Starting phenix.real_space_refine on Sat Jul 27 20:34:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5leg_4042/07_2024/5leg_4042_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5leg_4042/07_2024/5leg_4042.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5leg_4042/07_2024/5leg_4042.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5leg_4042/07_2024/5leg_4042.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5leg_4042/07_2024/5leg_4042_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5leg_4042/07_2024/5leg_4042_neut.cif" } resolution = 3.6 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= 1.048 sd= 8.826 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 75 5.49 5 S 320 5.16 5 C 28050 2.51 5 N 5680 2.21 5 O 7230 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1A ARG 39": "NH1" <-> "NH2" Residue "1B ARG 39": "NH1" <-> "NH2" Residue "1C ARG 39": "NH1" <-> "NH2" Residue "1D ARG 39": "NH1" <-> "NH2" Residue "1E ARG 39": "NH1" <-> "NH2" Residue "1F ARG 39": "NH1" <-> "NH2" Residue "1G ARG 39": "NH1" <-> "NH2" Residue "1H ARG 39": "NH1" <-> "NH2" Residue "1I ARG 39": "NH1" <-> "NH2" Residue "1J ARG 39": "NH1" <-> "NH2" Residue "1K ARG 39": "NH1" <-> "NH2" Residue "1L ARG 39": "NH1" <-> "NH2" Residue "1M ARG 39": "NH1" <-> "NH2" Residue "1N ARG 39": "NH1" <-> "NH2" Residue "1O ARG 39": "NH1" <-> "NH2" Residue "1P ARG 39": "NH1" <-> "NH2" Residue "2A ARG 39": "NH1" <-> "NH2" Residue "2B ARG 39": "NH1" <-> "NH2" Residue "2C ARG 39": "NH1" <-> "NH2" Residue "2D ARG 39": "NH1" <-> "NH2" Residue "2E ARG 39": "NH1" <-> "NH2" Residue "2F ARG 39": "NH1" <-> "NH2" Residue "2G ARG 39": "NH1" <-> "NH2" Residue "2H ARG 39": "NH1" <-> "NH2" Residue "2I ARG 39": "NH1" <-> "NH2" Residue "2J ARG 39": "NH1" <-> "NH2" Residue "2K ARG 39": "NH1" <-> "NH2" Residue "2L ARG 39": "NH1" <-> "NH2" Residue "2M ARG 39": "NH1" <-> "NH2" Residue "2N ARG 39": "NH1" <-> "NH2" Residue "2O ARG 39": "NH1" <-> "NH2" Residue "2P ARG 39": "NH1" <-> "NH2" Residue "3A ARG 39": "NH1" <-> "NH2" Residue "3B ARG 39": "NH1" <-> "NH2" Residue "3C ARG 39": "NH1" <-> "NH2" Residue "3D ARG 39": "NH1" <-> "NH2" Residue "3E ARG 39": "NH1" <-> "NH2" Residue "3F ARG 39": "NH1" <-> "NH2" Residue "3G ARG 39": "NH1" <-> "NH2" Residue "3H ARG 39": "NH1" <-> "NH2" Residue "3I ARG 39": "NH1" <-> "NH2" Residue "3J ARG 39": "NH1" <-> "NH2" Residue "3K ARG 39": "NH1" <-> "NH2" Residue "3L ARG 39": "NH1" <-> "NH2" Residue "3M ARG 39": "NH1" <-> "NH2" Residue "3N ARG 39": "NH1" <-> "NH2" Residue "3O ARG 39": "NH1" <-> "NH2" Residue "3P ARG 39": "NH1" <-> "NH2" Residue "4A ARG 39": "NH1" <-> "NH2" Residue "4B ARG 39": "NH1" <-> "NH2" Residue "4C ARG 39": "NH1" <-> "NH2" Residue "4D ARG 39": "NH1" <-> "NH2" Residue "4E ARG 39": "NH1" <-> "NH2" Residue "4F ARG 39": "NH1" <-> "NH2" Residue "4G ARG 39": "NH1" <-> "NH2" Residue "4H ARG 39": "NH1" <-> "NH2" Residue "4I ARG 39": "NH1" <-> "NH2" Residue "4J ARG 39": "NH1" <-> "NH2" Residue "4K ARG 39": "NH1" <-> "NH2" Residue "4L ARG 39": "NH1" <-> "NH2" Residue "4M ARG 39": "NH1" <-> "NH2" Residue "4N ARG 39": "NH1" <-> "NH2" Residue "4O ARG 39": "NH1" <-> "NH2" Residue "4P ARG 39": "NH1" <-> "NH2" Residue "5A ARG 39": "NH1" <-> "NH2" Residue "5B ARG 39": "NH1" <-> "NH2" Residue "5C ARG 39": "NH1" <-> "NH2" Residue "5D ARG 39": "NH1" <-> "NH2" Residue "5E ARG 39": "NH1" <-> "NH2" Residue "5F ARG 39": "NH1" <-> "NH2" Residue "5G ARG 39": "NH1" <-> "NH2" Residue "5H ARG 39": "NH1" <-> "NH2" Residue "5I ARG 39": "NH1" <-> "NH2" Residue "5J ARG 39": "NH1" <-> "NH2" Residue "5K ARG 39": "NH1" <-> "NH2" Residue "5L ARG 39": "NH1" <-> "NH2" Residue "5M ARG 39": "NH1" <-> "NH2" Residue "5N ARG 39": "NH1" <-> "NH2" Residue "5O ARG 39": "NH1" <-> "NH2" Residue "5P ARG 39": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 41355 Number of models: 1 Model: "" Number of chains: 155 Chain: "1A" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "1B" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "1C" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "1D" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "1E" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "1F" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "1G" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "1H" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "1I" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "1J" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "1K" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "1L" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "1M" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "1N" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "1O" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "1P" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "2A" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "2B" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "2C" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "2D" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "2E" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "2F" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "2G" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "2H" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "2I" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "2J" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "2K" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "2L" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "2M" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "2N" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "2O" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "2P" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "3A" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "3B" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "3C" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "3D" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "3E" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "3F" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "3G" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "3H" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "3I" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "3J" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "3K" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "3L" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "3M" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "3N" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "3O" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "3P" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "4A" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "4B" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "4C" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "4D" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "4E" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "4F" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "4G" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "4H" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "4I" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "4J" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "4K" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "4L" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "4M" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "4N" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "4O" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "4P" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "5A" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "5B" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "5C" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "5D" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "5E" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "5F" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "5G" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "5H" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "5I" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "5J" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "5K" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "5L" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "5M" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "5N" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "5O" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "5P" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 471 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "1A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "1B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "1C" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "1D" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "1E" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "1F" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "1G" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "1H" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "1I" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "1J" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "1K" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "1L" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "1M" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "1N" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "1O" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "2A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "2B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "2C" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "2D" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "2E" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "2F" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "2G" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "2H" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "2I" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "2J" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "2K" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "2L" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "2M" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "2N" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "2O" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "3A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "3B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "3C" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "3D" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "3E" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "3F" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "3G" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "3H" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "3I" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "3J" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "3K" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "3L" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "3M" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "3N" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "3O" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "4A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "4B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "4C" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "4D" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "4E" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "4F" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "4G" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "4H" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "4I" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "4J" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "4K" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "4L" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "4M" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "4N" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "4O" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "5A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "5B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "5C" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "5D" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "5E" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "5F" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "5G" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "5H" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "5I" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "5J" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "5K" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "5L" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "5M" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "5N" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Chain: "5O" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 21.39, per 1000 atoms: 0.52 Number of scatterers: 41355 At special positions: 0 Unit cell: (100.1, 100.1, 244.2, 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 320 16.00 P 75 15.00 O 7230 8.00 N 5680 7.00 C 28050 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: 16.12 Conformation dependent library (CDL) restraints added in 7.7 seconds 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9120 Finding SS restraints... Secondary structure from input PDB file: 240 helices and 0 sheets defined 66.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.27 Creating SS restraints... Processing helix chain '1A' and resid 10 through 16 Processing helix chain '1A' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE1A 26 " --> pdb=" O MET1A 22 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU1A 29 " --> pdb=" O ILE1A 25 " (cutoff:3.500A) Processing helix chain '1A' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL1A 51 " --> pdb=" O LEU1A 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL1A 52 " --> pdb=" O GLY1A 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR1A 61 " --> pdb=" O THR1A 57 " (cutoff:3.500A) Processing helix chain '1B' and resid 10 through 16 Processing helix chain '1B' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE1B 26 " --> pdb=" O MET1B 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU1B 29 " --> pdb=" O ILE1B 25 " (cutoff:3.500A) Processing helix chain '1B' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL1B 51 " --> pdb=" O LEU1B 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL1B 52 " --> pdb=" O GLY1B 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR1B 61 " --> pdb=" O THR1B 57 " (cutoff:3.500A) Processing helix chain '1C' and resid 10 through 16 Processing helix chain '1C' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE1C 26 " --> pdb=" O MET1C 22 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU1C 29 " --> pdb=" O ILE1C 25 " (cutoff:3.500A) Processing helix chain '1C' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL1C 51 " --> pdb=" O LEU1C 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL1C 52 " --> pdb=" O GLY1C 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR1C 61 " --> pdb=" O THR1C 57 " (cutoff:3.500A) Processing helix chain '1D' and resid 10 through 16 Processing helix chain '1D' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE1D 26 " --> pdb=" O MET1D 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU1D 29 " --> pdb=" O ILE1D 25 " (cutoff:3.500A) Processing helix chain '1D' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL1D 51 " --> pdb=" O LEU1D 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL1D 52 " --> pdb=" O GLY1D 48 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR1D 61 " --> pdb=" O THR1D 57 " (cutoff:3.500A) Processing helix chain '1E' and resid 10 through 16 Processing helix chain '1E' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE1E 26 " --> pdb=" O MET1E 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU1E 29 " --> pdb=" O ILE1E 25 " (cutoff:3.500A) Processing helix chain '1E' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL1E 51 " --> pdb=" O LEU1E 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL1E 52 " --> pdb=" O GLY1E 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR1E 61 " --> pdb=" O THR1E 57 " (cutoff:3.500A) Processing helix chain '1F' and resid 10 through 16 Processing helix chain '1F' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE1F 26 " --> pdb=" O MET1F 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU1F 29 " --> pdb=" O ILE1F 25 " (cutoff:3.500A) Processing helix chain '1F' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL1F 51 " --> pdb=" O LEU1F 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL1F 52 " --> pdb=" O GLY1F 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR1F 61 " --> pdb=" O THR1F 57 " (cutoff:3.500A) Processing helix chain '1G' and resid 10 through 16 Processing helix chain '1G' and resid 20 through 39 removed outlier: 3.530A pdb=" N ILE1G 26 " --> pdb=" O MET1G 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU1G 29 " --> pdb=" O ILE1G 25 " (cutoff:3.500A) Processing helix chain '1G' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL1G 51 " --> pdb=" O LEU1G 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL1G 52 " --> pdb=" O GLY1G 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR1G 61 " --> pdb=" O THR1G 57 " (cutoff:3.500A) Processing