Starting phenix.real_space_refine on Sat Mar 23 13:47:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cue_26999/03_2024/8cue_26999_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cue_26999/03_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_26999/03_2024/8cue_26999.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cue_26999/03_2024/8cue_26999.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cue_26999/03_2024/8cue_26999_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cue_26999/03_2024/8cue_26999_updated.pdb" } 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 16.75, per 1000 atoms: 0.45 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: 12.47 Conformation dependent library (CDL) restraints added in 6.1 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... running ksdssp... Secondary structure from input PDB file: 280 helices and 0 sheets defined 75.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.64 Creating SS restraints... Processing helix chain '1A' and resid 56 through 67 removed outlier: 3.554A pdb=" N ASN1A 61 " --> pdb=" O ALA1A 57 " (cutoff:3.500A) Processing helix chain '1A' and resid 70 through 87 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) Processing helix chain '1A' and resid 94 through 107 Processing helix chain '1A' and resid 110 through 118 Processing helix chain '1B' and resid 56 through 67 removed outlier: 3.554A pdb=" N ASN1B 61 " --> pdb=" O ALA1B 57 " (cutoff:3.500A) Processing helix chain '1B' and resid 70 through 87 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) Processing helix chain '1B' and resid 94 through 107 Processing helix chain '1B' and resid 110 through 118 Processing helix chain '1C' and resid 56 through 67 removed outlier: 3.554A pdb=" N ASN1C 61 " --> pdb=" O ALA1C 57 " (cutoff:3.500A) Processing helix chain '1C' and resid 70 through 87 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) Processing helix chain '1C' and resid 94 through 107 Processing helix chain '1C' and resid 110 through 118 Processing helix chain '1D' and resid 56 through 67 removed outlier: 3.554A pdb=" N ASN1D 61 " --> pdb=" O ALA1D 57 " (cutoff:3.500A) Processing helix chain '1D' and resid 70 through 87 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) Processing helix chain '1D' and resid 94 through 107 Processing helix chain '1D' and resid 110 through 118 Processing helix chain '1E' and resid 56 through 67 removed outlier: 3.554A pdb=" N ASN1E 61 " --> pdb=" O ALA1E 57 " (cutoff:3.500A) Processing helix chain '1E' and resid 70 through 87 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) Processing helix chain '1E' and resid 94 through 107 Processing helix chain '1E' and resid 110 through 118 Processing helix chain '1F' and resid 56 through 67 removed outlier: 3.554A pdb=" N ASN1F 61 " --> pdb=" O ALA1F 57 " (cutoff:3.500A) Processing helix chain '1F' and resid 70 through 87 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) Processing helix chain '1F' and resid 94 through 107 Processing helix chain '1F' and resid 110 through 118 Processing helix chain '1G' and resid 56 through 67 removed outlier: 3.555A pdb=" N ASN1G 61 " --> pdb=" O ALA1G 57 " (cutoff:3.500A) Processing helix chain '1G' and resid 70 through 87 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) Processing helix chain '1G' and resid 94 through 107 Processing helix chain '1G' and resid 110 through 118 Processing helix chain '1H' and resid 56 through 67 removed outlier: 3.555A pdb=" N ASN1H 61 " --> pdb=" O ALA1H 57 " (cutoff:3.500A) Processing helix chain '1H' and resid 70 through 87 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) Processing helix chain '1H' and resid 94 through 107 Processing helix chain '1H' and resid 110 through 118 Processing helix chain '1I' and resid 56 through 67 removed outlier: 3.554A pdb=" N ASN1I 61 " --> pdb=" O ALA1I 57 " (cutoff:3.500A) Processing helix chain '1I' and resid 70 through 87 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) Processing helix chain '1I' and resid 94 through 107 Processing helix chain '1I' and resid 110 through 118 Processing helix chain '1J' and resid 56 through 67 removed outlier: 3.553A pdb=" N ASN1J 61 " --> pdb=" O ALA1J 57 " (cutoff:3.500A) Processing helix chain '1J' and resid 70 through 87 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) Processing helix chain '1J' and resid 94 through 107 Processing helix chain '1J' and resid 110 through 118 Processing helix chain '1K' and resid 56 through 67 removed outlier: 3.553A pdb=" N ASN1K 61 " --> pdb=" O ALA1K 57 " (cutoff:3.500A) Processing helix chain '1K' and resid 70 through 87 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) Processing helix chain '1K' and resid 94 through 107 Processing helix chain '1K' and resid 110 through 118 Processing helix chain '1L' and resid 56 through 67 removed outlier: 3.554A pdb=" N ASN1L 61 " --> pdb=" O ALA1L 57 " (cutoff:3.500A) Processing helix chain '1L' and resid 70 through 87 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) Processing helix chain '1L' and resid 94 through 107 Processing helix chain '1L' and resid 110 through 118 Processing helix chain '1M' and resid 56 through 67 removed outlier: 3.554A pdb=" N ASN1M 61 " --> pdb=" O ALA1M 57 " (cutoff:3.500A) Processing helix chain '1M' and resid 70 through 87 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) Processing helix chain '1M' and resid 94 through 107 Processing helix chain '1M' and resid 110 through 118 Processing helix chain '1N' and resid 56 through 67 removed outlier: 3.554A pdb=" N ASN1N 61 " --> pdb=" O ALA1N 57 " (cutoff:3.500A) Processing helix chain '1N' and resid 70 through 87 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) Processing helix chain '1N' and resid 94 through 107 Processing helix chain '1N' and resid 110 through 118 Processing helix chain '2A' and resid 56 through 67 removed outlier: 3.554A pdb=" N ASN2A 61 " --> pdb=" O ALA2A 57 " (cutoff:3.500A) Processing helix chain '2A' and resid 70 through 87 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) Processing helix chain '2A' and resid 94 through 107 Processing helix chain '2A' and resid 110 through 118 Processing helix chain '2B' and resid 56 through 67 removed outlier: 3.555A pdb=" N ASN2B 61 " --> pdb=" O ALA2B 57 " (cutoff:3.500A) Processing helix chain '2B' and resid 70 through 87 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) Processing helix chain '2B' and resid 94 through 107 Processing helix chain '2B' and resid 110 through 118 Processing helix chain '2C' and resid 56 through 67 removed outlier: 3.554A pdb=" N ASN2C 61 " --> pdb=" O ALA2C 57 " (cutoff:3.500A) Processing helix chain '2C' and resid 70 through 87 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) Processing helix chain '2C' and resid 94 through 107 Processing helix chain '2C' and resid 110 through 118 Processing helix chain '2D' and resid 56 through 67 removed outlier: 3.554A pdb=" N ASN2D 61 " --> pdb=" O ALA2D 57 " (cutoff:3.500A) Processing helix chain '2D' and resid 70 through 87 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) Processing helix chain '2D' and resid 94 through 107 Processing helix chain '2D' and resid 110 through 118 Processing helix chain '2E' and resid 56 through 67 removed outlier: 3.553A pdb=" N ASN2E 61 " --> pdb=" O ALA2E 57 " (cutoff:3.500A) Processing helix chain '2E' and resid 70 through 87 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) Processing helix chain '2E' and resid 94 through 107 Processing helix chain '2E' and resid 110 through 118 Processing helix chain '2F' and