb=" O ILE4E 81 " (cutoff:3.500A) Processing helix chain '4E' and resid 86 through 93 removed outlier: 3.589A pdb=" N THR4E 93 " --> pdb=" O LEU4E 89 " (cutoff:3.500A) Processing helix chain '4F' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR4F 46 " --> pdb=" O THR4F 42 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TRP4F 47 " --> pdb=" O TRP4F 43 " (cutoff:3.500A) Proline residue: 4F 49 - end of helix Processing helix chain '4F' and resid 70 through 84 Proline residue: 4F 74 - end of helix removed outlier: 3.501A pdb=" N ILE4F 83 " --> pdb=" O LEU4F 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY4F 84 " --> pdb=" O ILE4F 81 " (cutoff:3.500A) Processing helix chain '4F' and resid 86 through 93 removed outlier: 3.590A pdb=" N THR4F 93 " --> pdb=" O LEU4F 89 " (cutoff:3.500A) Processing helix chain '4G' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR4G 46 " --> pdb=" O THR4G 42 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TRP4G 47 " --> pdb=" O TRP4G 43 " (cutoff:3.500A) Proline residue: 4G 49 - end of helix Processing helix chain '4G' and resid 70 through 84 Proline residue: 4G 74 - end of helix removed outlier: 3.502A pdb=" N ILE4G 83 " --> pdb=" O LEU4G 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY4G 84 " --> pdb=" O ILE4G 81 " (cutoff:3.500A) Processing helix chain '4G' and resid 86 through 93 removed outlier: 3.590A pdb=" N THR4G 93 " --> pdb=" O LEU4G 89 " (cutoff:3.500A) Processing helix chain '4H' and resid 34 through 64 removed outlier: 3.644A pdb=" N THR4H 46 " --> pdb=" O THR4H 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP4H 47 " --> pdb=" O TRP4H 43 " (cutoff:3.500A) Proline residue: 4H 49 - end of helix Processing helix chain '4H' and resid 70 through 84 Proline residue: 4H 74 - end of helix removed outlier: 3.501A pdb=" N ILE4H 83 " --> pdb=" O LEU4H 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY4H 84 " --> pdb=" O ILE4H 81 " (cutoff:3.500A) Processing helix chain '4H' and resid 86 through 93 removed outlier: 3.590A pdb=" N THR4H 93 " --> pdb=" O LEU4H 89 " (cutoff:3.500A) Processing helix chain '4I' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR4I 46 " --> pdb=" O THR4I 42 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TRP4I 47 " --> pdb=" O TRP4I 43 " (cutoff:3.500A) Proline residue: 4I 49 - end of helix Processing helix chain '4I' and resid 70 through 84 Proline residue: 4I 74 - end of helix removed outlier: 3.501A pdb=" N ILE4I 83 " --> pdb=" O LEU4I 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY4I 84 " --> pdb=" O ILE4I 81 " (cutoff:3.500A) Processing helix chain '4I' and resid 86 through 93 removed outlier: 3.590A pdb=" N THR4I 93 " --> pdb=" O LEU4I 89 " (cutoff:3.500A) Processing helix chain '4J' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR4J 46 " --> pdb=" O THR4J 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP4J 47 " --> pdb=" O TRP4J 43 " (cutoff:3.500A) Proline residue: 4J 49 - end of helix Processing helix chain '4J' and resid 70 through 84 Proline residue: 4J 74 - end of helix removed outlier: 3.501A pdb=" N ILE4J 83 " --> pdb=" O LEU4J 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY4J 84 " --> pdb=" O ILE4J 81 " (cutoff:3.500A) Processing helix chain '4J' and resid 86 through 93 removed outlier: 3.589A pdb=" N THR4J 93 " --> pdb=" O LEU4J 89 " (cutoff:3.500A) Processing helix chain '4K' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR4K 46 " --> pdb=" O THR4K 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP4K 47 " --> pdb=" O TRP4K 43 " (cutoff:3.500A) Proline residue: 4K 49 - end of helix Processing helix chain '4K' and resid 70 through 84 Proline residue: 4K 74 - end of helix removed outlier: 3.502A pdb=" N ILE4K 83 " --> pdb=" O LEU4K 80 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY4K 84 " --> pdb=" O ILE4K 81 " (cutoff:3.500A) Processing helix chain '4K' and resid 86 through 93 removed outlier: 3.590A pdb=" N THR4K 93 " --> pdb=" O LEU4K 89 " (cutoff:3.500A) Processing helix chain '4L' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR4L 46 " --> pdb=" O THR4L 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP4L 47 " --> pdb=" O TRP4L 43 " (cutoff:3.500A) Proline residue: 4L 49 - end of helix Processing helix chain '4L' and resid 70 through 84 Proline residue: 4L 74 - end of helix removed outlier: 3.501A pdb=" N ILE4L 83 " --> pdb=" O LEU4L 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY4L 84 " --> pdb=" O ILE4L 81 " (cutoff:3.500A) Processing helix chain '4L' and resid 86 through 93 removed outlier: 3.590A pdb=" N THR4L 93 " --> pdb=" O LEU4L 89 " (cutoff:3.500A) Processing helix chain '4M' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR4M 46 " --> pdb=" O THR4M 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP4M 47 " --> pdb=" O TRP4M 43 " (cutoff:3.500A) Proline residue: 4M 49 - end of helix Processing helix chain '4M' and resid 70 through 84 Proline residue: 4M 74 - end of helix removed outlier: 3.501A pdb=" N ILE4M 83 " --> pdb=" O LEU4M 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY4M 84 " --> pdb=" O ILE4M 81 " (cutoff:3.500A) Processing helix chain '4M' and resid 86 through 93 removed outlier: 3.590A pdb=" N THR4M 93 " --> pdb=" O LEU4M 89 " (cutoff:3.500A) Processing helix chain '4N' and resid 34 through 64 removed outlier: 3.644A pdb=" N THR4N 46 " --> pdb=" O THR4N 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP4N 47 " --> pdb=" O TRP4N 43 " (cutoff:3.500A) Proline residue: 4N 49 - end of helix Processing helix chain '4N' and resid 70 through 84 Proline residue: 4N 74 - end of helix removed outlier: 3.501A pdb=" N ILE4N 83 " --> pdb=" O LEU4N 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY4N 84 " --> pdb=" O ILE4N 81 " (cutoff:3.500A) Processing helix chain '4N' and resid 86 through 93 removed outlier: 3.590A pdb=" N THR4N 93 " --> pdb=" O LEU4N 89 " (cutoff:3.500A) Processing helix chain '5A' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR5A 46 " --> pdb=" O THR5A 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP5A 47 " --> pdb=" O TRP5A 43 " (cutoff:3.500A) Proline residue: 5A 49 - end of helix Processing helix chain '5A' and resid 70 through 84 Proline residue: 5A 74 - end of helix removed outlier: 3.502A pdb=" N ILE5A 83 " --> pdb=" O LEU5A 80 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY5A 84 " --> pdb=" O ILE5A 81 " (cutoff:3.500A) Processing helix chain '5A' and resid 86 through 93 removed outlier: 3.590A pdb=" N THR5A 93 " --> pdb=" O LEU5A 89 " (cutoff:3.500A) Processing helix chain '5B' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR5B 46 " --> pdb=" O THR5B 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP5B 47 " --> pdb=" O TRP5B 43 " (cutoff:3.500A) Proline residue: 5B 49 - end of helix Processing helix chain '5B' and resid 70 through 84 Proline residue: 5B 74 - end of helix removed outlier: 3.502A pdb=" N ILE5B 83 " --> pdb=" O LEU5B 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY5B 84 " --> pdb=" O ILE5B 81 " (cutoff:3.500A) Processing helix chain '5B' and resid 86 through 93 removed outlier: 3.589A pdb=" N THR5B 93 " --> pdb=" O