helix chain '1H' and resid 10 through 16 Processing helix chain '1H' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE1H 26 " --> pdb=" O MET1H 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU1H 29 " --> pdb=" O ILE1H 25 " (cutoff:3.500A) Processing helix chain '1H' and resid 47 through 61 removed outlier: 3.509A pdb=" N VAL1H 51 " --> pdb=" O LEU1H 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL1H 52 " --> pdb=" O GLY1H 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR1H 61 " --> pdb=" O THR1H 57 " (cutoff:3.500A) Processing helix chain '1I' and resid 10 through 16 Processing helix chain '1I' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE1I 26 " --> pdb=" O MET1I 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU1I 29 " --> pdb=" O ILE1I 25 " (cutoff:3.500A) Processing helix chain '1I' and resid 47 through 61 removed outlier: 3.509A pdb=" N VAL1I 51 " --> pdb=" O LEU1I 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL1I 52 " --> pdb=" O GLY1I 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR1I 61 " --> pdb=" O THR1I 57 " (cutoff:3.500A) Processing helix chain '1J' and resid 10 through 16 Processing helix chain '1J' and resid 20 through 39 removed outlier: 3.530A pdb=" N ILE1J 26 " --> pdb=" O MET1J 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU1J 29 " --> pdb=" O ILE1J 25 " (cutoff:3.500A) Processing helix chain '1J' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL1J 51 " --> pdb=" O LEU1J 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL1J 52 " --> pdb=" O GLY1J 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR1J 61 " --> pdb=" O THR1J 57 " (cutoff:3.500A) Processing helix chain '1K' and resid 10 through 16 Processing helix chain '1K' and resid 20 through 39 removed outlier: 3.530A pdb=" N ILE1K 26 " --> pdb=" O MET1K 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU1K 29 " --> pdb=" O ILE1K 25 " (cutoff:3.500A) Processing helix chain '1K' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL1K 51 " --> pdb=" O LEU1K 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL1K 52 " --> pdb=" O GLY1K 48 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR1K 61 " --> pdb=" O THR1K 57 " (cutoff:3.500A) Processing helix chain '1L' and resid 10 through 16 Processing helix chain '1L' and resid 20 through 39 removed outlier: 3.530A pdb=" N ILE1L 26 " --> pdb=" O MET1L 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU1L 29 " --> pdb=" O ILE1L 25 " (cutoff:3.500A) Processing helix chain '1L' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL1L 51 " --> pdb=" O LEU1L 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL1L 52 " --> pdb=" O GLY1L 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR1L 61 " --> pdb=" O THR1L 57 " (cutoff:3.500A) Processing helix chain '1M' and resid 10 through 16 Processing helix chain '1M' and resid 20 through 39 removed outlier: 3.531A pdb=" N ILE1M 26 " --> pdb=" O MET1M 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU1M 29 " --> pdb=" O ILE1M 25 " (cutoff:3.500A) Processing helix chain '1M' and resid 47 through 61 removed outlier: 3.511A pdb=" N VAL1M 51 " --> pdb=" O LEU1M 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL1M 52 " --> pdb=" O GLY1M 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR1M 61 " --> pdb=" O THR1M 57 " (cutoff:3.500A) Processing helix chain '1N' and resid 10 through 16 Processing helix chain '1N' and resid 20 through 39 removed outlier: 3.530A pdb=" N ILE1N 26 " --> pdb=" O MET1N 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU1N 29 " --> pdb=" O ILE1N 25 " (cutoff:3.500A) Processing helix chain '1N' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL1N 51 " --> pdb=" O LEU1N 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL1N 52 " --> pdb=" O GLY1N 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR1N 61 " --> pdb=" O THR1N 57 " (cutoff:3.500A) Processing helix chain '1O' and resid 10 through 16 Processing helix chain '1O' and resid 20 through 39 removed outlier: 3.531A pdb=" N ILE1O 26 " --> pdb=" O MET1O 22 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU1O 29 " --> pdb=" O ILE1O 25 " (cutoff:3.500A) Processing helix chain '1O' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL1O 51 " --> pdb=" O LEU1O 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL1O 52 " --> pdb=" O GLY1O 48 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR1O 61 " --> pdb=" O THR1O 57 " (cutoff:3.500A) Processing helix chain '1P' and resid 10 through 16 Processing helix chain '1P' and resid 20 through 39 removed outlier: 3.531A pdb=" N ILE1P 26 " --> pdb=" O MET1P 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU1P 29 " --> pdb=" O ILE1P 25 " (cutoff:3.500A) Processing helix chain '1P' and resid 47 through 61 removed outlier: 3.511A pdb=" N VAL1P 51 " --> pdb=" O LEU1P 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL1P 52 " --> pdb=" O GLY1P 48 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR1P 61 " --> pdb=" O THR1P 57 " (cutoff:3.500A) Processing helix chain '2A' and resid 10 through 16 Processing helix chain '2A' and resid 20 through 39 removed outlier: 3.528A pdb=" N ILE2A 26 " --> pdb=" O MET2A 22 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU2A 29 " --> pdb=" O ILE2A 25 " (cutoff:3.500A) Processing helix chain '2A' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL2A 51 " --> pdb=" O LEU2A 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL2A 52 " --> pdb=" O GLY2A 48 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR2A 61 " --> pdb=" O THR2A 57 " (cutoff:3.500A) Processing helix chain '2B' and resid 10 through 16 Processing helix chain '2B' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE2B 26 " --> pdb=" O MET2B 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU2B 29 " --> pdb=" O ILE2B 25 " (cutoff:3.500A) Processing helix chain '2B' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL2B 51 " --> pdb=" O LEU2B 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL2B 52 " --> pdb=" O GLY2B 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR2B 61 " --> pdb=" O THR2B 57 " (cutoff:3.500A) Processing helix chain '2C' and resid 10 through 16 Processing helix chain '2C' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE2C 26 " --> pdb=" O MET2C 22 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU2C 29 " --> pdb=" O ILE2C 25 " (cutoff:3.500A) Processing helix chain '2C' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL2C 51 " --> pdb=" O LEU2C 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL2C 52 " --> pdb=" O GLY2C 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR2C 61 " --> pdb=" O THR2C 57 " (cutoff:3.500A) Processing helix chain '2D' and resid 10 through 16 Processing helix chain '2D' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE2D 26 " --> pdb=" O MET2D 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU2D 29 " --> pdb=" O ILE2D 25 " (cutoff:3.500A) Processing helix chain '2D' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL2D 51 " --> pdb=" O LEU2D 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL2D 52 " --> pdb=" O GLY2D 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR2D 61 " --> pdb=" O THR2D 57 " (cutoff:3.500A) Processing helix chain '2E' and resid 10 through 16 Processing helix chain '2E' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE2E 26 " --> pdb=" O MET2E 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU2E 29 " --> pdb=" O ILE2E 25 " (cutoff:3.500A) Processing helix chain '2E' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL2E 51 " --> pdb=" O LEU2E 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL2E 52 " --> pdb=" O GLY2E 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR2E 61 " --> pdb=" O THR2E 57 " (cutoff:3.500A) Processing helix chain '2F' and resid 10 through 16 Processing helix chain '2F' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE2F 26 " --> pdb=" O MET2F 22 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU2F 29 " --> pdb=" O ILE2F 25 " (cutoff:3.500A) Processing helix chain '2F' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL2F 51 " --> pdb=" O LEU2F 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL2F 52 " --> pdb=" O GLY2F 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR2F 61 " --> pdb=" O THR2F 57 " (cutoff:3.500A) Processing helix chain '2G' and resid 10 through 16 Processing helix chain '2G' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE2G 26 " --> pdb=" O MET2G 22 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU2G 29 " --> pdb=" O ILE2G 25 " (cutoff:3.500A) Processing helix chain '2G' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL2G 51 " --> pdb=" O LEU2G 47 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL2G 52 " --> pdb=" O GLY2G 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR2G 61 " --> pdb=" O THR2G 57 " (cutoff:3.500A) Processing helix chain '2H' and resid 10 through 16 Processing helix chain '2H' and resid 20 through 39 removed outlier: 3.530A pdb=" N ILE2H 26 " --> pdb=" O MET2H 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU2H 29 " --> pdb=" O ILE2H 25 " (cutoff:3.500A) Processing helix chain '2H' and resid 47 through 61 removed outlier: 3.509A pdb=" N VAL2H 51 " --> pdb=" O LEU2H 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL2H 52 " --> pdb=" O GLY2H 48 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR2H 61 " --> pdb=" O THR2H 57 " (cutoff:3.500A) Processing helix chain '2I' and resid 10 through 16 Processing helix chain '2I' and resid 20 through 39 removed outlier: 3.530A pdb=" N ILE2I 26 " --> pdb=" O MET2I 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU2I 29 " --> pdb=" O ILE2I 25 " (cutoff:3.500A) Processing helix chain '2I' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL2I 51 " --> pdb=" O LEU2I 47 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL2I 52 " --> pdb=" O GLY2I 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR2I 61 " --> pdb=" O THR2I 57 " (cutoff:3.500A) Processing helix chain '2J' and resid 10 through 16 Processing helix chain '2J' and resid 20 through 39 removed outlier: 3.531A pdb=" N ILE2J 26 " --> pdb=" O MET2J 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU2J 29 " --> pdb=" O ILE2J 25 " (cutoff:3.500A) Processing helix chain '2J' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL2J 51 " --> pdb=" O LEU2J 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL2J 52 " --> pdb=" O GLY2J 48 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR2J 61 " --> pdb=" O THR2J 57 " (cutoff:3.500A) Processing helix chain '2K' and resid 10 through 16 Processing helix chain '2K' and resid 20 through 39 removed outlier: 3.530A pdb=" N ILE2K 26 " --> pdb=" O MET2K 22 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU2K 29 " --> pdb=" O ILE2K 25 " (cutoff:3.500A) Processing helix chain '2K' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL2K 51 " --> pdb=" O LEU2K 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL2K 52 " --> pdb=" O GLY2K 48 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR2K 61 " --> pdb=" O THR2K 57 " (cutoff:3.500A) Processing helix chain '2L' and resid 10 through 16 Processing helix chain '2L' and resid 20 through 39 removed outlier: 3.530A pdb=" N ILE2L 26 " --> pdb=" O MET2L 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU2L 29 " --> pdb=" O ILE2L 25 " (cutoff:3.500A) Processing helix chain '2L' and resid 47 through 61 removed outlier: 3.511A pdb=" N VAL2L 51 " --> pdb=" O LEU2L 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL2L 52 " --> pdb=" O GLY2L 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR2L 61 " --> pdb=" O THR2L 57 " (cutoff:3.500A) Processing helix chain '2M' and resid 10 through 16 Processing helix chain '2M' and resid 20 through 39 removed outlier: 3.531A pdb=" N ILE2M 26 " --> pdb=" O MET2M 22 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU2M 29 " --> pdb=" O ILE2M 25 " (cutoff:3.500A) Processing helix chain '2M' and resid 47 through 61 removed outlier: 3.511A pdb=" N VAL2M 51 " --> pdb=" O LEU2M 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL2M 52 " --> pdb=" O GLY2M 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR2M 61 " --> pdb=" O THR2M 57 " (cutoff:3.500A) Processing helix chain '2N' and resid 10 through 16 Processing helix chain '2N' and resid 20 through 39 removed outlier: 3.531A pdb=" N ILE2N 26 " --> pdb=" O MET2N 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU2N 29 " --> pdb=" O ILE2N 25 " (cutoff:3.500A) Processing helix chain '2N' and resid 47 through 61 removed outlier: 3.511A pdb=" N VAL2N 51 " --> pdb=" O LEU2N 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL2N 52 " --> pdb=" O GLY2N 48 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR2N 61 " --> pdb=" O THR2N 57 " (cutoff:3.500A) Processing helix chain '2O' and resid 10 through 16 Processing helix chain '2O' and resid 20 through 39 removed outlier: 3.531A pdb=" N ILE2O 26 " --> pdb=" O MET2O 22 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU2O 29 " --> pdb=" O ILE2O 25 " (cutoff:3.500A) Processing helix chain '2O' and resid 47 through 61 removed outlier: 3.511A pdb=" N VAL2O 51 " --> pdb=" O LEU2O 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL2O 52 " --> pdb=" O GLY2O 48 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR2O 61 " --> pdb=" O THR2O 57 " (cutoff:3.500A) Processing helix chain '2P' and resid 10 through 16 Processing helix chain '2P' and resid 20 through 39 removed outlier: 3.531A pdb=" N ILE2P 26 " --> pdb=" O MET2P 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU2P 29 " --> pdb=" O ILE2P 25 " (cutoff:3.500A) Processing helix chain '2P' and resid 47 through 61 removed outlier: 3.511A pdb=" N VAL2P 51 " --> pdb=" O LEU2P 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL2P 52 " --> pdb=" O GLY2P 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR2P 61 " --> pdb=" O THR2P 57 " (cutoff:3.500A) Processing helix chain '3A' and resid 10 through 16 Processing helix chain '3A' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE3A 26 " --> pdb=" O MET3A 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU3A 29 " --> pdb=" O ILE3A 25 " (cutoff:3.500A) Processing helix chain '3A' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL3A 51 " --> pdb=" O LEU3A 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL3A 52 " --> pdb=" O GLY3A 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR3A 61 " --> pdb=" O THR3A 57 " (cutoff:3.500A) Processing helix chain '3B' and resid 10 through 16 Processing helix chain '3B' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE3B 26 " --> pdb=" O MET3B 22 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU3B 29 " --> pdb=" O ILE3B 25 " (cutoff:3.500A) Processing helix chain '3B' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL3B 51 " --> pdb=" O LEU3B 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL3B 52 " --> pdb=" O GLY3B 48 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR3B 61 " --> pdb=" O THR3B 57 " (cutoff:3.500A) Processing helix chain '3C' and resid 10 through 16 Processing helix chain '3C' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE3C 26 " --> pdb=" O MET3C 22 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU3C 29 " --> pdb=" O ILE3C 25 " (cutoff:3.500A) Processing helix chain '3C' and resid 47 through 61 removed outlier: 3.511A pdb=" N VAL3C 51 " --> pdb=" O LEU3C 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL3C 52 " --> pdb=" O GLY3C 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR3C 61 " --> pdb=" O THR3C 57 " (cutoff:3.500A) Processing helix chain '3D' and resid 10 through 16 Processing helix chain '3D' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE3D 26 " --> pdb=" O MET3D 22 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU3D 29 " --> pdb=" O ILE3D 25 " (cutoff:3.500A) Processing helix chain '3D' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL3D 51 " --> pdb=" O LEU3D 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL3D 52 " --> pdb=" O GLY3D 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR3D 61 " --> pdb=" O THR3D 57 " (cutoff:3.500A) Processing helix chain '3E' and resid 10 through 16 Processing helix chain '3E' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE3E 26 " --> pdb=" O MET3E 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU3E 29 " --> pdb=" O ILE3E 25 " (cutoff:3.500A) Processing helix chain '3E' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL3E 51 " --> pdb=" O LEU3E 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL3E 52 " --> pdb=" O GLY3E 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR3E 61 " --> pdb=" O THR3E 57 " (cutoff:3.500A) Processing helix chain '3F' and resid 10 through 16 Processing helix chain '3F' and resid 20 through 39 removed outlier: 3.530A pdb=" N ILE3F 26 " --> pdb=" O MET3F 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU3F 29 " --> pdb=" O ILE3F 25 " (cutoff:3.500A) Processing helix chain '3F' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL3F 51 " --> pdb=" O LEU3F 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL3F 52 " --> pdb=" O GLY3F 48 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR3F 61 " --> pdb=" O THR3F 57 " (cutoff:3.500A) Processing helix chain '3G' and resid 10 through 16 Processing helix chain '3G' and resid 20 through 39 removed outlier: 3.530A pdb=" N ILE3G 26 " --> pdb=" O MET3G 22 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU3G 29 " --> pdb=" O ILE3G 25 " (cutoff:3.500A) Processing helix chain '3G' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL3G 51 " --> pdb=" O LEU3G 47 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL3G 52 " --> pdb=" O GLY3G 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR3G 61 " --> pdb=" O THR3G 57 " (cutoff:3.500A) Processing helix chain '3H' and resid 10 through 16 Processing helix chain '3H' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE3H 26 " --> pdb=" O MET3H 22 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU3H 29 " --> pdb=" O ILE3H 25 " (cutoff:3.500A) Processing helix chain '3H' and resid 47 through 61 removed outlier: 3.509A pdb=" N VAL3H 51 " --> pdb=" O LEU3H 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL3H 52 " --> pdb=" O GLY3H 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR3H 61 " --> pdb=" O THR3H 57 " (cutoff:3.500A) Processing helix chain '3I' and resid 10 through 16 Processing helix chain '3I' and resid 20 through 39 removed outlier: 3.530A pdb=" N ILE3I 26 " --> pdb=" O MET3I 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU3I 29 " --> pdb=" O ILE3I 25 " (cutoff:3.500A) Processing helix chain '3I' and resid 47 through 61 removed outlier: 3.509A pdb=" N VAL3I 51 " --> pdb=" O LEU3I 47 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL3I 52 " --> pdb=" O GLY3I 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR3I 61 " --> pdb=" O THR3I 57 " (cutoff:3.500A) Processing helix chain '3J' and resid 10 through 16 Processing helix chain '3J' and resid 20 through 39 removed outlier: 3.530A pdb=" N ILE3J 26 " --> pdb=" O MET3J 22 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU3J 29 " --> pdb=" O ILE3J 25 " (cutoff:3.500A) Processing helix chain '3J' and resid 47 through 61 removed outlier: 3.509A pdb=" N VAL3J 51 " --> pdb=" O LEU3J 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL3J 52 " --> pdb=" O GLY3J 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR3J 61 " --> pdb=" O THR3J 57 " (cutoff:3.500A) Processing helix chain '3K' and resid 10 through 16 Processing helix chain '3K' and resid 20 through 39 removed outlier: 3.531A pdb=" N ILE3K 26 " --> pdb=" O MET3K 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU3K 29 " --> pdb=" O ILE3K 25 " (cutoff:3.500A) Processing helix chain '3K' and resid 47 through 61 removed outlier: 3.509A pdb=" N VAL3K 51 " --> pdb=" O LEU3K 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL3K 52 " --> pdb=" O GLY3K 48 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR3K 61 " --> pdb=" O THR3K 57 " (cutoff:3.500A) Processing helix chain '3L' and resid 10 through 16 Processing helix chain '3L' and resid 20 through 39 removed outlier: 3.531A pdb=" N ILE3L 26 " --> pdb=" O MET3L 22 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU3L 29 " --> pdb=" O ILE3L 25 " (cutoff:3.500A) Processing helix chain '3L' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL3L 51 " --> pdb=" O LEU3L 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL3L 52 " --> pdb=" O GLY3L 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR3L 61 " --> pdb=" O THR3L 57 " (cutoff:3.500A) Processing helix chain '3M' and resid 10 through 16 Processing helix chain '3M' and resid 20 through 39 removed outlier: 3.531A pdb=" N ILE3M 26 " --> pdb=" O MET3M 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU3M 29 " --> pdb=" O ILE3M 25 " (cutoff:3.500A) Processing helix chain '3M' and resid 47 through 61 removed outlier: 3.511A pdb=" N VAL3M 51 " --> pdb=" O LEU3M 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL3M 52 " --> pdb=" O GLY3M 48 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR3M 61 " --> pdb=" O THR3M 57 " (cutoff:3.500A) Processing helix chain '3N' and resid 10 through 16 Processing helix chain '3N' and resid 20 through 39 removed outlier: 3.530A pdb=" N ILE3N 26 " --> pdb=" O MET3N 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU3N 29 " --> pdb=" O ILE3N 25 " (cutoff:3.500A) Processing helix chain '3N' and resid 47 through 61 removed outlier: 3.511A pdb=" N VAL3N 51 " --> pdb=" O LEU3N 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL3N 52 " --> pdb=" O GLY3N 48 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR3N 61 " --> pdb=" O THR3N 57 " (cutoff:3.500A) Processing helix chain '3O' and resid 10 through 16 Processing helix chain '3O' and resid 20 through 39 removed outlier: 3.531A pdb=" N ILE3O 26 " --> pdb=" O MET3O 22 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU3O 29 " --> pdb=" O ILE3O 25 " (cutoff:3.500A) Processing helix chain '3O' and resid 47 through 61 removed outlier: 3.511A pdb=" N VAL3O 51 " --> pdb=" O LEU3O 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL3O 52 " --> pdb=" O GLY3O 48 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR3O 61 " --> pdb=" O THR3O 57 " (cutoff:3.500A) Processing helix chain '3P' and resid 10 through 16 Processing helix chain '3P' and resid 20 through 39 removed outlier: 3.531A pdb=" N ILE3P 26 " --> pdb=" O MET3P 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU3P 29 " --> pdb=" O ILE3P 25 " (cutoff:3.500A) Processing helix chain '3P' and resid 47 through 61 removed outlier: 3.511A pdb=" N VAL3P 51 " --> pdb=" O LEU3P 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL3P 52 " --> pdb=" O GLY3P 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR3P 61 " --> pdb=" O THR3P 57 " (cutoff:3.500A) Processing helix chain '4A' and resid 10 through 16 Processing helix chain '4A' and resid 20 through 39 removed outlier: 3.528A pdb=" N ILE4A 26 " --> pdb=" O MET4A 22 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU4A 29 " --> pdb=" O ILE4A 25 " (cutoff:3.500A) Processing helix chain '4A' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL4A 51 " --> pdb=" O LEU4A 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL4A 52 " --> pdb=" O GLY4A 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR4A 61 " --> pdb=" O THR4A 57 " (cutoff:3.500A) Processing helix chain '4B' and resid 10 through 16 Processing helix chain '4B' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE4B 26 " --> pdb=" O MET4B 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU4B 29 " --> pdb=" O ILE4B 25 " (cutoff:3.500A) Processing helix chain '4B' and resid 47 through 61 removed outlier: 3.509A pdb=" N VAL4B 51 " --> pdb=" O LEU4B 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL4B 52 " --> pdb=" O GLY4B 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR4B 61 " --> pdb=" O THR4B 57 " (cutoff:3.500A) Processing helix chain '4C' and resid 10 through 16 Processing helix chain '4C' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE4C 26 " --> pdb=" O MET4C 22 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU4C 29 " --> pdb=" O ILE4C 25 " (cutoff:3.500A) Processing helix chain '4C' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL4C 51 " --> pdb=" O LEU4C 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL4C 52 " --> pdb=" O GLY4C 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR4C 61 " --> pdb=" O THR4C 57 " (cutoff:3.500A) Processing helix chain '4D' and resid 10 through 16 Processing helix chain '4D' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE4D 26 " --> pdb=" O MET4D 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU4D 29 " --> pdb=" O ILE4D 25 " (cutoff:3.500A) Processing helix chain '4D' and resid 47 through 61 removed outlier: 3.509A pdb=" N VAL4D 51 " --> pdb=" O LEU4D 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL4D 52 " --> pdb=" O GLY4D 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR4D 61 " --> pdb=" O THR4D 57 " (cutoff:3.500A) Processing helix chain '4E' and resid 10 through 16 Processing helix chain '4E' and resid 20 through 39 removed outlier: 3.528A pdb=" N ILE4E 26 " --> pdb=" O MET4E 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU4E 29 " --> pdb=" O ILE4E 25 " (cutoff:3.500A) Processing helix chain '4E' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL4E 51 " --> pdb=" O LEU4E 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL4E 52 " --> pdb=" O GLY4E 48 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR4E 61 " --> pdb=" O THR4E 57 " (cutoff:3.500A) Processing helix chain '4F' and resid 10 through 16 Processing helix chain '4F' and resid 20 through 39 removed outlier: 3.530A pdb=" N ILE4F 26 " --> pdb=" O MET4F 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU4F 29 " --> pdb=" O ILE4F 25 " (cutoff:3.500A) Processing helix chain '4F' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL4F 51 " --> pdb=" O LEU4F 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL4F 52 " --> pdb=" O GLY4F 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR4F 61 " --> pdb=" O THR4F 57 " (cutoff:3.500A) Processing helix chain '4G' and resid 10 through 16 Processing helix chain '4G' and resid 20 through 39 removed outlier: 3.530A pdb=" N ILE4G 26 " --> pdb=" O MET4G 22 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU4G 29 " --> pdb=" O ILE4G 25 " (cutoff:3.500A) Processing helix chain '4G' and resid 47 through 61 removed outlier: 3.509A pdb=" N VAL4G 51 " --> pdb=" O LEU4G 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL4G 52 " --> pdb=" O GLY4G 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR4G 61 " --> pdb=" O THR4G 57 " (cutoff:3.500A) Processing helix chain '4H' and resid 10 through 16 Processing helix chain '4H' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE4H 26 " --> pdb=" O MET4H 22 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU4H 29 " --> pdb=" O ILE4H 25 " (cutoff:3.500A) Processing helix chain '4H' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL4H 51 " --> pdb=" O LEU4H 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL4H 52 " --> pdb=" O GLY4H 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR4H 61 " --> pdb=" O THR4H 57 " (cutoff:3.500A) Processing helix chain '4I' and resid 10 through 16 Processing helix chain '4I' and resid 20 through 39 removed outlier: 3.530A pdb=" N ILE4I 26 " --> pdb=" O MET4I 22 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU4I 29 " --> pdb=" O ILE4I 25 " (cutoff:3.500A) Processing helix chain '4I' and resid 47 through 61 removed outlier: 3.509A pdb=" N VAL4I 51 " --> pdb=" O LEU4I 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL4I 52 " --> pdb=" O GLY4I 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR4I 61 " --> pdb=" O THR4I 57 " (cutoff:3.500A) Processing helix chain '4J' and resid 10 through 16 Processing helix chain '4J' and resid 20 through 39 removed outlier: 3.531A pdb=" N ILE4J 26 " --> pdb=" O MET4J 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU4J 29 " --> pdb=" O ILE4J 25 " (cutoff:3.500A) Processing helix chain '4J' and resid 47 through 61 removed outlier: 3.511A pdb=" N VAL4J 51 " --> pdb=" O LEU4J 47 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL4J 52 " --> pdb=" O GLY4J 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR4J 61 " --> pdb=" O THR4J 57 " (cutoff:3.500A) Processing helix chain '4K' and resid 10 through 16 Processing helix chain '4K' and resid 20 through 39 removed outlier: 3.531A pdb=" N ILE4K 26 " --> pdb=" O MET4K 22 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU4K 29 " --> pdb=" O ILE4K 25 " (cutoff:3.500A) Processing helix chain '4K' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL4K 51 " --> pdb=" O LEU4K 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL4K 52 " --> pdb=" O GLY4K 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR4K 61 " --> pdb=" O THR4K 57 " (cutoff:3.500A) Processing helix chain '4L' and resid 10 through 16 Processing helix chain '4L' and resid 20 through 39 removed outlier: 3.530A pdb=" N ILE4L 26 " --> pdb=" O MET4L 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU4L 29 " --> pdb=" O ILE4L 25 " (cutoff:3.500A) Processing helix chain '4L' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL4L 51 " --> pdb=" O LEU4L 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL4L 52 " --> pdb=" O GLY4L 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR4L 61 " --> pdb=" O THR4L 57 " (cutoff:3.500A) Processing helix chain '4M' and resid 10 through 16 Processing helix chain '4M' and resid 20 through 39 removed outlier: 3.531A pdb=" N ILE4M 26 " --> pdb=" O MET4M 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU4M 29 " --> pdb=" O ILE4M 25 " (cutoff:3.500A) Processing helix chain '4M' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL4M 51 " --> pdb=" O LEU4M 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL4M 52 " --> pdb=" O GLY4M 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR4M 61 " --> pdb=" O THR4M 57 " (cutoff:3.500A) Processing helix chain '4N' and resid 10 through 16 Processing helix chain '4N' and resid 20 through 39 removed outlier: 3.531A pdb=" N ILE4N 26 " --> pdb=" O MET4N 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU4N 29 " --> pdb=" O ILE4N 25 " (cutoff:3.500A) Processing helix chain '4N' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL4N 51 " --> pdb=" O LEU4N 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL4N 52 " --> pdb=" O GLY4N 48 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR4N 61 " --> pdb=" O THR4N 57 " (cutoff:3.500A) Processing helix chain '4O' and resid 10 through 16 Processing helix chain '4O' and resid 20 through 39 removed outlier: 3.531A pdb=" N ILE4O 26 " --> pdb=" O MET4O 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU4O 29 " --> pdb=" O ILE4O 25 " (cutoff:3.500A) Processing helix chain '4O' and resid 47 through 61 removed outlier: 3.511A pdb=" N VAL4O 51 " --> pdb=" O LEU4O 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL4O 52 " --> pdb=" O GLY4O 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR4O 61 " --> pdb=" O THR4O 57 " (cutoff:3.500A) Processing helix chain '4P' and resid 10 through 16 Processing helix chain '4P' and resid 20 through 39 removed outlier: 3.531A pdb=" N ILE4P 26 " --> pdb=" O MET4P 22 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU4P 29 " --> pdb=" O ILE4P 25 " (cutoff:3.500A) Processing helix chain '4P' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL4P 51 " --> pdb=" O LEU4P 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL4P 52 " --> pdb=" O GLY4P 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR4P 61 " --> pdb=" O THR4P 57 " (cutoff:3.500A) Processing helix chain '5A' and resid 10 through 16 Processing helix chain '5A' and resid 20 through 39 removed outlier: 3.528A pdb=" N ILE5A 26 " --> pdb=" O MET5A 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU5A 29 " --> pdb=" O ILE5A 25 " (cutoff:3.500A) Processing helix chain '5A' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL5A 51 " --> pdb=" O LEU5A 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL5A 52 " --> pdb=" O GLY5A 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR5A 61 " --> pdb=" O THR5A 57 " (cutoff:3.500A) Processing helix chain '5B' and resid 10 through 16 Processing helix chain '5B' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE5B 26 " --> pdb=" O MET5B 22 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU5B 29 " --> pdb=" O ILE5B 25 " (cutoff:3.500A) Processing helix chain '5B' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL5B 51 " --> pdb=" O LEU5B 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL5B 52 " --> pdb=" O GLY5B 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR5B 61 " --> pdb=" O THR5B 57 " (cutoff:3.500A) Processing helix chain '5C' and resid 10 through 16 Processing helix chain '5C' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE5C 26 " --> pdb=" O MET5C 22 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU5C 29 " --> pdb=" O ILE5C 25 " (cutoff:3.500A) Processing helix chain '5C' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL5C 51 " --> pdb=" O LEU5C 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL5C 52 " --> pdb=" O GLY5C 48 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR5C 61 " --> pdb=" O THR5C 57 " (cutoff:3.500A) Processing helix chain '5D' and resid 10 through 16 Processing helix chain '5D' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE5D 26 " --> pdb=" O MET5D 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU5D 29 " --> pdb=" O ILE5D 25 " (cutoff:3.500A) Processing helix chain '5D' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL5D 51 " --> pdb=" O LEU5D 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL5D 52 " --> pdb=" O GLY5D 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR5D 61 " --> pdb=" O THR5D 57 " (cutoff:3.500A) Processing helix chain '5E' and resid 10 through 16 Processing helix chain '5E' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE5E 26 " --> pdb=" O MET5E 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU5E 29 " --> pdb=" O ILE5E 25 " (cutoff:3.500A) Processing helix chain '5E' and resid 47 through 61 removed outlier: 3.509A pdb=" N VAL5E 51 " --> pdb=" O LEU5E 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL5E 52 " --> pdb=" O GLY5E 48 