resid 56 through 67 removed outlier: 3.553A pdb=" N ASN2F 61 " --> pdb=" O ALA2F 57 " (cutoff:3.500A) Processing helix chain '2F' and resid 70 through 87 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) Processing helix chain '2F' and resid 94 through 107 Processing helix chain '2F' and resid 110 through 118 Processing helix chain '2G' and resid 56 through 67 removed outlier: 3.553A pdb=" N ASN2G 61 " --> pdb=" O ALA2G 57 " (cutoff:3.500A) Processing helix chain '2G' and resid 70 through 87 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) Processing helix chain '2G' and resid 94 through 107 Processing helix chain '2G' and resid 110 through 118 Processing helix chain '2H' and resid 56 through 67 removed outlier: 3.554A pdb=" N ASN2H 61 " --> pdb=" O ALA2H 57 " (cutoff:3.500A) Processing helix chain '2H' and resid 70 through 87 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) Processing helix chain '2H' and resid 94 through 107 Processing helix chain '2H' and resid 110 through 118 Processing helix chain '2I' and resid 56 through 67 removed outlier: 3.554A pdb=" N ASN2I 61 " --> pdb=" O ALA2I 57 " (cutoff:3.500A) Processing helix chain '2I' and resid 70 through 87 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) Processing helix chain '2I' and resid 94 through 107 Processing helix chain '2I' and resid 110 through 118 Processing helix chain '2J' and resid 56 through 67 removed outlier: 3.554A pdb=" N ASN2J 61 " --> pdb=" O ALA2J 57 " (cutoff:3.500A) Processing helix chain '2J' and resid 70 through 87 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) Processing helix chain '2J' and resid 94 through 107 Processing helix chain '2J' and resid 110 through 118 Processing helix chain '2K' and resid 56 through 67 removed outlier: 3.554A pdb=" N ASN2K 61 " --> pdb=" O ALA2K 57 " (cutoff:3.500A) Processing helix chain '2K' and resid 70 through 87 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) Processing helix chain '2K' and resid 94 through 107 Processing helix chain '2K' and resid 110 through 118 Processing helix chain '2L' and resid 56 through 67 removed outlier: 3.554A pdb=" N ASN2L 61 " --> pdb=" O ALA2L 57 " (cutoff:3.500A) Processing helix chain '2L' and resid 70 through 87 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) Processing helix chain '2L' and resid 94 through 107 Processing helix chain '2L' and resid 110 through 118 Processing helix chain '2M' and resid 56 through 67 removed outlier: 3.554A pdb=" N ASN2M 61 " --> pdb=" O ALA2M 57 " (cutoff:3.500A) Processing helix chain '2M' and resid 70 through 87 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) Processing helix chain '2M' and resid 94 through 107 Processing helix chain '2M' and resid 110 through 118 Processing helix chain '2N' and resid 56 through 67 removed outlier: 3.554A pdb=" N ASN2N 61 " --> pdb=" O ALA2N 57 " (cutoff:3.500A) Processing helix chain '2N' and resid 70 through 87 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) Processing helix chain '2N' and resid 94 through 107 Processing helix chain '2N' and resid 110 through 118 Processing helix chain '3A' and resid 56 through 67 removed outlier: 3.553A pdb=" N ASN3A 61 " --> pdb=" O ALA3A 57 " (cutoff:3.500A) Processing helix chain '3A' and resid 70 through 87 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) Processing helix chain '3A' and resid 94 through 107 Processing helix chain '3A' and resid 110 through 118 Processing helix chain '3B' and resid 56 through 67 removed outlier: 3.554A pdb=" N ASN3B 61 " --> pdb=" O ALA3B 57 " (cutoff:3.500A) Processing helix chain '3B' and resid 70 through 87 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) Processing helix chain '3B' and resid 94 through 107 Processing helix chain '3B' and resid 110 through 118 Processing helix chain '3C' and resid 56 through 67 removed outlier: 3.554A pdb=" N ASN3C 61 " --> pdb=" O ALA3C 57 " (cutoff:3.500A) Processing helix chain '3C' and resid 70 through 87 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) Processing helix chain '3C' and resid 94 through 107 Processing helix chain '3C' and resid 110 through 118 Processing helix chain '3D' and resid 56 through 67 removed outlier: 3.554A pdb=" N ASN3D 61 " --> pdb=" O ALA3D 57 " (cutoff:3.500A) Processing helix chain '3D' and resid 70 through 87 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) Processing helix chain '3D' and resid 94 through 107 Processing helix chain '3D' and resid 110 through 118 Processing helix chain '3E' and resid 56 through 67 removed outlier: 3.554A pdb=" N ASN3E 61 " --> pdb=" O ALA3E 57 " (cutoff:3.500A) Processing helix chain '3E' and resid 70 through 87 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) Processing helix chain '3E' and resid 94 through 107 Processing helix chain '3E' and resid 110 through 118 Processing helix chain '3F' and resid 56 through 67 removed outlier: 3.553A pdb=" N ASN3F 61 " --> pdb=" O ALA3F 57 " (cutoff:3.500A) Processing helix chain '3F' and resid 70 through 87 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) Processing helix chain '3F' and resid 94 through 107 Processing helix chain '3F' and resid 110 through 118 Processing helix chain '3G' and resid 56 through 67 removed outlier: 3.554A pdb=" N ASN3G 61 " --> pdb=" O ALA3G 57 " (cutoff:3.500A) Processing helix chain '3G' and resid 70 through 87 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) Processing helix chain '3G' and resid 94 through 107 Processing helix chain '3G' and resid 110 through 118 Processing helix chain '3H' and resid 56 through 67 removed outlier: 3.553A pdb=" N ASN3H 61 " --> pdb=" O ALA3H 57 " (cutoff:3.500A) Processing helix chain '3H' and resid 70 through 87 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) Processing helix chain '3H' and resid 94 through 107 Processing helix chain '3H' and resid 110 through 118 Processing helix chain '3I' and resid 56 through 67 removed outlier: 3.554A pdb=" N ASN3I 61 " --> pdb=" O ALA3I 57 " (cutoff:3.500A) Processing helix chain '3I' and resid 70 through 87 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) Processing helix chain '3I' and resid 94 through 107 Processing helix chain '3I' and resid 110 through 118 Processing helix chain '3J' and resid 56 through 67 removed outlier: 3.554A pdb=" N ASN3J 61 " --> pdb=" O ALA3J 57 " (cutoff:3.500A) Processing helix chain '3J' and resid 70 through 87 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) Processing helix chain '3J' and resid 94 through 107 Processing helix chain '3J' and resid 110 through 118 Processing helix chain '3K' and resid 56 through 67 removed outlier: 3.554A pdb=" N ASN3K 61 " --> pdb=" O ALA3K 57 " (cutoff:3.500A) Processing helix chain '3K' and resid 70 through 87 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) Processing helix chain '3K' and resid 94 through 107 Processing helix chain '3K' and resid 110 through 118 Processing helix chain '3L' and resid 56 through 67 removed outlier: 3.554A pdb=" N ASN3L 61 " --> pdb=" O ALA3L 57 " (cutoff:3.500A) Processing helix chain '3L' and resid 70 through 87 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) Processing helix chain '3L' and resid 94 through 107 Processing helix chain '3L' and resid 110 through 118 Processing helix chain '3M' and resid 56 through 67 removed outlier: 3.554A pdb=" N ASN3M 61 " --> pdb=" O ALA3M 57 " (cutoff:3.500A) Processing helix chain '3M' and resid 70 through 87 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) Processing helix chain '3M' and resid 94 through 107 Processing helix chain '3M' and resid 110 through 