Starting phenix.real_space_refine on Sat Jul 27 08:16:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cue_26999/07_2024/8cue_26999.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cue_26999/07_2024/8cue_26999.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cue_26999/07_2024/8cue_26999.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cue_26999/07_2024/8cue_26999.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cue_26999/07_2024/8cue_26999.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cue_26999/07_2024/8cue_26999.cif" } resolution = 3.2 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= 0.011 sd= 0.135 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 280 5.16 5 C 24920 2.51 5 N 5530 2.21 5 O 6440 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1A PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1B PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1C PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1D PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1E PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1F PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1G PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1H PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1I PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1J PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1K PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1L PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1M PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1N PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2A PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2B PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2C PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2D PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2E PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2F PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2G PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2H PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2I PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2J PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2K PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2L PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2M PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2N PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3A PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3B PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3C PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3D PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3E PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3F PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3G PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3H PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3I PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3J PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3K PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3L PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3M PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3N PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4A PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4B PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4C PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4D PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4E PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4F PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4G PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4H PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4I PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4J PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4K PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4L PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4M PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4N PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5A PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5B PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5C PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5D PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5E PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5F PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5G PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5H PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5I PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5J PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5K PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5L PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5M PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5N PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 37240 Number of models: 1 Model: "" Number of chains: 140 Chain: "1A" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "1B" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "1C" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "1D" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "1E" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "1F" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "1G" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "1H" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "1I" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "1J" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "1K" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "1L" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "1M" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "1N" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "2A" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "2B" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "2C" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "2D" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "2E" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "2F" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "2G" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "2H" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "2I" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "2J" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "2K" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "2L" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "2M" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "2N" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "3A" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "3B" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "3C" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "3D" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "3E" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "3F" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "3G" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "3H" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "3I" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "3J" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "3K" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "3L" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "3M" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "3N" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "4A" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "4B" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "4C" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "4D" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "4E" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "4F" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "4G" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "4H" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "4I" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "4J" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "4K" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "4L" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "4M" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "4N" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "5A" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "5B" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "5C" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "5D" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "5E" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "5F" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "5G" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "5H" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "5I" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "5J" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "5K" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "5L" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "5M" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "5N" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 480 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "1A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "1B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "1C" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "1D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "1E" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "1F" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "1G" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "1H" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "1I" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "1J" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "1K" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "1L" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "1M" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "1N" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "2A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "2B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "2C" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "2D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "2E" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "2F" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "2G" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "2H" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "2I" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "2J" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "2K" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "2L" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "2M" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "2N" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "3A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "3B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "3C" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "3D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "3E" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "3F" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "3G" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "3H" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "3I" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "3J" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "3K" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "3L" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "3M" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "3N" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "4A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "4B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "4C" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "4D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "4E" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "4F" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "4G" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "4H" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "4I" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "4J" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "4K" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "4L" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "4M" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "4N" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "5A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "5B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "5C" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "5D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "5E" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "5F" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "5G" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "5H" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "5I" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "5J" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "5K" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "5L" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "5M" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "5N" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 18.75, per 1000 atoms: 0.50 Number of scatterers: 37240 At special positions: 0 Unit cell: (94.83, 94.83, 243.07, 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 280 16.00 P 70 15.00 O 6440 8.00 N 5530 7.00 C 24920 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: 14.24 Conformation dependent library (CDL) restraints added in 6.7 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: 7560 Finding SS restraints... Secondary structure from input PDB file: 280 helices and 0 sheets defined 87.