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR5E 61 " --> pdb=" O THR5E 57 " (cutoff:3.500A) Processing helix chain '5F' and resid 10 through 16 Processing helix chain '5F' and resid 20 through 39 removed outlier: 3.530A pdb=" N ILE5F 26 " --> pdb=" O MET5F 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU5F 29 " --> pdb=" O ILE5F 25 " (cutoff:3.500A) Processing helix chain '5F' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL5F 51 " --> pdb=" O LEU5F 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL5F 52 " --> pdb=" O GLY5F 48 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR5F 61 " --> pdb=" O THR5F 57 " (cutoff:3.500A) Processing helix chain '5G' and resid 10 through 16 Processing helix chain '5G' and resid 20 through 39 removed outlier: 3.530A pdb=" N ILE5G 26 " --> pdb=" O MET5G 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU5G 29 " --> pdb=" O ILE5G 25 " (cutoff:3.500A) Processing helix chain '5G' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL5G 51 " --> pdb=" O LEU5G 47 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL5G 52 " --> pdb=" O GLY5G 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR5G 61 " --> pdb=" O THR5G 57 " (cutoff:3.500A) Processing helix chain '5H' and resid 10 through 16 Processing helix chain '5H' and resid 20 through 39 removed outlier: 3.529A pdb=" N ILE5H 26 " --> pdb=" O MET5H 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU5H 29 " --> pdb=" O ILE5H 25 " (cutoff:3.500A) Processing helix chain '5H' and resid 47 through 61 removed outlier: 3.509A pdb=" N VAL5H 51 " --> pdb=" O LEU5H 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL5H 52 " --> pdb=" O GLY5H 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR5H 61 " --> pdb=" O THR5H 57 " (cutoff:3.500A) Processing helix chain '5I' and resid 10 through 16 Processing helix chain '5I' and resid 20 through 39 removed outlier: 3.530A pdb=" N ILE5I 26 " --> pdb=" O MET5I 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU5I 29 " --> pdb=" O ILE5I 25 " (cutoff:3.500A) Processing helix chain '5I' and resid 47 through 61 removed outlier: 3.509A pdb=" N VAL5I 51 " --> pdb=" O LEU5I 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL5I 52 " --> pdb=" O GLY5I 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR5I 61 " --> pdb=" O THR5I 57 " (cutoff:3.500A) Processing helix chain '5J' and resid 10 through 16 Processing helix chain '5J' and resid 20 through 39 removed outlier: 3.530A pdb=" N ILE5J 26 " --> pdb=" O MET5J 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU5J 29 " --> pdb=" O ILE5J 25 " (cutoff:3.500A) Processing helix chain '5J' and resid 47 through 61 removed outlier: 3.509A pdb=" N VAL5J 51 " --> pdb=" O LEU5J 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL5J 52 " --> pdb=" O GLY5J 48 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR5J 61 " --> pdb=" O THR5J 57 " (cutoff:3.500A) Processing helix chain '5K' and resid 10 through 16 Processing helix chain '5K' and resid 20 through 39 removed outlier: 3.530A pdb=" N ILE5K 26 " --> pdb=" O MET5K 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU5K 29 " --> pdb=" O ILE5K 25 " (cutoff:3.500A) Processing helix chain '5K' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL5K 51 " --> pdb=" O LEU5K 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL5K 52 " --> pdb=" O GLY5K 48 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR5K 61 " --> pdb=" O THR5K 57 " (cutoff:3.500A) Processing helix chain '5L' and resid 10 through 16 Processing helix chain '5L' and resid 20 through 39 removed outlier: 3.530A pdb=" N ILE5L 26 " --> pdb=" O MET5L 22 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU5L 29 " --> pdb=" O ILE5L 25 " (cutoff:3.500A) Processing helix chain '5L' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL5L 51 " --> pdb=" O LEU5L 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL5L 52 " --> pdb=" O GLY5L 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR5L 61 " --> pdb=" O THR5L 57 " (cutoff:3.500A) Processing helix chain '5M' and resid 10 through 16 Processing helix chain '5M' and resid 20 through 39 removed outlier: 3.531A pdb=" N ILE5M 26 " --> pdb=" O MET5M 22 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU5M 29 " --> pdb=" O ILE5M 25 " (cutoff:3.500A) Processing helix chain '5M' and resid 47 through 61 removed outlier: 3.511A pdb=" N VAL5M 51 " --> pdb=" O LEU5M 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL5M 52 " --> pdb=" O GLY5M 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR5M 61 " --> pdb=" O THR5M 57 " (cutoff:3.500A) Processing helix chain '5N' and resid 10 through 16 Processing helix chain '5N' and resid 20 through 39 removed outlier: 3.531A pdb=" N ILE5N 26 " --> pdb=" O MET5N 22 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU5N 29 " --> pdb=" O ILE5N 25 " (cutoff:3.500A) Processing helix chain '5N' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL5N 51 " --> pdb=" O LEU5N 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL5N 52 " --> pdb=" O GLY5N 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR5N 61 " --> pdb=" O THR5N 57 " (cutoff:3.500A) Processing helix chain '5O' and resid 10 through 16 Processing helix chain '5O' and resid 20 through 39 removed outlier: 3.531A pdb=" N ILE5O 26 " --> pdb=" O MET5O 22 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU5O 29 " --> pdb=" O ILE5O 25 " (cutoff:3.500A) Processing helix chain '5O' and resid 47 through 61 removed outlier: 3.510A pdb=" N VAL5O 51 " --> pdb=" O LEU5O 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL5O 52 " --> pdb=" O GLY5O 48 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR5O 61 " --> pdb=" O THR5O 57 " (cutoff:3.500A) Processing helix chain '5P' and resid 10 through 16 Processing helix chain '5P' and resid 20 through 39 removed outlier: 3.531A pdb=" N ILE5P 26 " --> pdb=" O MET5P 22 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU5P 29 " --> pdb=" O ILE5P 25 " (cutoff:3.500A) Processing helix chain '5P' and resid 47 through 61 removed outlier: 3.512A pdb=" N VAL5P 51 " --> pdb=" O LEU5P 47 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL5P 52 " --> pdb=" O GLY5P 48 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR5P 61 " --> pdb=" O THR5P 57 " (cutoff:3.500A) 2000 hydrogen bonds defined for protein. 6000 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.24 Time building geometry restraints manager: 17.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 6099 1.32 - 1.44: 8736 1.44 - 1.56: 26055 1.56 - 1.68: 150 1.68 - 1.80: 560 Bond restraints: 41600 Sorted by residual: bond pdb=" C15 LHG4J 101 " pdb=" C16 LHG4J 101 " ideal model delta sigma weight residual 1.524 1.315 0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C15 LHG2L 101 " pdb=" C16 LHG2L 101 " ideal model delta sigma weight residual 1.524 1.315 0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C15 LHG4I 101 " pdb=" C16 LHG4I 101 " ideal model delta sigma weight residual 1.524 1.315 0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C15 LHG3J 101 " pdb=" C16 LHG3J 101 " ideal model delta sigma weight residual 1.524 1.315 0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C15 LHG5J 101 " pdb=" C16 LHG5J 101 " ideal model delta sigma weight residual 1.524 1.315 0.209 2.00e-02 2.50e+03 1.09e+02 ... (remaining 41595 not shown) Histogram of bond angle deviations from ideal: 100.18 - 105.40: 315 105.40 - 110.63: 13519 110.63 - 115.85: 15600 115.85 - 121.07: 17379 121.07 - 126.29: 8597 Bond angle restraints: 55410 Sorted by residual: angle pdb=" C15 LHG5L 101 " pdb=" C16 LHG5L 101 " pdb=" C17 LHG5L 101 " ideal model delta sigma weight residual 112.69 126.29 -13.60 3.00e+00 1.11e-01 2.06e+01 angle pdb=" C15 LHG4K 101 " pdb=" C16 LHG4K 101 " pdb=" C17 LHG4K 101 " ideal model delta sigma weight residual 112.69 126.27 -13.58 3.00e+00 1.11e-01 2.05e+01 angle pdb=" C15 LHG2K 101 " pdb=" C16 LHG2K 101 " pdb=" C17 LHG2K 101 " ideal model delta sigma weight residual 112.69 126.27 -13.58 3.00e+00 1.11e-01 2.05e+01 angle pdb=" C15 LHG2L 101 " pdb=" C16 LHG2L 101 " pdb=" C17 LHG2L 101 " ideal model delta sigma weight residual 112.69 126.25 -13.56 3.00e+00 1.11e-01 2.04e+01 angle pdb=" C15 LHG5K 101 " pdb=" C16 LHG5K 101 " pdb=" C17 LHG5K 101 " ideal model delta sigma weight residual 112.69 126.24 -13.55 3.00e+00 1.11e-01 2.04e+01 ... (remaining 55405 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 23025 17.23 - 34.47: 1314 34.47 - 51.70: 896 51.70 - 68.94: 225 68.94 - 86.17: 315 Dihedral angle restraints: 25775 sinusoidal: 11615 harmonic: 14160 Sorted by residual: dihedral pdb=" CA GLY2C 7 " pdb=" C GLY2C 7 " pdb=" N LYS2C 8 " pdb=" CA LYS2C 8 " ideal model delta harmonic sigma weight residual 180.00 93.83 86.17 0 5.00e+00 4.00e-02 2.97e+02 dihedral pdb=" CA GLY3C 7 " pdb=" C GLY3C 7 " pdb=" N LYS3C 8 " pdb=" CA LYS3C 8 " ideal model delta harmonic sigma weight residual 180.00 93.88 86.12 0 5.00e+00 4.00e-02 2.97e+02 dihedral pdb=" CA GLY2B 7 " pdb=" C GLY2B 7 " pdb=" N LYS2B 8 " pdb=" CA LYS2B 8 " ideal model delta harmonic sigma weight residual 180.00 93.88 86.12 0 5.00e+00 4.00e-02 2.97e+02 ... (remaining 25772 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 3643 0.029 - 0.058: 2324 0.058 - 0.088: 1046 0.088 - 0.117: 97 0.117 - 0.146: 80 Chirality restraints: 7190 Sorted by residual: chirality pdb=" CB VAL5H 32 " pdb=" CA VAL5H 32 " pdb=" CG1 VAL5H 32 " pdb=" CG2 VAL5H 32 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.32e-01 chirality pdb=" CB VAL4F 32 " pdb=" CA VAL4F 32 " pdb=" CG1 VAL4F 32 " pdb=" CG2 VAL4F 32 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.29e-01 chirality pdb=" CB VAL3H 32 " pdb=" CA VAL3H 32 " pdb=" CG1 VAL3H 32 " pdb=" CG2 VAL3H 32 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.26e-01 ... (remaining 7187 not shown) Planarity restraints: 6070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET4L 23 " 0.003 2.00e-02 2.50e+03 6.31e-03 3.98e-01 pdb=" C MET4L 23 " -0.011 2.00e-02 2.50e+03 pdb=" O MET4L 23 " 0.004 2.00e-02 2.50e+03 pdb=" N CYS4L 24 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET5N 23 " 0.003 2.00e-02 2.50e+03 6.30e-03 3.97e-01 pdb=" C MET5N 23 " -0.011 2.00e-02 2.50e+03 pdb=" O MET5N 23 " 0.004 2.00e-02 2.50e+03 pdb=" N CYS5N 24 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET4A 23 " 0.003 2.00e-02 2.50e+03 6.27e-03 3.93e-01 pdb=" C MET4A 23 " -0.011 2.00e-02 2.50e+03 pdb=" O MET4A 23 " 0.004 2.00e-02 2.50e+03 pdb=" N CYS4A 24 " 0.004 2.00e-02 2.50e+03 ... (remaining 6067 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 15555 2.89 - 3.39: 42796 3.39 - 3.89: 67125 3.89 - 4.40: 74780 4.40 - 4.90: 119250 Nonbonded interactions: 319506 Sorted by model distance: nonbonded pdb=" O ASP4B 10 " pdb=" N ALA4B 13 " model vdw 2.383 2.520 nonbonded pdb=" O ASP5C 10 " pdb=" N ALA5C 13 " model vdw 2.383 2.520 nonbonded pdb=" O ASP4A 10 " pdb=" N ALA4A 13 " model vdw 2.383 2.520 nonbonded pdb=" O ASP3A 10 " pdb=" N ALA3A 13 " model vdw 2.383 2.520 nonbonded pdb=" O ASP2D 10 " pdb=" N ALA2D 13 " model vdw 2.384 2.520 ... (remaining 319501 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' and resid 2 through 64) selection = (chain '1B' and resid 2 through 64) selection = (chain '1C' and resid 2 through 64) selection = (chain '1D' and resid 2 through 64) selection = (chain '1E' and resid 2 through 64) selection = (chain '1F' and resid 2 through 64) selection = (chain '1G' and resid 2 through 64) selection = (chain '1H' and resid 2 through 64) selection = (chain '1I' and resid 2 through 64) selection = (chain '1J' and resid 2 through 64) selection = (chain '1K' and resid 2 through 64) selection = (chain '1L' and resid 2 through 64) selection = (chain '1M' and resid 2 through 64) selection = (chain '1N' and resid 2 through 64) selection = (chain '1O' and resid 2 through 64) selection = chain '1P' selection = (chain '2A' and resid 2 through 64) selection = (chain '2B' and resid 2 through 64) selection = (chain '2C' and resid 2 through 64) selection = (chain '2D' and resid 2 through 64) selection = (chain '2E' and resid 2 through 64) selection = (chain '2F' and resid 2 through 64) selection = (chain '2G' and resid 2 through 64) selection = (chain '2H' and resid 2 through 64) selection = (chain '2I' and resid 2 through 64) selection = (chain '2J' and resid 2 through 64) selection = (chain '2K' and resid 2 through 64) selection = (chain '2L' and resid 2 through 64) selection = (chain '2M' and resid 2 through 64) selection = (chain '2N' and resid 2 through 64) selection = (chain '2O' and resid 2 through 64) selection = chain '2P' selection = (chain '3A' and resid 2 through 64) selection = (chain '3B' and resid 2 through 64) selection = (chain '3C' and resid 2 through 64) selection = (chain '3D' and resid 2 through 64) selection = (chain '3E' and resid 2 through 64) selection = (chain '3F' and resid 2 through 64) selection = (chain '3G' and resid 2 through 64) selection = (chain '3H' and resid 2 through 64) selection = (chain '3I' and resid 2 through 64) selection = (chain '3J' and resid 2 through 64) selection = (chain '3K' and resid 2 through 64) selection = (chain '3L' and resid 2 through 64) selection = (chain '3M' and resid 2 through 64) selection = (chain '3N' and resid 2 through 64) selection = (chain '3O' and resid 2 through 64) selection = chain '3P' selection = (chain '4A' and resid 2 through 64) selection = (chain '4B' and resid 2 through 64) selection = (chain '4C' and resid 2 through 64) selection = (chain '4D' and resid 2 through 64) selection = (chain '4E' and resid 2 through 64) selection = (chain '4F' and resid 2 through 64) selection = (chain '4G' and resid 2 through 64) selection = (chain '4H' and resid 2 through 64) selection = (chain '4I' and resid 2 through 64) selection = (chain '4J' and resid 2 through 64) selection = (chain '4K' and resid 2 through 64) selection = (chain '4L' and resid 2 through 64) selection = (chain '4M' and resid 2 through 64) selection = (chain '4N' and resid 2 through 64) selection = (chain '4O' and resid 2 through 64) selection = chain '4P' selection = (chain '5A' and resid 2 through 64) selection = (chain '5B' and resid 2 through 64) selection = (chain '5C' and resid 2 through 64) selection = (chain '5D' and resid 2 through 64) selection = (chain '5E' and resid 2 through 64) selection = (chain '5F' and resid 2 through 64) selection = (chain '5G' and resid 2 through 64) selection = (chain '5H' and resid 2 through 64) selection = (chain '5I' and resid 2 through 64) selection = (chain '5J' and resid 2 through 64) selection = (chain '5K' and resid 2 through 64) selection = (chain '5L' and resid 2 through 64) selection = (chain '5M' and resid 2 through 64) selection = (chain '5N' and resid 2 through 64) selection = (chain '5O' and resid 2 through 64) selection = chain '5P' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.230 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: 0.050 Extract box with map and model: 1.320 Check model and map are aligned: 0.270 Set scattering table: 0.330 Process input model: 98.120 Find NCS groups from input model: 8.930 Set up NCS constraints: 0.570 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 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 : 0.012 0.209 41600 Z= 0.765 Angle : 1.206 13.603 55410 Z= 0.569 Chirality : 0.043 0.146 7190 Planarity : 0.002 0.006 6070 Dihedral : 18.495 86.173 16655 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 44.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % 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 : 9.68 % 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: -5.72 (0.09), residues: 4880 helix: -4.17 (0.05), residues: 3520 sheet: None (None), residues: 0 loop : -1.85 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.001 PHE5P 62 TYR 0.005 0.002 TYR4N 37 ARG 0.002 0.001 ARG4N 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2125 residues out of total 4160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2125 time to evaluate : 4.133 Fit side-chains REVERT: 1A 51 VAL cc_start: 0.8775 (m) cc_final: 0.8561 (t) REVERT: 1C 3 LEU cc_start: 0.7450 (tp) cc_final: 0.7238 (tp) REVERT: 1D 51 VAL cc_start: 0.8815 (m) cc_final: 0.8607 (t) REVERT: 1G 3 LEU cc_start: 0.7308 (tp) cc_final: 0.7031 (tp) REVERT: 1M 60 LEU cc_start: 0.8009 (mt) cc_final: 0.7717 (mt) REVERT: 2B 51 VAL cc_start: 0.8994 (m) cc_final: 0.8707 (t) REVERT: 2D 51 VAL cc_start: 0.8864 (m) cc_final: 0.8539 (t) REVERT: 3A 51 VAL cc_start: 0.8874 (m) cc_final: 0.8534 (t) REVERT: 3B 37 TYR cc_start: 0.8824 (t80) cc_final: 0.8559 (t80) REVERT: 3B 51 VAL cc_start: 0.9134 (m) cc_final: 0.8857 (t) REVERT: 4G 3 LEU cc_start: 0.7686 (tp) cc_final: 0.7461 (tp) REVERT: 4K 23 MET cc_start: 0.6289 (ttt) cc_final: 0.6023 (ttt) REVERT: 5B 20 PHE cc_start: 0.7913 (t80) cc_final: 0.7665 (t80) REVERT: 5B 29 GLU cc_start: 0.7265 (tp30) cc_final: 0.7045 (tp30) REVERT: 5C 3 LEU cc_start: 0.7638 (tp) cc_final: 0.7372 (tp) REVERT: 5G 3 LEU cc_start: 0.7351 (tp) cc_final: 0.7078 (tp) outliers start: 0 outliers final: 0 residues processed: 2125 average time/residue: 0.4809 time to fit residues: 1731.8858 Evaluate side-chains 1695 residues out of total 4160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1695 time to evaluate : 4.