LEU5B 89 " (cutoff:3.500A) Processing helix chain '5C' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR5C 46 " --> pdb=" O THR5C 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP5C 47 " --> pdb=" O TRP5C 43 " (cutoff:3.500A) Proline residue: 5C 49 - end of helix Processing helix chain '5C' and resid 70 through 84 Proline residue: 5C 74 - end of helix removed outlier: 3.502A pdb=" N ILE5C 83 " --> pdb=" O LEU5C 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY5C 84 " --> pdb=" O ILE5C 81 " (cutoff:3.500A) Processing helix chain '5C' and resid 86 through 93 removed outlier: 3.589A pdb=" N THR5C 93 " --> pdb=" O LEU5C 89 " (cutoff:3.500A) Processing helix chain '5D' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR5D 46 " --> pdb=" O THR5D 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP5D 47 " --> pdb=" O TRP5D 43 " (cutoff:3.500A) Proline residue: 5D 49 - end of helix Processing helix chain '5D' and resid 70 through 84 Proline residue: 5D 74 - end of helix removed outlier: 3.502A pdb=" N ILE5D 83 " --> pdb=" O LEU5D 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY5D 84 " --> pdb=" O ILE5D 81 " (cutoff:3.500A) Processing helix chain '5D' and resid 86 through 93 removed outlier: 3.589A pdb=" N THR5D 93 " --> pdb=" O LEU5D 89 " (cutoff:3.500A) Processing helix chain '5E' and resid 34 through 64 removed outlier: 3.646A pdb=" N THR5E 46 " --> pdb=" O THR5E 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP5E 47 " --> pdb=" O TRP5E 43 " (cutoff:3.500A) Proline residue: 5E 49 - end of helix Processing helix chain '5E' and resid 70 through 84 Proline residue: 5E 74 - end of helix removed outlier: 3.502A pdb=" N ILE5E 83 " --> pdb=" O LEU5E 80 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY5E 84 " --> pdb=" O ILE5E 81 " (cutoff:3.500A) Processing helix chain '5E' and resid 86 through 93 removed outlier: 3.589A pdb=" N THR5E 93 " --> pdb=" O LEU5E 89 " (cutoff:3.500A) Processing helix chain '5F' and resid 34 through 64 removed outlier: 3.644A pdb=" N THR5F 46 " --> pdb=" O THR5F 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP5F 47 " --> pdb=" O TRP5F 43 " (cutoff:3.500A) Proline residue: 5F 49 - end of helix Processing helix chain '5F' and resid 70 through 84 Proline residue: 5F 74 - end of helix removed outlier: 3.501A pdb=" N ILE5F 83 " --> pdb=" O LEU5F 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY5F 84 " --> pdb=" O ILE5F 81 " (cutoff:3.500A) Processing helix chain '5F' and resid 86 through 93 removed outlier: 3.590A pdb=" N THR5F 93 " --> pdb=" O LEU5F 89 " (cutoff:3.500A) Processing helix chain '5G' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR5G 46 " --> pdb=" O THR5G 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP5G 47 " --> pdb=" O TRP5G 43 " (cutoff:3.500A) Proline residue: 5G 49 - end of helix Processing helix chain '5G' and resid 70 through 84 Proline residue: 5G 74 - end of helix removed outlier: 3.501A pdb=" N ILE5G 83 " --> pdb=" O LEU5G 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY5G 84 " --> pdb=" O ILE5G 81 " (cutoff:3.500A) Processing helix chain '5G' and resid 86 through 93 removed outlier: 3.590A pdb=" N THR5G 93 " --> pdb=" O LEU5G 89 " (cutoff:3.500A) Processing helix chain '5H' and resid 34 through 64 removed outlier: 3.644A pdb=" N THR5H 46 " --> pdb=" O THR5H 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP5H 47 " --> pdb=" O TRP5H 43 " (cutoff:3.500A) Proline residue: 5H 49 - end of helix Processing helix chain '5H' and resid 70 through 84 Proline residue: 5H 74 - end of helix removed outlier: 3.501A pdb=" N ILE5H 83 " --> pdb=" O LEU5H 80 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY5H 84 " --> pdb=" O ILE5H 81 " (cutoff:3.500A) Processing helix chain '5H' and resid 86 through 93 removed outlier: 3.589A pdb=" N THR5H 93 " --> pdb=" O LEU5H 89 " (cutoff:3.500A) Processing helix chain '5I' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR5I 46 " --> pdb=" O THR5I 42 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TRP5I 47 " --> pdb=" O TRP5I 43 " (cutoff:3.500A) Proline residue: 5I 49 - end of helix Processing helix chain '5I' and resid 70 through 84 Proline residue: 5I 74 - end of helix removed outlier: 3.502A pdb=" N ILE5I 83 " --> pdb=" O LEU5I 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY5I 84 " --> pdb=" O ILE5I 81 " (cutoff:3.500A) Processing helix chain '5I' and resid 86 through 93 removed outlier: 3.589A pdb=" N THR5I 93 " --> pdb=" O LEU5I 89 " (cutoff:3.500A) Processing helix chain '5J' and resid 34 through 64 removed outlier: 3.646A pdb=" N THR5J 46 " --> pdb=" O THR5J 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP5J 47 " --> pdb=" O TRP5J 43 " (cutoff:3.500A) Proline residue: 5J 49 - end of helix Processing helix chain '5J' and resid 70 through 84 Proline residue: 5J 74 - end of helix removed outlier: 3.501A pdb=" N ILE5J 83 " --> pdb=" O LEU5J 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY5J 84 " --> pdb=" O ILE5J 81 " (cutoff:3.500A) Processing helix chain '5J' and resid 86 through 93 removed outlier: 3.589A pdb=" N THR5J 93 " --> pdb=" O LEU5J 89 " (cutoff:3.500A) Processing helix chain '5K' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR5K 46 " --> pdb=" O THR5K 42 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TRP5K 47 " --> pdb=" O TRP5K 43 " (cutoff:3.500A) Proline residue: 5K 49 - end of helix Processing helix chain '5K' and resid 70 through 84 Proline residue: 5K 74 - end of helix removed outlier: 3.502A pdb=" N ILE5K 83 " --> pdb=" O LEU5K 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY5K 84 " --> pdb=" O ILE5K 81 " (cutoff:3.500A) Processing helix chain '5K' and resid 86 through 93 removed outlier: 3.589A pdb=" N THR5K 93 " --> pdb=" O LEU5K 89 " (cutoff:3.500A) Processing helix chain '5L' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR5L 46 " --> pdb=" O THR5L 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP5L 47 " --> pdb=" O TRP5L 43 " (cutoff:3.500A) Proline residue: 5L 49 - end of helix Processing helix chain '5L' and resid 70 through 84 Proline residue: 5L 74 - end of helix removed outlier: 3.501A pdb=" N ILE5L 83 " --> pdb=" O LEU5L 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY5L 84 " --> pdb=" O ILE5L 81 " (cutoff:3.500A) Processing helix chain '5L' and resid 86 through 93 removed outlier: 3.590A pdb=" N THR5L 93 " --> pdb=" O LEU5L 89 " (cutoff:3.500A) Processing helix chain '5M' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR5M 46 " --> pdb=" O THR5M 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP5M 47 " --> pdb=" O TRP5M 43 " (cutoff:3.500A) Proline residue: 5M 49 - end of helix Processing helix chain '5M' and resid 70 through 84 Proline residue: 5M 74 - end of helix removed outlier: 3.502A pdb=" N ILE5M 83 " --> pdb=" O LEU5M 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY5M 84 " --> pdb=" O ILE5M 81 " (cutoff:3.500A) Processing helix chain '5M' and resid 86 through 93 removed outlier: 3.589A pdb=" N THR5M 93 " --> pdb=" O LEU5M 89 " (cutoff:3.500A) Processing helix chain '5N' and resid 34 through 64 removed outlier: 3.645A pdb=" N THR5N 46 " --> pdb=" O THR5N 42 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP5N 47 " --> pdb=" O TRP5N 43 " (cutoff:3.500A) Proline residue: 5N 49 - end of helix Processing helix chain '5N' and resid 70 through 84 Proline residue: 5N 74 - end of helix removed outlier: 3.502A pdb=" N ILE5N 83 " --> pdb=" O LEU5N 80 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY5N 84 " --> pdb=" O ILE5N 81 " (cutoff:3.500A) Processing helix chain '5N' and resid 86 through 93 removed outlier: 3.589A pdb=" N THR5N 93 " --> pdb=" O LEU5N 89 " (cutoff:3.500A) 2240 hydrogen bonds defined for protein. 