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.33 Creating SS restraints... Processing helix chain '1A' and resid 55 through 68 removed outlier: 3.603A pdb=" N MET1A 59 " --> pdb=" O ASP1A 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN1A 61 " --> pdb=" O ALA1A 57 " (cutoff:3.500A) Processing helix chain '1A' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL1A 77 " --> pdb=" O GLN1A 73 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU1A 78 " --> pdb=" O SER1A 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE1A 83 " --> pdb=" O GLY1A 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET1A 88 " --> pdb=" O GLY1A 84 " (cutoff:3.500A) Processing helix chain '1A' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL1A 97 " --> pdb=" O SER1A 93 " (cutoff:3.500A) Processing helix chain '1A' and resid 109 through 119 removed outlier: 3.543A pdb=" N LEU1A 113 " --> pdb=" O GLY1A 109 " (cutoff:3.500A) Processing helix chain '1B' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET1B 59 " --> pdb=" O ASP1B 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN1B 61 " --> pdb=" O ALA1B 57 " (cutoff:3.500A) Processing helix chain '1B' and resid 69 through 88 removed outlier: 3.578A pdb=" N VAL1B 77 " --> pdb=" O GLN1B 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU1B 78 " --> pdb=" O SER1B 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE1B 83 " --> pdb=" O GLY1B 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET1B 88 " --> pdb=" O GLY1B 84 " (cutoff:3.500A) Processing helix chain '1B' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL1B 97 " --> pdb=" O SER1B 93 " (cutoff:3.500A) Processing helix chain '1B' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU1B 113 " --> pdb=" O GLY1B 109 " (cutoff:3.500A) Processing helix chain '1C' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET1C 59 " --> pdb=" O ASP1C 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN1C 61 " --> pdb=" O ALA1C 57 " (cutoff:3.500A) Processing helix chain '1C' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL1C 77 " --> pdb=" O GLN1C 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU1C 78 " --> pdb=" O SER1C 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE1C 83 " --> pdb=" O GLY1C 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET1C 88 " --> pdb=" O GLY1C 84 " (cutoff:3.500A) Processing helix chain '1C' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL1C 97 " --> pdb=" O SER1C 93 " (cutoff:3.500A) Processing helix chain '1C' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU1C 113 " --> pdb=" O GLY1C 109 " (cutoff:3.500A) Processing helix chain '1D' and resid 55 through 68 removed outlier: 3.601A pdb=" N MET1D 59 " --> pdb=" O ASP1D 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN1D 61 " --> pdb=" O ALA1D 57 " (cutoff:3.500A) Processing helix chain '1D' and resid 69 through 88 removed outlier: 3.578A pdb=" N VAL1D 77 " --> pdb=" O GLN1D 73 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU1D 78 " --> pdb=" O SER1D 74 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE1D 83 " --> pdb=" O GLY1D 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET1D 88 " --> pdb=" O GLY1D 84 " (cutoff:3.500A) Processing helix chain '1D' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL1D 97 " --> pdb=" O SER1D 93 " (cutoff:3.500A) Processing helix chain '1D' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU1D 113 " --> pdb=" O GLY1D 109 " (cutoff:3.500A) Processing helix chain '1E' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET1E 59 " --> pdb=" O ASP1E 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN1E 61 " --> pdb=" O ALA1E 57 " (cutoff:3.500A) Processing helix chain '1E' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL1E 77 " --> pdb=" O GLN1E 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU1E 78 " --> pdb=" O SER1E 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE1E 83 " --> pdb=" O GLY1E 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET1E 88 " --> pdb=" O GLY1E 84 " (cutoff:3.500A) Processing helix chain '1E' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL1E 97 " --> pdb=" O SER1E 93 " (cutoff:3.500A) Processing helix chain '1E' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU1E 113 " --> pdb=" O GLY1E 109 " (cutoff:3.500A) Processing helix chain '1F' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET1F 59 " --> pdb=" O ASP1F 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN1F 61 " --> pdb=" O ALA1F 57 " (cutoff:3.500A) Processing helix chain '1F' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL1F 77 " --> pdb=" O GLN1F 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU1F 78 " --> pdb=" O SER1F 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE1F 83 " --> pdb=" O GLY1F 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET1F 88 " --> pdb=" O GLY1F 84 " (cutoff:3.500A) Processing helix chain '1F' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL1F 97 " --> pdb=" O SER1F 93 " (cutoff:3.500A) Processing helix chain '1F' and resid 109 through 119 removed outlier: 3.541A pdb=" N LEU1F 113 " --> pdb=" O GLY1F 109 " (cutoff:3.500A) Processing helix chain '1G' and resid 55 through 68 removed outlier: 3.601A pdb=" N MET1G 59 " --> pdb=" O ASP1G 55 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN1G 61 " --> pdb=" O ALA1G 57 " (cutoff:3.500A) Processing helix chain '1G' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL1G 77 " --> pdb=" O GLN1G 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU1G 78 " --> pdb=" O SER1G 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE1G 83 " --> pdb=" O GLY1G 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET1G 88 " --> pdb=" O GLY1G 84 " (cutoff:3.500A) Processing helix chain '1G' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL1G 97 " --> pdb=" O SER1G 93 " (cutoff:3.500A) Processing helix chain '1G' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU1G 113 " --> pdb=" O GLY1G 109 " (cutoff:3.500A) Processing helix chain '1H' and resid 55 through 68 removed outlier: 3.601A pdb=" N MET1H 59 " --> pdb=" O ASP1H 55 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN1H 61 " --> pdb=" O ALA1H 57 " (cutoff:3.500A) Processing helix chain '1H' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL1H 77 " --> pdb=" O GLN1H 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU1H 78 " --> pdb=" O SER1H 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE1H 83 " --> pdb=" O GLY1H 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET1H 88 " --> pdb=" O GLY1H 84 " (cutoff:3.500A) Processing helix chain '1H' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL1H 97 " --> pdb=" O SER1H 93 " (cutoff:3.500A) Processing helix chain '1H' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU1H 113 " --> pdb=" O GLY1H 109 " (cutoff:3.500A) Processing helix chain '1I' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET1I 59 " --> pdb=" O ASP1I 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN1I 61 " --> pdb=" O ALA1I 57 " (cutoff:3.500A) Processing helix chain '1I' and resid 69 through 88 removed outlier: 3.578A pdb=" N VAL1I 77 " --> pdb=" O GLN1I 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU1I 78 " --> pdb=" O SER1I 74 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE1I 83 " --> pdb=" O GLY1I 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET1I 88 " --> pdb=" O GLY1I 84 " (cutoff:3.500A) Processing helix chain '1I' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL1I 97 " --> pdb=" O SER1I 93 " (cutoff:3.500A) Processing helix chain '1I' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU1I 113 " --> pdb=" O GLY1I 109 " (cutoff:3.500A) Processing helix chain '1J' and resid 55 through 68 removed outlier: 3.601A pdb=" N MET1J 59 " --> pdb=" O ASP1J 55 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN1J 61 " --> pdb=" O ALA1J 57 " (cutoff:3.500A) Processing helix chain '1J' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL1J 77 " --> pdb=" O GLN1J 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU1J 78 " --> pdb=" O SER1J 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE1J 83 " --> pdb=" O GLY1J 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET1J 88 " --> pdb=" O GLY1J 84 " (cutoff:3.500A) Processing helix chain '1J' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL1J 97 " --> pdb=" O SER1J 93 " (cutoff:3.500A) Processing helix chain '1J' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU1J 113 " --> pdb=" O GLY1J 109 " (cutoff:3.500A) Processing helix chain '1K' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET1K 59 " --> pdb=" O ASP1K 55 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN1K 61 " --> pdb=" O ALA1K 57 " (cutoff:3.500A) Processing helix chain '1K' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL1K 77 " --> pdb=" O GLN1K 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU1K 78 " --> pdb=" O SER1K 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE1K 83 " --> pdb=" O GLY1K 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET1K 88 " --> pdb=" O GLY1K 84 " (cutoff:3.500A) Processing helix chain '1K' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL1K 97 " --> pdb=" O SER1K 93 " (cutoff:3.500A) Processing helix chain '1K' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU1K 113 " --> pdb=" O GLY1K 109 " (cutoff:3.500A) Processing helix chain '1L' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET1L 59 " --> pdb=" O ASP1L 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN1L 61 " --> pdb=" O ALA1L 57 " (cutoff:3.500A) Processing helix chain '1L' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL1L 77 " --> pdb=" O GLN1L 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU1L 78 " --> pdb=" O SER1L 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE1L 83 " --> pdb=" O GLY1L 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET1L 88 " --> pdb=" O GLY1L 84 " (cutoff:3.500A) Processing helix chain '1L' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL1L 97 " --> pdb=" O SER1L 93 " (cutoff:3.500A) Processing helix chain '1L' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU1L 113 " --> pdb=" O GLY1L 109 " (cutoff:3.500A) Processing helix chain '1M' and resid 55 through 68 removed outlier: 3.601A pdb=" N MET1M 59 " --> pdb=" O ASP1M 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN1M 61 " --> pdb=" O ALA1M 57 " (cutoff:3.500A) Processing helix chain '1M' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL1M 77 " --> pdb=" O GLN1M 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU1M 78 " --> pdb=" O SER1M 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE1M 83 " --> pdb=" O GLY1M 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET1M 88 " --> pdb=" O GLY1M 84 " (cutoff:3.500A) Processing helix chain '1M' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL1M 97 " --> pdb=" O SER1M 93 " (cutoff:3.500A) Processing helix chain '1M' and resid 109 through 119 removed outlier: 3.541A pdb=" N LEU1M 113 " --> pdb=" O GLY1M 109 " (cutoff:3.500A) Processing helix chain '1N' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET1N 59 " --> pdb=" O ASP1N 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN1N 61 " --> pdb=" O ALA1N 57 " (cutoff:3.500A) Processing helix chain '1N' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL1N 77 " --> pdb=" O GLN1N 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU1N 78 " --> pdb=" O SER1N 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE1N 83 " --> pdb=" O GLY1N 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET1N 88 " --> pdb=" O GLY1N 84 " (cutoff:3.500A) Processing helix chain '1N' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL1N 97 " --> pdb=" O SER1N 93 " (cutoff:3.500A) Processing helix chain '1N' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU1N 113 " --> pdb=" O GLY1N 109 " (cutoff:3.500A) Processing helix chain '2A' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET2A 59 " --> pdb=" O ASP2A 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN2A 61 " --> pdb=" O ALA2A 57 " (cutoff:3.500A) Processing helix chain '2A' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL2A 77 " --> pdb=" O GLN2A 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU2A 78 " --> pdb=" O SER2A 74 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE2A 83 " --> pdb=" O GLY2A 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET2A 88 " --> pdb=" O GLY2A 84 " (cutoff:3.500A) Processing helix chain '2A' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL2A 97 " --> pdb=" O SER2A 93 " (cutoff:3.500A) Processing helix chain '2A' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU2A 113 " --> pdb=" O GLY2A 109 " (cutoff:3.500A) Processing helix chain '2B' and resid 55 through 68 removed outlier: 3.601A pdb=" N MET2B 59 " --> pdb=" O ASP2B 55 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN2B 61 " --> pdb=" O ALA2B 57 " (cutoff:3.500A) Processing helix chain '2B' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL2B 77 " --> pdb=" O GLN2B 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU2B 78 " --> pdb=" O SER2B 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE2B 83 " --> pdb=" O GLY2B 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET2B 88 " --> pdb=" O GLY2B 84 " (cutoff:3.500A) Processing helix chain '2B' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL2B 97 " --> pdb=" O SER2B 93 " (cutoff:3.500A) Processing helix chain '2B' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU2B 113 " --> pdb=" O GLY2B 109 " (cutoff:3.500A) Processing helix chain '2C' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET2C 59 " --> pdb=" O ASP2C 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN2C 61 " --> pdb=" O ALA2C 57 " (cutoff:3.500A) Processing helix chain '2C' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL2C 77 " --> pdb=" O GLN2C 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU2C 78 " --> pdb=" O SER2C 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE2C 83 " --> pdb=" O GLY2C 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET2C 88 " --> pdb=" O GLY2C 84 " (cutoff:3.500A) Processing helix chain '2C' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL2C 97 " --> pdb=" O SER2C 93 " (cutoff:3.500A) Processing helix chain '2C' and resid 109 through 119 removed outlier: 3.541A pdb=" N LEU2C 113 " --> pdb=" O GLY2C 109 " (cutoff:3.500A) Processing helix chain '2D' and resid 55 through 68 removed outlier: 3.601A pdb=" N MET2D 59 " --> pdb=" O ASP2D 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN2D 61 " --> pdb=" O ALA2D 57 " (cutoff:3.500A) Processing helix chain '2D' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL2D 77 " --> pdb=" O GLN2D 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU2D 78 " --> pdb=" O SER2D 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE2D 83 " --> pdb=" O GLY2D 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET2D 88 " --> pdb=" O GLY2D 84 " (cutoff:3.500A) Processing helix chain '2D' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL2D 97 " --> pdb=" O SER2D 93 " (cutoff:3.500A) Processing helix chain '2D' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU2D 113 " --> pdb=" O GLY2D 109 " (cutoff:3.500A) Processing helix chain '2E' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET2E 59 " --> pdb=" O ASP2E 55 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN2E 61 " --> pdb=" O ALA2E 57 " (cutoff:3.500A) Processing helix chain '2E' and resid 69 through 88 removed outlier: 3.580A pdb=" N VAL2E 77 " --> pdb=" O GLN2E 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU2E 78 " --> pdb=" O SER2E 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE2E 83 " --> pdb=" O GLY2E 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET2E 88 " --> pdb=" O GLY2E 84 " (cutoff:3.500A) Processing helix chain '2E' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL2E 97 " --> pdb=" O SER2E 93 " (cutoff:3.500A) Processing helix chain '2E' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU2E 113 " --> pdb=" O GLY2E 109 " (cutoff:3.500A) Processing helix chain '2F' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET2F 59 " --> pdb=" O ASP2F 55 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN2F 61 " --> pdb=" O ALA2F 57 " (cutoff:3.500A) Processing helix chain '2F' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL2F 77 " --> pdb=" O GLN2F 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU2F 78 " --> pdb=" O SER2F 74 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE2F 83 " --> pdb=" O GLY2F 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET2F 88 " --> pdb=" O GLY2F 84 " (cutoff:3.500A) Processing helix chain '2F' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL2F 97 " --> pdb=" O SER2F 93 " (cutoff:3.500A) Processing helix chain '2F' and resid 109 through 119 removed outlier: 3.541A pdb=" N LEU2F 113 " --> pdb=" O GLY2F 109 " (cutoff:3.500A) Processing helix chain '2G' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET2G 59 " --> pdb=" O ASP2G 55 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN2G 61 " --> pdb=" O ALA2G 57 " (cutoff:3.500A) Processing helix chain '2G' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL2G 77 " --> pdb=" O GLN2G 73 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU2G 78 " --> pdb=" O SER2G 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE2G 83 " --> pdb=" O GLY2G 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET2G 88 " --> pdb=" O GLY2G 84 " (cutoff:3.500A) Processing helix chain '2G' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL2G 