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 405 optimal weight: 0.8980 chunk 363 optimal weight: 4.9990 chunk 201 optimal weight: 6.9990 chunk 124 optimal weight: 7.9990 chunk 245 optimal weight: 7.9990 chunk 194 optimal weight: 5.9990 chunk 376 optimal weight: 9.9990 chunk 145 optimal weight: 7.9990 chunk 228 optimal weight: 20.0000 chunk 280 optimal weight: 6.9990 chunk 435 optimal weight: 0.9980 overall best weight: 3.9786 ------------------------------------------------------------------------------- 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: 0.7646 moved from start: 0.4842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 41600 Z= 0.285 Angle : 0.746 9.761 55410 Z= 0.389 Chirality : 0.041 0.153 7190 Planarity : 0.004 0.014 6070 Dihedral : 17.124 74.156 8495 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 5.67 % Allowed : 13.46 % Favored : 80.87 % 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: -3.15 (0.11), residues: 4880 helix: -2.25 (0.07), residues: 3200 sheet: None (None), residues: 0 loop : -1.31 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.019 0.001 PHE4G 15 TYR 0.028 0.003 TYR5F 37 ARG 0.004 0.001 ARG2I 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2319 residues out of total 4160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 2083 time to evaluate : 3.889 Fit side-chains REVERT: 1A 53 ILE cc_start: 0.8958 (mm) cc_final: 0.8724 (mm) REVERT: 1B 54 VAL cc_start: 0.9091 (m) cc_final: 0.8831 (t) REVERT: 1C 54 VAL cc_start: 0.9147 (p) cc_final: 0.8861 (t) REVERT: 1E 37 TYR cc_start: 0.8565 (t80) cc_final: 0.8235 (t80) REVERT: 1G 45 ILE cc_start: 0.8672 (mm) cc_final: 0.8461 (mm) REVERT: 1O 60 LEU cc_start: 0.8107 (mt) cc_final: 0.7906 (mt) REVERT: 2A 37 TYR cc_start: 0.8808 (t80) cc_final: 0.8427 (t80) REVERT: 2E 22 MET cc_start: 0.7262 (tpp) cc_final: 0.7045 (tpp) REVERT: 2I 46 LEU cc_start: 0.8844 (mt) cc_final: 0.8628 (mt) REVERT: 2M 26 ILE cc_start: 0.8745 (mm) cc_final: 0.8454 (mt) REVERT: 3B 37 TYR cc_start: 0.8744 (t80) cc_final: 0.8503 (t80) REVERT: 3C 12 LYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7582 (tttp) REVERT: 3C 47 LEU cc_start: 0.8256 (tt) cc_final: 0.8038 (mt) REVERT: 3D 23 MET cc_start: 0.6716 (ttm) cc_final: 0.6407 (ttm) REVERT: 3G 23 MET cc_start: 0.6667 (ttm) cc_final: 0.6392 (ttm) REVERT: 3I 26 ILE cc_start: 0.8523 (tt) cc_final: 0.8259 (tt) REVERT: 3J 23 MET cc_start: 0.6593 (ttm) cc_final: 0.6366 (ttm) REVERT: 3N 26 ILE cc_start: 0.8834 (mm) cc_final: 0.8617 (mt) REVERT: 3N 37 TYR cc_start: 0.8337 (t80) cc_final: 0.8043 (t80) REVERT: 3P 37 TYR cc_start: 0.8093 (t80) cc_final: 0.7872 (t80) REVERT: 4C 37 TYR cc_start: 0.8465 (t80) cc_final: 0.8230 (t80) REVERT: 4G 54 VAL cc_start: 0.9236 (p) cc_final: 0.8975 (t) REVERT: 4I 54 VAL cc_start: 0.9257 (p) cc_final: 0.8994 (t) REVERT: 4L 26 ILE cc_start: 0.8891 (mm) cc_final: 0.8521 (mt) REVERT: 4M 10 ASP cc_start: 0.7873 (OUTLIER) cc_final: 0.7364 (p0) REVERT: 4N 60 LEU cc_start: 0.8114 (mt) cc_final: 0.7789 (mt) REVERT: 5E 12 LYS cc_start: 0.7760 (tttt) cc_final: 0.7509 (tttp) REVERT: 5F 23 MET cc_start: 0.6887 (ttm) cc_final: 0.6628 (ttm) REVERT: 5H 54 VAL cc_start: 0.9206 (p) cc_final: 0.8950 (t) REVERT: 5I 39 ARG cc_start: 0.7606 (ttp80) cc_final: 0.7402 (ttp-170) REVERT: 5J 54 VAL cc_start: 0.9179 (p) cc_final: 0.8935 (t) REVERT: 5L 60 LEU cc_start: 0.8266 (mt) cc_final: 0.8013 (mt) REVERT: 5N 26 ILE cc_start: 0.8891 (mm) cc_final: 0.8619 (mt) REVERT: 5N 60 LEU cc_start: 0.8097 (mt) cc_final: 0.7880 (mt) REVERT: 5O 39 ARG cc_start: 0.7610 (ttp80) cc_final: 0.7365 (ttp80) REVERT: 5P 29 GLU cc_start: 0.7077 (tp30) cc_final: 0.6475 (tp30) REVERT: 5P 34 VAL cc_start: 0.9024 (t) cc_final: 0.8727 (t) outliers start: 236 outliers final: 139 residues processed: 2138 average time/residue: 0.4982 time to fit residues: 1766.7727 Evaluate side-chains 1919 residues out of total 4160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 1778 time to evaluate : 4.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1B residue 26 ILE Chi-restraints excluded: chain 1C residue 50 VAL Chi-restraints excluded: chain 1D residue 26 ILE Chi-restraints excluded: chain 1D residue 58 VAL Chi-restraints excluded: chain 1E residue 21 VAL Chi-restraints excluded: chain 1E residue 31 ILE Chi-restraints excluded: chain 1E residue 58 VAL Chi-restraints excluded: chain 1F residue 58 VAL Chi-restraints excluded: chain 1G residue 11 VAL Chi-restraints excluded: chain 1G residue 26 ILE Chi-restraints excluded: chain 1G residue 50 VAL Chi-restraints excluded: chain 1G residue 58 VAL Chi-restraints excluded: chain 1H residue 26 ILE Chi-restraints excluded: chain 1H residue 58 VAL Chi-restraints excluded: chain 1I residue 26 ILE Chi-restraints excluded: chain 1I residue 58 VAL Chi-restraints excluded: chain 1J residue 21 VAL Chi-restraints excluded: chain 1J residue 58 VAL Chi-restraints excluded: chain 1L residue 58 VAL Chi-restraints excluded: chain 1L residue 61 THR Chi-restraints excluded: chain 1M residue 50 VAL Chi-restraints excluded: chain 1M residue 57 THR Chi-restraints excluded: chain 1M residue 58 VAL Chi-restraints excluded: chain 1M residue 61 THR Chi-restraints excluded: chain 1N residue 50 VAL Chi-restraints excluded: chain 1P residue 50 VAL Chi-restraints excluded: chain 1P residue 52 VAL Chi-restraints excluded: chain 1P residue 53 ILE Chi-restraints excluded: chain 2A residue 41 LYS Chi-restraints excluded: chain 2A residue 47 LEU Chi-restraints excluded: chain 2A residue 51 VAL Chi-restraints excluded: chain 2A residue 58 VAL Chi-restraints excluded: chain 2B residue 47 LEU Chi-restraints excluded: chain 2C residue 11 VAL Chi-restraints excluded: chain 2C residue 26 ILE Chi-restraints excluded: chain 2C residue 58 VAL Chi-restraints excluded: chain 2D residue 19 SER Chi-restraints excluded: chain 2D residue 50 VAL Chi-restraints excluded: chain 2E residue 26 ILE Chi-restraints excluded: chain 2E residue 51 VAL Chi-restraints excluded: chain 2E residue 53 ILE Chi-restraints excluded: chain 2G residue 26 ILE Chi-restraints excluded: chain 2G residue 58 VAL Chi-restraints excluded: chain 2H residue 31 ILE Chi-restraints excluded: chain 2I residue 21 VAL Chi-restraints excluded: chain 2I residue 26 ILE Chi-restraints excluded: chain 2K residue 50 VAL Chi-restraints excluded: chain 2K residue 61 THR Chi-restraints excluded: chain 2L residue 50 VAL Chi-restraints excluded: chain 2L residue 58 VAL Chi-restraints excluded: chain 2M residue 11 VAL Chi-restraints excluded: chain 2M residue 50 VAL Chi-restraints excluded: chain 2N residue 50 VAL Chi-restraints excluded: chain 2N residue 58 VAL Chi-restraints excluded: chain 2N residue 61 THR Chi-restraints excluded: chain 3A residue 4 LEU Chi-restraints excluded: chain 3A residue 21 VAL Chi-restraints excluded: chain 3A residue 58 VAL Chi-restraints excluded: chain 3C residue 12 LYS Chi-restraints excluded: chain 3C residue 61 THR Chi-restraints excluded: chain 3D residue 58 VAL Chi-restraints excluded: chain 3E residue 11 VAL Chi-restraints excluded: chain 3E residue 21 VAL Chi-restraints excluded: chain 3F residue 11 VAL Chi-restraints excluded: chain 3F residue 26 ILE Chi-restraints excluded: chain 3F residue 50 VAL Chi-restraints excluded: chain 3F residue 51 VAL Chi-restraints excluded: chain 3F residue 58 VAL Chi-restraints excluded: chain 3G residue 11 VAL Chi-restraints excluded: chain 3G residue 47 LEU Chi-restraints excluded: chain 3G residue 58 VAL Chi-restraints excluded: chain 3H residue 11 VAL Chi-restraints excluded: chain 3H residue 21 VAL Chi-restraints excluded: chain 3H residue 26 ILE Chi-restraints excluded: chain 3H residue 54 VAL Chi-restraints excluded: chain 3I residue 58 VAL Chi-restraints excluded: chain 3J residue 58 VAL Chi-restraints excluded: chain 3K residue 61 THR Chi-restraints excluded: chain 3L residue 21 VAL Chi-restraints excluded: chain 3N residue 21 VAL Chi-restraints excluded: chain 3N residue 50 VAL Chi-restraints excluded: chain 3O residue 50 VAL Chi-restraints excluded: chain 3O residue 61 THR Chi-restraints excluded: chain 3P residue 50 VAL Chi-restraints excluded: chain 3P residue 53 ILE Chi-restraints excluded: chain 4C residue 58 VAL Chi-restraints excluded: chain 4C residue 61 THR Chi-restraints excluded: chain 4D residue 58 VAL Chi-restraints excluded: chain 4E residue 58 VAL Chi-restraints excluded: chain 4F residue 11 VAL Chi-restraints excluded: chain 4F residue 26 ILE Chi-restraints excluded: chain 4F residue 51 VAL Chi-restraints excluded: chain 4F residue 53 ILE Chi-restraints excluded: chain 4F residue 57 THR Chi-restraints excluded: chain 4H residue 21 VAL Chi-restraints excluded: chain 4H residue 26 ILE Chi-restraints excluded: chain 4H residue 50 VAL Chi-restraints excluded: chain 4I residue 21 VAL Chi-restraints excluded: chain 4I residue 26 ILE Chi-restraints excluded: chain 4J residue 58 VAL Chi-restraints excluded: chain 4K residue 21 VAL Chi-restraints excluded: chain 4K residue 26 ILE Chi-restraints excluded: chain 4M residue 10 ASP Chi-restraints excluded: chain 4M residue 50 VAL Chi-restraints excluded: chain 4M residue 58 VAL Chi-restraints excluded: chain 4N residue 50 VAL Chi-restraints excluded: chain 4N residue 61 THR Chi-restraints excluded: chain 4O residue 57 THR Chi-restraints excluded: chain 5A residue 58 VAL Chi-restraints excluded: chain 5B residue 19 SER Chi-restraints excluded: chain 5B residue 26 ILE Chi-restraints excluded: chain 5B residue 53 ILE Chi-restraints excluded: chain 5B residue 58 VAL Chi-restraints excluded: chain 5C residue 50 VAL Chi-restraints excluded: chain 5C residue 61 THR Chi-restraints excluded: chain 5D residue 58 VAL Chi-restraints excluded: chain 5E residue 19 SER Chi-restraints excluded: chain 5E residue 21 VAL Chi-restraints excluded: chain 5E residue 50 VAL Chi-restraints excluded: chain 5F residue 4 LEU Chi-restraints excluded: chain 5F residue 58 VAL Chi-restraints excluded: chain 5G residue 58 VAL Chi-restraints excluded: chain 5H residue 26 ILE Chi-restraints excluded: chain 5I residue 50 VAL Chi-restraints excluded: chain 5I residue 53 ILE Chi-restraints excluded: chain 5I residue 58 VAL Chi-restraints excluded: chain 5I residue 61 THR Chi-restraints excluded: chain 5J residue 26 ILE Chi-restraints excluded: chain 5J residue 50 VAL Chi-restraints excluded: chain 5L residue 21 VAL Chi-restraints excluded: chain 5L residue 27 ILE Chi-restraints excluded: chain 5L residue 50 VAL Chi-restraints excluded: chain 5L residue 58 VAL Chi-restraints excluded: chain 5M residue 11 VAL Chi-restraints excluded: chain 5M residue 21 VAL Chi-restraints excluded: chain 5M residue 50 VAL Chi-restraints excluded: chain 5M residue 61 THR Chi-restraints excluded: chain 5N residue 50 VAL Chi-restraints excluded: chain 5N residue 61 THR Chi-restraints excluded: chain 5O residue 61 THR Chi-restraints excluded: chain 5P residue 52 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 242 optimal weight: 10.0000 chunk 135 optimal weight: 2.9990 chunk 362 optimal weight: 0.1980 chunk 296 optimal weight: 0.6980 chunk 120 optimal weight: 0.0070 chunk 436 optimal weight: 3.9990 chunk 471 optimal weight: 1.9990 chunk 388 optimal weight: 7.9990 chunk 433 optimal weight: 8.9990 chunk 148 optimal weight: 10.0000 chunk 350 optimal weight: 0.9990 overall best weight: 0.7802 ------------------------------------------------------------------------------- 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: 0.7556 moved from start: 0.5805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 41600 Z= 0.167 Angle : 0.582 8.394 55410 Z= 0.293 Chirality : 0.036 0.142 7190 Planarity : 0.002 0.010 6070 Dihedral : 15.160 76.160 8495 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 4.45 % Allowed : 20.38 % Favored : 75.17 % 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: -1.81 (0.11), residues: 4880 helix: -1.06 (0.08), residues: 3200 sheet: None (None), residues: 0 loop : -1.16 (0.16), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.001 PHE4C 15 TYR 0.018 0.002 TYR5E 37 ARG 0.004 0.001 ARG3K 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2071 residues out of total 4160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 1886 time to evaluate : 4.619 Fit side-chains REVERT: 1E 37 TYR cc_start: 0.8539 (t80) cc_final: 0.8291 (t80) REVERT: 2A 37 TYR cc_start: 0.8654 (t80) cc_final: 0.8350 (t80) REVERT: 2F 41 LYS cc_start: 0.8400 (mttp) cc_final: 0.8153 (mttp) REVERT: 2I 40 THR cc_start: 0.8909 (m) cc_final: 0.8551 (p) REVERT: 2I 46 LEU cc_start: 0.8765 (mt) cc_final: 0.8549 (mt) REVERT: 3D 40 THR cc_start: 0.8679 (m) cc_final: 0.8377 (p) REVERT: 3D 41 LYS cc_start: 0.8607 (mttp) cc_final: 0.8353 (ttmm) REVERT: 3H 40 THR cc_start: 0.8595 (m) cc_final: 0.8271 (p) REVERT: 3N 37 TYR cc_start: 0.8169 (t80) cc_final: 0.7906 (t80) REVERT: 3O 29 GLU cc_start: 0.7746 (tp30) cc_final: 0.7252 (tp30) REVERT: 3P 37 TYR cc_start: 0.8118 (t80) cc_final: 0.7766 (t80) REVERT: 3P 41 LYS cc_start: 0.8409 (mttp) cc_final: 0.8031 (mttp) REVERT: 4B 47 LEU cc_start: 0.8619 (tt) cc_final: 0.8374 (mt) REVERT: 4K 46 LEU cc_start: 0.8810 (mt) cc_final: 0.8583 (mt) REVERT: 4N 60 LEU cc_start: 0.8079 (mt) cc_final: 0.7805 (mt) REVERT: 4O 26 ILE cc_start: 0.8676 (mm) cc_final: 0.8377 (mt) REVERT: 4O 37 TYR cc_start: 0.8488 (t80) cc_final: 0.8234 (t80) REVERT: 5A 47 LEU cc_start: 0.8205 (tt) cc_final: 0.7774 (mp) REVERT: 5C 40 THR cc_start: 0.8650 (m) cc_final: 0.8398 (p) REVERT: 5F 23 MET cc_start: 0.6666 (ttm) cc_final: 0.6455 (ttm) REVERT: 5H 37 TYR cc_start: 0.8800 (t80) cc_final: 0.8551 (t80) REVERT: 5H 54 VAL cc_start: 0.9133 (p) cc_final: 0.8868 (t) REVERT: 5L 26 ILE cc_start: 0.8825 (mm) cc_final: 0.8556 (mt) REVERT: 5N 41 LYS cc_start: 0.8518 (mttp) cc_final: 0.8293 (tppt) REVERT: 5N 60 LEU cc_start: 0.8093 (mt) cc_final: 0.7795 (mt) REVERT: 5O 29 GLU cc_start: 0.6951 (tp30) cc_final: 0.6545 (tp30) REVERT: 5P 29 GLU cc_start: 0.6891 (tp30) cc_final: 0.6286 (tp30) REVERT: 5P 41 LYS cc_start: 0.8478 (mttp) cc_final: 0.8232 (mttp) outliers start: 185 outliers final: 104 residues processed: 1947 average time/residue: 0.4985 time to fit residues: 1606.0236 Evaluate side-chains 1781 residues out of total 4160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 1677 time to evaluate : 4.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 21 VAL Chi-restraints excluded: chain 1B residue 26 ILE Chi-restraints excluded: chain 1C residue 50 VAL Chi-restraints excluded: chain 1D residue 26 ILE Chi-restraints excluded: chain 1D residue 31 ILE Chi-restraints excluded: chain 1E residue 26 ILE Chi-restraints excluded: chain 1G residue 19 SER Chi-restraints excluded: chain 1G residue 26 ILE Chi-restraints excluded: chain 1G residue 31 ILE Chi-restraints excluded: chain 1H residue 26 ILE Chi-restraints excluded: chain 1I residue 26 ILE Chi-restraints excluded: chain 1I residue 31 ILE Chi-restraints excluded: chain 1I residue 50 VAL Chi-restraints excluded: chain 1J residue 21 VAL Chi-restraints excluded: chain 1J residue 26 ILE Chi-restraints excluded: chain 1J residue 58 VAL Chi-restraints excluded: chain 1L residue 41 LYS Chi-restraints excluded: chain 1M residue 50 VAL Chi-restraints excluded: chain 2A residue 23 MET Chi-restraints excluded: chain 2A residue 51 VAL Chi-restraints excluded: chain 2B residue 26 ILE Chi-restraints excluded: chain 2B residue 47 LEU Chi-restraints excluded: chain 2C residue 26 ILE Chi-restraints excluded: chain 2D residue 51 VAL Chi-restraints excluded: chain 2E residue 26 ILE Chi-restraints excluded: chain 2E residue 51 VAL Chi-restraints excluded: chain 2F residue 31 ILE Chi-restraints excluded: chain 2F residue 51 VAL Chi-restraints excluded: chain 2G residue 26 ILE Chi-restraints excluded: chain 2H residue 26 ILE Chi-restraints excluded: chain 2I residue 21 VAL Chi-restraints excluded: chain 2I residue 26 ILE Chi-restraints excluded: chain 2I residue 47 LEU Chi-restraints excluded: chain 2J residue 4 LEU Chi-restraints excluded: chain 2J residue 26 ILE Chi-restraints excluded: chain 2K residue 41 LYS Chi-restraints excluded: chain 2K residue 50 VAL Chi-restraints excluded: chain 2K residue 51 VAL Chi-restraints excluded: chain 2K residue 61 THR Chi-restraints excluded: chain 2L residue 58 VAL Chi-restraints excluded: chain 2M residue 50 VAL Chi-restraints excluded: chain 2M residue 58 VAL Chi-restraints excluded: chain 2N residue 63 ILE Chi-restraints excluded: chain 2P residue 53 ILE Chi-restraints excluded: chain 3A residue 21 VAL Chi-restraints excluded: chain 3C residue 26 ILE Chi-restraints excluded: chain 3C residue 31 ILE Chi-restraints excluded: chain 3C residue 51 VAL Chi-restraints excluded: chain 3E residue 21 VAL Chi-restraints excluded: chain 3F residue 11 VAL Chi-restraints excluded: chain 3F residue 26 ILE Chi-restraints excluded: chain 3F residue 47 LEU Chi-restraints excluded: chain 3F residue 51 VAL Chi-restraints excluded: chain 3G residue 31 ILE Chi-restraints excluded: chain 3G residue 58 VAL Chi-restraints excluded: chain 3H residue 21 VAL Chi-restraints excluded: chain 3H residue 26 ILE Chi-restraints excluded: chain 3H residue 