5250 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: 11.12 Time building geometry restraints manager: 14.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5461 1.32 - 1.44: 10359 1.44 - 1.56: 23520 1.56 - 1.68: 140 1.68 - 1.80: 560 Bond restraints: 40040 Sorted by residual: bond pdb=" C03 PGW5I 101 " pdb=" O11 PGW5I 101 " ideal model delta sigma weight residual 1.412 1.453 -0.041 2.00e-02 2.50e+03 4.11e+00 bond pdb=" C03 PGW2D 102 " pdb=" O11 PGW2D 102 " ideal model delta sigma weight residual 1.412 1.452 -0.040 2.00e-02 2.50e+03 4.06e+00 bond pdb=" C03 PGW3J 101 " pdb=" O11 PGW3J 101 " ideal model delta sigma weight residual 1.412 1.452 -0.040 2.00e-02 2.50e+03 4.06e+00 bond pdb=" C03 PGW4L 101 " pdb=" O11 PGW4L 101 " ideal model delta sigma weight residual 1.412 1.452 -0.040 2.00e-02 2.50e+03 4.03e+00 bond pdb=" C03 PGW5N 101 " pdb=" O11 PGW5N 101 " ideal model delta sigma weight residual 1.412 1.452 -0.040 2.00e-02 2.50e+03 4.03e+00 ... (remaining 40035 not shown) Histogram of bond angle deviations from ideal: 100.68 - 107.35: 1680 107.35 - 114.02: 24586 114.02 - 120.69: 16627 120.69 - 127.36: 10447 127.36 - 134.04: 630 Bond angle restraints: 53970 Sorted by residual: angle pdb=" O11 PGW4D 101 " pdb=" P PGW4D 101 " pdb=" O13 PGW4D 101 " ideal model delta sigma weight residual 111.26 102.76 8.50 3.00e+00 1.11e-01 8.03e+00 angle pdb=" O11 PGW4F 101 " pdb=" P PGW4F 101 " pdb=" O13 PGW4F 101 " ideal model delta sigma weight residual 111.26 102.76 8.50 3.00e+00 1.11e-01 8.02e+00 angle pdb=" O11 PGW1M 101 " pdb=" P PGW1M 101 " pdb=" O13 PGW1M 101 " ideal model delta sigma weight residual 111.26 102.76 8.50 3.00e+00 1.11e-01 8.02e+00 angle pdb=" O11 PGW4N 101 " pdb=" P PGW4N 101 " pdb=" O13 PGW4N 101 " ideal model delta sigma weight residual 111.26 102.77 8.49 3.00e+00 1.11e-01 8.01e+00 angle pdb=" O11 PGW2D 102 " pdb=" P PGW2D 102 " pdb=" O13 PGW2D 102 " ideal model delta sigma weight residual 111.26 102.77 8.49 3.00e+00 1.11e-01 8.01e+00 ... (remaining 53965 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.76: 22400 35.76 - 71.51: 910 71.51 - 107.27: 420 107.27 - 143.03: 280 143.03 - 178.79: 70 Dihedral angle restraints: 24080 sinusoidal: 10360 harmonic: 13720 Sorted by residual: dihedral pdb=" C07 PGW1B 102 " pdb=" C06 PGW1B 102 " pdb=" C10 PGW1B 102 " pdb=" C9 PGW1B 102 " ideal model delta sinusoidal sigma weight residual 110.06 -68.73 178.79 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C07 PGW2E 101 " pdb=" C06 PGW2E 101 " pdb=" C10 PGW2E 101 " pdb=" C9 PGW2E 101 " ideal model delta sinusoidal sigma weight residual 110.06 -68.72 178.78 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C07 PGW5N 101 " pdb=" C06 PGW5N 101 " pdb=" C10 PGW5N 101 " pdb=" C9 PGW5N 101 " ideal model delta sinusoidal sigma weight residual 110.06 -68.72 178.78 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 24077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 3064 0.022 - 0.044: 2301 0.044 - 0.066: 652 0.066 - 0.088: 213 0.088 - 0.111: 280 Chirality restraints: 6510 Sorted by residual: chirality pdb=" CA PRO5L 74 " pdb=" N PRO5L 74 " pdb=" C PRO5L 74 " pdb=" CB PRO5L 74 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.06e-01 chirality pdb=" CA PRO4L 74 " pdb=" N PRO4L 74 " pdb=" C PRO4L 74 " pdb=" CB PRO4L 74 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.05e-01 chirality pdb=" CA PRO3D 49 " pdb=" N PRO3D 49 " pdb=" C PRO3D 49 " pdb=" CB PRO3D 49 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.05e-01 ... (remaining 6507 not shown) Planarity restraints: 6020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C06 PGW1N 101 " 0.103 2.00e-02 2.50e+03 2.38e-01 5.67e+02 pdb=" C10 PGW1N 101 " -0.321 2.00e-02 2.50e+03 pdb=" C8 PGW1N 101 " -0.102 2.00e-02 2.50e+03 pdb=" C9 PGW1N 101 " 0.320 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW5L 101 " 0.103 2.00e-02 2.50e+03 2.38e-01 5.67e+02 pdb=" C10 PGW5L 101 " -0.322 2.00e-02 2.50e+03 pdb=" C8 PGW5L 101 " -0.102 2.00e-02 2.50e+03 pdb=" C9 PGW5L 101 " 0.320 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW5B 101 " 0.103 2.00e-02 2.50e+03 2.38e-01 5.67e+02 pdb=" C10 PGW5B 101 " -0.321 2.00e-02 2.50e+03 pdb=" C8 PGW5B 101 " -0.102 2.00e-02 2.50e+03 pdb=" C9 PGW5B 101 " 0.320 2.00e-02 2.50e+03 ... (remaining 6017 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 290 2.67 - 3.23: 38649 3.23 - 3.78: 57537 3.78 - 4.34: 87519 4.34 - 4.90: 140018 Nonbonded interactions: 324013 Sorted by model distance: nonbonded pdb=" O TRP3A 43 " pdb=" OG1 THR3A 46 " model vdw 2.109 2.440 nonbonded pdb=" O TRP4K 43 " pdb=" OG1 THR4K 46 " model vdw 2.109 2.440 nonbonded pdb=" O TRP2G 43 " pdb=" OG1 THR2G 46 " model vdw 2.109 2.440 nonbonded pdb=" O TRP3G 43 " pdb=" OG1 THR3G 46 " model vdw 2.109 2.440 nonbonded pdb=" O TRP1E 43 " pdb=" OG1 THR1E 46 " model vdw 2.109 2.440 ... (remaining 324008 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 '1A' selection = (chain '1B' and resid 28 through 97) selection = (chain '1C' and resid 28 through 97) selection = (chain '1D' and resid 28 through 97) selection = (chain '1E' and resid 28 through 97) selection = (chain '1F' and resid 28 through 97) selection = (chain '1G' and resid 28 through 97) selection = (chain '1H' and resid 28 through 97) selection = (chain '1I' and resid 28 through 97) selection = (chain '1J' and resid 28 through 97) selection = (chain '1K' and resid 28 through 97) selection = (chain '1L' and resid 28 through 97) selection = (chain '1M' and resid 28 through 97) selection = (chain '1N' and resid 28 through 97) selection = chain '2A' selection = (chain '2B' and resid 28 through 97) selection = (chain '2C' and resid 28 through 97) selection = (chain '2D' and resid 28 through 97) selection = (chain '2E' and resid 28 through 97) selection = (chain '2F' and resid 28 through 97) selection = (chain '2G' and resid 28 through 97) selection = (chain '2H' and resid 28 through 97) selection = (chain '2I' and resid 28 through 97) selection = (chain '2J' and resid 28 through 97) selection = (chain '2K' and resid 28 through 97) selection = (chain '2L' and resid 28 through 97) selection = (chain '2M' and resid 28 through 97) selection = (chain '2N' and resid 28 through 97) selection = chain '3A' selection = (chain '3B' and resid 28 through 97) selection = (chain '3C' and resid 28 through 97) selection = (chain '3D' and resid 28 through 97) selection = (chain '3E' and resid 28 through 97) selection = (chain '3F' and resid 28 through 97) selection = (chain '3G' and resid 28 through 97) selection = (chain '3H' and resid 28 through 97) selection = (chain '3I' and resid 28 through 97) selection = (chain '3J' and resid 28 through 97) selection = (chain '3K' and resid 28 through 97) selection = (chain '3L' and resid 28 through 97) selection = (chain '3M' and resid 28 through 97) selection = (chain '3N' and resid 28 through 97) selection = chain '4A' selection = (chain '4B' and resid 28 through 97) selection = (chain '4C' and resid 28 through 97) selection = (chain '4D' and resid 28 through 97) selection = (chain '4E' and resid 28 through 97) selection = (chain '4F' and resid 28 through 97) selection = (chain '4G' and resid 28 through 97) selection = (chain '4H' and resid 28 through 97) selection = (chain '4I' and resid 28 through 97) selection = (chain '4J' and resid 28 through 97) selection = (chain '4K' and resid 28 through 97) selection = (chain '4L' and resid 28 through 97) selection = (chain '4M' and resid 28 through 97) selection = (chain '4N' and resid 28 through 97) selection = chain '5A' selection = (chain '5B' and resid 28 through 97) selection = (chain '5C' and resid 28 through 97) selection = (chain '5D' and resid 28 through 97) selection = (chain '5E' and resid 28 through 97) selection = (chain '5F' and resid 28 through 97) selection = (chain '5G' and resid 28 through 97) selection = (chain '5H' and resid 28 through 97) selection = (chain '5I' and resid 28 through 97) selection = (chain '5J' and resid 28 through 97) selection = (chain '5K' and resid 28 through 97) selection = (chain '5L' and resid 28 through 97) selection = (chain '5M' and resid 28 through 97) selection = (chain '5N' and resid 28 through 97) } 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=1.00 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: 1.170 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: 0.030 Extract box with map and model: 5.890 Check model and map are aligned: 0.520 Set scattering table: 0.310 Process input model: 88.650 Find NCS groups from input model: 3.110 Set up NCS constraints: 0.730 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 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 : 0.007 0.041 40040 Z= 0.410 Angle : 0.795 8.504 53970 Z= 0.335 Chirality : 0.038 0.111 6510 Planarity : 0.026 0.238 6020 Dihedral : 28.783 178.787 15260 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.21 (0.12), residues: 4760 helix: 2.48 (0.08), residues: 3710 sheet: None (None), residues: 0 loop : -2.50 (0.17), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP1G 47 HIS 0.001 0.000 HIS1K 66 PHE 0.003 0.001 PHE1H 72 TYR 0.003 0.001 TYR5E 88 ARG 0.004 0.002 ARG5J 75 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 506 time to evaluate : 4.174 Fit side-chains revert: symmetry clash REVERT: 1A 56 ILE cc_start: 0.8454 (mt) cc_final: 0.8215 (pt) REVERT: 1F 57 MET cc_start: 0.9017 (ttp) cc_final: 0.8809 (ttp) REVERT: 1L 57 MET cc_start: 0.9022 (ttp) cc_final: 0.8764 (ttm) REVERT: 2B 88 TYR cc_start: 0.9072 (t80) cc_final: 0.8849 (t80) REVERT: 2G 64 MET cc_start: 0.8838 (ttm) cc_final: 0.8574 (ttp) REVERT: 2H 64 MET cc_start: 0.8877 (ttm) cc_final: 0.8604 (ttp) REVERT: 2L 64 MET cc_start: 0.8775 (ttm) cc_final: 0.8555 (ttp) REVERT: 2N 57 MET cc_start: 0.8605 (ttp) cc_final: 0.8259 (ttm) REVERT: 3H 30 THR cc_start: 0.8975 (p) cc_final: 0.8727 (p) REVERT: 3J 64 MET cc_start: 0.8866 (ttm) cc_final: 0.8650 (ttp) REVERT: 3L 57 MET cc_start: 0.8955 (ttp) cc_final: 0.8741 (ttm) REVERT: 3N 88 TYR cc_start: 0.9141 (t80) cc_final: 0.8851 (t80) REVERT: 4L 57 MET cc_start: 0.8930 (ttp) cc_final: 0.8715 (ttm) REVERT: 5A 56 ILE cc_start: 0.8378 (mt) cc_final: 0.8088 (pt) REVERT: 5C 30 THR cc_start: 0.8874 (p) cc_final: 0.8591 (p) REVERT: 5F 57 MET cc_start: 0.8886 (ttp) cc_final: 0.8559 (ttm) REVERT: 5I 57 MET cc_start: 0.8925 (ttp) cc_final: 0.8655 (ttm) REVERT: 5L 62 MET cc_start: 0.8747 (mmp) cc_final: 0.8524 (mmp) outliers start: 0 outliers final: 0 residues processed: 506 average time/residue: 1.4993 time to fit residues: 918.5696 Evaluate side-chains 397 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 397 time to evaluate : 3.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 413 optimal weight: 10.0000 chunk 371 optimal weight: 0.0270 chunk 206 optimal weight: 1.9990 chunk 126 optimal weight: 9.9990 chunk 250 optimal weight: 0.9980 chunk 198 optimal weight: 3.9990 chunk 384 optimal weight: 1.9990 chunk 148 optimal weight: 0.8980 chunk 233 optimal weight: 6.9990 chunk 285 optimal weight: 3.9990 chunk 444 optimal weight: 0.9980 overall best weight: 0.9840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1G 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 40040 Z= 0.169 Angle : 0.497 5.135 53970 Z= 0.250 Chirality : 0.041 0.130 6510 Planarity : 0.006 0.042 6020 Dihedral : 26.195 83.451 8260 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.58 % Allowed : 6.62 % Favored : 92.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.06 (0.12), residues: 4760 helix: 2.11 (0.08), residues: 3780 sheet: None (None), residues: 0 loop : -1.69 (0.21), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP5A 47 HIS 0.008 0.001 HIS1B 66 PHE 0.006 0.002 PHE2A 61 TYR 0.009 0.001 TYR4N 88 ARG 0.003 0.001 ARG1F 75 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 523 time to evaluate : 3.849 Fit side-chains REVERT: 2N 57 MET cc_start: 0.8560 (ttp) cc_final: 0.8240 (ttm) REVERT: 3A 57 MET cc_start: 0.7106 (ttp) cc_final: 0.6899 (ttm) REVERT: 3H 30 THR cc_start: 0.8965 (p) cc_final: 0.8754 (p) REVERT: 5C 30 THR cc_start: 0.8889 (p) cc_final: 0.8582 (p) REVERT: 5L 62 MET cc_start: 0.8720 (mmp) cc_final: 0.8481 (mmp) outliers start: 23 outliers final: 5 residues processed: 533 average time/residue: 1.0601 time to fit residues: 734.9251 Evaluate side-chains 453 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 448 time to evaluate : 3.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1B residue 45 SER Chi-restraints excluded: chain 2B residue 45 SER Chi-restraints excluded: chain 3B residue 45 SER Chi-restraints excluded: chain 4B residue 45 SER Chi-restraints excluded: chain 5B residue 48 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 247 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 chunk 370 optimal weight: 6.9990 chunk 303 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 445 optimal weight: 0.0070 chunk 481 optimal weight: 0.0970 chunk 397 optimal weight: 6.9990 chunk 442 optimal weight: 0.9990 chunk 151 optimal weight: 0.3980 chunk 357 optimal weight: 0.7980 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 40040 Z= 0.146 Angle : 0.412 5.462 53970 Z= 0.202 Chirality : 0.039 0.120 6510 Planarity : 0.004 0.030 6020 Dihedral : 23.360 89.983 8260 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.33 % Allowed : 8.97 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.18 (0.13), residues: 4760 helix: 2.15 (0.08), residues: 3780 sheet: None (None), residues: 0 loop : -1.48 (0.21), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP5F 47 HIS 0.008 0.001 HIS5B 66 PHE 0.003 0.001 PHE3E 61 TYR 0.012 0.000 TYR4N 88 ARG 0.003 0.000 ARG5A 75 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 496 time to evaluate : 3.466 Fit side-chains REVERT: 2N 57 MET cc_start: 0.8539 (ttp) cc_final: 0.8246 (ttm) REVERT: 3N 88 TYR cc_start: 0.9006 (t80) cc_final: 0.8672 (t80) REVERT: 4I 64 MET cc_start: 0.8719 (ttm) cc_final: 0.8266 (ttm) REVERT: 5C 30 THR cc_start: 0.8831 (p) cc_final: 0.8528 (p) REVERT: 5H 62 MET cc_start: 0.8643 (mmp) cc_final: 0.8353 (mmp) REVERT: 5L 62 MET cc_start: 0.8730 (mmp) cc_final: 0.8490 (mmp) outliers start: 53 outliers final: 38 residues processed: 529 average time/residue: 1.0881 time to fit residues: 743.1838 Evaluate side-chains 513 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 475 time to evaluate : 3.