97 " --> pdb=" O SER2G 93 " (cutoff:3.500A) Processing helix chain '2G' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU2G 113 " --> pdb=" O GLY2G 109 " (cutoff:3.500A) Processing helix chain '2H' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET2H 59 " --> pdb=" O ASP2H 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN2H 61 " --> pdb=" O ALA2H 57 " (cutoff:3.500A) Processing helix chain '2H' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL2H 77 " --> pdb=" O GLN2H 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU2H 78 " --> pdb=" O SER2H 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE2H 83 " --> pdb=" O GLY2H 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET2H 88 " --> pdb=" O GLY2H 84 " (cutoff:3.500A) Processing helix chain '2H' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL2H 97 " --> pdb=" O SER2H 93 " (cutoff:3.500A) Processing helix chain '2H' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU2H 113 " --> pdb=" O GLY2H 109 " (cutoff:3.500A) Processing helix chain '2I' and resid 55 through 68 removed outlier: 3.601A pdb=" N MET2I 59 " --> pdb=" O ASP2I 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN2I 61 " --> pdb=" O ALA2I 57 " (cutoff:3.500A) Processing helix chain '2I' and resid 69 through 88 removed outlier: 3.578A pdb=" N VAL2I 77 " --> pdb=" O GLN2I 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU2I 78 " --> pdb=" O SER2I 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE2I 83 " --> pdb=" O GLY2I 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET2I 88 " --> pdb=" O GLY2I 84 " (cutoff:3.500A) Processing helix chain '2I' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL2I 97 " --> pdb=" O SER2I 93 " (cutoff:3.500A) Processing helix chain '2I' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU2I 113 " --> pdb=" O GLY2I 109 " (cutoff:3.500A) Processing helix chain '2J' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET2J 59 " --> pdb=" O ASP2J 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN2J 61 " --> pdb=" O ALA2J 57 " (cutoff:3.500A) Processing helix chain '2J' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL2J 77 " --> pdb=" O GLN2J 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU2J 78 " --> pdb=" O SER2J 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE2J 83 " --> pdb=" O GLY2J 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET2J 88 " --> pdb=" O GLY2J 84 " (cutoff:3.500A) Processing helix chain '2J' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL2J 97 " --> pdb=" O SER2J 93 " (cutoff:3.500A) Processing helix chain '2J' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU2J 113 " --> pdb=" O GLY2J 109 " (cutoff:3.500A) Processing helix chain '2K' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET2K 59 " --> pdb=" O ASP2K 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN2K 61 " --> pdb=" O ALA2K 57 " (cutoff:3.500A) Processing helix chain '2K' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL2K 77 " --> pdb=" O GLN2K 73 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU2K 78 " --> pdb=" O SER2K 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE2K 83 " --> pdb=" O GLY2K 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET2K 88 " --> pdb=" O GLY2K 84 " (cutoff:3.500A) Processing helix chain '2K' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL2K 97 " --> pdb=" O SER2K 93 " (cutoff:3.500A) Processing helix chain '2K' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU2K 113 " --> pdb=" O GLY2K 109 " (cutoff:3.500A) Processing helix chain '2L' and resid 55 through 68 removed outlier: 3.603A pdb=" N MET2L 59 " --> pdb=" O ASP2L 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN2L 61 " --> pdb=" O ALA2L 57 " (cutoff:3.500A) Processing helix chain '2L' and resid 69 through 88 removed outlier: 3.578A pdb=" N VAL2L 77 " --> pdb=" O GLN2L 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU2L 78 " --> pdb=" O SER2L 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE2L 83 " --> pdb=" O GLY2L 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET2L 88 " --> pdb=" O GLY2L 84 " (cutoff:3.500A) Processing helix chain '2L' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL2L 97 " --> pdb=" O SER2L 93 " (cutoff:3.500A) Processing helix chain '2L' and resid 109 through 119 removed outlier: 3.541A pdb=" N LEU2L 113 " --> pdb=" O GLY2L 109 " (cutoff:3.500A) Processing helix chain '2M' and resid 55 through 68 removed outlier: 3.601A pdb=" N MET2M 59 " --> pdb=" O ASP2M 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN2M 61 " --> pdb=" O ALA2M 57 " (cutoff:3.500A) Processing helix chain '2M' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL2M 77 " --> pdb=" O GLN2M 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU2M 78 " --> pdb=" O SER2M 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE2M 83 " --> pdb=" O GLY2M 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET2M 88 " --> pdb=" O GLY2M 84 " (cutoff:3.500A) Processing helix chain '2M' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL2M 97 " --> pdb=" O SER2M 93 " (cutoff:3.500A) Processing helix chain '2M' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU2M 113 " --> pdb=" O GLY2M 109 " (cutoff:3.500A) Processing helix chain '2N' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET2N 59 " --> pdb=" O ASP2N 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN2N 61 " --> pdb=" O ALA2N 57 " (cutoff:3.500A) Processing helix chain '2N' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL2N 77 " --> pdb=" O GLN2N 73 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU2N 78 " --> pdb=" O SER2N 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE2N 83 " --> pdb=" O GLY2N 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET2N 88 " --> pdb=" O GLY2N 84 " (cutoff:3.500A) Processing helix chain '2N' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL2N 97 " --> pdb=" O SER2N 93 " (cutoff:3.500A) Processing helix chain '2N' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU2N 113 " --> pdb=" O GLY2N 109 " (cutoff:3.500A) Processing helix chain '3A' and resid 55 through 68 removed outlier: 3.601A pdb=" N MET3A 59 " --> pdb=" O ASP3A 55 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN3A 61 " --> pdb=" O ALA3A 57 " (cutoff:3.500A) Processing helix chain '3A' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL3A 77 " --> pdb=" O GLN3A 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU3A 78 " --> pdb=" O SER3A 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE3A 83 " --> pdb=" O GLY3A 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET3A 88 " --> pdb=" O GLY3A 84 " (cutoff:3.500A) Processing helix chain '3A' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL3A 97 " --> pdb=" O SER3A 93 " (cutoff:3.500A) Processing helix chain '3A' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU3A 113 " --> pdb=" O GLY3A 109 " (cutoff:3.500A) Processing helix chain '3B' and resid 55 through 68 removed outlier: 3.603A pdb=" N MET3B 59 " --> pdb=" O ASP3B 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN3B 61 " --> pdb=" O ALA3B 57 " (cutoff:3.500A) Processing helix chain '3B' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL3B 77 " --> pdb=" O GLN3B 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU3B 78 " --> pdb=" O SER3B 74 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE3B 83 " --> pdb=" O GLY3B 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET3B 88 " --> pdb=" O GLY3B 84 " (cutoff:3.500A) Processing helix chain '3B' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL3B 97 " --> pdb=" O SER3B 93 " (cutoff:3.500A) Processing helix chain '3B' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU3B 113 " --> pdb=" O GLY3B 109 " (cutoff:3.500A) Processing helix chain '3C' and resid 55 through 68 removed outlier: 3.601A pdb=" N MET3C 59 " --> pdb=" O ASP3C 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN3C 61 " --> pdb=" O ALA3C 57 " (cutoff:3.500A) Processing helix chain '3C' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL3C 77 " --> pdb=" O GLN3C 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU3C 78 " --> pdb=" O SER3C 74 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE3C 83 " --> pdb=" O GLY3C 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET3C 88 " --> pdb=" O GLY3C 84 " (cutoff:3.500A) Processing helix chain '3C' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL3C 97 " --> pdb=" O SER3C 93 " (cutoff:3.500A) Processing helix chain '3C' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU3C 113 " --> pdb=" O GLY3C 109 " (cutoff:3.500A) Processing helix chain '3D' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET3D 59 " --> pdb=" O ASP3D 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN3D 61 " --> pdb=" O ALA3D 57 " (cutoff:3.500A) Processing helix chain '3D' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL3D 77 " --> pdb=" O GLN3D 73 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU3D 78 " --> pdb=" O SER3D 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE3D 83 " --> pdb=" O GLY3D 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET3D 88 " --> pdb=" O GLY3D 84 " (cutoff:3.500A) Processing helix chain '3D' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL3D 97 " --> pdb=" O SER3D 93 " (cutoff:3.500A) Processing helix chain '3D' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU3D 113 " --> pdb=" O GLY3D 109 " (cutoff:3.500A) Processing helix chain '3E' and resid 55 through 68 removed outlier: 3.601A pdb=" N MET3E 59 " --> pdb=" O ASP3E 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN3E 61 " --> pdb=" O ALA3E 57 " (cutoff:3.500A) Processing helix chain '3E' and resid 69 through 88 removed outlier: 3.578A pdb=" N VAL3E 77 " --> pdb=" O GLN3E 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU3E 78 " --> pdb=" O SER3E 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE3E 83 " --> pdb=" O GLY3E 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET3E 88 " --> pdb=" O GLY3E 84 " (cutoff:3.500A) Processing helix chain '3E' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL3E 97 " --> pdb=" O SER3E 93 " (cutoff:3.500A) Processing helix chain '3E' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU3E 113 " --> pdb=" O GLY3E 109 " (cutoff:3.500A) Processing helix chain '3F' and resid 55 through 68 removed outlier: 3.603A pdb=" N MET3F 59 " --> pdb=" O ASP3F 55 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN3F 61 " --> pdb=" O ALA3F 57 " (cutoff:3.500A) Processing helix chain '3F' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL3F 77 " --> pdb=" O GLN3F 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU3F 78 " --> pdb=" O SER3F 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE3F 83 " --> pdb=" O GLY3F 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET3F 88 " --> pdb=" O GLY3F 84 " (cutoff:3.500A) Processing helix chain '3F' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL3F 97 " --> pdb=" O SER3F 93 " (cutoff:3.500A) Processing helix chain '3F' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU3F 113 " --> pdb=" O GLY3F 109 " (cutoff:3.500A) Processing helix chain '3G' and resid 55 through 68 removed outlier: 3.601A pdb=" N MET3G 59 " --> pdb=" O ASP3G 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN3G 61 " --> pdb=" O ALA3G 57 " (cutoff:3.500A) Processing helix chain '3G' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL3G 77 " --> pdb=" O GLN3G 73 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU3G 78 " --> pdb=" O SER3G 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE3G 83 " --> pdb=" O GLY3G 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET3G 88 " --> pdb=" O GLY3G 84 " (cutoff:3.500A) Processing helix chain '3G' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL3G 97 " --> pdb=" O SER3G 93 " (cutoff:3.500A) Processing helix chain '3G' and resid 109 through 119 removed outlier: 3.541A pdb=" N LEU3G 113 " --> pdb=" O GLY3G 109 " (cutoff:3.500A) Processing helix chain '3H' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET3H 59 " --> pdb=" O ASP3H 55 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN3H 61 " --> pdb=" O ALA3H 57 " (cutoff:3.500A) Processing helix chain '3H' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL3H 77 " --> pdb=" O GLN3H 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU3H 78 " --> pdb=" O SER3H 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE3H 83 " --> pdb=" O GLY3H 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET3H 88 " --> pdb=" O GLY3H 84 " (cutoff:3.500A) Processing helix chain '3H' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL3H 97 " --> pdb=" O SER3H 93 " (cutoff:3.500A) Processing helix chain '3H' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU3H 113 " --> pdb=" O GLY3H 109 " (cutoff:3.500A) Processing helix chain '3I' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET3I 59 " --> pdb=" O ASP3I 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN3I 61 " --> pdb=" O ALA3I 57 " (cutoff:3.500A) Processing helix chain '3I' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL3I 77 " --> pdb=" O GLN3I 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU3I 78 " --> pdb=" O SER3I 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE3I 83 " --> pdb=" O GLY3I 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET3I 88 " --> pdb=" O GLY3I 84 " (cutoff:3.500A) Processing helix chain '3I' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL3I 97 " --> pdb=" O SER3I 93 " (cutoff:3.500A) Processing helix chain '3I' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU3I 113 " --> pdb=" O GLY3I 109 " (cutoff:3.500A) Processing helix chain '3J' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET3J 59 " --> pdb=" O ASP3J 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN3J 61 " --> pdb=" O ALA3J 57 " (cutoff:3.500A) Processing helix chain '3J' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL3J 77 " --> pdb=" O GLN3J 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU3J 78 " --> pdb=" O SER3J 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE3J 83 " --> pdb=" O GLY3J 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET3J 88 " --> pdb=" O GLY3J 84 " (cutoff:3.500A) Processing helix chain '3J' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL3J 97 " --> pdb=" O SER3J 93 " (cutoff:3.500A) Processing helix chain '3J' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU3J 113 " --> pdb=" O GLY3J 109 " (cutoff:3.500A) Processing helix chain '3K' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET3K 59 " --> pdb=" O ASP3K 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN3K 61 " --> pdb=" O ALA3K 57 " (cutoff:3.500A) Processing helix chain '3K' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL3K 77 " --> pdb=" O GLN3K 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU3K 78 " --> pdb=" O SER3K 74 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE3K 83 " --> pdb=" O GLY3K 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET3K 88 " --> pdb=" O GLY3K 84 " (cutoff:3.500A) Processing helix chain '3K' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL3K 97 " --> pdb=" O SER3K 93 " (cutoff:3.500A) Processing helix chain '3K' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU3K 113 " --> pdb=" O GLY3K 109 " (cutoff:3.500A) Processing helix chain '3L' and resid 55 through 68 removed outlier: 3.601A pdb=" N MET3L 59 " --> pdb=" O ASP3L 