30 LEU Chi-restraints excluded: chain 3I residue 26 ILE Chi-restraints excluded: chain 3I residue 50 VAL Chi-restraints excluded: chain 3I residue 51 VAL Chi-restraints excluded: chain 3K residue 50 VAL Chi-restraints excluded: chain 3N residue 21 VAL Chi-restraints excluded: chain 3O residue 50 VAL Chi-restraints excluded: chain 3O residue 61 THR Chi-restraints excluded: chain 3O residue 62 PHE Chi-restraints excluded: chain 3P residue 53 ILE Chi-restraints excluded: chain 4B residue 31 ILE Chi-restraints excluded: chain 4B residue 41 LYS Chi-restraints excluded: chain 4C residue 26 ILE Chi-restraints excluded: chain 4D residue 31 ILE Chi-restraints excluded: chain 4D residue 54 VAL Chi-restraints excluded: chain 4E residue 26 ILE Chi-restraints excluded: chain 4F residue 26 ILE Chi-restraints excluded: chain 4F residue 54 VAL Chi-restraints excluded: chain 4H residue 21 VAL Chi-restraints excluded: chain 4H residue 31 ILE Chi-restraints excluded: chain 4I residue 21 VAL Chi-restraints excluded: chain 4I residue 26 ILE Chi-restraints excluded: chain 4I residue 31 ILE Chi-restraints excluded: chain 4I residue 43 LEU Chi-restraints excluded: chain 4K residue 21 VAL Chi-restraints excluded: chain 4K residue 26 ILE Chi-restraints excluded: chain 4K residue 52 VAL Chi-restraints excluded: chain 4L residue 31 ILE Chi-restraints excluded: chain 4N residue 50 VAL Chi-restraints excluded: chain 5B residue 26 ILE Chi-restraints excluded: chain 5B residue 53 ILE Chi-restraints excluded: chain 5C residue 31 ILE Chi-restraints excluded: chain 5D residue 4 LEU Chi-restraints excluded: chain 5E residue 21 VAL Chi-restraints excluded: chain 5E residue 53 ILE Chi-restraints excluded: chain 5F residue 11 VAL Chi-restraints excluded: chain 5F residue 26 ILE Chi-restraints excluded: chain 5H residue 26 ILE Chi-restraints excluded: chain 5I residue 31 ILE Chi-restraints excluded: chain 5I residue 58 VAL Chi-restraints excluded: chain 5L residue 21 VAL Chi-restraints excluded: chain 5L residue 50 VAL Chi-restraints excluded: chain 5L residue 53 ILE Chi-restraints excluded: chain 5M residue 21 VAL Chi-restraints excluded: chain 5N residue 53 ILE Chi-restraints excluded: chain 5P residue 43 LEU Chi-restraints excluded: chain 5P residue 53 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 431 optimal weight: 8.9990 chunk 328 optimal weight: 7.9990 chunk 226 optimal weight: 8.9990 chunk 48 optimal weight: 20.0000 chunk 208 optimal weight: 9.9990 chunk 293 optimal weight: 7.9990 chunk 438 optimal weight: 0.0670 chunk 463 optimal weight: 9.9990 chunk 228 optimal weight: 0.0980 chunk 415 optimal weight: 9.9990 chunk 125 optimal weight: 9.9990 overall best weight: 5.0324 ------------------------------------------------------------------------------- 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: 0.7779 moved from start: 0.6264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 41600 Z= 0.282 Angle : 0.648 8.514 55410 Z= 0.320 Chirality : 0.038 0.165 7190 Planarity : 0.002 0.027 6070 Dihedral : 15.223 78.952 8495 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 5.17 % Allowed : 22.84 % Favored : 72.00 % 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: -1.51 (0.12), residues: 4880 helix: -0.81 (0.08), residues: 3280 sheet: None (None), residues: 0 loop : -1.07 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.023 0.001 PHE2B 15 TYR 0.020 0.002 TYR1F 37 ARG 0.005 0.000 ARG3A 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1982 residues out of total 4160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 1767 time to evaluate : 3.944 Fit side-chains REVERT: 1C 54 VAL cc_start: 0.9171 (p) cc_final: 0.8889 (t) REVERT: 1E 40 THR cc_start: 0.8872 (m) cc_final: 0.8650 (p) REVERT: 1I 40 THR cc_start: 0.8896 (m) cc_final: 0.8530 (p) REVERT: 1N 41 LYS cc_start: 0.8554 (mttp) cc_final: 0.8323 (mttp) REVERT: 1P 41 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8362 (mttm) REVERT: 2A 37 TYR cc_start: 0.8782 (t80) cc_final: 0.8404 (t80) REVERT: 2I 40 THR cc_start: 0.8931 (m) cc_final: 0.8626 (p) REVERT: 2K 53 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8589 (mm) REVERT: 2M 47 LEU cc_start: 0.8213 (tt) cc_final: 0.7970 (tt) REVERT: 2N 60 LEU cc_start: 0.8128 (mt) cc_final: 0.7889 (mt) REVERT: 3C 26 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8570 (mt) REVERT: 3C 40 THR cc_start: 0.8675 (m) cc_final: 0.8365 (p) REVERT: 3C 54 VAL cc_start: 0.9194 (p) cc_final: 0.8951 (t) REVERT: 3D 40 THR cc_start: 0.8767 (m) cc_final: 0.8505 (p) REVERT: 3H 40 THR cc_start: 0.8769 (m) cc_final: 0.8440 (p) REVERT: 3L 40 THR cc_start: 0.8622 (m) cc_final: 0.8278 (p) REVERT: 3P 37 TYR cc_start: 0.8543 (t80) cc_final: 0.8202 (t80) REVERT: 3P 41 LYS cc_start: 0.8423 (mttp) cc_final: 0.8209 (mttp) REVERT: 4D 41 LYS cc_start: 0.7843 (mttp) cc_final: 0.7585 (mttp) REVERT: 4K 47 LEU cc_start: 0.8603 (tt) cc_final: 0.8386 (tt) REVERT: 4L 40 THR cc_start: 0.8812 (m) cc_final: 0.8566 (p) REVERT: 4N 60 LEU cc_start: 0.8152 (mt) cc_final: 0.7874 (mt) REVERT: 4O 37 TYR cc_start: 0.8905 (t80) cc_final: 0.8605 (t80) REVERT: 4O 46 LEU cc_start: 0.8733 (mt) cc_final: 0.8451 (mt) REVERT: 4O 60 LEU cc_start: 0.7951 (mt) cc_final: 0.7681 (mt) REVERT: 5B 29 GLU cc_start: 0.7853 (tp30) cc_final: 0.7240 (tp30) REVERT: 5E 26 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8370 (mt) REVERT: 5F 23 MET cc_start: 0.6736 (ttm) cc_final: 0.6496 (ttm) REVERT: 5H 54 VAL cc_start: 0.9257 (p) cc_final: 0.9041 (t) REVERT: 5J 40 THR cc_start: 0.8741 (m) cc_final: 0.8398 (p) REVERT: 5L 40 THR cc_start: 0.8811 (m) cc_final: 0.8532 (p) REVERT: 5N 60 LEU cc_start: 0.8097 (mt) cc_final: 0.7855 (mt) REVERT: 5P 29 GLU cc_start: 0.7339 (tp30) cc_final: 0.7059 (tp30) outliers start: 215 outliers final: 157 residues processed: 1847 average time/residue: 0.5605 time to fit residues: 1712.8322 Evaluate side-chains 1811 residues out of total 4160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 1650 time to evaluate : 4.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 11 VAL Chi-restraints excluded: chain 1A residue 21 VAL Chi-restraints excluded: chain 1A residue 23 MET Chi-restraints excluded: chain 1A residue 51 VAL Chi-restraints excluded: chain 1B residue 11 VAL Chi-restraints excluded: chain 1B residue 26 ILE Chi-restraints excluded: chain 1B residue 29 GLU Chi-restraints excluded: chain 1C residue 26 ILE Chi-restraints excluded: chain 1C residue 50 VAL Chi-restraints excluded: chain 1D residue 26 ILE Chi-restraints excluded: chain 1D residue 31 ILE Chi-restraints excluded: chain 1E residue 21 VAL Chi-restraints excluded: chain 1E residue 26 ILE Chi-restraints excluded: chain 1E residue 31 ILE Chi-restraints excluded: chain 1E residue 50 VAL Chi-restraints excluded: chain 1F residue 26 ILE Chi-restraints excluded: chain 1G residue 25 ILE Chi-restraints excluded: chain 1G residue 26 ILE Chi-restraints excluded: chain 1G residue 31 ILE Chi-restraints excluded: chain 1G residue 47 LEU Chi-restraints excluded: chain 1G residue 51 VAL Chi-restraints excluded: chain 1G residue 58 VAL Chi-restraints excluded: chain 1H residue 19 SER Chi-restraints excluded: chain 1H residue 23 MET Chi-restraints excluded: chain 1H residue 26 ILE Chi-restraints excluded: chain 1I residue 23 MET Chi-restraints excluded: chain 1I residue 26 ILE Chi-restraints excluded: chain 1I residue 31 ILE Chi-restraints excluded: chain 1J residue 21 VAL Chi-restraints excluded: chain 1J residue 26 ILE Chi-restraints excluded: chain 1J residue 58 VAL Chi-restraints excluded: chain 1K residue 23 MET Chi-restraints excluded: chain 1L residue 26 ILE Chi-restraints excluded: chain 1L residue 41 LYS Chi-restraints excluded: chain 1L residue 58 VAL Chi-restraints excluded: chain 1M residue 23 MET Chi-restraints excluded: chain 1M residue 50 VAL Chi-restraints excluded: chain 1O residue 31 ILE Chi-restraints excluded: chain 1O residue 52 VAL Chi-restraints excluded: chain 1P residue 41 LYS Chi-restraints excluded: chain 1P residue 53 ILE Chi-restraints excluded: chain 2A residue 4 LEU Chi-restraints excluded: chain 2A residue 11 VAL Chi-restraints excluded: chain 2A residue 23 MET Chi-restraints excluded: chain 2A residue 51 VAL Chi-restraints excluded: chain 2B residue 23 MET Chi-restraints excluded: chain 2B residue 24 CYS Chi-restraints excluded: chain 2B residue 26 ILE Chi-restraints excluded: chain 2B residue 47 LEU Chi-restraints excluded: chain 2B residue 57 THR Chi-restraints excluded: chain 2C residue 4 LEU Chi-restraints excluded: chain 2C residue 26 ILE Chi-restraints excluded: chain 2D residue 4 LEU Chi-restraints excluded: chain 2D residue 26 ILE Chi-restraints excluded: chain 2D residue 43 LEU Chi-restraints excluded: chain 2D residue 51 VAL Chi-restraints excluded: chain 2E residue 26 ILE Chi-restraints excluded: chain 2E residue 47 LEU Chi-restraints excluded: chain 2F residue 31 ILE Chi-restraints excluded: chain 2G residue 23 MET Chi-restraints excluded: chain 2G residue 26 ILE Chi-restraints excluded: chain 2H residue 26 ILE Chi-restraints excluded: chain 2H residue 31 ILE Chi-restraints excluded: chain 2I residue 21 VAL Chi-restraints excluded: chain 2I residue 26 ILE Chi-restraints excluded: chain 2I residue 47 LEU Chi-restraints excluded: chain 2I residue 51 VAL Chi-restraints excluded: chain 2J residue 4 LEU Chi-restraints excluded: chain 2J residue 26 ILE Chi-restraints excluded: chain 2J residue 47 LEU Chi-restraints excluded: chain 2K residue 53 ILE Chi-restraints excluded: chain 2K residue 61 THR Chi-restraints excluded: chain 2L residue 23 MET Chi-restraints excluded: chain 2L residue 58 VAL Chi-restraints excluded: chain 2L residue 61 THR Chi-restraints excluded: chain 2M residue 31 ILE Chi-restraints excluded: chain 2M residue 50 VAL Chi-restraints excluded: chain 2N residue 50 VAL Chi-restraints excluded: chain 2N residue 58 VAL Chi-restraints excluded: chain 2N residue 63 ILE Chi-restraints excluded: chain 2P residue 50 VAL Chi-restraints excluded: chain 3B residue 26 ILE Chi-restraints excluded: chain 3C residue 26 ILE Chi-restraints excluded: chain 3C residue 41 LYS Chi-restraints excluded: chain 3C residue 51 VAL Chi-restraints excluded: chain 3C residue 57 THR Chi-restraints excluded: chain 3D residue 50 VAL Chi-restraints excluded: chain 3E residue 50 VAL Chi-restraints excluded: chain 3F residue 11 VAL Chi-restraints excluded: chain 3F residue 23 MET Chi-restraints excluded: chain 3F residue 26 ILE Chi-restraints excluded: chain 3F residue 47 LEU Chi-restraints excluded: chain 3G residue 31 ILE Chi-restraints excluded: chain 3G residue 51 VAL Chi-restraints excluded: chain 3G residue 58 VAL Chi-restraints excluded: chain 3H residue 21 VAL Chi-restraints excluded: chain 3I residue 51 VAL Chi-restraints excluded: chain 3I residue 58 VAL Chi-restraints excluded: chain 3I residue 61 THR Chi-restraints excluded: chain 3J residue 4 LEU Chi-restraints excluded: chain 3J residue 11 VAL Chi-restraints excluded: chain 3J residue 50 VAL Chi-restraints excluded: chain 3K residue 23 MET Chi-restraints excluded: chain 3K residue 51 VAL Chi-restraints excluded: chain 3L residue 51 VAL Chi-restraints excluded: chain 3M residue 63 ILE Chi-restraints excluded: chain 3N residue 21 VAL Chi-restraints excluded: chain 3N residue 43 LEU Chi-restraints excluded: chain 3O residue 61 THR Chi-restraints excluded: chain 3P residue 53 ILE Chi-restraints excluded: chain 4A residue 11 VAL Chi-restraints excluded: chain 4A residue 50 VAL Chi-restraints excluded: chain 4A residue 58 VAL Chi-restraints excluded: chain 4B residue 31 ILE Chi-restraints excluded: chain 4C residue 26 ILE Chi-restraints excluded: chain 4D residue 31 ILE Chi-restraints excluded: chain 4E residue 50 VAL Chi-restraints excluded: chain 4F residue 11 VAL Chi-restraints excluded: chain 4H residue 21 VAL Chi-restraints excluded: chain 4I residue 21 VAL Chi-restraints excluded: chain 4I residue 23 MET Chi-restraints excluded: chain 4I residue 26 ILE Chi-restraints excluded: chain 4I residue 31 ILE Chi-restraints excluded: chain 4K residue 21 VAL Chi-restraints excluded: chain 4K residue 26 ILE Chi-restraints excluded: chain 4K residue 52 VAL Chi-restraints excluded: chain 4L residue 4 LEU Chi-restraints excluded: chain 4L residue 23 MET Chi-restraints excluded: chain 4L residue 31 ILE Chi-restraints excluded: chain 5B residue 11 VAL Chi-restraints excluded: chain 5B residue 26 ILE Chi-restraints excluded: chain 5B residue 57 THR Chi-restraints excluded: chain 5C residue 11 VAL Chi-restraints excluded: chain 5C residue 31 ILE Chi-restraints excluded: chain 5C residue 61 THR Chi-restraints excluded: chain 5D residue 4 LEU Chi-restraints excluded: chain 5D residue 43 LEU Chi-restraints excluded: chain 5E residue 19 SER Chi-restraints excluded: chain 5E residue 21 VAL Chi-restraints excluded: chain 5E residue 26 ILE Chi-restraints excluded: chain 5E residue 31 ILE Chi-restraints excluded: chain 5E residue 54 VAL Chi-restraints excluded: chain 5F residue 11 VAL Chi-restraints excluded: chain 5F residue 26 ILE Chi-restraints excluded: chain 5F residue 31 ILE Chi-restraints excluded: chain 5F residue 53 ILE Chi-restraints excluded: chain 5H residue 26 ILE Chi-restraints excluded: chain 5I residue 26 ILE Chi-restraints excluded: chain 5I residue 31 ILE Chi-restraints excluded: chain 5I residue 53 ILE Chi-restraints excluded: chain 5I residue 61 THR Chi-restraints excluded: chain 5J residue 23 MET Chi-restraints excluded: chain 5K residue 23 MET Chi-restraints excluded: chain 5L residue 21 VAL Chi-restraints excluded: chain 5M residue 11 VAL Chi-restraints excluded: chain 5M residue 50 VAL Chi-restraints excluded: chain 5M residue 61 THR Chi-restraints excluded: chain 5N residue 47 LEU Chi-restraints excluded: chain 5N residue 53 ILE Chi-restraints excluded: chain 5N residue 57 THR Chi-restraints excluded: chain 5P residue 52 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 386 optimal weight: 5.9990 chunk 263 optimal weight: 2.9990 chunk 6 optimal weight: 0.0020 chunk 345 optimal weight: 8.9990 chunk 191 optimal weight: 8.9990 chunk 395 optimal weight: 6.9990 chunk 320 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 236 optimal weight: 8.9990 chunk 416 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 overall best weight: 3.9996 ------------------------------------------------------------------------------- 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: 0.7759 moved from start: 0.6698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 41600 Z= 0.233 Angle : 0.596 8.592 55410 Z= 0.294 Chirality : 0.038 0.158 7190 Planarity : 0.002 0.028 6070 Dihedral : 14.649 78.198 8495 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 5.46 % Allowed : 24.50 % Favored : 70.05 % 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: -1.32 (0.12), residues: 4880 helix: -0.61 (0.08), residues: 3280 sheet: None (None), residues: 0 loop : -1.14 (0.16), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.018 0.001 PHE2B 15 TYR 0.020 0.002 TYR4L 37 ARG 0.006 0.000 ARG1I 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1944 residues out of total 4160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 1717 time to evaluate : 4.130 Fit side-chains REVERT: 1D 40 THR cc_start: 0.8714 (m) cc_final: 0.8353 (p) REVERT: 1E 40 THR cc_start: 0.8871 (m) cc_final: 0.8669 (p) REVERT: 1I 40 THR cc_start: 0.8878 (m) cc_final: 0.8416 (p) REVERT: 1K 26 ILE cc_start: 0.8550 (mm) cc_final: 0.8261 (mt) REVERT: 1N 41 LYS cc_start: 0.8557 (mttp) cc_final: 0.8318 (tppt) REVERT: 2A 37 TYR cc_start: 0.8797 (t80) cc_final: 0.8395 (t80) REVERT: 2I 40 THR cc_start: 0.8961 (m) cc_final: 0.8682 (p) REVERT: 2L 29 GLU cc_start: 0.7408 (tp30) cc_final: 0.6963 (tp30) REVERT: 2N 60 LEU cc_start: 0.8059 (mt) cc_final: 0.7850 (mt) REVERT: 3C 40 THR cc_start: 0.8659 (m) cc_final: 0.8338 (p) REVERT: 3C 54 VAL cc_start: 0.9177 (p) cc_final: 0.8943 (t) REVERT: 3D 40 THR cc_start: 0.8765 (m) cc_final: 0.8500 (p) REVERT: 3H 40 THR cc_start: 0.8792 (m) cc_final: 0.8471 (p) REVERT: 3I 40 THR cc_start: 0.8862 (m) cc_final: 0.8430 (p) REVERT: 3L 40 THR cc_start: 0.8567 (m) cc_final: 0.8068 (p) REVERT: 3P 37 TYR cc_start: 0.8612 (t80) cc_final: 0.8198 (t80) REVERT: 3P 40 THR cc_start: 0.8409 (m) cc_final: 0.8175 (p) REVERT: 4G 26 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8598 (mt) REVERT: 4H 40 THR cc_start: 0.8741 (m) cc_final: 0.8470 (p) REVERT: 4K 40 THR cc_start: 0.8789 (m) cc_final: 0.8471 (p) REVERT: 4L 40 THR cc_start: 0.8731 (m) cc_final: 0.8432 (p) REVERT: 4N 60 LEU cc_start: 0.8216 (mt) cc_final: 0.7931 (mt) REVERT: 4O 37 TYR cc_start: 0.8971 (t80) cc_final: 0.8662 (t80) REVERT: 4O 46 LEU cc_start: 0.8888 (mt) cc_final: 0.8634 (mt) REVERT: 5B 29 GLU cc_start: 0.7784 (tp30) cc_final: 0.7039 (tp30) REVERT: 5E 12 LYS cc_start: 0.7923 (ttmt) cc_final: 0.7697 (ttmt) REVERT: 5E 26 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8207 (mt) REVERT: 5I 4 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7807 (mt) REVERT: 5I 40 THR cc_start: 0.8715 (m) cc_final: 0.8439 (p) REVERT: 5J 40 THR cc_start: 0.8619 (m) cc_final: 0.8280 (p) REVERT: 5K 37 TYR cc_start: 0.8803 (t80) cc_final: 0.8517 (t80) REVERT: 5L 40 THR cc_start: 0.8722 (m) cc_final: 0.8388 (p) REVERT: 5O 29 GLU cc_start: 0.7603 (tp30) cc_final: 0.7258 (tp30) REVERT: 5P 41 LYS cc_start: 0.8408 (mttp) cc_final: 0.8157 (mttp) outliers start: 227 outliers final: 166 residues processed: 1812 average time/residue: 0.5136 time to fit residues: 1525.1587 Evaluate side-chains 1805 residues out of total 4160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 1636 time to evaluate : 4.