118 Processing helix chain '3N' and resid 56 through 67 removed outlier: 3.554A pdb=" N ASN3N 61 " --> pdb=" O ALA3N 57 " (cutoff:3.500A) Processing helix chain '3N' and resid 70 through 87 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) Processing helix chain '3N' and resid 94 through 107 Processing helix chain '3N' and resid 110 through 118 Processing helix chain '4A' and resid 56 through 67 removed outlier: 3.553A pdb=" N ASN4A 61 " --> pdb=" O ALA4A 57 " (cutoff:3.500A) Processing helix chain '4A' and resid 70 through 87 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) Processing helix chain '4A' and resid 94 through 107 Processing helix chain '4A' and resid 110 through 118 Processing helix chain '4B' and resid 56 through 67 removed outlier: 3.554A pdb=" N ASN4B 61 " --> pdb=" O ALA4B 57 " (cutoff:3.500A) Processing helix chain '4B' and resid 70 through 87 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) Processing helix chain '4B' and resid 94 through 107 Processing helix chain '4B' and resid 110 through 118 Processing helix chain '4C' and resid 56 through 67 removed outlier: 3.554A pdb=" N ASN4C 61 " --> pdb=" O ALA4C 57 " (cutoff:3.500A) Processing helix chain '4C' and resid 70 through 87 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) Processing helix chain '4C' and resid 94 through 107 Processing helix chain '4C' and resid 110 through 118 Processing helix chain '4D' and resid 56 through 67 removed outlier: 3.554A pdb=" N ASN4D 61 " --> pdb=" O ALA4D 57 " (cutoff:3.500A) Processing helix chain '4D' and resid 70 through 87 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) Processing helix chain '4D' and resid 94 through 107 Processing helix chain '4D' and resid 110 through 118 Processing helix chain '4E' and resid 56 through 67 removed outlier: 3.554A pdb=" N ASN4E 61 " --> pdb=" O ALA4E 57 " (cutoff:3.500A) Processing helix chain '4E' and resid 70 through 87 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) Processing helix chain '4E' and resid 94 through 107 Processing helix chain '4E' and resid 110 through 118 Processing helix chain '4F' and resid 56 through 67 removed outlier: 3.554A pdb=" N ASN4F 61 " --> pdb=" O ALA4F 57 " (cutoff:3.500A) Processing helix chain '4F' and resid 70 through 87 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) Processing helix chain '4F' and resid 94 through 107 Processing helix chain '4F' and resid 110 through 118 Processing helix chain '4G' and resid 56 through 67 removed outlier: 3.554A pdb=" N ASN4G 61 " --> pdb=" O ALA4G 57 " (cutoff:3.500A) Processing helix chain '4G' and resid 70 through 87 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) Processing helix chain '4G' and resid 94 through 107 Processing helix chain '4G' and resid 110 through 118 Processing helix chain '4H' and resid 56 through 67 removed outlier: 3.554A pdb=" N ASN4H 61 " --> pdb=" O ALA4H 57 " (cutoff:3.500A) Processing helix chain '4H' and resid 70 through 87 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) Processing helix chain '4H' and resid 94 through 107 Processing helix chain '4H' and resid 110 through 118 Processing helix chain '4I' and resid 56 through 67 removed outlier: 3.554A pdb=" N ASN4I 61 " --> pdb=" O ALA4I 57 " (cutoff:3.500A) Processing helix chain '4I' and resid 70 through 87 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) Processing helix chain '4I' and resid 94 through 107 Processing helix chain '4I' and resid 110 through 118 Processing helix chain '4J' and resid 56 through 67 removed outlier: 3.554A pdb=" N ASN4J 61 " --> pdb=" O ALA4J 57 " (cutoff:3.500A) Processing helix chain '4J' and resid 70 through 87 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) Processing helix chain '4J' and resid 94 through 107 Processing helix chain '4J' and resid 110 through 118 Processing helix chain '4K' and resid 56 through 67 removed outlier: 3.554A pdb=" N ASN4K 61 " --> pdb=" O ALA4K 57 " (cutoff:3.500A) Processing helix chain '4K' and resid 70 through 87 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) Processing helix chain '4K' and resid 94 through 107 Processing helix chain '4K' and resid 110 through 118 Processing helix chain '4L' and resid 56 through 67 removed outlier: 3.554A pdb=" N ASN4L 61 " --> pdb=" O ALA4L 57 " (cutoff:3.500A) Processing helix chain '4L' and resid 70 through 87 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) Processing helix chain '4L' and resid 94 through 107 Processing helix chain '4L' and resid 110 through 118 Processing helix chain '4M' and resid 56 through 67 removed outlier: 3.554A pdb=" N ASN4M 61 " --> pdb=" O ALA4M 57 " (cutoff:3.500A) Processing helix chain '4M' and resid 70 through 87 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) Processing helix chain '4M' and resid 94 through 107 Processing helix chain '4M' and resid 110 through 118 Processing helix chain '4N' and resid 56 through 67 removed outlier: 3.554A pdb=" N ASN4N 61 " --> pdb=" O ALA4N 57 " (cutoff:3.500A) Processing helix chain '4N' and resid 70 through 87 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) Processing helix chain '4N' and resid 94 through 107 Processing helix chain '4N' and resid 110 through 118 Processing helix chain '5A' and resid 56 through 67 removed outlier: 3.553A pdb=" N ASN5A 61 " --> pdb=" O ALA5A 57 " (cutoff:3.500A) Processing helix chain '5A' and resid 70 through 87 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) Processing helix chain '5A' and resid 94 through 107 Processing helix chain '5A' and resid 110 through 118 Processing helix chain '5B' and resid 56 through 67 removed outlier: 3.553A pdb=" N ASN5B 61 " --> pdb=" O ALA5B 57 " (cutoff:3.500A) Processing helix chain '5B' and resid 70 through 87 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) Processing helix chain '5B' and resid 94 through 107 Processing helix chain '5B' and resid 110 through 118 Processing helix chain '5C' and resid 56 through 67 removed outlier: 3.555A pdb=" N ASN5C 61 " --> pdb=" O ALA5C 57 " (cutoff:3.500A) Processing helix chain '5C' and resid 70 through 87 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) Processing helix chain '5C' and resid 94 through 107 Processing helix chain '5C' and resid 110 through 118 Processing helix chain '5D' and resid 56 through 67 removed outlier: 3.554A pdb=" N ASN5D 61 " --> pdb=" O ALA5D 57 " (cutoff:3.500A) Processing helix chain '5D' and resid 70 through 87 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) Processing helix chain '5D' and resid 94 through 107 Processing helix chain '5D' and resid 110 through 118 Processing helix chain '5E' and resid 56 through 67 removed outlier: 3.555A pdb=" N ASN5E 61 " --> pdb=" O ALA5E 57 " (cutoff:3.500A) Processing helix chain '5E' and resid 70 through 87 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) Processing helix chain '5E' and resid 94 through 107 Processing helix chain '5E' and resid 110 through 118 Processing helix chain '5F' and resid 56 through 67 removed outlier: 3.554A pdb=" N ASN5F 61 " --> pdb=" O ALA5F 57 " (cutoff:3.500A) Processing helix chain '5F' and resid 70 through 87 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) Processing helix chain '5F' and resid 94 through 107 Processing helix chain '5F' and resid 110 through 118 Processing helix chain '5G' and resid 56 through 67 removed outlier: 3.553A pdb=" N ASN5G 61 " --> pdb=" O ALA5G 57 " (cutoff:3.500A) Processing helix chain '5G' and resid 70 through 87 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) Processing helix chain '5G' and resid 94 through 107 Processing helix