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN3L 61 " --> pdb=" O ALA3L 57 " (cutoff:3.500A) Processing helix chain '3L' and resid 69 through 88 removed outlier: 3.578A pdb=" N VAL3L 77 " --> pdb=" O GLN3L 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU3L 78 " --> pdb=" O SER3L 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE3L 83 " --> pdb=" O GLY3L 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET3L 88 " --> pdb=" O GLY3L 84 " (cutoff:3.500A) Processing helix chain '3L' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL3L 97 " --> pdb=" O SER3L 93 " (cutoff:3.500A) Processing helix chain '3L' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU3L 113 " --> pdb=" O GLY3L 109 " (cutoff:3.500A) Processing helix chain '3M' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET3M 59 " --> pdb=" O ASP3M 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN3M 61 " --> pdb=" O ALA3M 57 " (cutoff:3.500A) Processing helix chain '3M' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL3M 77 " --> pdb=" O GLN3M 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU3M 78 " --> pdb=" O SER3M 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE3M 83 " --> pdb=" O GLY3M 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET3M 88 " --> pdb=" O GLY3M 84 " (cutoff:3.500A) Processing helix chain '3M' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL3M 97 " --> pdb=" O SER3M 93 " (cutoff:3.500A) Processing helix chain '3M' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU3M 113 " --> pdb=" O GLY3M 109 " (cutoff:3.500A) Processing helix chain '3N' and resid 55 through 68 removed outlier: 3.601A pdb=" N MET3N 59 " --> pdb=" O ASP3N 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN3N 61 " --> pdb=" O ALA3N 57 " (cutoff:3.500A) Processing helix chain '3N' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL3N 77 " --> pdb=" O GLN3N 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU3N 78 " --> pdb=" O SER3N 74 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE3N 83 " --> pdb=" O GLY3N 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET3N 88 " --> pdb=" O GLY3N 84 " (cutoff:3.500A) Processing helix chain '3N' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL3N 97 " --> pdb=" O SER3N 93 " (cutoff:3.500A) Processing helix chain '3N' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU3N 113 " --> pdb=" O GLY3N 109 " (cutoff:3.500A) Processing helix chain '4A' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET4A 59 " --> pdb=" O ASP4A 55 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN4A 61 " --> pdb=" O ALA4A 57 " (cutoff:3.500A) Processing helix chain '4A' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL4A 77 " --> pdb=" O GLN4A 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU4A 78 " --> pdb=" O SER4A 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE4A 83 " --> pdb=" O GLY4A 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET4A 88 " --> pdb=" O GLY4A 84 " (cutoff:3.500A) Processing helix chain '4A' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL4A 97 " --> pdb=" O SER4A 93 " (cutoff:3.500A) Processing helix chain '4A' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU4A 113 " --> pdb=" O GLY4A 109 " (cutoff:3.500A) Processing helix chain '4B' and resid 55 through 68 removed outlier: 3.601A pdb=" N MET4B 59 " --> pdb=" O ASP4B 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN4B 61 " --> pdb=" O ALA4B 57 " (cutoff:3.500A) Processing helix chain '4B' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL4B 77 " --> pdb=" O GLN4B 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU4B 78 " --> pdb=" O SER4B 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE4B 83 " --> pdb=" O GLY4B 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET4B 88 " --> pdb=" O GLY4B 84 " (cutoff:3.500A) Processing helix chain '4B' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL4B 97 " --> pdb=" O SER4B 93 " (cutoff:3.500A) Processing helix chain '4B' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU4B 113 " --> pdb=" O GLY4B 109 " (cutoff:3.500A) Processing helix chain '4C' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET4C 59 " --> pdb=" O ASP4C 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN4C 61 " --> pdb=" O ALA4C 57 " (cutoff:3.500A) Processing helix chain '4C' and resid 69 through 88 removed outlier: 3.580A pdb=" N VAL4C 77 " --> pdb=" O GLN4C 73 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU4C 78 " --> pdb=" O SER4C 74 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE4C 83 " --> pdb=" O GLY4C 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET4C 88 " --> pdb=" O GLY4C 84 " (cutoff:3.500A) Processing helix chain '4C' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL4C 97 " --> pdb=" O SER4C 93 " (cutoff:3.500A) Processing helix chain '4C' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU4C 113 " --> pdb=" O GLY4C 109 " (cutoff:3.500A) Processing helix chain '4D' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET4D 59 " --> pdb=" O ASP4D 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN4D 61 " --> pdb=" O ALA4D 57 " (cutoff:3.500A) Processing helix chain '4D' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL4D 77 " --> pdb=" O GLN4D 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU4D 78 " --> pdb=" O SER4D 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE4D 83 " --> pdb=" O GLY4D 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET4D 88 " --> pdb=" O GLY4D 84 " (cutoff:3.500A) Processing helix chain '4D' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL4D 97 " --> pdb=" O SER4D 93 " (cutoff:3.500A) Processing helix chain '4D' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU4D 113 " --> pdb=" O GLY4D 109 " (cutoff:3.500A) Processing helix chain '4E' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET4E 59 " --> pdb=" O ASP4E 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN4E 61 " --> pdb=" O ALA4E 57 " (cutoff:3.500A) Processing helix chain '4E' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL4E 77 " --> pdb=" O GLN4E 73 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU4E 78 " --> pdb=" O SER4E 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE4E 83 " --> pdb=" O GLY4E 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET4E 88 " --> pdb=" O GLY4E 84 " (cutoff:3.500A) Processing helix chain '4E' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL4E 97 " --> pdb=" O SER4E 93 " (cutoff:3.500A) Processing helix chain '4E' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU4E 113 " --> pdb=" O GLY4E 109 " (cutoff:3.500A) Processing helix chain '4F' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET4F 59 " --> pdb=" O ASP4F 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN4F 61 " --> pdb=" O ALA4F 57 " (cutoff:3.500A) Processing helix chain '4F' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL4F 77 " --> pdb=" O GLN4F 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU4F 78 " --> pdb=" O SER4F 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE4F 83 " --> pdb=" O GLY4F 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET4F 88 " --> pdb=" O GLY4F 84 " (cutoff:3.500A) Processing helix chain '4F' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL4F 97 " --> pdb=" O SER4F 93 " (cutoff:3.500A) Processing helix chain '4F' and resid 109 through 119 removed outlier: 3.541A pdb=" N LEU4F 113 " --> pdb=" O GLY4F 109 " (cutoff:3.500A) Processing helix chain '4G' and resid 55 through 68 removed outlier: 3.601A pdb=" N MET4G 59 " --> pdb=" O ASP4G 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN4G 61 " --> pdb=" O ALA4G 57 " (cutoff:3.500A) Processing helix chain '4G' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL4G 77 " --> pdb=" O GLN4G 73 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU4G 78 " --> pdb=" O SER4G 74 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE4G 83 " --> pdb=" O GLY4G 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET4G 88 " --> pdb=" O GLY4G 84 " (cutoff:3.500A) Processing helix chain '4G' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL4G 97 " --> pdb=" O SER4G 93 " (cutoff:3.500A) Processing helix chain '4G' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU4G 113 " --> pdb=" O GLY4G 109 " (cutoff:3.500A) Processing helix chain '4H' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET4H 59 " --> pdb=" O ASP4H 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN4H 61 " --> pdb=" O ALA4H 57 " (cutoff:3.500A) Processing helix chain '4H' and resid 69 through 88 removed outlier: 3.578A pdb=" N VAL4H 77 " --> pdb=" O GLN4H 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU4H 78 " --> pdb=" O SER4H 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE4H 83 " --> pdb=" O GLY4H 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET4H 88 " --> pdb=" O GLY4H 84 " (cutoff:3.500A) Processing helix chain '4H' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL4H 97 " --> pdb=" O SER4H 93 " (cutoff:3.500A) Processing helix chain '4H' and resid 109 through 119 removed outlier: 3.541A pdb=" N LEU4H 113 " --> pdb=" O GLY4H 109 " (cutoff:3.500A) Processing helix chain '4I' and resid 55 through 68 removed outlier: 3.601A pdb=" N MET4I 59 " --> pdb=" O ASP4I 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN4I 61 " --> pdb=" O ALA4I 57 " (cutoff:3.500A) Processing helix chain '4I' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL4I 77 " --> pdb=" O GLN4I 73 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU4I 78 " --> pdb=" O SER4I 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE4I 83 " --> pdb=" O GLY4I 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET4I 88 " --> pdb=" O GLY4I 84 " (cutoff:3.500A) Processing helix chain '4I' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL4I 97 " --> pdb=" O SER4I 93 " (cutoff:3.500A) Processing helix chain '4I' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU4I 113 " --> pdb=" O GLY4I 109 " (cutoff:3.500A) Processing helix chain '4J' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET4J 59 " --> pdb=" O ASP4J 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN4J 61 " --> pdb=" O ALA4J 57 " (cutoff:3.500A) Processing helix chain '4J' and resid 69 through 88 removed outlier: 3.580A pdb=" N VAL4J 77 " --> pdb=" O GLN4J 73 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU4J 78 " --> pdb=" O SER4J 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE4J 83 " --> pdb=" O GLY4J 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET4J 88 " --> pdb=" O GLY4J 84 " (cutoff:3.500A) Processing helix chain '4J' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL4J 97 " --> pdb=" O SER4J 93 " (cutoff:3.500A) Processing helix chain '4J' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU4J 113 " --> pdb=" O GLY4J 109 " (cutoff:3.500A) Processing helix chain '4K' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET4K 59 " --> pdb=" O ASP4K 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN4K 61 " --> pdb=" O ALA4K 57 " (cutoff:3.500A) Processing helix chain '4K' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL4K 77 " --> pdb=" O GLN4K 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU4K 78 " --> pdb=" O SER4K 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE4K 83 " --> pdb=" O GLY4K 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET4K 88 " --> pdb=" O GLY4K 84 " (cutoff:3.500A) Processing helix chain '4K' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL4K 97 " --> pdb=" O SER4K 93 " (cutoff:3.500A) Processing helix chain '4K' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU4K 113 " --> pdb=" O GLY4K 109 " (cutoff:3.500A) Processing helix chain '4L' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET4L 59 " --> pdb=" O ASP4L 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN4L 61 " --> pdb=" O ALA4L 57 " (cutoff:3.500A) Processing helix chain '4L' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL4L 77 " --> pdb=" O GLN4L 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU4L 78 " --> pdb=" O SER4L 74 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE4L 83 " --> pdb=" O GLY4L 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET4L 88 " --> pdb=" O GLY4L 84 " (cutoff:3.500A) Processing helix chain '4L' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL4L 97 " --> pdb=" O SER4L 93 " (cutoff:3.500A) Processing helix chain '4L' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU4L 113 " --> pdb=" O GLY4L 109 " (cutoff:3.500A) Processing helix chain '4M' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET4M 59 " --> pdb=" O ASP4M 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN4M 61 " --> pdb=" O ALA4M 57 " (cutoff:3.500A) Processing helix chain '4M' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL4M 77 " --> pdb=" O GLN4M 73 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU4M 78 " --> pdb=" O SER4M 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE4M 83 " --> pdb=" O GLY4M 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET4M 88 " --> pdb=" O GLY4M 84 " (cutoff:3.500A) Processing helix chain '4M' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL4M 97 " --> pdb=" O SER4M 93 " (cutoff:3.500A) Processing helix chain '4M' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU4M 113 " --> pdb=" O GLY4M 109 " (cutoff:3.500A) Processing helix chain '4N' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET4N 59 " --> pdb=" O ASP4N 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN4N 61 " --> pdb=" O ALA4N 57 " (cutoff:3.500A) Processing helix chain '4N' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL4N 77 " --> pdb=" O GLN4N 73 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU4N 78 " --> pdb=" O SER4N 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE4N 83 " --> pdb=" O GLY4N 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET4N 88 " --> pdb=" O GLY4N 84 " (cutoff:3.500A) Processing helix chain '4N' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL4N 97 " --> pdb=" O SER4N 93 " (cutoff:3.500A) Processing helix chain '4N' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU4N 113 " --> pdb=" O GLY4N 109 " (cutoff:3.500A) Processing helix chain '5A' and resid 55 through 68 removed outlier: 3.601A pdb=" N MET5A 59 " --> pdb=" O ASP5A 55 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN5A 61 " --> pdb=" O ALA5A 57 " (cutoff:3.500A) Processing helix chain '5A' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL5A 77 " --> pdb=" O GLN5A 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU5A 78 " --> pdb=" O SER5A 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE5A 83 " --> pdb=" O GLY5A 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET5A 88 " --> pdb=" O GLY5A 84 " (cutoff:3.500A) Processing helix chain '5A' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL5A 97 " --> pdb=" O SER5A 93 " (cutoff:3.500A) Processing helix chain '5A' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU5A 113 " --> pdb=" O GLY5A 109 " (cutoff:3.500A) Processing helix chain '5B' and resid 55 through 68 removed outlier: 3.601A pdb=" N MET5B 59 " --> pdb=" O ASP5B 55 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN5B 61 " --> pdb=" O ALA5B 57 " (cutoff:3.500A) Processing helix chain '5B' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL5B 77 " --> pdb=" O GLN5B 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU5B 78 " --> pdb=" O SER5B 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE5B 