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1D residue 91 SER Chi-restraints excluded: chain 1E residue 91 SER Chi-restraints excluded: chain 1G residue 91 SER Chi-restraints excluded: chain 1L residue 62 MET Chi-restraints excluded: chain 1L residue 91 SER Chi-restraints excluded: chain 2A residue 30 THR Chi-restraints excluded: chain 2A residue 45 SER Chi-restraints excluded: chain 2B residue 45 SER Chi-restraints excluded: chain 2B residue 59 SER Chi-restraints excluded: chain 2D residue 91 SER Chi-restraints excluded: chain 2E residue 91 SER Chi-restraints excluded: chain 2F residue 91 SER Chi-restraints excluded: chain 3A residue 30 THR Chi-restraints excluded: chain 3A residue 45 SER Chi-restraints excluded: chain 3B residue 45 SER Chi-restraints excluded: chain 3C residue 91 SER Chi-restraints excluded: chain 3D residue 91 SER Chi-restraints excluded: chain 3E residue 91 SER Chi-restraints excluded: chain 3F residue 91 SER Chi-restraints excluded: chain 3G residue 91 SER Chi-restraints excluded: chain 3H residue 91 SER Chi-restraints excluded: chain 3I residue 91 SER Chi-restraints excluded: chain 3J residue 91 SER Chi-restraints excluded: chain 4B residue 45 SER Chi-restraints excluded: chain 4E residue 91 SER Chi-restraints excluded: chain 4F residue 91 SER Chi-restraints excluded: chain 4G residue 91 SER Chi-restraints excluded: chain 4I residue 91 SER Chi-restraints excluded: chain 4L residue 91 SER Chi-restraints excluded: chain 5A residue 30 THR Chi-restraints excluded: chain 5B residue 48 ILE Chi-restraints excluded: chain 5C residue 45 SER Chi-restraints excluded: chain 5D residue 91 SER Chi-restraints excluded: chain 5E residue 91 SER Chi-restraints excluded: chain 5F residue 91 SER Chi-restraints excluded: chain 5H residue 91 SER Chi-restraints excluded: chain 5I residue 91 SER Chi-restraints excluded: chain 5J residue 91 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 440 optimal weight: 5.9990 chunk 335 optimal weight: 0.2980 chunk 231 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 212 optimal weight: 2.9990 chunk 299 optimal weight: 8.9990 chunk 447 optimal weight: 5.9990 chunk 473 optimal weight: 0.8980 chunk 233 optimal weight: 1.9990 chunk 424 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1C 66 HIS 1G 66 HIS 2A 41 GLN 2E 66 HIS 2H 66 HIS 3A 41 GLN 3E 66 HIS 3J 66 HIS 4D 66 HIS 5E 66 HIS 5G 66 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 40040 Z= 0.242 Angle : 0.491 5.564 53970 Z= 0.240 Chirality : 0.041 0.131 6510 Planarity : 0.005 0.029 6020 Dihedral : 22.074 87.311 8260 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.15 % Allowed : 9.22 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.13), residues: 4760 helix: 1.95 (0.09), residues: 3780 sheet: None (None), residues: 0 loop : -1.61 (0.21), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP5D 47 HIS 0.006 0.001 HIS1K 66 PHE 0.006 0.001 PHE3B 61 TYR 0.007 0.001 TYR5N 88 ARG 0.006 0.001 ARG3J 75 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 475 time to evaluate : 3.276 Fit side-chains REVERT: 1A 75 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.6636 (ttp80) REVERT: 2A 75 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.6479 (ttp80) REVERT: 2N 57 MET cc_start: 0.8626 (ttp) cc_final: 0.8339 (ttm) REVERT: 3D 71 SER cc_start: 0.9009 (p) cc_final: 0.8688 (m) REVERT: 3M 91 SER cc_start: 0.9160 (t) cc_final: 0.8771 (p) REVERT: 3N 88 TYR cc_start: 0.9025 (t80) cc_final: 0.8715 (t80) REVERT: 5C 30 THR cc_start: 0.8842 (p) cc_final: 0.8528 (p) REVERT: 5H 62 MET cc_start: 0.8651 (mmp) cc_final: 0.8423 (mmp) outliers start: 46 outliers final: 32 residues processed: 503 average time/residue: 1.1530 time to fit residues: 743.3716 Evaluate side-chains 482 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 448 time to evaluate : 3.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 75 ARG Chi-restraints excluded: chain 1B residue 45 SER Chi-restraints excluded: chain 1B residue 91 SER Chi-restraints excluded: chain 1E residue 91 SER Chi-restraints excluded: chain 1G residue 91 SER Chi-restraints excluded: chain 1H residue 91 SER Chi-restraints excluded: chain 1L residue 91 SER Chi-restraints excluded: chain 2A residue 30 THR Chi-restraints excluded: chain 2A residue 45 SER Chi-restraints excluded: chain 2A residue 75 ARG Chi-restraints excluded: chain 2A residue 80 LEU Chi-restraints excluded: chain 2B residue 45 SER Chi-restraints excluded: chain 2B residue 59 SER Chi-restraints excluded: chain 2E residue 91 SER Chi-restraints excluded: chain 2F residue 91 SER Chi-restraints excluded: chain 3A residue 30 THR Chi-restraints excluded: chain 3A residue 45 SER Chi-restraints excluded: chain 3B residue 45 SER Chi-restraints excluded: chain 3B residue 91 SER Chi-restraints excluded: chain 3E residue 91 SER Chi-restraints excluded: chain 3F residue 91 SER Chi-restraints excluded: chain 3H residue 91 SER Chi-restraints excluded: chain 4A residue 30 THR Chi-restraints excluded: chain 4B residue 45 SER Chi-restraints excluded: chain 4B residue 59 SER Chi-restraints excluded: chain 4E residue 91 SER Chi-restraints excluded: chain 4F residue 91 SER Chi-restraints excluded: chain 5A residue 30 THR Chi-restraints excluded: chain 5B residue 45 SER Chi-restraints excluded: chain 5B residue 48 ILE Chi-restraints excluded: chain 5B residue 91 SER Chi-restraints excluded: chain 5C residue 45 SER Chi-restraints excluded: chain 5F residue 91 SER Chi-restraints excluded: chain 5H residue 91 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 394 optimal weight: 4.9990 chunk 268 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 352 optimal weight: 1.9990 chunk 195 optimal weight: 3.9990 chunk 404 optimal weight: 3.9990 chunk 327 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 241 optimal weight: 0.6980 chunk 425 optimal weight: 7.9990 chunk 119 optimal weight: 0.