chain '5G' and resid 110 through 118 Processing helix chain '5H' and resid 56 through 67 removed outlier: 3.554A pdb=" N ASN5H 61 " --> pdb=" O ALA5H 57 " (cutoff:3.500A) Processing helix chain '5H' and resid 70 through 87 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) Processing helix chain '5H' and resid 94 through 107 Processing helix chain '5H' and resid 110 through 118 Processing helix chain '5I' and resid 56 through 67 removed outlier: 3.553A pdb=" N ASN5I 61 " --> pdb=" O ALA5I 57 " (cutoff:3.500A) Processing helix chain '5I' and resid 70 through 87 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) Processing helix chain '5I' and resid 94 through 107 Processing helix chain '5I' and resid 110 through 118 Processing helix chain '5J' and resid 56 through 67 removed outlier: 3.554A pdb=" N ASN5J 61 " --> pdb=" O ALA5J 57 " (cutoff:3.500A) Processing helix chain '5J' and resid 70 through 87 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) Processing helix chain '5J' and resid 94 through 107 Processing helix chain '5J' and resid 110 through 118 Processing helix chain '5K' and resid 56 through 67 removed outlier: 3.554A pdb=" N ASN5K 61 " --> pdb=" O ALA5K 57 " (cutoff:3.500A) Processing helix chain '5K' and resid 70 through 87 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) Processing helix chain '5K' and resid 94 through 107 Processing helix chain '5K' and resid 110 through 118 Processing helix chain '5L' and resid 56 through 67 removed outlier: 3.554A pdb=" N ASN5L 61 " --> pdb=" O ALA5L 57 " (cutoff:3.500A) Processing helix chain '5L' and resid 70 through 87 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) Processing helix chain '5L' and resid 94 through 107 Processing helix chain '5L' and resid 110 through 118 Processing helix chain '5M' and resid 56 through 67 removed outlier: 3.554A pdb=" N ASN5M 61 " --> pdb=" O ALA5M 57 " (cutoff:3.500A) Processing helix chain '5M' and resid 70 through 87 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) Processing helix chain '5M' and resid 94 through 107 Processing helix chain '5M' and resid 110 through 118 Processing helix chain '5N' and resid 56 through 67 removed outlier: 3.555A pdb=" N ASN5N 61 " --> pdb=" O ALA5N 57 " (cutoff:3.500A) Processing helix chain '5N' and resid 70 through 87 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) Processing helix chain '5N' and resid 94 through 107 Processing helix chain '5N' and resid 110 through 118 2310 hydrogen bonds defined for protein. 6930 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: 12.01 Time building geometry restraints manager: 13.56 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: 20415 3.01 - 3.48: 35136 3.48 - 3.96: 57754 3.96 - 4.43: 64763 4.43 - 4.90: 108215 Nonbonded interactions: 286283 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 286278 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: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 5.890 Check model and map are aligned: 0.570 Set scattering table: 0.330 Process input model: 87.500 Find NCS groups from input model: 3.240 Set up NCS constraints: 1.270 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.170 ------------------------------------------------------------------------------- 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= 0.642 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 : 3.846 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: 0.5068 time to fit residues: 649.9768 Evaluate side-chains 652 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 652 time to evaluate : 3.564 ------------------------------------------------------------------------------- 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: 4.9990 chunk 371 optimal weight: 0.8980 chunk 206 optimal weight: 0.9990 chunk 126 optimal weight: 7.9990 chunk 250 optimal weight: 3.9990 chunk 198 optimal weight: 2.9990 chunk 384 optimal weight: 4.9990 chunk 148 optimal weight: 0.0010 chunk 233 optimal weight: 0.8980 chunk 285 optimal weight: 6.9990 chunk 444 optimal weight: 0.9980 overall best weight: 0.7588 ------------------------------------------------------------------------------- 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: 0.7945 moved from start: 0.2381 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= 0.126 Angle : 0.434 8.065 50330 Z= 0.219 Chirality : 0.033 0.104 5670 Planarity : 0.003 0.022 6020 Dihedral : 25.248 175.552 7910 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 1.04 % Allowed : 6.99 % Favored : 91.96 % 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: 2.14 (0.12), residues: 4760 helix: 1.85 (0.08), residues: 3990 sheet: None (None), residues: 0 loop : -0.81 (0.18), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP4L 87 PHE 0.009 0.001 PHE3M 89 ARG 0.001 0.000 ARG3G 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 730 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 695 time to evaluate : 3.906 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: 0.8554 (mtt) cc_final: 0.8264 (mtt) REVERT: 1B 59 MET cc_start: 0.8597 (mtt) cc_final: 0.8291 (mtt) REVERT: 1F 107 MET cc_start: 0.8777 (ttt) cc_final: 0.8488 (ttp) REVERT: 1G 115 LYS cc_start: 0.8230 (mtpt) cc_final: 0.7998 (ttmm) REVERT: 1J 107 MET cc_start: 0.8801 (ttt) cc_final: 0.8548 (ttp) REVERT: 1L 107 MET cc_start: 0.8696 (ttt) cc_final: 0.8450 (ttt) REVERT: 1M 107 MET cc_start: 0.8532 (ttt) cc_final: 0.8262 (ttt) REVERT: 2A 59 MET cc_start: 0.8658 (mtt) cc_final: 0.7968 (mtt) REVERT: 2B 59 MET cc_start: 0.8546 (mtt) cc_final: 0.8117 (mtt) REVERT: 2H 107 MET cc_start: 0.8858 (ttt) cc_final: 0.8617 (ttt) REVERT: 2J 59 MET cc_start: 0.8556 (mtt) cc_final: 0.8243 (mtt) REVERT: 2K 59 MET cc_start: 0.8460 (mtt) cc_final: 0.8220 (mtt) REVERT: 3B 115 LYS cc_start: 0.8597 (mtpp) cc_final: 0.8150 (ttpp) REVERT: 3E 107 MET cc_start: 0.8887 (ttt) cc_final: 0.8629 (ttp) REVERT: 3G 59 MET cc_start: 0.8384 (mtt) cc_final: 0.7788 (mtt) REVERT: 3G 107 MET cc_start: 0.8857 (ttt) cc_final: 0.8429 (ttp) REVERT: 4B 115 LYS cc_start: 0.8419 (mtpp) cc_final: 0.8019 (ttpp) REVERT: 4C 83 ILE cc_start: 0.8925 (mm) cc_final: 0.8709 (mm) REVERT: 4G 59 MET cc_start: 0.8381 (mtt) cc_final: 0.7955 (mtt) REVERT: 4I 59 MET cc_start: 0.8365 (mtt) cc_final: 0.7989 (mtt) REVERT: 4I 88 MET cc_start: 0.7978 (ptt) cc_final: 0.7758 (ptt) REVERT: 4K 59 MET cc_start: 0.8576 (mtt) cc_final: 0.8273 (mtt) REVERT: 4M 115 LYS cc_start: 0.8293 (ttpp) cc_final: 0.8080 (ttmm) REVERT: 5G 59 MET cc_start: 0.8370 (mtt) cc_final: 0.8159 (mtt) REVERT: 5G 107 MET cc_start: 0.8797 (ttt) cc_final: 0.8576 (ttp) REVERT: 5N 61 ASN cc_start: 0.8171 (m-40) cc_final: 0.7860 (m-40) outliers start: 35 outliers final: 16 residues processed: 710 average time/residue: 0.5243 time to fit residues: 585.4564 Evaluate side-chains 641 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 625 time to evaluate : 3.696 ------------------------------------------------------------------------------- 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 3M residue 59 MET Chi-restraints excluded: chain 3N residue 60 VAL 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: 5.9990 chunk 370 optimal weight: 6.9990 chunk 303 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 445 optimal weight: 0.4980 chunk 481 optimal weight: 0.7980 chunk 397 optimal weight: 6.9990 chunk 442 optimal weight: 1.9990 chunk 151 optimal weight: 0.9980 chunk 357 optimal weight: 7.