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 11 VAL Chi-restraints excluded: chain 1A residue 21 VAL Chi-restraints excluded: chain 1A residue 51 VAL Chi-restraints excluded: chain 1B residue 11 VAL Chi-restraints excluded: chain 1B residue 26 ILE Chi-restraints excluded: chain 1C residue 26 ILE Chi-restraints excluded: chain 1C residue 50 VAL Chi-restraints excluded: chain 1D residue 26 ILE Chi-restraints excluded: chain 1D residue 31 ILE Chi-restraints excluded: chain 1D residue 51 VAL Chi-restraints excluded: chain 1E residue 21 VAL Chi-restraints excluded: chain 1E residue 26 ILE Chi-restraints excluded: chain 1E residue 31 ILE Chi-restraints excluded: chain 1F residue 26 ILE Chi-restraints excluded: chain 1G residue 25 ILE Chi-restraints excluded: chain 1G residue 26 ILE Chi-restraints excluded: chain 1G residue 31 ILE Chi-restraints excluded: chain 1G residue 47 LEU Chi-restraints excluded: chain 1G residue 51 VAL Chi-restraints excluded: chain 1H residue 19 SER Chi-restraints excluded: chain 1H residue 23 MET Chi-restraints excluded: chain 1H residue 26 ILE Chi-restraints excluded: chain 1H residue 47 LEU Chi-restraints excluded: chain 1I residue 26 ILE Chi-restraints excluded: chain 1I residue 31 ILE Chi-restraints excluded: chain 1J residue 21 VAL Chi-restraints excluded: chain 1J residue 26 ILE Chi-restraints excluded: chain 1L residue 26 ILE Chi-restraints excluded: chain 1L residue 41 LYS Chi-restraints excluded: chain 1L residue 49 LEU Chi-restraints excluded: chain 1L residue 53 ILE Chi-restraints excluded: chain 1M residue 11 VAL Chi-restraints excluded: chain 1M residue 23 MET Chi-restraints excluded: chain 1M residue 31 ILE Chi-restraints excluded: chain 1N residue 31 ILE Chi-restraints excluded: chain 1N residue 50 VAL Chi-restraints excluded: chain 1O residue 31 ILE Chi-restraints excluded: chain 1P residue 52 VAL Chi-restraints excluded: chain 2A residue 11 VAL Chi-restraints excluded: chain 2A residue 23 MET Chi-restraints excluded: chain 2A residue 51 VAL Chi-restraints excluded: chain 2B residue 23 MET Chi-restraints excluded: chain 2B residue 26 ILE Chi-restraints excluded: chain 2B residue 47 LEU Chi-restraints excluded: chain 2B residue 57 THR Chi-restraints excluded: chain 2C residue 26 ILE Chi-restraints excluded: chain 2D residue 26 ILE Chi-restraints excluded: chain 2D residue 53 ILE Chi-restraints excluded: chain 2E residue 26 ILE Chi-restraints excluded: chain 2E residue 47 LEU Chi-restraints excluded: chain 2F residue 31 ILE Chi-restraints excluded: chain 2F residue 51 VAL Chi-restraints excluded: chain 2G residue 23 MET Chi-restraints excluded: chain 2G residue 26 ILE Chi-restraints excluded: chain 2H residue 26 ILE Chi-restraints excluded: chain 2H residue 31 ILE Chi-restraints excluded: chain 2I residue 21 VAL Chi-restraints excluded: chain 2I residue 26 ILE Chi-restraints excluded: chain 2I residue 47 LEU Chi-restraints excluded: chain 2I residue 51 VAL Chi-restraints excluded: chain 2I residue 52 VAL Chi-restraints excluded: chain 2J residue 4 LEU Chi-restraints excluded: chain 2J residue 23 MET Chi-restraints excluded: chain 2J residue 26 ILE Chi-restraints excluded: chain 2J residue 47 LEU Chi-restraints excluded: chain 2K residue 51 VAL Chi-restraints excluded: chain 2K residue 61 THR Chi-restraints excluded: chain 2L residue 57 THR Chi-restraints excluded: chain 2L residue 58 VAL Chi-restraints excluded: chain 2L residue 61 THR Chi-restraints excluded: chain 2M residue 11 VAL Chi-restraints excluded: chain 2M residue 31 ILE Chi-restraints excluded: chain 2M residue 50 VAL Chi-restraints excluded: chain 2N residue 31 ILE Chi-restraints excluded: chain 2N residue 58 VAL Chi-restraints excluded: chain 2N residue 63 ILE Chi-restraints excluded: chain 3A residue 21 VAL Chi-restraints excluded: chain 3B residue 26 ILE Chi-restraints excluded: chain 3C residue 12 LYS Chi-restraints excluded: chain 3C residue 41 LYS Chi-restraints excluded: chain 3C residue 51 VAL Chi-restraints excluded: chain 3C residue 53 ILE Chi-restraints excluded: chain 3C residue 57 THR Chi-restraints excluded: chain 3D residue 50 VAL Chi-restraints excluded: chain 3F residue 11 VAL Chi-restraints excluded: chain 3F residue 26 ILE Chi-restraints excluded: chain 3F residue 43 LEU Chi-restraints excluded: chain 3G residue 31 ILE Chi-restraints excluded: chain 3G residue 47 LEU Chi-restraints excluded: chain 3G residue 51 VAL Chi-restraints excluded: chain 3G residue 58 VAL Chi-restraints excluded: chain 3H residue 21 VAL Chi-restraints excluded: chain 3H residue 23 MET Chi-restraints excluded: chain 3I residue 11 VAL Chi-restraints excluded: chain 3I residue 23 MET Chi-restraints excluded: chain 3I residue 51 VAL Chi-restraints excluded: chain 3I residue 58 VAL Chi-restraints excluded: chain 3J residue 4 LEU Chi-restraints excluded: chain 3J residue 11 VAL Chi-restraints excluded: chain 3J residue 50 VAL Chi-restraints excluded: chain 3L residue 11 VAL Chi-restraints excluded: chain 3L residue 21 VAL Chi-restraints excluded: chain 3L residue 23 MET Chi-restraints excluded: chain 3M residue 21 VAL Chi-restraints excluded: chain 3M residue 58 VAL Chi-restraints excluded: chain 3N residue 21 VAL Chi-restraints excluded: chain 3N residue 43 LEU Chi-restraints excluded: chain 4A residue 4 LEU Chi-restraints excluded: chain 4A residue 50 VAL Chi-restraints excluded: chain 4B residue 31 ILE Chi-restraints excluded: chain 4C residue 26 ILE Chi-restraints excluded: chain 4D residue 31 ILE Chi-restraints excluded: chain 4D residue 47 LEU Chi-restraints excluded: chain 4E residue 50 VAL Chi-restraints excluded: chain 4F residue 11 VAL Chi-restraints excluded: chain 4F residue 19 SER Chi-restraints excluded: chain 4F residue 26 ILE Chi-restraints excluded: chain 4G residue 26 ILE Chi-restraints excluded: chain 4H residue 21 VAL Chi-restraints excluded: chain 4I residue 21 VAL Chi-restraints excluded: chain 4I residue 23 MET Chi-restraints excluded: chain 4I residue 26 ILE Chi-restraints excluded: chain 4I residue 31 ILE Chi-restraints excluded: chain 4I residue 43 LEU Chi-restraints excluded: chain 4J residue 51 VAL Chi-restraints excluded: chain 4K residue 21 VAL Chi-restraints excluded: chain 4K residue 26 ILE Chi-restraints excluded: chain 4L residue 4 LEU Chi-restraints excluded: chain 4L residue 31 ILE Chi-restraints excluded: chain 4L residue 49 LEU Chi-restraints excluded: chain 4N residue 49 LEU Chi-restraints excluded: chain 4O residue 23 MET Chi-restraints excluded: chain 4O residue 27 ILE Chi-restraints excluded: chain 4O residue 31 ILE Chi-restraints excluded: chain 4P residue 52 VAL Chi-restraints excluded: chain 5B residue 26 ILE Chi-restraints excluded: chain 5B residue 53 ILE Chi-restraints excluded: chain 5C residue 11 VAL Chi-restraints excluded: chain 5C residue 23 MET Chi-restraints excluded: chain 5C residue 31 ILE Chi-restraints excluded: chain 5C residue 57 THR Chi-restraints excluded: chain 5D residue 4 LEU Chi-restraints excluded: chain 5E residue 19 SER Chi-restraints excluded: chain 5E residue 21 VAL Chi-restraints excluded: chain 5E residue 26 ILE Chi-restraints excluded: chain 5E residue 31 ILE Chi-restraints excluded: chain 5E residue 50 VAL Chi-restraints excluded: chain 5F residue 11 VAL Chi-restraints excluded: chain 5F residue 26 ILE Chi-restraints excluded: chain 5F residue 31 ILE Chi-restraints excluded: chain 5F residue 47 LEU Chi-restraints excluded: chain 5G residue 31 ILE Chi-restraints excluded: chain 5H residue 11 VAL Chi-restraints excluded: chain 5H residue 26 ILE Chi-restraints excluded: chain 5H residue 31 ILE Chi-restraints excluded: chain 5I residue 4 LEU Chi-restraints excluded: chain 5I residue 31 ILE Chi-restraints excluded: chain 5I residue 61 THR Chi-restraints excluded: chain 5J residue 23 MET Chi-restraints excluded: chain 5J residue 52 VAL Chi-restraints excluded: chain 5K residue 31 ILE Chi-restraints excluded: chain 5L residue 4 LEU Chi-restraints excluded: chain 5L residue 21 VAL Chi-restraints excluded: chain 5L residue 52 VAL Chi-restraints excluded: chain 5M residue 11 VAL Chi-restraints excluded: chain 5N residue 23 MET Chi-restraints excluded: chain 5N residue 47 LEU Chi-restraints excluded: chain 5N residue 57 THR Chi-restraints excluded: chain 5P residue 52 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 156 optimal weight: 0.0670 chunk 417 optimal weight: 7.9990 chunk 91 optimal weight: 50.0000 chunk 272 optimal weight: 6.9990 chunk 114 optimal weight: 30.0000 chunk 464 optimal weight: 7.9990 chunk 385 optimal weight: 6.9990 chunk 215 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 153 optimal weight: 8.9990 chunk 243 optimal weight: 8.9990 overall best weight: 5.4126 ------------------------------------------------------------------------------- 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: 0.7813 moved from start: 0.6893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 41600 Z= 0.282 Angle : 0.635 10.022 55410 Z= 0.312 Chirality : 0.039 0.201 7190 Planarity : 0.002 0.029 6070 Dihedral : 14.975 77.714 8495 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 5.77 % Allowed : 26.73 % Favored : 67.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.12), residues: 4880 helix: -0.60 (0.08), residues: 3280 sheet: None (None), residues: 0 loop : -1.16 (0.17), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.020 0.001 PHE3N 15 TYR 0.020 0.002 TYR3N 37 ARG 0.005 0.000 ARG1I 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1952 residues out of total 4160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 1712 time to evaluate : 4.330 Fit side-chains REVERT: 1H 60 LEU cc_start: 0.7829 (mt) cc_final: 0.7626 (mt) REVERT: 1I 40 THR cc_start: 0.8934 (m) cc_final: 0.8508 (p) REVERT: 1J 40 THR cc_start: 0.8623 (m) cc_final: 0.8128 (p) REVERT: 1K 26 ILE cc_start: 0.8649 (mm) cc_final: 0.8441 (mt) REVERT: 1N 41 LYS cc_start: 0.8523 (mttp) cc_final: 0.8318 (tppt) REVERT: 2A 37 TYR cc_start: 0.8766 (t80) cc_final: 0.8350 (t80) REVERT: 2D 3 LEU cc_start: 0.7169 (tp) cc_final: 0.6964 (tp) REVERT: 2I 40 THR cc_start: 0.8944 (m) cc_final: 0.8678 (p) REVERT: 2J 40 THR cc_start: 0.8610 (m) cc_final: 0.8373 (p) REVERT: 2K 46 LEU cc_start: 0.8807 (mt) cc_final: 0.8539 (tp) REVERT: 2K 54 VAL cc_start: 0.9157 (p) cc_final: 0.8841 (t) REVERT: 2L 29 GLU cc_start: 0.7478 (tp30) cc_final: 0.7030 (tp30) REVERT: 2L 40 THR cc_start: 0.8880 (m) cc_final: 0.8642 (p) REVERT: 2N 60 LEU cc_start: 0.8146 (mt) cc_final: 0.7909 (mt) REVERT: 2O 46 LEU cc_start: 0.8986 (mt) cc_final: 0.8771 (mt) REVERT: 3B 37 TYR cc_start: 0.8735 (t80) cc_final: 0.8491 (t80) REVERT: 3C 40 THR cc_start: 0.8683 (m) cc_final: 0.8457 (p) REVERT: 3C 54 VAL cc_start: 0.9255 (p) cc_final: 0.9021 (t) REVERT: 3D 40 THR cc_start: 0.8905 (m) cc_final: 0.8673 (p) REVERT: 3E 40 THR cc_start: 0.8778 (m) cc_final: 0.8560 (p) REVERT: 3F 40 THR cc_start: 0.8607 (m) cc_final: 0.8296 (p) REVERT: 3H 40 THR cc_start: 0.8700 (m) cc_final: 0.8440 (p) REVERT: 3I 40 THR cc_start: 0.8891 (m) cc_final: 0.8552 (p) REVERT: 3L 40 THR cc_start: 0.8602 (m) cc_final: 0.8252 (p) REVERT: 3P 37 TYR cc_start: 0.8686 (t80) cc_final: 0.8278 (t80) REVERT: 4G 26 ILE cc_start: 0.9039 (OUTLIER) cc_final: 0.8604 (mt) REVERT: 4H 40 THR cc_start: 0.8735 (m) cc_final: 0.8529 (p) REVERT: 4L 40 THR cc_start: 0.8684 (m) cc_final: 0.8450 (p) REVERT: 4N 60 LEU cc_start: 0.8134 (mt) cc_final: 0.7904 (mt) REVERT: 5B 12 LYS cc_start: 0.7977 (tttt) cc_final: 0.7771 (tttp) REVERT: 5B 29 GLU cc_start: 0.7756 (tp30) cc_final: 0.7177 (tp30) REVERT: 5E 40 THR cc_start: 0.8867 (m) cc_final: 0.8500 (p) REVERT: 5I 40 THR cc_start: 0.8711 (m) cc_final: 0.8403 (p) REVERT: 5J 40 THR cc_start: 0.8762 (m) cc_final: 0.8436 (p) REVERT: 5K 37 TYR cc_start: 0.8872 (t80) cc_final: 0.8598 (t80) REVERT: 5K 40 THR cc_start: 0.8760 (m) cc_final: 0.8518 (p) outliers start: 240 outliers final: 202 residues processed: 1813 average time/residue: 0.5037 time to fit residues: 1499.8831 Evaluate side-chains 1857 residues out of total 4160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 1654 time to evaluate : 4.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 11 VAL Chi-restraints excluded: chain 1A residue 21 VAL Chi-restraints excluded: chain 1A residue 23 MET Chi-restraints excluded: chain 1A residue 51 VAL Chi-restraints excluded: chain 1B residue 11 VAL Chi-restraints excluded: chain 1B residue 26 ILE Chi-restraints excluded: chain 1C residue 21 VAL Chi-restraints excluded: chain 1C residue 23 MET Chi-restraints excluded: chain 1C residue 26 ILE Chi-restraints excluded: chain 1C residue 53 ILE Chi-restraints excluded: chain 1C residue 61 THR Chi-restraints excluded: chain 1D residue 26 ILE Chi-restraints excluded: chain 1D residue 31 ILE Chi-restraints excluded: chain 1E residue 21 VAL Chi-restraints excluded: chain 1E residue 26 ILE Chi-restraints excluded: chain 1E residue 31 ILE Chi-restraints excluded: chain 1F residue 23 MET Chi-restraints excluded: chain 1F residue 26 ILE Chi-restraints excluded: chain 1G residue 26 ILE Chi-restraints excluded: chain 1G residue 31 ILE Chi-restraints excluded: chain 1G residue 47 LEU Chi-restraints excluded: chain 1G residue 51 VAL Chi-restraints excluded: chain 1G residue 52 VAL Chi-restraints excluded: chain 1G residue 53 ILE Chi-restraints excluded: chain 1G residue 58 VAL Chi-restraints excluded: chain 1H residue 23 MET Chi-restraints excluded: chain 1H residue 26 ILE Chi-restraints excluded: chain 1I residue 23 MET Chi-restraints excluded: chain 1I residue 26 ILE Chi-restraints excluded: chain 1I residue 31 ILE Chi-restraints excluded: chain 1I residue 51 VAL Chi-restraints excluded: chain 1J residue 21 VAL Chi-restraints excluded: chain 1J residue 26 ILE Chi-restraints excluded: chain 1J residue 58 VAL Chi-restraints excluded: chain 1K residue 23 MET Chi-restraints excluded: chain 1L residue 23 MET Chi-restraints excluded: chain 1L residue 26 ILE Chi-restraints excluded: chain 1L residue 41 LYS Chi-restraints excluded: chain 1L residue 49 LEU Chi-restraints excluded: chain 1L residue 53 ILE Chi-restraints excluded: chain 1M residue 11 VAL Chi-restraints excluded: chain 1M residue 23 MET Chi-restraints excluded: chain 1N residue 11 VAL Chi-restraints excluded: chain 1N residue 23 MET Chi-restraints excluded: chain 1N residue 31 ILE Chi-restraints excluded: chain 1N residue 43 LEU Chi-restraints excluded: chain 1O residue 31 ILE Chi-restraints excluded: chain 1P residue 52 VAL Chi-restraints excluded: chain 2A residue 11 VAL Chi-restraints excluded: chain 2A residue 23 MET Chi-restraints excluded: chain 2A residue 51 VAL Chi-restraints excluded: chain 2B residue 23 MET Chi-restraints excluded: chain 2B residue 24 CYS Chi-restraints excluded: chain 2B residue 26 ILE Chi-restraints excluded: chain 2B residue 57 THR Chi-restraints excluded: chain 2C residue 26 ILE Chi-restraints excluded: chain 2D residue 4 LEU Chi-restraints excluded: chain 2D residue 26 ILE Chi-restraints excluded: chain 2D residue 43 LEU Chi-restraints excluded: chain 2D residue 53 ILE Chi-restraints excluded: chain 2F residue 31 ILE Chi-restraints excluded: chain 2G residue 23 MET Chi-restraints excluded: chain 2G residue 26 ILE Chi-restraints excluded: chain 2H residue 31 ILE Chi-restraints excluded: chain 2I residue 21 VAL Chi-restraints excluded: chain 2I residue 26 ILE Chi-restraints excluded: chain 2I residue 47 LEU Chi-restraints excluded: chain 2I residue 51 VAL Chi-restraints excluded: chain 2I residue 52 VAL Chi-restraints excluded: chain 2I residue 53 ILE Chi-restraints excluded: chain 2J residue 4 LEU Chi-restraints excluded: chain 2J residue 26 ILE Chi-restraints excluded: chain 2J residue 47 LEU Chi-restraints excluded: chain 2K residue 26 ILE Chi-restraints excluded: chain 2K residue 51 VAL Chi-restraints excluded: chain 2K residue 61 THR Chi-restraints excluded: chain 2L residue 23 MET Chi-restraints excluded: chain 2L residue 57 THR Chi-restraints excluded: chain 2L residue 58 VAL Chi-restraints excluded: chain 2L residue 61 THR Chi-restraints excluded: chain 2M residue 11 VAL Chi-restraints excluded: chain 2M residue 31 ILE Chi-restraints excluded: chain 2M residue 50 VAL Chi-restraints excluded: chain 2N residue 31 ILE Chi-restraints excluded: chain 2N residue 58 VAL Chi-restraints excluded: chain 2N residue 63 ILE Chi-restraints excluded: chain 3B residue 23 MET Chi-restraints excluded: chain 3B residue 26 ILE Chi-restraints excluded: chain 3C residue 12 LYS Chi-restraints excluded: chain 3C residue 31 ILE Chi-restraints excluded: chain 3C residue 41 LYS Chi-restraints excluded: chain 3C residue 51 VAL Chi-restraints excluded: chain 3C residue 57 THR Chi-restraints excluded: chain 3D residue 50 VAL Chi-restraints excluded: chain 3E residue 