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1E 66 HIS 1F 66 HIS 2A 41 GLN 2H 66 HIS 3A 41 GLN 3L 66 HIS 4D 66 HIS 4E 66 HIS 5E 66 HIS 5G 66 HIS 5L 66 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 40040 Z= 0.183 Angle : 0.452 5.376 53970 Z= 0.217 Chirality : 0.040 0.120 6510 Planarity : 0.004 0.028 6020 Dihedral : 19.242 86.703 8260 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.95 % Allowed : 10.10 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.13), residues: 4760 helix: 1.95 (0.09), residues: 3780 sheet: None (None), residues: 0 loop : -1.55 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP1F 47 HIS 0.006 0.001 HIS5B 66 PHE 0.004 0.001 PHE3H 72 TYR 0.007 0.001 TYR4N 88 ARG 0.003 0.001 ARG2J 75 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 470 time to evaluate : 4.073 Fit side-chains REVERT: 1A 75 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.6722 (ttp80) REVERT: 2A 75 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.6537 (ttp80) REVERT: 2N 57 MET cc_start: 0.8647 (ttp) cc_final: 0.8397 (ttm) REVERT: 3D 71 SER cc_start: 0.8987 (p) cc_final: 0.8670 (m) REVERT: 3N 88 TYR cc_start: 0.9031 (t80) cc_final: 0.8711 (t80) REVERT: 4B 75 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.7107 (ttm110) REVERT: 4E 66 HIS cc_start: 0.8478 (m90) cc_final: 0.8248 (m90) REVERT: 5C 30 THR cc_start: 0.8836 (p) cc_final: 0.8518 (p) REVERT: 5H 62 MET cc_start: 0.8643 (mmp) cc_final: 0.8420 (mmp) outliers start: 38 outliers final: 29 residues processed: 492 average time/residue: 1.1346 time to fit residues: 711.7192 Evaluate side-chains 484 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 452 time to evaluate : 4.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 75 ARG Chi-restraints excluded: chain 1B residue 45 SER Chi-restraints excluded: chain 1B residue 91 SER Chi-restraints excluded: chain 1E residue 91 SER Chi-restraints excluded: chain 2A residue 30 THR Chi-restraints excluded: chain 2A residue 45 SER Chi-restraints excluded: chain 2A residue 75 ARG Chi-restraints excluded: chain 2A residue 80 LEU Chi-restraints excluded: chain 2B residue 45 SER Chi-restraints excluded: chain 2B residue 59 SER Chi-restraints excluded: chain 2C residue 79 SER Chi-restraints excluded: chain 2E residue 91 SER Chi-restraints excluded: chain 2F residue 91 SER Chi-restraints excluded: chain 2G residue 91 SER Chi-restraints excluded: chain 3A residue 30 THR Chi-restraints excluded: chain 3B residue 45 SER Chi-restraints excluded: chain 3B residue 91 SER Chi-restraints excluded: chain 3C residue 91 SER Chi-restraints excluded: chain 3E residue 91 SER Chi-restraints excluded: chain 3G residue 91 SER Chi-restraints excluded: chain 3H residue 30 THR Chi-restraints excluded: chain 4A residue 30 THR Chi-restraints excluded: chain 4B residue 45 SER Chi-restraints excluded: chain 4B residue 75 ARG Chi-restraints excluded: chain 4E residue 91 SER Chi-restraints excluded: chain 4L residue 91 SER Chi-restraints excluded: chain 4M residue 79 SER Chi-restraints excluded: chain 5A residue 30 THR Chi-restraints excluded: chain 5B residue 45 SER Chi-restraints excluded: chain 5B residue 48 ILE Chi-restraints excluded: chain 5B residue 64 MET Chi-restraints excluded: chain 5E residue 91 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 159 optimal weight: 0.8980 chunk 426 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 278 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 474 optimal weight: 0.8980 chunk 393 optimal weight: 5.9990 chunk 219 optimal weight: 4.9990 chunk 39 optimal weight: 0.0980 chunk 156 optimal weight: 2.9990 chunk 248 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2A 41 GLN 2H 66 HIS 3A 41 GLN 5G 66 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 40040 Z= 0.145 Angle : 0.418 5.819 53970 Z= 0.204 Chirality : 0.039 0.120 6510 Planarity : 0.004 0.028 6020 Dihedral : 17.971 88.716 8260 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.78 % Allowed : 10.75 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.13), residues: 4760 helix: 2.01 (0.09), residues: 3780 sheet: None (None), residues: 0 loop : -1.53 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP3F 47 HIS 0.003 0.001 HIS1K 66 PHE 0.004 0.001 PHE1C 61 TYR 0.005 0.001 TYR5N 88 ARG 0.002 0.000 ARG1H 75 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 479 time to evaluate : 4.345 Fit side-chains REVERT: 2N 57 MET cc_start: 0.8618 (ttp) cc_final: 0.8369 (ttm) REVERT: 3B 41 GLN cc_start: 0.9177 (tt0) cc_final: 0.8964 (tt0) REVERT: 3D 71 SER cc_start: 0.8936 (p) cc_final: 0.8668 (m) REVERT: 3N 88 TYR cc_start: 0.9035 (t80) cc_final: 0.8725 (t80) REVERT: 4B 75 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.7204 (ttm110) REVERT: 4I 64 MET cc_start: 0.8742 (ttm) cc_final: 0.8478 (ttm) REVERT: 5C 30 THR cc_start: 0.8820 (p) cc_final: 0.8498 (p) REVERT: 5H 62 MET cc_start: 0.8622 (mmp) cc_final: 0.8385 (mmp) REVERT: 5K 71 SER cc_start: 0.9001 (p) cc_final: 0.8695 (m) outliers start: 31 outliers final: 21 residues processed: 490 average time/residue: 1.1128 time to fit residues: 700.3582 Evaluate side-chains 485 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 463 time to evaluate : 3.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1B residue 45 SER Chi-restraints excluded: chain 1B residue 91 SER Chi-restraints excluded: chain 1D residue 91 SER Chi-restraints excluded: chain 1G residue 91 SER Chi-restraints excluded: chain 2A residue 30 THR Chi-restraints excluded: chain 2A residue 45 SER Chi-restraints excluded: chain 2B residue 45 SER Chi-restraints excluded: chain 2B residue 59 SER Chi-restraints excluded: chain 2M residue 79 SER Chi-restraints excluded: chain 3A residue 30 THR Chi-restraints excluded: chain 3A residue 45 SER Chi-restraints excluded: chain 3B residue 45 SER Chi-restraints excluded: chain 3B residue 91 SER Chi-restraints excluded: chain 3F residue 91 SER Chi-restraints excluded: chain 4A residue 30 THR Chi-restraints excluded: chain 4B residue 75 ARG Chi-restraints excluded: chain 4K residue 91 SER Chi-restraints excluded: chain 4L residue 91 SER Chi-restraints excluded: chain 5A residue 30 THR Chi-restraints excluded: chain 5B residue 45 SER Chi-restraints excluded: chain 5B residue 48 ILE Chi-restraints excluded: chain 5E residue 91 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 457 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 270 optimal weight: 6.9990 chunk 346 optimal weight: 4.9990 chunk 268 optimal weight: 0.9990 chunk 399 optimal weight: 9.9990 chunk 264 optimal weight: 5.9990 chunk 472 optimal weight: 1.9990 chunk 295 optimal weight: 9.9990 chunk 287 optimal weight: 20.0000 chunk 218 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1F 66 HIS 2A 41 GLN 2H 66 HIS 3A 41 GLN 5A 41 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 40040 Z= 0.201 Angle : 0.454 6.358 53970 Z= 0.220 Chirality : 0.040 0.122 6510 Planarity : 0.004 0.026 6020 Dihedral : 17.990 89.959 8260 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.03 % Allowed : 10.48 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.13), residues: 4760 helix: 1.93 (0.09), residues: 3780 sheet: None (None), residues: 0 loop : -1.50 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP4D 47 HIS 0.005 0.001 HIS2B 66 PHE 0.004 0.001 PHE1C 61 TYR 0.007 0.001 TYR5N 88 ARG 0.003 0.001 ARG1H 75 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 464 time to evaluate : 3.530 Fit side-chains REVERT: 1D 71 SER cc_start: 0.9113 (OUTLIER) cc_final: 0.8545 (m) REVERT: 2A 75 ARG cc_start: 0.7393 (OUTLIER) cc_final: 0.6674 (ttp80) REVERT: 2N 57 MET cc_start: 0.8625 (ttp) cc_final: 0.8379 (ttm) REVERT: 3B 41 GLN cc_start: 0.9193 (tt0) cc_final: 0.8960 (tt0) REVERT: 3D 71 SER cc_start: 0.8970 (p) cc_final: 0.8708 (m) REVERT: 3N 88 TYR cc_start: 0.9056 (t80) cc_final: 0.8724 (t80) REVERT: 4B 75 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.7095 (ttm110) REVERT: 5K 71 SER cc_start: 0.9056 (p) cc_final: 0.8767 (m) outliers start: 41 outliers final: 33 residues processed: 490 average time/residue: 1.1202 time to fit residues: 701.6632 Evaluate side-chains 496 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 460 time to evaluate : 3.