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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: 0.8011 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 37730 Z= 0.174 Angle : 0.432 6.055 50330 Z= 0.225 Chirality : 0.034 0.113 5670 Planarity : 0.003 0.022 6020 Dihedral : 23.720 179.609 7910 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 0.57 % Allowed : 9.85 % Favored : 89.58 % 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: 2.52 (0.12), residues: 4760 helix: 2.18 (0.08), residues: 3920 sheet: None (None), residues: 0 loop : -0.81 (0.16), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP1N 87 PHE 0.008 0.001 PHE1A 112 ARG 0.001 0.000 ARG5L 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 646 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 627 time to evaluate : 4.129 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: 0.8689 (mtt) cc_final: 0.8301 (mtt) REVERT: 1B 59 MET cc_start: 0.8686 (mtt) cc_final: 0.8476 (mtt) REVERT: 1G 115 LYS cc_start: 0.8262 (mtpt) cc_final: 0.8058 (ttmm) REVERT: 1J 107 MET cc_start: 0.8827 (ttt) cc_final: 0.8513 (ttp) REVERT: 1L 107 MET cc_start: 0.8809 (ttt) cc_final: 0.8520 (ttt) REVERT: 1M 115 LYS cc_start: 0.8467 (ttpp) cc_final: 0.8233 (ttpp) REVERT: 2A 59 MET cc_start: 0.8758 (mtt) cc_final: 0.8127 (mtt) REVERT: 2B 59 MET cc_start: 0.8652 (mtt) cc_final: 0.8295 (mtt) REVERT: 2B 88 MET cc_start: 0.6991 (ptp) cc_final: 0.6754 (ptt) REVERT: 2I 107 MET cc_start: 0.8702 (ttt) cc_final: 0.8499 (ttp) REVERT: 2J 59 MET cc_start: 0.8633 (mtt) cc_final: 0.8379 (mtt) REVERT: 2K 59 MET cc_start: 0.8512 (mtt) cc_final: 0.8293 (mtt) REVERT: 2N 115 LYS cc_start: 0.8033 (mttp) cc_final: 0.7827 (mtpt) REVERT: 3B 115 LYS cc_start: 0.8491 (mtpp) cc_final: 0.8131 (ttpp) REVERT: 3E 107 MET cc_start: 0.8870 (ttt) cc_final: 0.8604 (ttp) REVERT: 3G 107 MET cc_start: 0.8877 (ttt) cc_final: 0.8471 (ttp) REVERT: 3K 88 MET cc_start: 0.7474 (ptt) cc_final: 0.7268 (ptt) REVERT: 3N 61 ASN cc_start: 0.8457 (m-40) cc_final: 0.8084 (m-40) REVERT: 4B 115 LYS cc_start: 0.8450 (mtpp) cc_final: 0.7988 (ttpp) REVERT: 4G 59 MET cc_start: 0.8434 (mtt) cc_final: 0.8132 (mtt) REVERT: 4I 59 MET cc_start: 0.8358 (mtt) cc_final: 0.8017 (mtt) REVERT: 4K 59 MET cc_start: 0.8652 (mtt) cc_final: 0.8356 (mtt) REVERT: 4M 115 LYS cc_start: 0.8331 (ttpp) cc_final: 0.8115 (ttmm) REVERT: 5G 59 MET cc_start: 0.8364 (mtt) cc_final: 0.8150 (mtt) REVERT: 5N 61 ASN cc_start: 0.8230 (m-40) cc_final: 0.7943 (m-40) outliers start: 19 outliers final: 15 residues processed: 641 average time/residue: 0.5592 time to fit residues: 555.2439 Evaluate side-chains 603 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 588 time to evaluate : 3.771 ------------------------------------------------------------------------------- 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 3M residue 59 MET 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: 7.9990 chunk 335 optimal weight: 6.9990 chunk 231 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 212 optimal weight: 2.9990 chunk 299 optimal weight: 20.0000 chunk 447 optimal weight: 0.9990 chunk 473 optimal weight: 3.9990 chunk 233 optimal weight: 6.9990 chunk 424 optimal weight: 5.9990 chunk 127 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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: 0.8089 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 37730 Z= 0.296 Angle : 0.510 5.298 50330 Z= 0.267 Chirality : 0.036 0.123 5670 Planarity : 0.003 0.023 6020 Dihedral : 23.105 179.730 7910 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 0.89 % Allowed : 12.62 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.12), residues: 4760 helix: 1.81 (0.08), residues: 3990 sheet: None (None), residues: 0 loop : -1.29 (0.17), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP4N 87 PHE 0.013 0.001 PHE3L 89 ARG 0.001 0.000 ARG2N 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 644 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 614 time to evaluate : 2.947 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: symmetry clash REVERT: 1A 59 MET cc_start: 0.8835 (mtt) cc_final: 0.8429 (mtt) REVERT: 1A 93 SER cc_start: 0.8081 (p) cc_final: 0.7792 (m) REVERT: 1B 59 MET cc_start: 0.8708 (mtt) cc_final: 0.8377 (mtt) REVERT: 1J 107 MET cc_start: 0.8776 (ttt) cc_final: 0.8478 (ttp) REVERT: 1L 107 MET cc_start: 0.8852 (ttt) cc_final: 0.8557 (ttt) REVERT: 2A 59 MET cc_start: 0.8800 (mtt) cc_final: 0.8279 (mtt) REVERT: 2J 59 MET cc_start: 0.8687 (mtt) cc_final: 0.8436 (mtt) REVERT: 2K 59 MET cc_start: 0.8599 (mtt) cc_final: 0.8343 (mtt) REVERT: 2N 115 LYS cc_start: 0.7990 (mttp) cc_final: 0.7773 (mtpt) REVERT: 3B 115 LYS cc_start: 0.8481 (mtpp) cc_final: 0.8214 (ttpp) REVERT: 3E 107 MET cc_start: 0.8889 (ttt) cc_final: 0.8557 (ttp) REVERT: 3F 59 MET cc_start: 0.8474 (mtt) cc_final: 0.8071 (mtt) REVERT: 3G 107 MET cc_start: 0.8877 (ttt) cc_final: 0.8630 (ttp) REVERT: 3N 61 ASN cc_start: 0.8484 (m-40) cc_final: 0.8120 (m-40) REVERT: 4B 115 LYS cc_start: 0.8514 (mtpp) cc_final: 0.8115 (ttpp) REVERT: 4C 61 ASN cc_start: 0.8020 (m-40) cc_final: 0.7815 (m-40) REVERT: 4G 59 MET cc_start: 0.8409 (mtt) cc_final: 0.8137 (mtt) REVERT: 4H 59 MET cc_start: 0.8440 (mtt) cc_final: 0.8024 (mtt) REVERT: 4I 59 MET cc_start: 0.8430 (mtt) cc_final: 0.8081 (mtt) REVERT: 4K 59 MET cc_start: 0.8695 (mtt) cc_final: 0.8345 (mtt) REVERT: 4K 107 MET cc_start: 0.8731 (ttp) cc_final: 0.8505 (ttp) REVERT: 4M 115 LYS cc_start: 0.8435 (ttpp) cc_final: 0.8182 (ttmm) REVERT: 5H 107 MET cc_start: 0.8999 (ttt) cc_final: 0.8788 (ttt) REVERT: 5I 107 MET cc_start: 0.8904 (ttt) cc_final: 0.8670 (ttp) REVERT: 5N 59 MET cc_start: 0.8030 (mtp) cc_final: 0.7765 (mtp) REVERT: 5N 61 ASN cc_start: 0.8239 (m-40) cc_final: 0.7956 (m-40) REVERT: 5N 108 PHE cc_start: 0.8499 (m-80) cc_final: 0.8273 (m-80) outliers start: 30 outliers final: 22 residues processed: 627 average time/residue: 0.5423 time to fit residues: 524.0053 Evaluate side-chains 612 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 590 time to evaluate : 3.132 ------------------------------------------------------------------------------- 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 2A residue 55 ASP Chi-restraints excluded: chain 2B residue 55 ASP Chi-restraints excluded: chain 2C residue 88 MET 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 3M residue 59 MET 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 4N residue 67 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 104 ILE Chi-restraints excluded: chain 5I residue 67 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 394 optimal weight: 10.0000 chunk 268 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 352 optimal weight: 0.8980 chunk 195 optimal weight: 9.9990 chunk 404 optimal weight: 10.0000 chunk 327 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 241 optimal weight: 0.9980 chunk 425 optimal weight: 8.9990 chunk 119 optimal weight: 6.