83 " --> pdb=" O GLY5B 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET5B 88 " --> pdb=" O GLY5B 84 " (cutoff:3.500A) Processing helix chain '5B' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL5B 97 " --> pdb=" O SER5B 93 " (cutoff:3.500A) Processing helix chain '5B' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU5B 113 " --> pdb=" O GLY5B 109 " (cutoff:3.500A) Processing helix chain '5C' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET5C 59 " --> pdb=" O ASP5C 55 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN5C 61 " --> pdb=" O ALA5C 57 " (cutoff:3.500A) Processing helix chain '5C' and resid 69 through 88 removed outlier: 3.580A pdb=" N VAL5C 77 " --> pdb=" O GLN5C 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU5C 78 " --> pdb=" O SER5C 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE5C 83 " --> pdb=" O GLY5C 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET5C 88 " --> pdb=" O GLY5C 84 " (cutoff:3.500A) Processing helix chain '5C' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL5C 97 " --> pdb=" O SER5C 93 " (cutoff:3.500A) Processing helix chain '5C' and resid 109 through 119 removed outlier: 3.541A pdb=" N LEU5C 113 " --> pdb=" O GLY5C 109 " (cutoff:3.500A) Processing helix chain '5D' and resid 55 through 68 removed outlier: 3.601A pdb=" N MET5D 59 " --> pdb=" O ASP5D 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN5D 61 " --> pdb=" O ALA5D 57 " (cutoff:3.500A) Processing helix chain '5D' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL5D 77 " --> pdb=" O GLN5D 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU5D 78 " --> pdb=" O SER5D 74 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE5D 83 " --> pdb=" O GLY5D 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET5D 88 " --> pdb=" O GLY5D 84 " (cutoff:3.500A) Processing helix chain '5D' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL5D 97 " --> pdb=" O SER5D 93 " (cutoff:3.500A) Processing helix chain '5D' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU5D 113 " --> pdb=" O GLY5D 109 " (cutoff:3.500A) Processing helix chain '5E' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET5E 59 " --> pdb=" O ASP5E 55 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN5E 61 " --> pdb=" O ALA5E 57 " (cutoff:3.500A) Processing helix chain '5E' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL5E 77 " --> pdb=" O GLN5E 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU5E 78 " --> pdb=" O SER5E 74 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE5E 83 " --> pdb=" O GLY5E 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET5E 88 " --> pdb=" O GLY5E 84 " (cutoff:3.500A) Processing helix chain '5E' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL5E 97 " --> pdb=" O SER5E 93 " (cutoff:3.500A) Processing helix chain '5E' and resid 109 through 119 removed outlier: 3.541A pdb=" N LEU5E 113 " --> pdb=" O GLY5E 109 " (cutoff:3.500A) Processing helix chain '5F' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET5F 59 " --> pdb=" O ASP5F 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN5F 61 " --> pdb=" O ALA5F 57 " (cutoff:3.500A) Processing helix chain '5F' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL5F 77 " --> pdb=" O GLN5F 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU5F 78 " --> pdb=" O SER5F 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE5F 83 " --> pdb=" O GLY5F 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET5F 88 " --> pdb=" O GLY5F 84 " (cutoff:3.500A) Processing helix chain '5F' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL5F 97 " --> pdb=" O SER5F 93 " (cutoff:3.500A) Processing helix chain '5F' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU5F 113 " --> pdb=" O GLY5F 109 " (cutoff:3.500A) Processing helix chain '5G' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET5G 59 " --> pdb=" O ASP5G 55 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN5G 61 " --> pdb=" O ALA5G 57 " (cutoff:3.500A) Processing helix chain '5G' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL5G 77 " --> pdb=" O GLN5G 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU5G 78 " --> pdb=" O SER5G 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE5G 83 " --> pdb=" O GLY5G 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET5G 88 " --> pdb=" O GLY5G 84 " (cutoff:3.500A) Processing helix chain '5G' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL5G 97 " --> pdb=" O SER5G 93 " (cutoff:3.500A) Processing helix chain '5G' and resid 109 through 119 removed outlier: 3.541A pdb=" N LEU5G 113 " --> pdb=" O GLY5G 109 " (cutoff:3.500A) Processing helix chain '5H' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET5H 59 " --> pdb=" O ASP5H 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN5H 61 " --> pdb=" O ALA5H 57 " (cutoff:3.500A) Processing helix chain '5H' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL5H 77 " --> pdb=" O GLN5H 73 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU5H 78 " --> pdb=" O SER5H 74 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE5H 83 " --> pdb=" O GLY5H 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET5H 88 " --> pdb=" O GLY5H 84 " (cutoff:3.500A) Processing helix chain '5H' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL5H 97 " --> pdb=" O SER5H 93 " (cutoff:3.500A) Processing helix chain '5H' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU5H 113 " --> pdb=" O GLY5H 109 " (cutoff:3.500A) Processing helix chain '5I' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET5I 59 " --> pdb=" O ASP5I 55 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN5I 61 " --> pdb=" O ALA5I 57 " (cutoff:3.500A) Processing helix chain '5I' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL5I 77 " --> pdb=" O GLN5I 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU5I 78 " --> pdb=" O SER5I 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE5I 83 " --> pdb=" O GLY5I 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET5I 88 " --> pdb=" O GLY5I 84 " (cutoff:3.500A) Processing helix chain '5I' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL5I 97 " --> pdb=" O SER5I 93 " (cutoff:3.500A) Processing helix chain '5I' and resid 109 through 119 removed outlier: 3.541A pdb=" N LEU5I 113 " --> pdb=" O GLY5I 109 " (cutoff:3.500A) Processing helix chain '5J' and resid 55 through 68 removed outlier: 3.601A pdb=" N MET5J 59 " --> pdb=" O ASP5J 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN5J 61 " --> pdb=" O ALA5J 57 " (cutoff:3.500A) Processing helix chain '5J' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL5J 77 " --> pdb=" O GLN5J 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU5J 78 " --> pdb=" O SER5J 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE5J 83 " --> pdb=" O GLY5J 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET5J 88 " --> pdb=" O GLY5J 84 " (cutoff:3.500A) Processing helix chain '5J' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL5J 97 " --> pdb=" O SER5J 93 " (cutoff:3.500A) Processing helix chain '5J' and resid 109 through 119 removed outlier: 3.541A pdb=" N LEU5J 113 " --> pdb=" O GLY5J 109 " (cutoff:3.500A) Processing helix chain '5K' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET5K 59 " --> pdb=" O ASP5K 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN5K 61 " --> pdb=" O ALA5K 57 " (cutoff:3.500A) Processing helix chain '5K' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL5K 77 " --> pdb=" O GLN5K 73 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU5K 78 " --> pdb=" O SER5K 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE5K 83 " --> pdb=" O GLY5K 79 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET5K 88 " --> pdb=" O GLY5K 84 " (cutoff:3.500A) Processing helix chain '5K' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL5K 97 " --> pdb=" O SER5K 93 " (cutoff:3.500A) Processing helix chain '5K' and resid 109 through 119 removed outlier: 3.541A pdb=" N LEU5K 113 " --> pdb=" O GLY5K 109 " (cutoff:3.500A) Processing helix chain '5L' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET5L 59 " --> pdb=" O ASP5L 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN5L 61 " --> pdb=" O ALA5L 57 " (cutoff:3.500A) Processing helix chain '5L' and resid 69 through 88 removed outlier: 3.579A pdb=" N VAL5L 77 " --> pdb=" O GLN5L 73 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU5L 78 " --> pdb=" O SER5L 74 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE5L 83 " --> pdb=" O GLY5L 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET5L 88 " --> pdb=" O GLY5L 84 " (cutoff:3.500A) Processing helix chain '5L' and resid 93 through 108 removed outlier: 3.803A pdb=" N VAL5L 97 " --> pdb=" O SER5L 93 " (cutoff:3.500A) Processing helix chain '5L' and resid 109 through 119 removed outlier: 3.542A pdb=" N LEU5L 113 " --> pdb=" O GLY5L 109 " (cutoff:3.500A) Processing helix chain '5M' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET5M 59 " --> pdb=" O ASP5M 55 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN5M 61 " --> pdb=" O ALA5M 57 " (cutoff:3.500A) Processing helix chain '5M' and resid 69 through 88 removed outlier: 3.580A pdb=" N VAL5M 77 " --> pdb=" O GLN5M 73 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU5M 78 " --> pdb=" O SER5M 74 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE5M 83 " --> pdb=" O GLY5M 79 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET5M 88 " --> pdb=" O GLY5M 84 " (cutoff:3.500A) Processing helix chain '5M' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL5M 97 " --> pdb=" O SER5M 93 " (cutoff:3.500A) Processing helix chain '5M' and resid 109 through 119 removed outlier: 3.541A pdb=" N LEU5M 113 " --> pdb=" O GLY5M 109 " (cutoff:3.500A) Processing helix chain '5N' and resid 55 through 68 removed outlier: 3.602A pdb=" N MET5N 59 " --> pdb=" O ASP5N 55 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN5N 61 " --> pdb=" O ALA5N 57 " (cutoff:3.500A) Processing helix chain '5N' and resid 69 through 88 removed outlier: 3.580A pdb=" N VAL5N 77 " --> pdb=" O GLN5N 73 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU5N 78 " --> pdb=" O SER5N 74 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE5N 83 " --> pdb=" O GLY5N 79 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET5N 88 " --> pdb=" O GLY5N 84 " (cutoff:3.500A) Processing helix chain '5N' and resid 93 through 108 removed outlier: 3.802A pdb=" N VAL5N 97 " --> pdb=" O SER5N 93 " (cutoff:3.500A) Processing helix chain '5N' and resid 109 through 119 removed outlier: 3.541A pdb=" N LEU5N 113 " --> pdb=" O GLY5N 109 " (cutoff:3.500A) 2590 hydrogen bonds defined for protein. 7770 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: 11.19 Time building geometry restraints manager: 15.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 5390 1.31 - 1.43: 9234 1.43 - 1.56: 22409 1.56 - 1.68: 207 1.68 - 1.81: 490 Bond restraints: 37730 Sorted by residual: bond pdb=" C11 CPL3A 201 " pdb=" O3 CPL3A 201 " ideal model delta sigma weight residual 1.327 1.424 -0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" C11 CPL5F 201 " pdb=" O3 CPL5F 201 " ideal model delta sigma weight residual 1.327 1.424 -0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" C11 CPL1M 201 " pdb=" O3 CPL1M 201 " ideal model delta sigma weight residual 1.327 1.424 -0.097 2.00e-02 2.50e+03 2.35e+01 bond pdb=" C11 CPL5G 201 " pdb=" O3 CPL5G 201 " ideal model delta sigma weight residual 1.327 1.424 -0.097 2.00e-02 2.50e+03 2.35e+01 bond pdb=" C11 CPL1A 201 " pdb=" O3 CPL1A 201 " ideal model delta sigma weight residual 1.327 1.424 -0.097 2.00e-02 2.50e+03 2.35e+01 ... (remaining 37725 not shown) Histogram of bond angle deviations from ideal: 100.23 - 110.96: 15394 110.96 - 121.70: 28672 121.70 - 132.43: 6054 132.43 - 143.17: 70 143.17 - 153.91: 140 Bond angle restraints: 50330 Sorted by residual: angle pdb=" C39 CPL5B 201 " pdb=" C40 CPL5B 201 " pdb=" C41 CPL5B 201 " ideal model delta sigma weight residual 127.51 153.76 -26.25 3.00e+00 1.11e-01 7.66e+01 angle pdb=" C39 CPL3B 201 " pdb=" C40 CPL3B 201 " pdb=" C41 CPL3B 201 " ideal model delta sigma weight residual 127.51 153.75 -26.24 3.00e+00 1.11e-01 7.65e+01 angle pdb=" C39 CPL1L 201 " pdb=" C40 CPL1L 201 " pdb=" C41 CPL1L 201 " ideal model delta sigma weight residual 127.51 153.75 -26.24 3.00e+00 1.11e-01 7.65e+01 angle pdb=" C39 CPL5D 201 " pdb=" C40 CPL5D 201 " pdb=" C41 CPL5D 201 " ideal model delta sigma weight residual 127.51 153.75 -26.24 3.00e+00 1.11e-01 7.65e+01 angle pdb=" C39 CPL5F 201 " pdb=" C40 CPL5F 201 " pdb=" C41 CPL5F 201 " ideal model delta sigma weight residual 127.51 153.74 -26.23 3.00e+00 1.11e-01 7.65e+01 ... (remaining 50325 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 20300 35.84 - 71.67: 1120 71.67 - 107.51: 210 107.51 - 143.35: 0 143.35 - 179.18: 70 Dihedral angle restraints: 21700 sinusoidal: 9310 harmonic: 12390 Sorted by residual: dihedral pdb=" C33 CPL1D 201 " pdb=" C31 CPL1D 201 " pdb=" C32 CPL1D 201 " pdb=" O2 CPL1D 201 " ideal model delta sinusoidal sigma weight residual 171.65 -9.17 -179.18 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C33 CPL3M 201 " pdb=" C31 CPL3M 201 " pdb=" C32 CPL3M 201 " pdb=" O2 CPL3M 201 " ideal model delta sinusoidal sigma weight residual 171.65 -9.18 -179.17 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C33 CPL3F 201 " pdb=" C31 CPL3F 201 " pdb=" C32 CPL3F 201 " pdb=" O2 CPL3F 201 " ideal model delta sinusoidal sigma weight residual 171.65 -9.18 -179.17 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 21697 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 4627 0.047 - 0.093: 904 0.093 - 0.140: 69 0.140 - 0.187: 0 0.187 - 0.233: 70 Chirality restraints: 5670 Sorted by residual: chirality pdb=" C2 CPL2H 201 " pdb=" C1 CPL2H 201 " pdb=" C3 CPL2H 201 " pdb=" O2 CPL2H 201 " both_signs ideal model delta sigma weight residual False -2.32 -2.55 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" C2 CPL4L 201 " pdb=" C1 CPL4L 201 " pdb=" C3 CPL4L 201 " pdb=" O2 CPL4L 201 " both_signs ideal model delta sigma weight residual False -2.32 -2.55 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" C2 CPL5L 201 " pdb=" C1 CPL5L 201 " pdb=" C3 CPL5L 201 " pdb=" O2 CPL5L 201 " both_signs ideal model delta sigma weight residual False -2.32 -2.55 0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 5667 not shown) Planarity restraints: 6020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP1A 55 " -0.014 5.00e-02 4.00e+02 2.18e-02 7.59e-01 pdb=" N PRO1A 56 " 0.038 5.00e-02 4.00e+02 pdb=" CA PRO1A 56 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO1A 56 " -0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP1L 55 " -0.014 5.00e-02 4.00e+02 2.17e-02 7.56e-01 pdb=" N PRO1L 56 " 0.038 5.00e-02 4.00e+02 pdb=" CA PRO1L 56 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO1L 56 " -0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP5C 55 " -0.014 5.00e-02 4.00e+02 2.17e-02 7.55e-01 pdb=" N PRO5C 56 " 0.038 5.00e-02 4.00e+02 pdb=" CA PRO5C 56 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO5C 56 " -0.012 5.00e-02 4.00e+02 ... (remaining 6017 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 20275 3.01 - 3.48: 34926 3.48 - 3.96: 57404 3.96 - 4.43: 64413 4.43 - 4.90: 108145 Nonbonded interactions: 285163 Sorted by model distance: nonbonded pdb=" OD1 ASP1H 55 " pdb=" OG1 THR1H 58 " model vdw 2.541 2.440 nonbonded pdb=" OD1 ASP1K 55 " pdb=" OG1 THR1K 58 " model vdw 2.541 2.440 nonbonded pdb=" OD1 ASP2L 