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1B residue 45 SER Chi-restraints excluded: chain 1B residue 91 SER Chi-restraints excluded: chain 1D residue 71 SER Chi-restraints excluded: chain 1D residue 91 SER Chi-restraints excluded: chain 1E residue 91 SER Chi-restraints excluded: chain 1G residue 91 SER Chi-restraints excluded: chain 2A residue 30 THR Chi-restraints excluded: chain 2A residue 45 SER Chi-restraints excluded: chain 2A residue 75 ARG Chi-restraints excluded: chain 2B residue 45 SER Chi-restraints excluded: chain 2B residue 59 SER Chi-restraints excluded: chain 2C residue 79 SER Chi-restraints excluded: chain 2E residue 91 SER Chi-restraints excluded: chain 2F residue 91 SER Chi-restraints excluded: chain 2G residue 91 SER Chi-restraints excluded: chain 2M residue 71 SER Chi-restraints excluded: chain 2M residue 79 SER Chi-restraints excluded: chain 3A residue 30 THR Chi-restraints excluded: chain 3A residue 45 SER Chi-restraints excluded: chain 3B residue 45 SER Chi-restraints excluded: chain 3B residue 91 SER Chi-restraints excluded: chain 3D residue 64 MET Chi-restraints excluded: chain 3E residue 91 SER Chi-restraints excluded: chain 3F residue 91 SER Chi-restraints excluded: chain 3G residue 91 SER Chi-restraints excluded: chain 3H residue 91 SER Chi-restraints excluded: chain 4A residue 30 THR Chi-restraints excluded: chain 4B residue 75 ARG Chi-restraints excluded: chain 4E residue 91 SER Chi-restraints excluded: chain 4K residue 91 SER Chi-restraints excluded: chain 4L residue 91 SER Chi-restraints excluded: chain 5A residue 30 THR Chi-restraints excluded: chain 5B residue 45 SER Chi-restraints excluded: chain 5B residue 48 ILE Chi-restraints excluded: chain 5E residue 91 SER Chi-restraints excluded: chain 5N residue 71 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 292 optimal weight: 0.5980 chunk 188 optimal weight: 0.9990 chunk 282 optimal weight: 3.9990 chunk 142 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 300 optimal weight: 8.9990 chunk 321 optimal weight: 3.9990 chunk 233 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 371 optimal weight: 0.0770 overall best weight: 0.9344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1F 66 HIS 2A 41 GLN 3A 41 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 40040 Z= 0.141 Angle : 0.414 6.735 53970 Z= 0.201 Chirality : 0.039 0.118 6510 Planarity : 0.004 0.026 6020 Dihedral : 17.513 84.693 8260 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 0.68 % Allowed : 10.78 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.04 (0.13), residues: 4760 helix: 2.03 (0.09), residues: 3780 sheet: None (None), residues: 0 loop : -1.39 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP2J 47 HIS 0.004 0.001 HIS2B 66 PHE 0.004 0.001 PHE2C 61 TYR 0.006 0.001 TYR1B 88 ARG 0.001 0.000 ARG2A 75 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 474 time to evaluate : 4.493 Fit side-chains revert: symmetry clash REVERT: 1H 30 THR cc_start: 0.8952 (p) cc_final: 0.8702 (p) REVERT: 2N 57 MET cc_start: 0.8574 (ttp) cc_final: 0.8329 (ttm) REVERT: 3B 41 GLN cc_start: 0.9157 (tt0) cc_final: 0.8925 (tt0) REVERT: 3D 71 SER cc_start: 0.8915 (p) cc_final: 0.8681 (m) REVERT: 3N 88 TYR cc_start: 0.9048 (t80) cc_final: 0.8732 (t80) REVERT: 4B 75 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.7216 (ttm110) REVERT: 5C 71 SER cc_start: 0.9090 (p) cc_final: 0.8526 (m) REVERT: 5K 71 SER cc_start: 0.8982 (p) cc_final: 0.8730 (m) outliers start: 27 outliers final: 21 residues processed: 491 average time/residue: 1.1770 time to fit residues: 746.9984 Evaluate side-chains 487 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 465 time to evaluate : 4.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1B residue 45 SER Chi-restraints excluded: chain 1G residue 91 SER Chi-restraints excluded: chain 2A residue 45 SER Chi-restraints excluded: chain 2A residue 75 ARG Chi-restraints excluded: chain 2B residue 45 SER Chi-restraints excluded: chain 2C residue 79 SER Chi-restraints excluded: chain 2F residue 91 SER Chi-restraints excluded: chain 2M residue 71 SER Chi-restraints excluded: chain 2M residue 79 SER Chi-restraints excluded: chain 3A residue 45 SER Chi-restraints excluded: chain 3B residue 45 SER Chi-restraints excluded: chain 3B residue 91 SER Chi-restraints excluded: chain 3D residue 64 MET Chi-restraints excluded: chain 3F residue 91 SER Chi-restraints excluded: chain 3H residue 91 SER Chi-restraints excluded: chain 4B residue 75 ARG Chi-restraints excluded: chain 4E residue 91 SER Chi-restraints excluded: chain 4K residue 91 SER Chi-restraints excluded: chain 4L residue 91 SER Chi-restraints excluded: chain 5B residue 45 SER Chi-restraints excluded: chain 5B residue 48 ILE Chi-restraints excluded: chain 5E residue 91 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 429 optimal weight: 1.9990 chunk 452 optimal weight: 0.3980 chunk 412 optimal weight: 3.9990 chunk 440 optimal weight: 2.9990 chunk 264 optimal weight: 8.9990 chunk 191 optimal weight: 6.9990 chunk 345 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 397 optimal weight: 6.9990 chunk 416 optimal weight: 6.9990 chunk 438 optimal weight: 0.6980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1F 66 HIS 2A 41 GLN 2B 66 HIS 2H 66 HIS 3A 41 GLN 4C 66 HIS 5A 41 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 40040 Z= 0.178 Angle : 0.441 7.222 53970 Z= 0.213 Chirality : 0.040 0.156 6510 Planarity : 0.004 0.026 6020 Dihedral : 17.568 82.072 8260 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.85 % Allowed : 10.85 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.13), residues: 4760 helix: 1.97 (0.09), residues: 3780 sheet: None (None), residues: 0 loop : -1.42 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP1F 47 HIS 0.004 0.001 HIS1K 66 PHE 0.005 0.001 PHE5A 72 TYR 0.007 0.001 TYR1B 88 ARG 0.003 0.001 ARG1J 75 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 462 time to evaluate : 3.762 Fit side-chains REVERT: 1B 75 ARG cc_start: 0.7363 (OUTLIER) cc_final: 0.6895 (ttm170) REVERT: 2M 71 SER cc_start: 0.9202 (OUTLIER) cc_final: 0.8593 (m) REVERT: 2N 57 MET cc_start: 0.8617 (ttp) cc_final: 0.8380 (ttm) REVERT: 3B 41 GLN cc_start: 0.9178 (tt0) cc_final: 0.8941 (tt0) REVERT: 3D 71 SER cc_start: 0.8948 (p) cc_final: 0.8697 (m) REVERT: 3M 90 VAL cc_start: 0.9054 (t) cc_final: 0.8798 (t) REVERT: 3N 88 TYR cc_start: 0.9084 (t80) cc_final: 0.8761 (t80) REVERT: 4B 75 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.7162 (ttm110) REVERT: 5K 71 SER cc_start: 0.8983 (p) cc_final: 0.8739 (m) outliers start: 34 outliers final: 28 residues processed: 486 average time/residue: 1.1220 time to fit residues: 696.7038 Evaluate side-chains 489 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 458 time to evaluate : 3.