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- 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: 0.8066 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 37730 Z= 0.242 Angle : 0.461 4.534 50330 Z= 0.241 Chirality : 0.035 0.115 5670 Planarity : 0.003 0.023 6020 Dihedral : 21.901 166.783 7910 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 1.13 % Allowed : 14.43 % Favored : 84.43 % 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: 2.16 (0.12), residues: 4760 helix: 1.98 (0.08), residues: 3920 sheet: None (None), residues: 0 loop : -1.24 (0.16), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP1N 87 PHE 0.011 0.001 PHE1L 89 ARG 0.001 0.000 ARG5D 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 638 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 600 time to evaluate : 3.603 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: 1A 59 MET cc_start: 0.8806 (mtt) cc_final: 0.8389 (mtt) REVERT: 1B 59 MET cc_start: 0.8703 (mtt) cc_final: 0.8428 (mtt) REVERT: 1J 107 MET cc_start: 0.8803 (ttt) cc_final: 0.8527 (ttp) REVERT: 1L 107 MET cc_start: 0.8827 (ttt) cc_final: 0.8546 (ttt) REVERT: 2A 59 MET cc_start: 0.8798 (mtt) cc_final: 0.8269 (mtt) REVERT: 2J 59 MET cc_start: 0.8617 (mtt) cc_final: 0.8348 (mtt) REVERT: 2K 59 MET cc_start: 0.8560 (mtt) cc_final: 0.8316 (mtt) REVERT: 2N 115 LYS cc_start: 0.7982 (mttp) cc_final: 0.7745 (mtpt) REVERT: 3B 115 LYS cc_start: 0.8471 (mtpp) cc_final: 0.8216 (ttpp) REVERT: 3E 107 MET cc_start: 0.8914 (ttt) cc_final: 0.8595 (ttp) REVERT: 3G 107 MET cc_start: 0.8863 (ttt) cc_final: 0.8586 (ttp) REVERT: 3N 61 ASN cc_start: 0.8476 (m-40) cc_final: 0.8087 (m-40) REVERT: 4B 115 LYS cc_start: 0.8519 (mtpp) cc_final: 0.8150 (ttpp) REVERT: 4I 59 MET cc_start: 0.8370 (mtt) cc_final: 0.8004 (mtt) REVERT: 4K 59 MET cc_start: 0.8632 (mtt) cc_final: 0.8286 (mtt) REVERT: 4M 115 LYS cc_start: 0.8421 (ttpp) cc_final: 0.8173 (ttmm) REVERT: 5I 107 MET cc_start: 0.8871 (ttt) cc_final: 0.8660 (ttp) REVERT: 5N 59 MET cc_start: 0.7978 (mtp) cc_final: 0.7708 (mtp) REVERT: 5N 61 ASN cc_start: 0.8194 (m-40) cc_final: 0.7916 (m-40) REVERT: 5N 108 PHE cc_start: 0.8393 (m-80) cc_final: 0.8138 (m-80) outliers start: 38 outliers final: 28 residues processed: 624 average time/residue: 0.5561 time to fit residues: 535.6584 Evaluate side-chains 617 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 589 time to evaluate : 3.859 ------------------------------------------------------------------------------- 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 1C residue 117 LEU Chi-restraints excluded: chain 1D residue 54 THR Chi-restraints excluded: chain 1G residue 116 THR Chi-restraints excluded: chain 1I residue 115 LYS Chi-restraints excluded: chain 1J 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 3F residue 67 ILE Chi-restraints excluded: chain 3G residue 96 LEU Chi-restraints excluded: chain 3I 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 4E residue 115 LYS 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 104 ILE Chi-restraints excluded: chain 5I residue 67 ILE Chi-restraints excluded: chain 5M residue 116 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 159 optimal weight: 3.9990 chunk 426 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 278 optimal weight: 3.9990 chunk 116 optimal weight: 10.0000 chunk 474 optimal weight: 6.9990 chunk 393 optimal weight: 8.9990 chunk 219 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 chunk 248 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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: 0.8101 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 37730 Z= 0.313 Angle : 0.515 4.989 50330 Z= 0.270 Chirality : 0.036 0.122 5670 Planarity : 0.003 0.025 6020 Dihedral : 21.949 174.353 7910 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 1.55 % Allowed : 15.42 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.12), residues: 4760 helix: 1.86 (0.08), residues: 3920 sheet: None (None), residues: 0 loop : -1.39 (0.16), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP3M 87 PHE 0.011 0.001 PHE5L 89 ARG 0.003 0.000 ARG3E 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 649 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 597 time to evaluate : 3.615 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: 1A 59 MET cc_start: 0.8841 (mtt) cc_final: 0.8459 (mtt) REVERT: 1B 59 MET cc_start: 0.8752 (mtt) cc_final: 0.8432 (mtt) REVERT: 1J 107 MET cc_start: 0.8817 (ttt) cc_final: 0.8537 (ttp) REVERT: 1L 107 MET cc_start: 0.8848 (ttt) cc_final: 0.8548 (ttt) REVERT: 2A 59 MET cc_start: 0.8793 (mtt) cc_final: 0.8298 (mtt) REVERT: 2J 59 MET cc_start: 0.8667 (mtt) cc_final: 0.8403 (mtt) REVERT: 2K 59 MET cc_start: 0.8659 (mtt) cc_final: 0.8425 (mtt) REVERT: 3B 115 LYS cc_start: 0.8467 (mtpp) cc_final: 0.8215 (ttpp) REVERT: 3E 107 MET cc_start: 0.8925 (ttt) cc_final: 0.8594 (ttp) REVERT: 3G 107 MET cc_start: 0.8898 (ttt) cc_final: 0.8630 (ttp) REVERT: 3N 61 ASN cc_start: 0.8487 (m-40) cc_final: 0.8113 (m-40) REVERT: 4B 115 LYS cc_start: 0.8526 (mtpp) cc_final: 0.8159 (ttpp) REVERT: 4H 59 MET cc_start: 0.8447 (mtt) cc_final: 0.8032 (mtt) REVERT: 4I 59 MET cc_start: 0.8415 (mtt) cc_final: 0.8067 (mtt) REVERT: 4K 59 MET cc_start: 0.8654 (mtt) cc_final: 0.8296 (mtt) REVERT: 4M 115 LYS cc_start: 0.8431 (ttpp) cc_final: 0.8176 (ttmm) REVERT: 5I 107 MET cc_start: 0.8927 (ttt) cc_final: 0.8674 (ttp) REVERT: 5N 59 MET cc_start: 0.8037 (mtp) cc_final: 0.7784 (mtp) REVERT: 5N 61 ASN cc_start: 0.8193 (m-40) cc_final: 0.7921 (m-40) REVERT: 5N 108 PHE cc_start: 0.8502 (m-80) cc_final: 0.8293 (m-80) outliers start: 52 outliers final: 38 residues processed: 630 average time/residue: 0.5521 time to fit residues: 537.6796 Evaluate side-chains 624 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 586 time to evaluate : 3.638 ------------------------------------------------------------------------------- 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 1C residue 117 LEU Chi-restraints excluded: chain 1D residue 54 THR Chi-restraints excluded: chain 1E residue 55 ASP Chi-restraints excluded: chain 1G residue 116 THR Chi-restraints excluded: chain 1I residue 115 LYS Chi-restraints excluded: chain 1J 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 3D residue 54 THR Chi-restraints excluded: chain 3E residue 55 ASP Chi-restraints excluded: chain 3F residue 67 ILE Chi-restraints excluded: chain 3H residue 115 LYS 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 3M residue 59 MET Chi-restraints excluded: chain 3N residue 74 SER Chi-restraints excluded: chain 4A residue 55 ASP Chi-restraints excluded: chain 4E residue 115 LYS Chi-restraints excluded: chain 4L residue 116 THR Chi-restraints excluded: chain 4M residue 83 ILE Chi-restraints excluded: chain 4N residue 65 THR 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 5B residue 104 ILE Chi-restraints excluded: chain 5E residue 55 ASP Chi-restraints excluded: chain 5I residue 67 ILE Chi-restraints excluded: chain 5M residue 116 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 457 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 270 optimal weight: 0.0670 chunk 346 optimal weight: 4.9990 chunk 268 optimal weight: 0.7980 chunk 399 optimal weight: 10.0000 chunk 264 optimal weight: 3.9990 chunk 472 optimal weight: 2.9990 chunk 295 optimal weight: 5.9990 chunk 287 optimal weight: 20.0000 chunk 218 optimal weight: 5.9990 overall best weight: 1.9724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5A 73 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3492 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= 0.198 Angle : 0.440 5.391 50330 Z= 0.230 Chirality : 0.034 0.112 5670 Planarity : 0.003 0.023 6020 Dihedral : 20.698 173.576 7910 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 1.31 % Allowed : 16.67 % Favored : 82.02 % 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: 2.20 (0.12), residues: 4760 helix: 2.03 (0.08), residues: 3920 sheet: None (None), residues: 0 loop : -1.34 (0.16), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP3M 87 PHE 0.010 0.001 PHE3K 89 ARG 0.002 0.000 ARG2C 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 646 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 602 time to evaluate : 3.438 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: 1A 59 MET cc_start: 0.8782 (mtt) cc_final: 0.8370 (mtt) REVERT: 1B 59 MET cc_start: 0.8675 (mtt) cc_final: 0.8402 (mtt) REVERT: 1J 107 MET cc_start: 0.8811 (ttt) cc_final: 0.8524 (ttp) REVERT: 1L 107 MET cc_start: 0.8817 (ttt) cc_final: 0.8528 (ttt) REVERT: 2A 59 MET cc_start: 0.8750 (mtt) cc_final: 0.8228 (mtt) REVERT: 2I 107 MET cc_start: 0.8811 (ttt) cc_final: 0.8564 (ttp) REVERT: 2J 59 MET cc_start: 0.8594 (mtt) cc_final: 0.8324 (mtt) REVERT: 2K 59 MET cc_start: 0.8559 (mtt) cc_final: 0.8328 (mtt) REVERT: 3B 115 LYS cc_start: 0.8490 (mtpp) cc_final: 0.8256 (ttpp) REVERT: 3E 107 MET cc_start: 0.8923 (ttt) cc_final: 0.8621 (ttp) REVERT: 3G 107 MET cc_start: 0.8875 (ttt) cc_final: 0.8539 (ttp) REVERT: 3M 88 MET cc_start: 0.7909 (ptt) cc_final: 0.7598 (ptt) REVERT: 3N 61 ASN cc_start: 0.8454 (m-40) cc_final: 0.8069 (m-40) REVERT: 4B 115 LYS cc_start: 0.8526 (mtpp) cc_final: 0.8167 (ttpp) REVERT: 4H 59 MET cc_start: 0.8398 (mtt) cc_final: 0.8009 (mtt) REVERT: 4I 59 MET cc_start: 0.8357 (mtt) cc_final: 0.7992 (mtt) REVERT: 4K 59 MET cc_start: 0.8580 (mtt) cc_final: 0.8234 (mtt) REVERT: 4M 115 LYS cc_start: 0.8394 (ttpp) cc_final: 0.8146 (ttmm) REVERT: 5N 59 MET cc_start: 0.7945 (mtp) cc_final: 0.7677 (mtp) REVERT: 5N 61 ASN cc_start: 0.8167 (m-40) cc_final: 0.7909 (m-40) REVERT: 5N 108 PHE cc_start: 0.8376 (m-80) cc_final: 0.8107 (m-80) outliers start: 44 outliers final: 33 residues processed: 631 average time/residue: 0.5376 time to fit residues: 523.8034 Evaluate side-chains 616 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 583 time to evaluate : 3.546 ------------------------------------------------------------------------------- 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 1G residue 116 THR 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 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 3D residue 55 ASP Chi-restraints excluded: chain 3F residue 67 ILE Chi-restraints excluded: chain 3G residue 96 LEU Chi-restraints excluded: chain 3I residue 116 THR Chi-restraints excluded: chain 3J 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 88 MET Chi-restraints excluded: chain 4D residue 55 ASP Chi-restraints excluded: chain 4E residue 55 ASP Chi-restraints excluded: chain 4E residue 115 LYS 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 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: 8.9990 chunk 188 optimal weight: 1.9990 chunk 282 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 92 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 chunk 300 optimal weight: 4.9990 chunk 321 optimal weight: 7.9990 chunk 233 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 371 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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: 0.8077 moved from start: 0.3514 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= 0.251 Angle : 0.478 6.200 50330 Z= 0.250 Chirality : 0.035 0.118 5670 Planarity : 0.003 0.024 6020 Dihedral : 20.670 174.295 7910 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 1.52 % Allowed : 16.99 % Favored : 81.49 % 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: 2.10 (0.12), residues: 4760 helix: 1.97 (0.08), residues: 3920 sheet: None (None), residues: 0 loop : -1.40 (0.16), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP5N 87 PHE 0.011 0.001 PHE4D 89 ARG 0.003 0.000 ARG4D 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 638 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 587 time to evaluate : 3.588 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: 0.8777 (mtt) cc_final: 0.8416 (mtt) REVERT: 1B 59 MET cc_start: 0.8733 (mtt) cc_final: 0.8409 (mtt) REVERT: 1J 107 MET cc_start: 0.8853 (ttt) cc_final: 0.8563 (ttp) REVERT: 1L 107 MET cc_start: 0.8834 (ttt) cc_final: 0.8536 (ttt) REVERT: 2A 59 MET cc_start: 0.8799 (mtt) cc_final: 0.8315 (mtt) REVERT: 2J 59 MET cc_start: 0.8624 (mtt) cc_final: 0.8358 (mtt) REVERT: 3B 60 VAL cc_start: 0.8778 (m) cc_final: 0.8560 (m) REVERT: 3B 115 LYS cc_start: 0.8471 (mtpp) cc_final: 0.8232 (ttpp) REVERT: 3E 107 MET cc_start: 0.8949 (ttt) cc_final: 0.8610 (ttp) REVERT: 3G 107 MET cc_start: 0.8895 (ttt) cc_final: 0.8626 (ttp) REVERT: 3N 61 ASN cc_start: 0.8485 (m-40) cc_final: 0.8122 (m-40) REVERT: 4B 115 LYS cc_start: 0.8508 (mtpp) cc_final: 0.8137 (ttpp) REVERT: 4H 59 MET cc_start: 0.8430 (mtt) cc_final: 0.8029 (mtt) REVERT: 4I 59 MET cc_start: 0.8381 (mtt) cc_final: 0.8028 (mtt) REVERT: 4K 59 MET cc_start: 0.8587 (mtt) cc_final: 0.8229 (mtt) REVERT: 4M 115 LYS cc_start: 0.8416 (ttpp) cc_final: 0.8162 (ttmm) REVERT: 5I 107 MET cc_start: 0.8903 (ttt) cc_final: 0.8689 (ttp) REVERT: 5N 59 MET cc_start: 0.8007 (mtp) cc_final: 0.7745 (mtp) REVERT: 5N 61 ASN cc_start: 0.8191 (m-40) cc_final: 0.7940 (m-40) REVERT: 5N 108 PHE cc_start: 0.8507 (m-80) cc_final: 0.8234 (m-80) outliers start: 51 outliers final: 42 residues processed: 621 average time/residue: 0.5808 time to fit residues: 561.4767 Evaluate side-chains 624 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 582 time to evaluate : 3.431 ------------------------------------------------------------------------------- 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 1E residue 55 ASP Chi-restraints excluded: chain 1G residue 116 THR Chi-restraints excluded: chain 1I residue 115 LYS Chi-restraints excluded: chain 1J residue 116 THR Chi-restraints excluded: chain 2A residue 55 ASP Chi-restraints excluded: chain 2A residue 83 ILE Chi-restraints excluded: chain 2B residue 55 ASP Chi-restraints excluded: chain 2E residue 55 ASP Chi-restraints excluded: chain 2I 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 3D residue 54 THR Chi-restraints excluded: chain 3E residue 55 ASP Chi-restraints excluded: chain 3F residue 67 ILE Chi-restraints excluded: chain 3G residue 96 LEU Chi-restraints excluded: chain 3H residue 115 LYS Chi-restraints excluded: chain 3I residue 116 THR Chi-restraints excluded: chain 3J 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 88 MET Chi-restraints excluded: chain 4E residue 55 ASP Chi-restraints excluded: chain 4E residue 115 LYS 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 5B residue 104 ILE Chi-restraints excluded: chain 5E residue 55 ASP Chi-restraints excluded: chain 5I residue 55 ASP Chi-restraints excluded: chain 5I residue 67 ILE Chi-restraints excluded: chain 5M residue 116 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 429 optimal weight: 4.9990 chunk 452 optimal weight: 0.9980 chunk 412 optimal weight: 1.9990 chunk 440 optimal weight: 0.6980 chunk 264 optimal weight: 4.9990 chunk 191 optimal weight: 10.0000 chunk 345 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 397 optimal weight: 20.0000 chunk 416 optimal weight: 10.0000 chunk 438 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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: 0.8042 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 37730 Z= 0.197 Angle : 0.438 6.632 50330 Z= 0.228 Chirality : 0.034 0.116 5670 Planarity : 0.003 0.023 6020 Dihedral : 19.775 176.999 7910 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 1.40 % Allowed : 17.47 % Favored : 81.13 % 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: 2.27 (0.12), residues: 4760 helix: 2.09 (0.08), residues: 3920 sheet: None (None), residues: 0 loop : -1.35 (0.16), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP5N 87 PHE 0.010 0.001 PHE4D 89 ARG 0.003 0.000 ARG5E 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 646 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 599 time to evaluate : 3.908 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: 0.8400 (mtt) REVERT: 1B 59 MET cc_start: 0.8722 (mtt) cc_final: 0.8481 (mtt) REVERT: 1J 107 MET cc_start: 0.8831 (ttt) cc_final: 0.8545 (ttp) REVERT: 1L 107 MET cc_start: 0.8815 (ttt) cc_final: 0.8527 (ttt) REVERT: 2A 59 MET cc_start: 0.8820 (mtt) cc_final: 0.8338 (mtt) REVERT: 2J 59 MET cc_start: 0.8594 (mtt) cc_final: 0.8342 (mtt) REVERT: 3B 60 VAL cc_start: 0.8784 (m) cc_final: 0.8560 (m) REVERT: 3B 115 LYS cc_start: 0.8456 (mtpp) cc_final: 0.8223 (ttpp) REVERT: 3E 107 MET cc_start: 0.8930 (ttt) cc_final: 0.8629 (ttp) REVERT: 3G 107 MET cc_start: 0.8871 (ttt) cc_final: 0.8535 (ttp) REVERT: 3N 61 ASN cc_start: 0.8444 (m-40) cc_final: 0.8067 (m-40) REVERT: 4B 115 LYS cc_start: 0.8494 (mtpp) cc_final: 0.8106 (ttpp) REVERT: 4H 59 MET cc_start: 0.8390 (mtt) cc_final: 0.8001 (mtt) REVERT: 4I 59 MET cc_start: 0.8342 (mtt) cc_final: 0.7993 (mtt) REVERT: 4K 59 MET cc_start: 0.8532 (mtt) cc_final: 0.8182 (mtt) REVERT: 4M 115 LYS cc_start: 0.8364 (ttpp) cc_final: 0.8104 (ttmm) REVERT: 5N 59 MET cc_start: 0.7944 (mtp) cc_final: 0.7670 (mtp) REVERT: 5N 61 ASN cc_start: 0.8155 (m-40) cc_final: 0.7909 (m-40) outliers start: 47 outliers final: 44 residues processed: 632 average time/residue: 0.5558 time to fit residues: 542.3279 Evaluate side-chains 625 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 581 time to evaluate : 3.592 ------------------------------------------------------------------------------- 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 1D residue 55 ASP Chi-restraints excluded: chain 1E residue 55 ASP Chi-restraints excluded: chain 1G residue 116 THR Chi-restraints excluded: chain 1I residue 115 LYS Chi-restraints excluded: chain 1J residue 116 THR Chi-restraints excluded: chain 1M residue 97 VAL 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 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 3B residue 55 ASP Chi-restraints excluded: chain 3D residue 54 THR 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 3H residue 115 LYS Chi-restraints excluded: chain 3I residue 116 THR Chi-restraints excluded: chain 3J residue 116 THR Chi-restraints excluded: chain 3M residue 59 MET Chi-restraints excluded: chain 4A residue 55 ASP Chi-restraints excluded: chain 4A residue 88 MET Chi-restraints excluded: chain 4D residue 55 ASP Chi-restraints excluded: chain 4E residue 55 ASP Chi-restraints excluded: chain 4E residue 115 LYS 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 5B residue 104 ILE Chi-restraints excluded: chain 5E residue 55 ASP Chi-restraints excluded: chain 5I residue 67 ILE Chi-restraints excluded: chain 5M residue 116 THR Chi-restraints excluded: chain 5N residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 289 optimal weight: 7.9990 chunk 465 optimal weight: 4.9990 chunk 284 optimal weight: 0.9980 chunk 220 optimal weight: 7.9990 chunk 323 optimal weight: 7.9990 chunk 488 optimal weight: 5.9990 chunk 449 optimal weight: 1.9990 chunk 388 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 300 optimal weight: 6.9990 chunk 238 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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: 0.8051 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 37730 Z= 0.205 Angle : 0.452 6.755 50330 Z= 0.236 Chirality : 0.034 0.119 5670 Planarity : 0.003 0.023 6020 Dihedral : 19.370 176.887 7910 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 1.31 % Allowed : 18.10 % Favored : 80.60 % 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: 2.25 (0.12), residues: 4760 helix: 2.08 (0.08), residues: 3920 sheet: None (None), residues: 0 loop : -1.39 (0.16), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP5N 87 PHE 0.013 0.001 PHE5A 112 ARG 0.001 0.000 ARG4N 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 628 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 584 time to evaluate : 4.155 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: 0.8784 (mtt) cc_final: 0.8384 (mtt) REVERT: 1B 59 MET cc_start: 0.8730 (mtt) cc_final: 0.8470 (mtt) REVERT: 1J 107 MET cc_start: 0.8853 (ttt) cc_final: 0.8556 (ttp) REVERT: 1L 107 MET cc_start: 0.8823 (ttt) cc_final: 0.8522 (ttt) REVERT: 2A 59 MET cc_start: 0.8836 (mtt) cc_final: 0.8389 (mtt) REVERT: 2J 59 MET cc_start: 0.8608 (mtt) cc_final: 0.8337 (mtt) REVERT: 3B 60 VAL cc_start: 0.8741 (m) cc_final: 0.8503 (m) REVERT: 3B 115 LYS cc_start: 0.8457 (mtpp) cc_final: 0.8221 (ttpp) REVERT: 3E 107 MET cc_start: 0.8949 (ttt) cc_final: 0.8627 (ttp) REVERT: 3G 107 MET cc_start: 0.8886 (ttt) cc_final: 0.8581 (ttp) REVERT: 3N 61 ASN cc_start: 0.8452 (m-40) cc_final: 0.8101 (m-40) REVERT: 4B 115 LYS cc_start: 0.8499 (mtpp) cc_final: 0.8113 (ttpp) REVERT: 4H 59 MET cc_start: 0.8405 (mtt) cc_final: 0.7998 (mtt) REVERT: 4I 59 MET cc_start: 0.8358 (mtt) cc_final: 0.7998 (mtt) REVERT: 4K 59 MET cc_start: 0.8584 (mtt) cc_final: 0.8236 (mtt) REVERT: 4M 115 LYS cc_start: 0.8362 (ttpp) cc_final: 0.8105 (ttmm) REVERT: 5I 107 MET cc_start: 0.8899 (ttt) cc_final: 0.8696 (ttp) REVERT: 5N 59 MET cc_start: 0.7953 (mtp) cc_final: 0.7686 (mtp) REVERT: 5N 61 ASN cc_start: 0.8170 (m-40) cc_final: 0.7930 (m-40) outliers start: 44 outliers final: 42 residues processed: 617 average time/residue: 0.5640 time to fit residues: 538.7640 Evaluate side-chains 619 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 577 time to evaluate : 3.288 ------------------------------------------------------------------------------- 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 1E residue 55 ASP Chi-restraints excluded: chain 1I residue 115 LYS Chi-restraints excluded: chain 1J residue 116 THR Chi-restraints excluded: chain 1M residue 97 VAL 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 2I 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 3B residue 55 ASP Chi-restraints excluded: chain 3D residue 54 THR 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 116 THR Chi-restraints excluded: chain 3J 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 88 MET 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 111 SER Chi-restraints excluded: chain 5B residue 55 ASP Chi-restraints excluded: chain 5B residue 88 MET Chi-restraints excluded: chain 5B residue 104 ILE Chi-restraints excluded: chain 5D residue 55 ASP Chi-restraints excluded: chain 5E residue 55 ASP Chi-restraints excluded: chain 5I residue 67 ILE Chi-restraints excluded: chain 5M residue 116 THR Chi-restraints excluded: chain 5N residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 490 random chunks: chunk 308 optimal weight: 6.9990 chunk 414 optimal weight: 7.9990 chunk 119 optimal weight: 6.9990 chunk 358 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 389 optimal weight: 4.9990 chunk 162 optimal weight: 0.0570 chunk 399 optimal weight: 9.9990 chunk 49 optimal weight: 8.9990 chunk 71 optimal weight: 0.0570 overall best weight: 2.2222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.119268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.088884 restraints weight = 44090.804| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.85 r_work: 0.2891 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 37730 Z= 0.220 Angle : 0.458 6.900 50330 Z= 0.239 Chirality : 0.034 0.119 5670 Planarity : 0.003 0.022 6020 Dihedral : 19.048 175.668 7910 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 1.43 % Allowed : 18.10 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.12), residues: 4760 helix: 2.05 (0.08), residues: 3920 sheet: None (None), residues: 0 loop : -1.40 (0.16), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP5N 87 PHE 0.012 0.001 PHE5A 112 ARG 0.001 0.000 ARG3N 91 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9433.54 seconds wall clock time: 174 minutes 8.66 seconds (10448.66 seconds total)