55 " pdb=" OG1 THR2L 58 " model vdw 2.541 2.440 nonbonded pdb=" OD1 ASP2C 55 " pdb=" OG1 THR2C 58 " model vdw 2.541 2.440 nonbonded pdb=" OD1 ASP2K 55 " pdb=" OG1 THR2K 58 " model vdw 2.542 2.440 ... (remaining 285158 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' selection = chain '1C' selection = chain '1D' selection = chain '1E' selection = chain '1F' selection = chain '1G' selection = chain '1H' selection = chain '1I' selection = chain '1J' selection = chain '1K' selection = chain '1L' selection = chain '1M' selection = chain '1N' selection = chain '2A' selection = chain '2B' selection = chain '2C' selection = chain '2D' selection = chain '2E' selection = chain '2F' selection = chain '2G' selection = chain '2H' selection = chain '2I' selection = chain '2J' selection = chain '2K' selection = chain '2L' selection = chain '2M' selection = chain '2N' selection = chain '3A' selection = chain '3B' selection = chain '3C' selection = chain '3D' selection = chain '3E' selection = chain '3F' selection = chain '3G' selection = chain '3H' selection = chain '3I' selection = chain '3J' selection = chain '3K' selection = chain '3L' selection = chain '3M' selection = chain '3N' selection = chain '4A' selection = chain '4B' selection = chain '4C' selection = chain '4D' selection = chain '4E' selection = chain '4F' selection = chain '4G' selection = chain '4H' selection = chain '4I' selection = chain '4J' selection = chain '4K' selection = chain '4L' selection = chain '4M' selection = chain '4N' selection = chain '5A' selection = chain '5B' selection = chain '5C' selection = chain '5D' selection = chain '5E' selection = chain '5F' selection = chain '5G' selection = chain '5H' selection = chain '5I' selection = chain '5J' selection = chain '5K' selection = chain '5L' selection = chain '5M' selection = chain '5N' } 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: 0.940 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: 0.040 Extract box with map and model: 1.280 Check model and map are aligned: 0.280 Set scattering table: 0.310 Process input model: 88.820 Find NCS groups from input model: 14.160 Set up NCS constraints: 0.480 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 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 : 0.010 0.097 37730 Z= 0.650 Angle : 1.825 26.252 50330 Z= 0.629 Chirality : 0.042 0.233 5670 Planarity : 0.003 0.022 6020 Dihedral : 24.543 179.182 14140 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % 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: 0.78 (0.11), residues: 4760 helix: 0.64 (0.07), residues: 3920 sheet: None (None), residues: 0 loop : 0.53 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP3H 87 PHE 0.005 0.001 PHE2F 89 ARG 0.001 0.000 ARG4I 91 *********************** 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 810 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 810 time to evaluate : 3.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1A 59 MET cc_start: 0.8766 (mtt) cc_final: 0.8449 (mtt) REVERT: 1B 59 MET cc_start: 0.8858 (mtt) cc_final: 0.8550 (mtt) REVERT: 1E 107 MET cc_start: 0.8806 (ttt) cc_final: 0.8554 (ttt) REVERT: 1F 107 MET cc_start: 0.8765 (ttt) cc_final: 0.8392 (ttt) REVERT: 1G 115 LYS cc_start: 0.8204 (mtpt) cc_final: 0.7991 (ttmm) REVERT: 1I 107 MET cc_start: 0.8884 (ttt) cc_final: 0.8603 (ttp) REVERT: 1J 107 MET cc_start: 0.8696 (ttt) cc_final: 0.8356 (ttp) REVERT: 1J 117 LEU cc_start: 0.8750 (tp) cc_final: 0.8538 (tt) REVERT: 1K 59 MET cc_start: 0.8783 (mtt) cc_final: 0.8531 (mtt) REVERT: 1K 107 MET cc_start: 0.8784 (ttt) cc_final: 0.8437 (ttp) REVERT: 1L 107 MET cc_start: 0.8680 (ttt) cc_final: 0.8456 (ttt) REVERT: 1M 107 MET cc_start: 0.8610 (ttt) cc_final: 0.8345 (ttt) REVERT: 2A 59 MET cc_start: 0.8793 (mtt) cc_final: 0.8342 (mtt) REVERT: 2B 59 MET cc_start: 0.8767 (mtt) cc_final: 0.8264 (mtt) REVERT: 2E 59 MET cc_start: 0.8657 (mtt) cc_final: 0.8389 (mtt) REVERT: 2E 107 MET cc_start: 0.8738 (ttt) cc_final: 0.8469 (ttt) REVERT: 2H 107 MET cc_start: 0.8866 (ttt) cc_final: 0.8590 (ttt) REVERT: 2J 59 MET cc_start: 0.8773 (mtt) cc_final: 0.8483 (mtt) REVERT: 2J 107 MET cc_start: 0.8645 (ttt) cc_final: 0.8435 (ttp) REVERT: 2J 117 LEU cc_start: 0.8832 (tp) cc_final: 0.8610 (tt) REVERT: 2K 59 MET cc_start: 0.8720 (mtt) cc_final: 0.8513 (mtt) REVERT: 2L 107 MET cc_start: 0.8569 (ttt) cc_final: 0.8325 (ttp) REVERT: 2M 107 MET cc_start: 0.8438 (ttt) cc_final: 0.8141 (ttt) REVERT: 3B 59 MET cc_start: 0.8680 (mtt) cc_final: 0.8396 (mtt) REVERT: 3E 107 MET cc_start: 0.8764 (ttt) cc_final: 0.8388 (ttp) REVERT: 3G 59 MET cc_start: 0.8575 (mtt) cc_final: 0.8132 (mtt) REVERT: 3G 107 MET cc_start: 0.8885 (ttt) cc_final: 0.8624 (ttt) REVERT: 3K 107 MET cc_start: 0.8803 (ttt) cc_final: 0.8516 (ttt) REVERT: 3K 112 PHE cc_start: 0.8262 (m-80) cc_final: 0.7902 (m-80) REVERT: 3L 59 MET cc_start: 0.8710 (mtt) cc_final: 0.8425 (mtt) REVERT: 3L 107 MET cc_start: 0.8703 (ttt) cc_final: 0.8414 (ttp) REVERT: 3M 107 MET cc_start: 0.8525 (ttt) cc_final: 0.8287 (ttp) REVERT: 4B 107 MET cc_start: 0.8803 (ttt) cc_final: 0.8580 (ttt) REVERT: 4G 59 MET cc_start: 0.8674 (mtt) cc_final: 0.8419 (mtt) REVERT: 4H 59 MET cc_start: 0.8671 (mtt) cc_final: 0.8345 (mtt) REVERT: 4I 59 MET cc_start: 0.8625 (mtt) cc_final: 0.8328 (mtt) REVERT: 4I 107 MET cc_start: 0.8803 (ttt) cc_final: 0.8599 (ttp) REVERT: 4I 115 LYS cc_start: 0.8161 (mtpt) cc_final: 0.7812 (mptt) REVERT: 4K 59 MET cc_start: 0.8857 (mtt) cc_final: 0.8613 (mtt) REVERT: 4K 112 PHE cc_start: 0.8062 (m-80) cc_final: 0.7828 (m-80) REVERT: 4N 61 ASN cc_start: 0.8241 (m-40) cc_final: 0.7984 (m-40) REVERT: 5G 59 MET cc_start: 0.8606 (mtt) cc_final: 0.8382 (mtt) REVERT: 5I 107 MET cc_start: 0.8760 (ttt) cc_final: 0.8510 (ttp) REVERT: 5K 59 MET cc_start: 0.8830 (mtt) cc_final: 0.8429 (mtt) REVERT: 5N 61 ASN cc_start: 0.8292 (m-40) cc_final: 0.8066 (m-40) outliers start: 0 outliers final: 0 residues processed: 810 average time/residue: 0.5043 time to fit residues: 648.9199 Evaluate side-chains 652 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 652 time to evaluate : 3.504 ------------------------------------------------------------------------------- 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: 0.0170 chunk 371 optimal weight: 7.9990 chunk 206 optimal weight: 0.9990 chunk 126 optimal weight: 7.9990 chunk 250 optimal weight: 3.9990 chunk 198 optimal weight: 3.9990 chunk 384 optimal weight: 3.9990 chunk 148 optimal weight: 0.5980 chunk 233 optimal weight: 0.7980 chunk 285 optimal weight: 5.9990 chunk 444 optimal weight: 0.9980 overall best weight: 0.6820 ------------------------------------------------------------------------------- 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: 0.7927 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 37730 Z= 0.130 Angle : 0.441 8.328 50330 Z= 0.229 Chirality : 0.034 0.104 5670 Planarity : 0.003 0.023 6020 Dihedral : 25.183 174.926 7910 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.89 % Allowed : 7.17 % Favored : 91.93 % 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: 2.61 (0.12), residues: 4760 helix: 2.20 (0.08), residues: 3990 sheet: None (None), residues: 0 loop : -0.86 (0.17), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP3B 87 PHE 0.009 0.001 PHE3M 89 ARG 0.002 0.000 ARG1F 91 *********************** 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 726 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 696 time to evaluate : 3.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1A 59 MET cc_start: 0.8551 (mtt) cc_final: 0.8044 (mtt) REVERT: 1F 107 MET cc_start: 0.8764 (ttt) cc_final: 0.8456 (ttp) REVERT: 1J 107 MET cc_start: 0.8732 (ttt) cc_final: 0.8529 (ttp) REVERT: 1L 107 MET cc_start: 0.8737 (ttt) cc_final: 0.8481 (ttt) REVERT: 1M 107 MET cc_start: 0.8541 (ttt) cc_final: 0.8260 (ttt) REVERT: 2A 59 MET cc_start: 0.8637 (mtt) cc_final: 0.7943 (mtt) REVERT: 2B 59 MET cc_start: 0.8440 (mtt) cc_final: 0.8080 (mtt) REVERT: 2E 59 MET cc_start: 0.8283 (mtt) cc_final: 0.7754 (mtt) REVERT: 2H 107 MET cc_start: 0.8877 (ttt) cc_final: 0.8619 (ttt) REVERT: 2J 59 MET cc_start: 0.8545 (mtt) cc_final: 0.8247 (mtt) REVERT: 2K 59 MET cc_start: 0.8426 (mtt) cc_final: 0.8192 (mtt) REVERT: 3B 115 LYS cc_start: 0.8519 (mtpp) cc_final: 0.8147 (ttpp) REVERT: 3E 107 MET cc_start: 0.8879 (ttt) cc_final: 0.8616 (ttp) REVERT: 3G 107 MET cc_start: 0.8814 (ttt) cc_final: 0.8389 (ttp) REVERT: 3J 107 MET cc_start: 0.8755 (ttt) cc_final: 0.8478 (ttp) REVERT: 4B 115 LYS cc_start: 0.8312 (mtpp) cc_final: 0.7948 (ttpp) REVERT: 4C 83 ILE cc_start: 0.8936 (mm) cc_final: 0.8730 (mm) REVERT: 4G 59 MET cc_start: 0.8391 (mtt) cc_final: 0.8005 (mtt) REVERT: 4H 59 MET cc_start: 0.8381 (mtt) cc_final: 0.7982 (mtt) REVERT: 4I 59 MET cc_start: 0.8354 (mtt) cc_final: 0.7993 (mtt) REVERT: 4I 88 MET cc_start: 0.7916 (ptt) cc_final: 0.7708 (ptt) REVERT: 4K 59 MET cc_start: 0.8591 (mtt) cc_final: 0.8303 (mtt) REVERT: 4L 73 GLN cc_start: 0.8475 (mt0) cc_final: 0.8275 (mm110) REVERT: 4M 115 LYS cc_start: 0.8280 (ttpp) cc_final: 0.8058 (ttmm) REVERT: 5G 59 MET cc_start: 0.8380 (mtt) cc_final: 0.8179 (mtt) REVERT: 5G 107 MET cc_start: 0.8740 (ttt) cc_final: 0.8515 (ttp) REVERT: 5N 61 ASN cc_start: 0.8205 (m-40) cc_final: 0.7894 (m-40) outliers start: 30 outliers final: 14 residues processed: 712 average time/residue: 0.5230 time to fit residues: 586.3354 Evaluate side-chains 635 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 621 time to evaluate : 3.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 55 ASP Chi-restraints excluded: chain 1A residue 111 SER Chi-restraints excluded: chain 1B residue 55 ASP Chi-restraints excluded: chain 2A residue 55 ASP Chi-restraints excluded: chain 2B residue 55 ASP Chi-restraints excluded: chain 3A residue 55 ASP Chi-restraints excluded: chain 3A residue 111 SER Chi-restraints excluded: chain 3N residue 74 SER Chi-restraints excluded: chain 4A residue 55 ASP Chi-restraints excluded: chain 4M residue 88 MET Chi-restraints excluded: chain 5A residue 55 ASP Chi-restraints excluded: chain 5A residue 111 SER Chi-restraints excluded: chain 5B residue 55 ASP Chi-restraints excluded: chain 5N residue 74 SER 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: 0.8980 chunk 370 optimal weight: 3.9990 chunk 303 optimal weight: 9.9990 chunk 122 optimal weight: 0.9990 chunk 445 optimal weight: 0.8980 chunk 481 optimal weight: 5.9990 chunk 397 optimal weight: 5.9990 chunk 442 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 chunk 357 optimal weight: 7.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3B 61 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 37730 Z= 0.142 Angle : 0.412 6.278 50330 Z= 0.217 Chirality : 0.034 0.112 5670 Planarity : 0.003 0.022 6020 Dihedral : 23.187 179.713 7910 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.57 % Allowed : 9.88 % Favored : 89.55 % 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: 2.89 (0.12), residues: 4760 helix: 2.44 (0.08), residues: 3990 sheet: None (None), residues: 0 loop : -1.05 (0.17), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP4N 87 PHE 0.009 0.001 PHE1C 89 ARG 0.002 0.000 ARG2G 91 *********************** 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 641 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 622 time to evaluate : 3.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1A 59 MET cc_start: 0.8673 (mtt) cc_final: 0.8230 (mtt) REVERT: 1A 68 LEU cc_start: 0.8778 (mt) cc_final: 0.8535 (mt) REVERT: 1F 107 MET cc_start: 0.8810 (ttt) cc_final: 0.8592 (ttp) REVERT: 1J 107 MET cc_start: 0.8791 (ttt) cc_final: 0.8573 (ttp) REVERT: 1L 107 MET cc_start: 0.8823 (ttt) cc_final: 0.8531 (ttt) REVERT: 1N 61 ASN cc_start: 0.8553 (m-40) cc_final: 0.8312 (m-40) REVERT: 2A 59 MET cc_start: 0.8737 (mtt) cc_final: 0.8106 (mtt) REVERT: 2B 59 MET cc_start: 0.8521 (mtt) cc_final: 0.8152 (mtt) REVERT: 2B 115 LYS cc_start: 0.8543 (mtpp) cc_final: 0.8225 (ttpp) REVERT: 2E 59 MET cc_start: 0.8281 (mtt) cc_final: 0.7909 (mtt) REVERT: 2J 59 MET cc_start: 0.8571 (mtt) cc_final: 0.8312 (mtt) REVERT: 2N 61 ASN cc_start: 0.8308 (m-40) cc_final: 0.8063 (m-40) REVERT: 3B 115 LYS cc_start: 0.8406 (mtpp) cc_final: 0.8125 (ttpp) REVERT: 3E 107 MET cc_start: 0.8854 (ttt) cc_final: 0.8611 (ttp) REVERT: 3G 107 MET cc_start: 0.8815 (ttt) cc_final: 0.8360 (ttp) REVERT: 3J 107 MET cc_start: 0.8717 (ttt) cc_final: 0.8457 (ttp) REVERT: 4B 61 ASN cc_start: 0.8337 (m-40) cc_final: 0.8115 (m-40) REVERT: 4B 115 LYS cc_start: 0.8355 (mtpp) cc_final: 0.8001 (ttpp) REVERT: 4G 59 MET cc_start: 0.8390 (mtt) cc_final: 0.8085 (mtt) REVERT: 4H 59 MET cc_start: 0.8420 (mtt) cc_final: 0.8025 (mtt) REVERT: 4I 59 MET cc_start: 0.8328 (mtt) cc_final: 0.8055 (mtt) REVERT: 4K 59 MET cc_start: 0.8579 (mtt) cc_final: 0.8307 (mtt) REVERT: 4L 73 GLN cc_start: 0.8478 (mt0) cc_final: 0.8250 (mm-40) REVERT: 5G 59 MET cc_start: 0.8339 (mtt) cc_final: 0.8047 (mtt) REVERT: 5N 61 ASN cc_start: 0.8143 (m-40) cc_final: 0.7917 (m-40) outliers start: 19 outliers final: 17 residues processed: 637 average time/residue: 0.5962 time to fit residues: 594.2546 Evaluate side-chains 604 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 587 time to evaluate : 4.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 55 ASP Chi-restraints excluded: chain 1A residue 111 SER Chi-restraints excluded: chain 1B residue 55 ASP Chi-restraints excluded: chain 2A residue 55 ASP Chi-restraints excluded: chain 2B residue 55 ASP Chi-restraints excluded: chain 3A residue 55 ASP Chi-restraints excluded: chain 3A residue 111 SER Chi-restraints excluded: chain 3K residue 116 THR Chi-restraints excluded: chain 3M residue 59 MET Chi-restraints excluded: chain 3N residue 74 SER Chi-restraints excluded: chain 4A residue 55 ASP Chi-restraints excluded: chain 4A residue 85 ILE Chi-restraints excluded: chain 4M residue 83 ILE Chi-restraints excluded: chain 5A residue 55 ASP Chi-restraints excluded: chain 5A residue 111 SER Chi-restraints excluded: chain 5B residue 55 ASP Chi-restraints excluded: chain 5N residue 74 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 440 optimal weight: 2.9990 chunk 335 optimal weight: 0.9990 chunk 231 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 chunk 212 optimal weight: 2.9990 chunk 299 optimal weight: 8.9990 chunk 447 optimal weight: 5.9990 chunk 473 optimal weight: 0.0770 chunk 233 optimal weight: 0.9980 chunk 424 optimal weight: 0.8980 chunk 127 optimal weight: 9.9990 overall best weight: 1.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2M 61 ASN 4L 61 ASN 4M 61 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 37730 Z= 0.143 Angle : 0.407 6.319 50330 Z= 0.213 Chirality : 0.034 0.111 5670 Planarity : 0.003 0.022 6020 Dihedral : 21.716 178.864 7910 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.57 % Allowed : 12.80 % Favored : 86.64 % 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: 2.97 (0.12), residues: 4760 helix: 2.51 (0.08), residues: 3990 sheet: None (None), residues: 0 loop : -1.13 (0.17), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP4N 87 PHE 0.010 0.001 PHE5A 112 ARG 0.001 0.000 ARG3N 91 *********************** 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 628 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 609 time to evaluate : 4.