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1B residue 45 SER Chi-restraints excluded: chain 1B residue 75 ARG Chi-restraints excluded: chain 1D residue 91 SER Chi-restraints excluded: chain 1G residue 91 SER Chi-restraints excluded: chain 2A residue 45 SER Chi-restraints excluded: chain 2B residue 45 SER Chi-restraints excluded: chain 2C residue 79 SER Chi-restraints excluded: chain 2E residue 91 SER Chi-restraints excluded: chain 2F residue 91 SER Chi-restraints excluded: chain 2M residue 71 SER Chi-restraints excluded: chain 2M residue 79 SER Chi-restraints excluded: chain 3A residue 45 SER Chi-restraints excluded: chain 3B residue 45 SER Chi-restraints excluded: chain 3B residue 91 SER Chi-restraints excluded: chain 3D residue 64 MET Chi-restraints excluded: chain 3E residue 91 SER Chi-restraints excluded: chain 3F residue 91 SER Chi-restraints excluded: chain 3G residue 91 SER Chi-restraints excluded: chain 3H residue 91 SER Chi-restraints excluded: chain 3N residue 45 SER Chi-restraints excluded: chain 4A residue 30 THR Chi-restraints excluded: chain 4B residue 45 SER Chi-restraints excluded: chain 4B residue 75 ARG Chi-restraints excluded: chain 4E residue 91 SER Chi-restraints excluded: chain 4G residue 91 SER Chi-restraints excluded: chain 4L residue 91 SER Chi-restraints excluded: chain 4M residue 79 SER Chi-restraints excluded: chain 5B residue 45 SER Chi-restraints excluded: chain 5B residue 48 ILE Chi-restraints excluded: chain 5E residue 91 SER Chi-restraints excluded: chain 5F residue 91 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 289 optimal weight: 4.9990 chunk 465 optimal weight: 5.9990 chunk 284 optimal weight: 0.7980 chunk 220 optimal weight: 7.9990 chunk 323 optimal weight: 1.9990 chunk 488 optimal weight: 10.0000 chunk 449 optimal weight: 7.9990 chunk 388 optimal weight: 8.9990 chunk 40 optimal weight: 7.9990 chunk 300 optimal weight: 0.4980 chunk 238 optimal weight: 4.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1F 66 HIS 2A 41 GLN 2H 66 HIS 3A 41 GLN 3H 66 HIS 3J 66 HIS 4C 66 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 40040 Z= 0.246 Angle : 0.493 8.063 53970 Z= 0.237 Chirality : 0.041 0.126 6510 Planarity : 0.005 0.026 6020 Dihedral : 18.089 85.011 8260 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.95 % Allowed : 10.78 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.13), residues: 4760 helix: 1.84 (0.09), residues: 3780 sheet: None (None), residues: 0 loop : -1.51 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP5D 47 HIS 0.005 0.001 HIS1K 66 PHE 0.006 0.001 PHE5A 61 TYR 0.009 0.001 TYR1B 88 ARG 0.005 0.001 ARG1J 75 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9520 Ramachandran restraints generated. 4760 Oldfield, 0 Emsley, 4760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 461 time to evaluate : 3.749 Fit side-chains REVERT: 1B 75 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.7069 (ttm170) REVERT: 2M 71 SER cc_start: 0.9246 (OUTLIER) cc_final: 0.8633 (m) REVERT: 2N 57 MET cc_start: 0.8607 (ttp) cc_final: 0.8350 (ttm) REVERT: 3D 71 SER cc_start: 0.8995 (p) cc_final: 0.8704 (m) REVERT: 3M 90 VAL cc_start: 0.9085 (t) cc_final: 0.8797 (t) REVERT: 3N 88 TYR cc_start: 0.9102 (t80) cc_final: 0.8766 (t80) REVERT: 4B 75 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.7069 (ttm110) REVERT: 5K 71 SER cc_start: 0.9060 (p) cc_final: 0.8779 (m) outliers start: 38 outliers final: 33 residues processed: 492 average time/residue: 1.0961 time to fit residues: 689.2622 Evaluate side-chains 489 residues out of total 3990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 453 time to evaluate : 4.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1B residue 45 SER Chi-restraints excluded: chain 1B residue 75 ARG Chi-restraints excluded: chain 1C residue 66 HIS Chi-restraints excluded: chain 1D residue 71 SER Chi-restraints excluded: chain 1D residue 91 SER Chi-restraints excluded: chain 1E residue 91 SER Chi-restraints excluded: chain 1G residue 91 SER Chi-restraints excluded: chain 2A residue 45 SER Chi-restraints excluded: chain 2B residue 45 SER Chi-restraints excluded: chain 2C residue 79 SER Chi-restraints excluded: chain 2E residue 91 SER Chi-restraints excluded: chain 2F residue 91 SER Chi-restraints excluded: chain 2G residue 91 SER Chi-restraints excluded: chain 2M residue 71 SER Chi-restraints excluded: chain 2M residue 79 SER Chi-restraints excluded: chain 3A residue 45 SER Chi-restraints excluded: chain 3B residue 45 SER Chi-restraints excluded: chain 3B residue 91 SER Chi-restraints excluded: chain 3E residue 91 SER Chi-restraints excluded: chain 3F residue 91 SER Chi-restraints excluded: chain 3H residue 30 THR Chi-restraints excluded: chain 3H residue 91 SER Chi-restraints excluded: chain 4A residue 30 THR Chi-restraints excluded: chain 4B residue 45 SER Chi-restraints excluded: chain 4B residue 75 ARG Chi-restraints excluded: chain 4E residue 91 SER Chi-restraints excluded: chain 4G residue 91 SER Chi-restraints excluded: chain 4J residue 91 SER Chi-restraints excluded: chain 4L residue 91 SER Chi-restraints excluded: chain 4M residue 79 SER Chi-restraints excluded: chain 5A residue 30 THR Chi-restraints excluded: chain 5B residue 45 SER Chi-restraints excluded: chain 5B residue 48 ILE Chi-restraints excluded: chain 5E residue 91 SER Chi-restraints excluded: chain 5F residue 91 SER Chi-restraints excluded: chain 5N residue 71 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 308 optimal weight: 10.0000 chunk 414 optimal weight: 1.9990 chunk 119 optimal weight: 0.2980 chunk 358 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 108 optimal weight: 9.9990 chunk 389 optimal weight: 0.7980 chunk 162 optimal weight: 0.9990 chunk 399 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1F 66 HIS 2A 41 GLN 2H 66 HIS 3A 41 GLN 3L 66 HIS 4A 41 GLN 4C 66 HIS 5I 66 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.104523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.077678 restraints weight = 45123.219| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 1.55 r_work: 0.2668 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2533 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 40040 Z= 0.140 Angle : 0.424 8.774 53970 Z= 0.206 Chirality : 0.039 0.119 6510 Planarity : 0.004 0.026 6020 Dihedral : 17.590 80.935 8260 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 0.75 % Allowed : 10.98 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.13), residues: 4760 helix: 1.98 (0.09), residues: 3780 sheet: None (None), residues: 0 loop : -1.35 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP5D 47 HIS 0.003 0.001 HIS1B 66 PHE 0.004 0.001 PHE2C 61 TYR 0.006 0.001 TYR1B 88 ARG 0.003 0.000 ARG2A 75 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11487.16 seconds wall clock time: 209 minutes 15.63 seconds (12555.63 seconds total)