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1A 59 MET cc_start: 0.8649 (mtt) cc_final: 0.8273 (mtt) REVERT: 1A 68 LEU cc_start: 0.8777 (mt) cc_final: 0.8519 (mt) REVERT: 1J 107 MET cc_start: 0.8800 (ttt) cc_final: 0.8555 (ttp) REVERT: 1L 107 MET cc_start: 0.8817 (ttt) cc_final: 0.8519 (ttt) REVERT: 1N 61 ASN cc_start: 0.8528 (m-40) cc_final: 0.8324 (m-40) REVERT: 2A 59 MET cc_start: 0.8746 (mtt) cc_final: 0.8148 (mtt) REVERT: 2B 59 MET cc_start: 0.8517 (mtt) cc_final: 0.8060 (mtt) REVERT: 2E 59 MET cc_start: 0.8199 (mtt) cc_final: 0.7731 (mtt) REVERT: 2J 59 MET cc_start: 0.8549 (mtt) cc_final: 0.8258 (mtt) REVERT: 2N 61 ASN cc_start: 0.8338 (m-40) cc_final: 0.8127 (m-40) REVERT: 3B 115 LYS cc_start: 0.8414 (mtpp) cc_final: 0.8164 (ttpp) REVERT: 3E 107 MET cc_start: 0.8855 (ttt) cc_final: 0.8594 (ttp) REVERT: 3F 59 MET cc_start: 0.8340 (mtt) cc_final: 0.7875 (mtt) REVERT: 3G 107 MET cc_start: 0.8811 (ttt) cc_final: 0.8364 (ttp) REVERT: 3J 107 MET cc_start: 0.8688 (ttt) cc_final: 0.8416 (ttp) REVERT: 4B 61 ASN cc_start: 0.8265 (m-40) cc_final: 0.8037 (m-40) REVERT: 4B 115 LYS cc_start: 0.8399 (mtpp) cc_final: 0.8055 (ttpp) REVERT: 4G 59 MET cc_start: 0.8327 (mtt) cc_final: 0.8019 (mtt) REVERT: 4H 59 MET cc_start: 0.8389 (mtt) cc_final: 0.7951 (mtt) REVERT: 4H 107 MET cc_start: 0.8902 (ttt) cc_final: 0.8637 (ttp) REVERT: 4I 59 MET cc_start: 0.8316 (mtt) cc_final: 0.8000 (mtt) REVERT: 4J 107 MET cc_start: 0.8709 (ttt) cc_final: 0.8475 (ttp) REVERT: 4K 59 MET cc_start: 0.8544 (mtt) cc_final: 0.8212 (mtt) REVERT: 4L 73 GLN cc_start: 0.8520 (mt0) cc_final: 0.8274 (mm-40) REVERT: 5G 59 MET cc_start: 0.8281 (mtt) cc_final: 0.7883 (mtt) REVERT: 5N 61 ASN cc_start: 0.8080 (m-40) cc_final: 0.7870 (m-40) outliers start: 19 outliers final: 15 residues processed: 624 average time/residue: 0.5630 time to fit residues: 545.0449 Evaluate side-chains 593 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 578 time to evaluate : 3.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 55 ASP Chi-restraints excluded: chain 1A residue 111 SER Chi-restraints excluded: chain 1B residue 55 ASP Chi-restraints excluded: chain 2A residue 55 ASP Chi-restraints excluded: chain 2B residue 55 ASP Chi-restraints excluded: chain 2I residue 83 ILE Chi-restraints excluded: chain 2K residue 96 LEU Chi-restraints excluded: chain 3A residue 55 ASP Chi-restraints excluded: chain 3A residue 111 SER Chi-restraints excluded: chain 4A residue 55 ASP Chi-restraints excluded: chain 4M residue 83 ILE Chi-restraints excluded: chain 5A residue 55 ASP Chi-restraints excluded: chain 5A residue 97 VAL Chi-restraints excluded: chain 5A residue 111 SER Chi-restraints excluded: chain 5B residue 55 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 394 optimal weight: 1.9990 chunk 268 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 352 optimal weight: 0.8980 chunk 195 optimal weight: 3.9990 chunk 404 optimal weight: 2.9990 chunk 327 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 241 optimal weight: 7.9990 chunk 425 optimal weight: 3.9990 chunk 119 optimal weight: 8.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4L 61 ASN 4M 61 ASN 5B 73 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 37730 Z= 0.219 Angle : 0.457 5.586 50330 Z= 0.241 Chirality : 0.035 0.119 5670 Planarity : 0.003 0.022 6020 Dihedral : 21.675 175.046 7910 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.01 % Allowed : 15.03 % Favored : 83.96 % 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: 2.70 (0.12), residues: 4760 helix: 2.34 (0.08), residues: 3990 sheet: None (None), residues: 0 loop : -1.32 (0.17), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP3M 87 PHE 0.011 0.001 PHE3L 89 ARG 0.004 0.000 ARG2C 91 *********************** 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 632 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 598 time to evaluate : 4.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1A 59 MET cc_start: 0.8712 (mtt) cc_final: 0.8299 (mtt) REVERT: 1B 59 MET cc_start: 0.8457 (mtt) cc_final: 0.8240 (mtt) REVERT: 1J 107 MET cc_start: 0.8809 (ttt) cc_final: 0.8423 (ttp) REVERT: 1L 107 MET cc_start: 0.8836 (ttt) cc_final: 0.8549 (ttt) REVERT: 1N 61 ASN cc_start: 0.8543 (m-40) cc_final: 0.8298 (m-40) REVERT: 2A 59 MET cc_start: 0.8786 (mtt) cc_final: 0.8227 (mtt) REVERT: 2B 59 MET cc_start: 0.8674 (mtt) cc_final: 0.8234 (mtt) REVERT: 2E 59 MET cc_start: 0.8232 (mtt) cc_final: 0.7873 (mtt) REVERT: 2J 59 MET cc_start: 0.8645 (mtt) cc_final: 0.8361 (mtt) REVERT: 2N 61 ASN cc_start: 0.8464 (m-40) cc_final: 0.8196 (m-40) REVERT: 3B 115 LYS cc_start: 0.8448 (mtpp) cc_final: 0.8213 (ttpp) REVERT: 3E 107 MET cc_start: 0.8868 (ttt) cc_final: 0.8520 (ttp) REVERT: 3F 59 MET cc_start: 0.8404 (mtt) cc_final: 0.7995 (mtt) REVERT: 3G 107 MET cc_start: 0.8843 (ttt) cc_final: 0.8584 (ttp) REVERT: 3J 107 MET cc_start: 0.8689 (ttt) cc_final: 0.8416 (ttp) REVERT: 4B 115 LYS cc_start: 0.8436 (mtpp) cc_final: 0.8083 (ttpp) REVERT: 4G 59 MET cc_start: 0.8423 (mtt) cc_final: 0.8130 (mtt) REVERT: 4H 59 MET cc_start: 0.8464 (mtt) cc_final: 0.8028 (mtt) REVERT: 4I 59 MET cc_start: 0.8399 (mtt) cc_final: 0.8038 (mtt) REVERT: 4K 59 MET cc_start: 0.8603 (mtt) cc_final: 0.8255 (mtt) REVERT: 4L 73 GLN cc_start: 0.8657 (mt0) cc_final: 0.8352 (mm-40) REVERT: 5N 61 ASN cc_start: 0.8125 (m-40) cc_final: 0.7911 (m-40) outliers start: 34 outliers final: 24 residues processed: 622 average time/residue: 0.5472 time to fit residues: 527.7118 Evaluate side-chains 601 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 577 time to evaluate : 3.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 55 ASP Chi-restraints excluded: chain 1A residue 111 SER Chi-restraints excluded: chain 1B residue 55 ASP Chi-restraints excluded: chain 1D residue 54 THR Chi-restraints excluded: chain 1J residue 116 THR Chi-restraints excluded: chain 1M residue 116 THR Chi-restraints excluded: chain 2A residue 55 ASP Chi-restraints excluded: chain 2B residue 55 ASP Chi-restraints excluded: chain 2I residue 83 ILE Chi-restraints excluded: chain 2K residue 96 LEU Chi-restraints excluded: chain 3A residue 55 ASP Chi-restraints excluded: chain 3A residue 111 SER Chi-restraints excluded: chain 3I residue 116 THR Chi-restraints excluded: chain 3J residue 116 THR Chi-restraints excluded: chain 4A residue 55 ASP Chi-restraints excluded: chain 4M residue 83 ILE Chi-restraints excluded: chain 5A residue 55 ASP Chi-restraints excluded: chain 5A residue 97 VAL Chi-restraints excluded: chain 5A residue 111 SER Chi-restraints excluded: chain 5B residue 55 ASP Chi-restraints excluded: chain 5B residue 88 MET Chi-restraints excluded: chain 5I residue 67 ILE Chi-restraints excluded: chain 5M residue 116 THR Chi-restraints excluded: chain 5N residue 74 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 159 optimal weight: 0.9990 chunk 426 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 278 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 474 optimal weight: 7.9990 chunk 393 optimal weight: 9.9990 chunk 219 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 156 optimal weight: 0.9980 chunk 248 optimal weight: 6.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2B 73 GLN 3B 73 GLN 4L 61 ASN 4M 61 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 37730 Z= 0.187 Angle : 0.431 6.301 50330 Z= 0.227 Chirality : 0.034 0.113 5670 Planarity : 0.003 0.020 6020 Dihedral : 20.718 176.386 7910 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.13 % Allowed : 16.01 % Favored : 82.86 % 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: 2.72 (0.12), residues: 4760 helix: 2.36 (0.08), residues: 3990 sheet: None (None), residues: 0 loop : -1.38 (0.17), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP5N 87 PHE 0.010 0.001 PHE5A 112 ARG 0.002 0.000 ARG5C 91 *********************** 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 614 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 576 time to evaluate : 3.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1A 59 MET cc_start: 0.8740 (mtt) cc_final: 0.8340 (mtt) REVERT: 1B 59 MET cc_start: 0.8514 (mtt) cc_final: 0.8275 (mtt) REVERT: 1J 107 MET cc_start: 0.8831 (ttt) cc_final: 0.8449 (ttp) REVERT: 1L 107 MET cc_start: 0.8818 (ttt) cc_final: 0.8528 (ttt) REVERT: 1N 61 ASN cc_start: 0.8515 (m-40) cc_final: 0.8272 (m-40) REVERT: 2A 59 MET cc_start: 0.8773 (mtt) cc_final: 0.8208 (mtt) REVERT: 2B 59 MET cc_start: 0.8644 (mtt) cc_final: 0.8184 (mtt) REVERT: 2E 59 MET cc_start: 0.8235 (mtt) cc_final: 0.7805 (mtt) REVERT: 2G 91 ARG cc_start: 0.6915 (OUTLIER) cc_final: 0.6704 (tpm170) REVERT: 2J 59 MET cc_start: 0.8598 (mtt) cc_final: 0.8322 (mtt) REVERT: 2N 61 ASN cc_start: 0.8440 (m-40) cc_final: 0.8151 (m-40) REVERT: 3B 60 VAL cc_start: 0.8485 (m) cc_final: 0.8276 (m) REVERT: 3B 115 LYS cc_start: 0.8432 (mtpp) cc_final: 0.8213 (ttpp) REVERT: 3E 107 MET cc_start: 0.8873 (ttt) cc_final: 0.8547 (ttp) REVERT: 3G 107 MET cc_start: 0.8801 (ttt) cc_final: 0.8563 (ttp) REVERT: 3J 107 MET cc_start: 0.8667 (ttt) cc_final: 0.8404 (ttp) REVERT: 4B 115 LYS cc_start: 0.8441 (mtpp) cc_final: 0.8089 (ttpp) REVERT: 4H 59 MET cc_start: 0.8400 (mtt) cc_final: 0.7956 (mtt) REVERT: 4I 59 MET cc_start: 0.8357 (mtt) cc_final: 0.7988 (mtt) REVERT: 4K 59 MET cc_start: 0.8547 (mtt) cc_final: 0.8196 (mtt) REVERT: 4M 115 LYS cc_start: 0.8291 (ttpp) cc_final: 0.7871 (ttmm) outliers start: 38 outliers final: 32 residues processed: 601 average time/residue: 0.5449 time to fit residues: 506.5791 Evaluate side-chains 594 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 561 time to evaluate : 3.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 55 ASP Chi-restraints excluded: chain 1A residue 111 SER Chi-restraints excluded: chain 1B residue 55 ASP Chi-restraints excluded: chain 1B residue 88 MET Chi-restraints excluded: chain 1D residue 54 THR Chi-restraints excluded: chain 1J residue 116 THR Chi-restraints excluded: chain 1N residue 115 LYS Chi-restraints excluded: chain 2A residue 55 ASP Chi-restraints excluded: chain 2B residue 55 ASP Chi-restraints excluded: chain 2G residue 91 ARG Chi-restraints excluded: chain 2I residue 83 ILE Chi-restraints excluded: chain 2K residue 96 LEU Chi-restraints excluded: chain 3A residue 55 ASP Chi-restraints excluded: chain 3A residue 111 SER Chi-restraints excluded: chain 3F residue 67 ILE Chi-restraints excluded: chain 3I residue 116 THR Chi-restraints excluded: chain 3J residue 116 THR Chi-restraints excluded: chain 3K residue 116 THR Chi-restraints excluded: chain 3M residue 59 MET Chi-restraints excluded: chain 3M residue 116 THR Chi-restraints excluded: chain 3N residue 74 SER Chi-restraints excluded: chain 4A residue 55 ASP Chi-restraints excluded: chain 4A residue 88 MET Chi-restraints excluded: chain 4L residue 116 THR Chi-restraints excluded: chain 4M residue 83 ILE Chi-restraints excluded: chain 5A residue 55 ASP Chi-restraints excluded: chain 5A residue 97 VAL Chi-restraints excluded: chain 5A residue 111 SER Chi-restraints excluded: chain 5B residue 55 ASP Chi-restraints excluded: chain 5B residue 88 MET Chi-restraints excluded: chain 5H residue 116 THR Chi-restraints excluded: chain 5M residue 116 THR Chi-restraints excluded: chain 5N residue 74 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 457 optimal weight: 4.9990 chunk 53 optimal weight: 0.5980 chunk 270 optimal weight: 0.9980 chunk 346 optimal weight: 6.9990 chunk 268 optimal weight: 2.9990 chunk 399 optimal weight: 10.0000 chunk 264 optimal weight: 0.9990 chunk 472 optimal weight: 4.9990 chunk 295 optimal weight: 6.9990 chunk 287 optimal weight: 20.0000 chunk 218 optimal weight: 8.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3A 73 GLN 4L 61 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 37730 Z= 0.215 Angle : 0.457 5.589 50330 Z= 0.240 Chirality : 0.035 0.121 5670 Planarity : 0.003 0.020 6020 Dihedral : 20.414 175.974 7910 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.40 % Allowed : 16.28 % Favored : 82.32 % 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: 2.61 (0.12), residues: 4760 helix: 2.31 (0.08), residues: 3990 sheet: None (None), residues: 0 loop : -1.52 (0.17), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP5N 87 PHE 0.011 0.001 PHE5A 112 ARG 0.002 0.000 ARG5C 91 *********************** 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 632 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 585 time to evaluate : 3.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1A 59 MET cc_start: 0.8757 (mtt) cc_final: 0.8360 (mtt) REVERT: 1J 107 MET cc_start: 0.8795 (ttt) cc_final: 0.8428 (ttp) REVERT: 1L 107 MET cc_start: 0.8844 (ttt) cc_final: 0.8545 (ttt) REVERT: 1N 61 ASN cc_start: 0.8516 (m-40) cc_final: 0.8286 (m-40) REVERT: 2A 59 MET cc_start: 0.8805 (mtt) cc_final: 0.8269 (mtt) REVERT: 2B 59 MET cc_start: 0.8658 (mtt) cc_final: 0.8201 (mtt) REVERT: 2F 107 MET cc_start: 0.8911 (ttt) cc_final: 0.8707 (ttt) REVERT: 2G 91 ARG cc_start: 0.6954 (OUTLIER) cc_final: 0.6746 (tpm170) REVERT: 2J 59 MET cc_start: 0.8642 (mtt) cc_final: 0.8363 (mtt) REVERT: 2N 61 ASN cc_start: 0.8462 (m-40) cc_final: 0.8176 (m-40) REVERT: 3B 60 VAL cc_start: 0.8632 (m) cc_final: 0.8429 (m) REVERT: 3E 107 MET cc_start: 0.8915 (ttt) cc_final: 0.8567 (ttp) REVERT: 3G 107 MET cc_start: 0.8840 (ttt) cc_final: 0.8586 (ttp) REVERT: 3J 107 MET cc_start: 0.8678 (ttt) cc_final: 0.8418 (ttp) REVERT: 4B 115 LYS cc_start: 0.8452 (mtpp) cc_final: 0.8092 (ttpp) REVERT: 4H 59 MET cc_start: 0.8452 (mtt) cc_final: 0.7988 (mtt) REVERT: 4I 59 MET cc_start: 0.8398 (mtt) cc_final: 0.8037 (mtt) REVERT: 4J 115 LYS cc_start: 0.7993 (mtpp) cc_final: 0.7776 (mtpt) REVERT: 4K 59 MET cc_start: 0.8584 (mtt) cc_final: 0.8238 (mtt) REVERT: 4M 115 LYS cc_start: 0.8302 (ttpp) cc_final: 0.7886 (ttmm) outliers start: 47 outliers final: 39 residues processed: 618 average time/residue: 0.5306 time to fit residues: 508.2421 Evaluate side-chains 613 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 573 time to evaluate : 3.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 55 ASP Chi-restraints excluded: chain 1A residue 111 SER Chi-restraints excluded: chain 1B residue 55 ASP Chi-restraints excluded: chain 1B residue 88 MET Chi-restraints excluded: chain 1D residue 54 THR Chi-restraints excluded: chain 1D residue 55 ASP Chi-restraints excluded: chain 1J residue 116 THR Chi-restraints excluded: chain 1M residue 116 THR Chi-restraints excluded: chain 1N residue 115 LYS Chi-restraints excluded: chain 2A residue 55 ASP Chi-restraints excluded: chain 2B residue 55 ASP Chi-restraints excluded: chain 2D residue 55 ASP Chi-restraints excluded: chain 2G residue 91 ARG Chi-restraints excluded: chain 2I residue 83 ILE Chi-restraints excluded: chain 2J residue 116 THR Chi-restraints excluded: chain 2K residue 96 LEU Chi-restraints excluded: chain 3A residue 55 ASP Chi-restraints excluded: chain 3A residue 111 SER Chi-restraints excluded: chain 3F residue 67 ILE Chi-restraints excluded: chain 3I residue 67 ILE Chi-restraints excluded: chain 3I residue 88 MET Chi-restraints excluded: chain 3I residue 116 THR Chi-restraints excluded: chain 3J residue 116 THR Chi-restraints excluded: chain 3K residue 116 THR Chi-restraints excluded: chain 3M residue 59 MET Chi-restraints excluded: chain 3M residue 116 THR Chi-restraints excluded: chain 3N residue 74 SER Chi-restraints excluded: chain 4A residue 55 ASP Chi-restraints excluded: chain 4D residue 55 ASP Chi-restraints excluded: chain 4L residue 116 THR Chi-restraints excluded: chain 4M residue 83 ILE Chi-restraints excluded: chain 5A residue 55 ASP Chi-restraints excluded: chain 5A residue 97 VAL Chi-restraints excluded: chain 5A residue 107 MET Chi-restraints excluded: chain 5A residue 111 SER Chi-restraints excluded: chain 5B residue 55 ASP Chi-restraints excluded: chain 5B residue 88 MET Chi-restraints excluded: chain 5H residue 116 THR Chi-restraints excluded: chain 5I residue 67 ILE Chi-restraints excluded: chain 5M residue 116 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 292 optimal weight: 10.0000 chunk 188 optimal weight: 0.9990 chunk 282 optimal weight: 4.9990 chunk 142 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 300 optimal weight: 4.9990 chunk 321 optimal weight: 5.9990 chunk 233 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 371 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3A 73 GLN 4B 73 GLN 4L 61 ASN 4M 61 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 37730 Z= 0.268 Angle : 0.492 6.644 50330 Z= 0.259 Chirality : 0.036 0.123 5670 Planarity : 0.003 0.020 6020 Dihedral : 20.442 165.324 7910 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.67 % Allowed : 16.34 % Favored : 81.99 % 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: 2.41 (0.12), residues: 4760 helix: 2.18 (0.09), residues: 3990 sheet: None (None), residues: 0 loop : -1.69 (0.17), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP5N 87 PHE 0.012 0.001 PHE1L 89 ARG 0.001 0.000 ARG4G 91 *********************** 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 648 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 592 time to evaluate : 4.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1A 59 MET cc_start: 0.8766 (mtt) cc_final: 0.8385 (mtt) REVERT: 1A 93 SER cc_start: 0.7980 (p) cc_final: 0.7717 (m) REVERT: 1J 107 MET cc_start: 0.8775 (ttt) cc_final: 0.8411 (ttp) REVERT: 1L 107 MET cc_start: 0.8845 (ttt) cc_final: 0.8552 (ttt) REVERT: 1N 61 ASN cc_start: 0.8575 (m-40) cc_final: 0.8323 (m-40) REVERT: 2A 59 MET cc_start: 0.8850 (mtt) cc_final: 0.8334 (mtt) REVERT: 2F 107 MET cc_start: 0.8943 (ttt) cc_final: 0.8735 (ttt) REVERT: 2G 91 ARG cc_start: 0.6866 (OUTLIER) cc_final: 0.6665 (tpm170) REVERT: 2J 59 MET cc_start: 0.8673 (mtt) cc_final: 0.8407 (mtt) REVERT: 2N 61 ASN cc_start: 0.8473 (m-40) cc_final: 0.8176 (m-40) REVERT: 3E 107 MET cc_start: 0.8911 (ttt) cc_final: 0.8544 (ttp) REVERT: 3G 107 MET cc_start: 0.8860 (ttt) cc_final: 0.8603 (ttp) REVERT: 4B 115 LYS cc_start: 0.8474 (mtpp) cc_final: 0.8102 (ttpp) REVERT: 4H 59 MET cc_start: 0.8444 (mtt) cc_final: 0.7986 (mtt) REVERT: 4I 59 MET cc_start: 0.8399 (mtt) cc_final: 0.8026 (mtt) REVERT: 4K 59 MET cc_start: 0.8662 (mtt) cc_final: 0.8331 (mtt) REVERT: 4M 115 LYS cc_start: 0.8321 (ttpp) cc_final: 0.7918 (ttmm) REVERT: 5C 73 GLN cc_start: 0.8003 (mt0) cc_final: 0.7717 (mm-40) outliers start: 56 outliers final: 45 residues processed: 632 average time/residue: 0.5435 time to fit residues: 533.6070 Evaluate side-chains 627 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 581 time to evaluate : 3.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 55 ASP Chi-restraints excluded: chain 1A residue 111 SER Chi-restraints excluded: chain 1B residue 55 ASP Chi-restraints excluded: chain 1B residue 88 MET Chi-restraints excluded: chain 1C residue 97 VAL Chi-restraints excluded: chain 1D residue 54 THR Chi-restraints excluded: chain 1G residue 116 THR Chi-restraints excluded: chain 1J residue 116 THR Chi-restraints excluded: chain 1M residue 116 THR Chi-restraints excluded: chain 1N residue 115 LYS Chi-restraints excluded: chain 2A residue 55 ASP Chi-restraints excluded: chain 2B residue 55 ASP Chi-restraints excluded: chain 2D residue 55 ASP Chi-restraints excluded: chain 2G residue 91 ARG Chi-restraints excluded: chain 2I residue 55 ASP Chi-restraints excluded: chain 2I residue 83 ILE Chi-restraints excluded: chain 2J residue 116 THR Chi-restraints excluded: chain 2K residue 96 LEU Chi-restraints excluded: chain 3A residue 55 ASP Chi-restraints excluded: chain 3A residue 111 SER Chi-restraints excluded: chain 3E residue 55 ASP Chi-restraints excluded: chain 3F residue 67 ILE Chi-restraints excluded: chain 3I residue 67 ILE Chi-restraints excluded: chain 3I residue 116 THR Chi-restraints excluded: chain 3J residue 116 THR Chi-restraints excluded: chain 3K residue 116 THR Chi-restraints excluded: chain 3M residue 59 MET Chi-restraints excluded: chain 3M residue 116 THR Chi-restraints excluded: chain 3N residue 74 SER Chi-restraints excluded: chain 4A residue 55 ASP Chi-restraints excluded: chain 4A residue 83 ILE Chi-restraints excluded: chain 4D residue 55 ASP Chi-restraints excluded: chain 4E residue 55 ASP Chi-restraints excluded: chain 4L residue 116 THR Chi-restraints excluded: chain 4M residue 83 ILE Chi-restraints excluded: chain 5A residue 55 ASP Chi-restraints excluded: chain 5A residue 97 VAL Chi-restraints excluded: chain 5A residue 107 MET Chi-restraints excluded: chain 5A residue 111 SER Chi-restraints excluded: chain 5B residue 55 ASP Chi-restraints excluded: chain 5B residue 88 MET Chi-restraints excluded: chain 5E residue 55 ASP Chi-restraints excluded: chain 5H residue 116 THR Chi-restraints excluded: chain 5I residue 67 ILE Chi-restraints excluded: chain 5M residue 116 THR Chi-restraints excluded: chain 5N residue 74 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 429 optimal weight: 0.8980 chunk 452 optimal weight: 2.9990 chunk 412 optimal weight: 3.9990 chunk 440 optimal weight: 1.9990 chunk 264 optimal weight: 7.9990 chunk 191 optimal weight: 7.9990 chunk 345 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 397 optimal weight: 0.6980 chunk 416 optimal weight: 3.9990 chunk 438 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3A 73 GLN 4L 61 ASN 4M 61 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 37730 Z= 0.198 Angle : 0.444 5.673 50330 Z= 0.234 Chirality : 0.034 0.117 5670 Planarity : 0.003 0.019 6020 Dihedral : 19.548 174.311 7910 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.49 % Allowed : 16.73 % Favored : 81.79 % 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: 2.56 (0.12), residues: 4760 helix: 2.29 (0.08), residues: 3990 sheet: None (None), residues: 0 loop : -1.67 (0.17), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP5N 87 PHE 0.012 0.001 PHE1A 112 ARG 0.002 0.000 ARG3N 91 *********************** 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 622 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 572 time to evaluate : 3.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1A 59 MET cc_start: 0.8789 (mtt) cc_final: 0.8399 (mtt) REVERT: 1A 93 SER cc_start: 0.7887 (p) cc_final: 0.7660 (m) REVERT: 1J 107 MET cc_start: 0.8804 (ttt) cc_final: 0.8439 (ttp) REVERT: 1L 107 MET cc_start: 0.8845 (ttt) cc_final: 0.8546 (ttt) REVERT: 1N 61 ASN cc_start: 0.8536 (m-40) cc_final: 0.8302 (m-40) REVERT: 2A 59 MET cc_start: 0.8831 (mtt) cc_final: 0.8297 (mtt) REVERT: 2F 107 MET cc_start: 0.8935 (ttt) cc_final: 0.8716 (ttt) REVERT: 2G 91 ARG cc_start: 0.6905 (OUTLIER) cc_final: 0.6704 (tpm170) REVERT: 2J 59 MET cc_start: 0.8591 (mtt) cc_final: 0.8293 (mtt) REVERT: 2N 61 ASN cc_start: 0.8407 (m-40) cc_final: 0.8161 (m-40) REVERT: 3E 107 MET cc_start: 0.8936 (ttt) cc_final: 0.8602 (ttp) REVERT: 3G 107 MET cc_start: 0.8818 (ttt) cc_final: 0.8570 (ttp) REVERT: 4B 115 LYS cc_start: 0.8446 (mtpp) cc_final: 0.8104 (ttpp) REVERT: 4H 59 MET cc_start: 0.8426 (mtt) cc_final: 0.8018 (mtt) REVERT: 4I 59 MET cc_start: 0.8369 (mtt) cc_final: 0.7995 (mtt) REVERT: 4J 115 LYS cc_start: 0.8044 (mtpp) cc_final: 0.7841 (mtpt) REVERT: 4K 59 MET cc_start: 0.8535 (mtt) cc_final: 0.8212 (mtt) REVERT: 4M 115 LYS cc_start: 0.8286 (ttpp) cc_final: 0.7871 (ttmm) outliers start: 50 outliers final: 45 residues processed: 608 average time/residue: 0.5685 time to fit residues: 535.9302 Evaluate side-chains 606 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 560 time to evaluate : 3.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 55 ASP Chi-restraints excluded: chain 1A residue 111 SER Chi-restraints excluded: chain 1B residue 55 ASP Chi-restraints excluded: chain 1B residue 88 MET Chi-restraints excluded: chain 1C residue 97 VAL Chi-restraints excluded: chain 1D residue 54 THR Chi-restraints excluded: chain 1D residue 55 ASP Chi-restraints excluded: chain 1E residue 55 ASP Chi-restraints excluded: chain 1J residue 116 THR Chi-restraints excluded: chain 1M residue 116 THR Chi-restraints excluded: chain 1N residue 115 LYS Chi-restraints excluded: chain 2A residue 55 ASP Chi-restraints excluded: chain 2B residue 55 ASP Chi-restraints excluded: chain 2D residue 55 ASP Chi-restraints excluded: chain 2E residue 55 ASP Chi-restraints excluded: chain 2G residue 91 ARG Chi-restraints excluded: chain 2I residue 55 ASP Chi-restraints excluded: chain 2I residue 83 ILE Chi-restraints excluded: chain 2J residue 116 THR Chi-restraints excluded: chain 2K residue 96 LEU Chi-restraints excluded: chain 3A residue 55 ASP Chi-restraints excluded: chain 3A residue 111 SER Chi-restraints excluded: chain 3D residue 55 ASP Chi-restraints excluded: chain 3E residue 55 ASP Chi-restraints excluded: chain 3F residue 67 ILE Chi-restraints excluded: chain 3I residue 67 ILE Chi-restraints excluded: chain 3I residue 116 THR Chi-restraints excluded: chain 3J residue 116 THR Chi-restraints excluded: chain 3K residue 116 THR Chi-restraints excluded: chain 3M residue 59 MET Chi-restraints excluded: chain 3M residue 116 THR Chi-restraints excluded: chain 3N residue 74 SER Chi-restraints excluded: chain 4A residue 55 ASP Chi-restraints excluded: chain 4A residue 88 MET Chi-restraints excluded: chain 4L residue 116 THR Chi-restraints excluded: chain 4M residue 83 ILE Chi-restraints excluded: chain 4N residue 117 LEU Chi-restraints excluded: chain 5A residue 55 ASP Chi-restraints excluded: chain 5A residue 97 VAL Chi-restraints excluded: chain 5A residue 111 SER Chi-restraints excluded: chain 5B residue 55 ASP Chi-restraints excluded: chain 5B residue 88 MET Chi-restraints excluded: chain 5H residue 116 THR Chi-restraints excluded: chain 5I residue 67 ILE Chi-restraints excluded: chain 5K residue 107 MET Chi-restraints excluded: chain 5M residue 116 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 289 optimal weight: 9.9990 chunk 465 optimal weight: 5.9990 chunk 284 optimal weight: 0.7980 chunk 220 optimal weight: 0.8980 chunk 323 optimal weight: 6.9990 chunk 488 optimal weight: 0.0270 chunk 449 optimal weight: 0.9980 chunk 388 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 300 optimal weight: 9.9990 chunk 238 optimal weight: 0.4980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1B 73 GLN 2G 73 GLN 3A 73 GLN 3G 73 GLN 4L 61 ASN 5G 73 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 37730 Z= 0.114 Angle : 0.393 5.489 50330 Z= 0.205 Chirality : 0.033 0.105 5670 Planarity : 0.002 0.019 6020 Dihedral : 17.961 174.419 7910 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.95 % Allowed : 17.32 % Favored : 81.73 % 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: 2.94 (0.12), residues: 4760 helix: 2.55 (0.08), residues: 3990 sheet: None (None), residues: 0 loop : -1.53 (0.17), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP4M 87 PHE 0.011 0.001 PHE1A 112 ARG 0.002 0.000 ARG1L 91 ********************** 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 623 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 591 time to evaluate : 3.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1A 59 MET cc_start: 0.8593 (mtt) cc_final: 0.8263 (mtt) REVERT: 1J 107 MET cc_start: 0.8844 (ttt) cc_final: 0.8582 (ttp) REVERT: 1L 107 MET cc_start: 0.8776 (ttt) cc_final: 0.8503 (ttt) REVERT: 1N 61 ASN cc_start: 0.8459 (m-40) cc_final: 0.8239 (m-40) REVERT: 2A 59 MET cc_start: 0.8757 (mtt) cc_final: 0.8216 (mtt) REVERT: 2F 107 MET cc_start: 0.8910 (ttt) cc_final: 0.8691 (ttt) REVERT: 2G 91 ARG cc_start: 0.6867 (OUTLIER) cc_final: 0.6644 (tpm170) REVERT: 2I 107 MET cc_start: 0.8806 (ttp) cc_final: 0.8594 (ttp) REVERT: 2J 59 MET cc_start: 0.8492 (mtt) cc_final: 0.8189 (mtt) REVERT: 2N 61 ASN cc_start: 0.8363 (m-40) cc_final: 0.8146 (m-40) REVERT: 3A 105 VAL cc_start: 0.8918 (t) cc_final: 0.8702 (m) REVERT: 3E 107 MET cc_start: 0.8907 (ttt) cc_final: 0.8606 (ttp) REVERT: 3G 107 MET cc_start: 0.8816 (ttt) cc_final: 0.8565 (ttp) REVERT: 4B 115 LYS cc_start: 0.8462 (mtpp) cc_final: 0.8122 (ttpp) REVERT: 4H 59 MET cc_start: 0.8312 (mtt) cc_final: 0.7948 (mtt) REVERT: 4I 59 MET cc_start: 0.8268 (mtt) cc_final: 0.7904 (mtt) REVERT: 4K 59 MET cc_start: 0.8400 (mtt) cc_final: 0.8135 (mtt) REVERT: 4M 115 LYS cc_start: 0.8298 (ttpp) cc_final: 0.7882 (ttmm) outliers start: 32 outliers final: 26 residues processed: 614 average time/residue: 0.5669 time to fit residues: 539.2603 Evaluate side-chains 594 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 567 time to evaluate : 4.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 55 ASP Chi-restraints excluded: chain 1B residue 55 ASP Chi-restraints excluded: chain 1D residue 55 ASP Chi-restraints excluded: chain 1E residue 55 ASP Chi-restraints excluded: chain 1J residue 116 THR Chi-restraints excluded: chain 1M residue 116 THR Chi-restraints excluded: chain 1N residue 115 LYS Chi-restraints excluded: chain 2A residue 55 ASP Chi-restraints excluded: chain 2B residue 55 ASP Chi-restraints excluded: chain 2E residue 55 ASP Chi-restraints excluded: chain 2G residue 91 ARG Chi-restraints excluded: chain 2I residue 83 ILE Chi-restraints excluded: chain 2K residue 96 LEU Chi-restraints excluded: chain 3A residue 55 ASP Chi-restraints excluded: chain 3I residue 116 THR Chi-restraints excluded: chain 3J residue 116 THR Chi-restraints excluded: chain 3K residue 116 THR Chi-restraints excluded: chain 4A residue 55 ASP Chi-restraints excluded: chain 4D residue 55 ASP Chi-restraints excluded: chain 4L residue 116 THR Chi-restraints excluded: chain 4M residue 83 ILE Chi-restraints excluded: chain 5A residue 55 ASP Chi-restraints excluded: chain 5A residue 97 VAL Chi-restraints excluded: chain 5A residue 111 SER Chi-restraints excluded: chain 5B residue 55 ASP Chi-restraints excluded: chain 5H residue 116 THR Chi-restraints excluded: chain 5K residue 107 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 308 optimal weight: 0.1980 chunk 414 optimal weight: 1.9990 chunk 119 optimal weight: 7.9990 chunk 358 optimal weight: 8.9990 chunk 57 optimal weight: 0.8980 chunk 108 optimal weight: 10.0000 chunk 389 optimal weight: 9.9990 chunk 162 optimal weight: 5.9990 chunk 399 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5L 61 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.124536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.097832 restraints weight = 43413.755| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.49 r_work: 0.3046 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 37730 Z= 0.258 Angle : 0.489 7.469 50330 Z= 0.257 Chirality : 0.036 0.124 5670 Planarity : 0.003 0.020 6020 Dihedral : 18.846 168.204 7910 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.07 % Allowed : 17.41 % Favored : 81.52 % 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: 2.61 (0.13), residues: 4760 helix: 2.33 (0.09), residues: 3990 sheet: None (None), residues: 0 loop : -1.68 (0.17), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP5N 87 PHE 0.013 0.001 PHE5E 89 ARG 0.007 0.000 ARG4D 91 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9583.88 seconds wall clock time: 171 minutes 2.42 seconds (10262.42 seconds total)