11 VAL Chi-restraints excluded: chain 3E residue 50 VAL Chi-restraints excluded: chain 3F residue 11 VAL Chi-restraints excluded: chain 3F residue 26 ILE Chi-restraints excluded: chain 3F residue 43 LEU Chi-restraints excluded: chain 3G residue 11 VAL Chi-restraints excluded: chain 3G residue 23 MET Chi-restraints excluded: chain 3G residue 31 ILE Chi-restraints excluded: chain 3G residue 51 VAL Chi-restraints excluded: chain 3G residue 57 THR Chi-restraints excluded: chain 3G residue 58 VAL Chi-restraints excluded: chain 3H residue 21 VAL Chi-restraints excluded: chain 3H residue 31 ILE Chi-restraints excluded: chain 3I residue 11 VAL Chi-restraints excluded: chain 3I residue 41 LYS Chi-restraints excluded: chain 3I residue 51 VAL Chi-restraints excluded: chain 3I residue 58 VAL Chi-restraints excluded: chain 3J residue 4 LEU Chi-restraints excluded: chain 3J residue 11 VAL Chi-restraints excluded: chain 3J residue 50 VAL Chi-restraints excluded: chain 3K residue 23 MET Chi-restraints excluded: chain 3K residue 53 ILE Chi-restraints excluded: chain 3L residue 11 VAL Chi-restraints excluded: chain 3L residue 21 VAL Chi-restraints excluded: chain 3L residue 23 MET Chi-restraints excluded: chain 3L residue 51 VAL Chi-restraints excluded: chain 3M residue 21 VAL Chi-restraints excluded: chain 3M residue 58 VAL Chi-restraints excluded: chain 3N residue 21 VAL Chi-restraints excluded: chain 3N residue 43 LEU Chi-restraints excluded: chain 3N residue 47 LEU Chi-restraints excluded: chain 3O residue 23 MET Chi-restraints excluded: chain 3O residue 50 VAL Chi-restraints excluded: chain 4A residue 4 LEU Chi-restraints excluded: chain 4A residue 50 VAL Chi-restraints excluded: chain 4B residue 31 ILE Chi-restraints excluded: chain 4C residue 26 ILE Chi-restraints excluded: chain 4D residue 31 ILE Chi-restraints excluded: chain 4D residue 41 LYS Chi-restraints excluded: chain 4D residue 47 LEU Chi-restraints excluded: chain 4E residue 50 VAL Chi-restraints excluded: chain 4F residue 4 LEU Chi-restraints excluded: chain 4F residue 11 VAL Chi-restraints excluded: chain 4F residue 26 ILE Chi-restraints excluded: chain 4G residue 26 ILE Chi-restraints excluded: chain 4H residue 4 LEU Chi-restraints excluded: chain 4H residue 21 VAL Chi-restraints excluded: chain 4H residue 31 ILE Chi-restraints excluded: chain 4H residue 57 THR Chi-restraints excluded: chain 4I residue 4 LEU Chi-restraints excluded: chain 4I residue 21 VAL Chi-restraints excluded: chain 4I residue 23 MET Chi-restraints excluded: chain 4I residue 26 ILE Chi-restraints excluded: chain 4I residue 31 ILE Chi-restraints excluded: chain 4I residue 43 LEU Chi-restraints excluded: chain 4K residue 21 VAL Chi-restraints excluded: chain 4K residue 26 ILE Chi-restraints excluded: chain 4K residue 57 THR Chi-restraints excluded: chain 4L residue 4 LEU Chi-restraints excluded: chain 4L residue 31 ILE Chi-restraints excluded: chain 4L residue 49 LEU Chi-restraints excluded: chain 4N residue 49 LEU Chi-restraints excluded: chain 4N residue 57 THR Chi-restraints excluded: chain 4O residue 21 VAL Chi-restraints excluded: chain 4O residue 27 ILE Chi-restraints excluded: chain 4O residue 31 ILE Chi-restraints excluded: chain 5A residue 57 THR Chi-restraints excluded: chain 5B residue 11 VAL Chi-restraints excluded: chain 5B residue 26 ILE Chi-restraints excluded: chain 5B residue 53 ILE Chi-restraints excluded: chain 5B residue 57 THR Chi-restraints excluded: chain 5C residue 11 VAL Chi-restraints excluded: chain 5C residue 23 MET Chi-restraints excluded: chain 5C residue 31 ILE Chi-restraints excluded: chain 5C residue 57 THR Chi-restraints excluded: chain 5C residue 61 THR Chi-restraints excluded: chain 5D residue 4 LEU Chi-restraints excluded: chain 5E residue 19 SER Chi-restraints excluded: chain 5E residue 21 VAL Chi-restraints excluded: chain 5E residue 26 ILE Chi-restraints excluded: chain 5E residue 31 ILE Chi-restraints excluded: chain 5E residue 50 VAL Chi-restraints excluded: chain 5F residue 11 VAL Chi-restraints excluded: chain 5F residue 26 ILE Chi-restraints excluded: chain 5F residue 31 ILE Chi-restraints excluded: chain 5F residue 47 LEU Chi-restraints excluded: chain 5F residue 53 ILE Chi-restraints excluded: chain 5G residue 23 MET Chi-restraints excluded: chain 5G residue 31 ILE Chi-restraints excluded: chain 5G residue 57 THR Chi-restraints excluded: chain 5H residue 4 LEU Chi-restraints excluded: chain 5H residue 11 VAL Chi-restraints excluded: chain 5H residue 26 ILE Chi-restraints excluded: chain 5H residue 31 ILE Chi-restraints excluded: chain 5H residue 61 THR Chi-restraints excluded: chain 5I residue 31 ILE Chi-restraints excluded: chain 5I residue 53 ILE Chi-restraints excluded: chain 5I residue 61 THR Chi-restraints excluded: chain 5J residue 23 MET Chi-restraints excluded: chain 5K residue 31 ILE Chi-restraints excluded: chain 5L residue 21 VAL Chi-restraints excluded: chain 5M residue 11 VAL Chi-restraints excluded: chain 5M residue 61 THR Chi-restraints excluded: chain 5N residue 23 MET Chi-restraints excluded: chain 5N residue 47 LEU Chi-restraints excluded: chain 5N residue 53 ILE Chi-restraints excluded: chain 5N residue 57 THR Chi-restraints excluded: chain 5N residue 63 ILE Chi-restraints excluded: chain 5P residue 52 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 447 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 264 optimal weight: 0.3980 chunk 339 optimal weight: 3.9990 chunk 262 optimal weight: 10.0000 chunk 390 optimal weight: 4.9990 chunk 259 optimal weight: 20.0000 chunk 462 optimal weight: 10.0000 chunk 289 optimal weight: 8.9990 chunk 282 optimal weight: 50.0000 chunk 213 optimal weight: 0.9980 overall best weight: 3.2786 ------------------------------------------------------------------------------- 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: 0.7763 moved from start: 0.7143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 41600 Z= 0.212 Angle : 0.602 10.278 55410 Z= 0.295 Chirality : 0.038 0.177 7190 Planarity : 0.002 0.022 6070 Dihedral : 14.343 80.534 8495 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 5.19 % Allowed : 28.73 % Favored : 66.08 % 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: -1.07 (0.12), residues: 4880 helix: -0.39 (0.08), residues: 3280 sheet: None (None), residues: 0 loop : -1.11 (0.17), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.001 PHE4A 15 TYR 0.020 0.002 TYR4K 37 ARG 0.005 0.000 ARG1I 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1902 residues out of total 4160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 1686 time to evaluate : 4.205 Fit side-chains REVERT: 1D 40 THR cc_start: 0.8703 (m) cc_final: 0.8320 (p) REVERT: 1H 46 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8558 (mp) REVERT: 1I 40 THR cc_start: 0.8892 (m) cc_final: 0.8480 (p) REVERT: 2A 37 TYR cc_start: 0.8777 (t80) cc_final: 0.8396 (t80) REVERT: 2I 40 THR cc_start: 0.8948 (m) cc_final: 0.8686 (p) REVERT: 2L 29 GLU cc_start: 0.7421 (tp30) cc_final: 0.7075 (tp30) REVERT: 3B 37 TYR cc_start: 0.8755 (t80) cc_final: 0.8544 (t80) REVERT: 3C 40 THR cc_start: 0.8664 (m) cc_final: 0.8445 (p) REVERT: 3D 40 THR cc_start: 0.8822 (m) cc_final: 0.8598 (p) REVERT: 3F 40 THR cc_start: 0.8565 (m) cc_final: 0.8220 (p) REVERT: 3H 40 THR cc_start: 0.8577 (m) cc_final: 0.8350 (p) REVERT: 3I 40 THR cc_start: 0.8880 (m) cc_final: 0.8563 (p) REVERT: 3L 40 THR cc_start: 0.8552 (m) cc_final: 0.8126 (p) REVERT: 3M 37 TYR cc_start: 0.8605 (t80) cc_final: 0.8370 (t80) REVERT: 4K 40 THR cc_start: 0.8708 (m) cc_final: 0.8419 (p) REVERT: 4K 41 LYS cc_start: 0.8595 (mttp) cc_final: 0.8353 (mttp) REVERT: 4L 40 THR cc_start: 0.8611 (m) cc_final: 0.8394 (p) REVERT: 4M 10 ASP cc_start: 0.7676 (OUTLIER) cc_final: 0.7367 (p0) REVERT: 4N 60 LEU cc_start: 0.8052 (mt) cc_final: 0.7823 (mt) REVERT: 5B 29 GLU cc_start: 0.7723 (tp30) cc_final: 0.7093 (tp30) REVERT: 5E 40 THR cc_start: 0.8871 (m) cc_final: 0.8456 (p) REVERT: 5I 40 THR cc_start: 0.8744 (m) cc_final: 0.8467 (p) REVERT: 5J 40 THR cc_start: 0.8689 (m) cc_final: 0.8358 (p) REVERT: 5K 40 THR cc_start: 0.8761 (m) cc_final: 0.8499 (p) REVERT: 5N 47 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8042 (tt) outliers start: 216 outliers final: 180 residues processed: 1762 average time/residue: 0.4981 time to fit residues: 1438.0171 Evaluate side-chains 1822 residues out of total 4160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 1639 time to evaluate : 4.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 57 THR Chi-restraints excluded: chain 1B residue 25 ILE Chi-restraints excluded: chain 1B residue 26 ILE Chi-restraints excluded: chain 1C residue 21 VAL Chi-restraints excluded: chain 1C residue 23 MET Chi-restraints excluded: chain 1C residue 26 ILE Chi-restraints excluded: chain 1C residue 53 ILE Chi-restraints excluded: chain 1D residue 26 ILE Chi-restraints excluded: chain 1D residue 31 ILE Chi-restraints excluded: chain 1D residue 47 LEU Chi-restraints excluded: chain 1D residue 51 VAL Chi-restraints excluded: chain 1E residue 21 VAL Chi-restraints excluded: chain 1E residue 26 ILE Chi-restraints excluded: chain 1E residue 31 ILE Chi-restraints excluded: chain 1E residue 41 LYS Chi-restraints excluded: chain 1F residue 26 ILE Chi-restraints excluded: chain 1G residue 25 ILE Chi-restraints excluded: chain 1G residue 26 ILE Chi-restraints excluded: chain 1G residue 31 ILE Chi-restraints excluded: chain 1G residue 51 VAL Chi-restraints excluded: chain 1G residue 52 VAL Chi-restraints excluded: chain 1H residue 23 MET Chi-restraints excluded: chain 1H residue 26 ILE Chi-restraints excluded: chain 1H residue 46 LEU Chi-restraints excluded: chain 1H residue 47 LEU Chi-restraints excluded: chain 1I residue 23 MET Chi-restraints excluded: chain 1I residue 26 ILE Chi-restraints excluded: chain 1I residue 31 ILE Chi-restraints excluded: chain 1I residue 47 LEU Chi-restraints excluded: chain 1J residue 21 VAL Chi-restraints excluded: chain 1J residue 26 ILE Chi-restraints excluded: chain 1J residue 46 LEU Chi-restraints excluded: chain 1J residue 47 LEU Chi-restraints excluded: chain 1J residue 58 VAL Chi-restraints excluded: chain 1K residue 23 MET Chi-restraints excluded: chain 1L residue 21 VAL Chi-restraints excluded: chain 1L residue 23 MET Chi-restraints excluded: chain 1L residue 26 ILE Chi-restraints excluded: chain 1L residue 41 LYS Chi-restraints excluded: chain 1L residue 49 LEU Chi-restraints excluded: chain 1L residue 53 ILE Chi-restraints excluded: chain 1M residue 11 VAL Chi-restraints excluded: chain 1M residue 23 MET Chi-restraints excluded: chain 1N residue 31 ILE Chi-restraints excluded: chain 1N residue 43 LEU Chi-restraints excluded: chain 1O residue 31 ILE Chi-restraints excluded: chain 1O residue 52 VAL Chi-restraints excluded: chain 1P residue 52 VAL Chi-restraints excluded: chain 2A residue 11 VAL Chi-restraints excluded: chain 2A residue 51 VAL Chi-restraints excluded: chain 2B residue 23 MET Chi-restraints excluded: chain 2B residue 24 CYS Chi-restraints excluded: chain 2B residue 26 ILE Chi-restraints excluded: chain 2B residue 57 THR Chi-restraints excluded: chain 2C residue 26 ILE Chi-restraints excluded: chain 2D residue 26 ILE Chi-restraints excluded: chain 2D residue 43 LEU Chi-restraints excluded: chain 2D residue 52 VAL Chi-restraints excluded: chain 2D residue 53 ILE Chi-restraints excluded: chain 2F residue 51 VAL Chi-restraints excluded: chain 2G residue 26 ILE Chi-restraints excluded: chain 2H residue 31 ILE Chi-restraints excluded: chain 2I residue 21 VAL Chi-restraints excluded: chain 2I residue 26 ILE Chi-restraints excluded: chain 2I residue 47 LEU Chi-restraints excluded: chain 2I residue 51 VAL Chi-restraints excluded: chain 2I residue 52 VAL Chi-restraints excluded: chain 2J residue 4 LEU Chi-restraints excluded: chain 2J residue 26 ILE Chi-restraints excluded: chain 2J residue 47 LEU Chi-restraints excluded: chain 2K residue 26 ILE Chi-restraints excluded: chain 2L residue 23 MET Chi-restraints excluded: chain 2L residue 61 THR Chi-restraints excluded: chain 2M residue 31 ILE Chi-restraints excluded: chain 2M residue 47 LEU Chi-restraints excluded: chain 2M residue 50 VAL Chi-restraints excluded: chain 2N residue 31 ILE Chi-restraints excluded: chain 2N residue 58 VAL Chi-restraints excluded: chain 2O residue 60 LEU Chi-restraints excluded: chain 3B residue 23 MET Chi-restraints excluded: chain 3B residue 25 ILE Chi-restraints excluded: chain 3B residue 26 ILE Chi-restraints excluded: chain 3C residue 12 LYS Chi-restraints excluded: chain 3C residue 51 VAL Chi-restraints excluded: chain 3C residue 57 THR Chi-restraints excluded: chain 3D residue 10 ASP Chi-restraints excluded: chain 3D residue 50 VAL Chi-restraints excluded: chain 3E residue 11 VAL Chi-restraints excluded: chain 3E residue 50 VAL Chi-restraints excluded: chain 3F residue 11 VAL Chi-restraints excluded: chain 3F residue 26 ILE Chi-restraints excluded: chain 3F residue 43 LEU Chi-restraints excluded: chain 3F residue 51 VAL Chi-restraints excluded: chain 3G residue 23 MET Chi-restraints excluded: chain 3G residue 31 ILE Chi-restraints excluded: chain 3G residue 51 VAL Chi-restraints excluded: chain 3G residue 58 VAL Chi-restraints excluded: chain 3H residue 21 VAL Chi-restraints excluded: chain 3H residue 23 MET Chi-restraints excluded: chain 3H residue 49 LEU Chi-restraints excluded: chain 3I residue 11 VAL Chi-restraints excluded: chain 3I residue 23 MET Chi-restraints excluded: chain 3I residue 51 VAL Chi-restraints excluded: chain 3I residue 58 VAL Chi-restraints excluded: chain 3J residue 4 LEU Chi-restraints excluded: chain 3J residue 11 VAL Chi-restraints excluded: chain 3K residue 31 ILE Chi-restraints excluded: chain 3K residue 47 LEU Chi-restraints excluded: chain 3K residue 51 VAL Chi-restraints excluded: chain 3K residue 53 ILE Chi-restraints excluded: chain 3L residue 11 VAL Chi-restraints excluded: chain 3L residue 21 VAL Chi-restraints excluded: chain 3L residue 23 MET Chi-restraints excluded: chain 3L residue 53 ILE Chi-restraints excluded: chain 3M residue 21 VAL Chi-restraints excluded: chain 3M residue 58 VAL Chi-restraints excluded: chain 3N residue 10 ASP Chi-restraints excluded: chain 3N residue 21 VAL Chi-restraints excluded: chain 3N residue 47 LEU Chi-restraints excluded: chain 3O residue 50 VAL Chi-restraints excluded: chain 3O residue 58 VAL Chi-restraints excluded: chain 4A residue 4 LEU Chi-restraints excluded: chain 4A residue 50 VAL Chi-restraints excluded: chain 4B residue 31 ILE Chi-restraints excluded: chain 4C residue 26 ILE Chi-restraints excluded: chain 4D residue 31 ILE Chi-restraints excluded: chain 4D residue 41 LYS Chi-restraints excluded: chain 4D residue 47 LEU Chi-restraints excluded: chain 4E residue 23 MET Chi-restraints excluded: chain 4E residue 50 VAL Chi-restraints excluded: chain 4F residue 4 LEU Chi-restraints excluded: chain 4F residue 11 VAL Chi-restraints excluded: chain 4F residue 26 ILE Chi-restraints excluded: chain 4G residue 25 ILE Chi-restraints excluded: chain 4H residue 21 VAL Chi-restraints excluded: chain 4I residue 4 LEU Chi-restraints excluded: chain 4I residue 21 VAL Chi-restraints excluded: chain 4I residue 23 MET Chi-restraints excluded: chain 4I residue 26 ILE Chi-restraints excluded: chain 4I residue 43 LEU Chi-restraints excluded: chain 4J residue 51 VAL Chi-restraints excluded: chain 4K residue 21 VAL Chi-restraints excluded: chain 4K residue 26 ILE Chi-restraints excluded: chain 4L residue 4 LEU Chi-restraints excluded: chain 4L residue 23 MET Chi-restraints excluded: chain 4L residue 31 ILE Chi-restraints excluded: chain 4L residue 49 LEU Chi-restraints excluded: chain 4M residue 10 ASP Chi-restraints excluded: chain 4O residue 27 ILE Chi-restraints excluded: chain 4O residue 31 ILE Chi-restraints excluded: chain 5B residue 11 VAL Chi-restraints excluded: chain 5B residue 26 ILE Chi-restraints excluded: chain 5B residue 47 LEU Chi-restraints excluded: chain 5B residue 53 ILE Chi-restraints excluded: chain 5C residue 23 MET Chi-restraints excluded: chain 5C residue 31 ILE Chi-restraints excluded: chain 5D residue 4 LEU Chi-restraints excluded: chain 5E residue 10 ASP Chi-restraints excluded: chain 5E residue 11 VAL Chi-restraints excluded: chain 5E residue 19 SER Chi-restraints excluded: chain 5E residue 21 VAL Chi-restraints excluded: chain 5E residue 26 ILE Chi-restraints excluded: chain 5E residue 31 ILE Chi-restraints excluded: chain 5E residue 50 VAL Chi-restraints excluded: chain 5F residue 11 VAL Chi-restraints excluded: chain 5F residue 26 ILE Chi-restraints excluded: chain 5F residue 31 ILE Chi-restraints excluded: chain 5F residue 53 ILE Chi-restraints excluded: chain 5G residue 31 ILE Chi-restraints excluded: chain 5G residue 57 THR Chi-restraints excluded: chain 5H residue 11 VAL Chi-restraints excluded: chain 5H residue 26 ILE Chi-restraints excluded: chain 5I residue 31 ILE Chi-restraints excluded: chain 5I residue 53 ILE Chi-restraints excluded: chain 5I residue 61 THR Chi-restraints excluded: chain 5J residue 23 MET Chi-restraints excluded: chain 5L residue 21 VAL Chi-restraints excluded: chain 5M residue 11 VAL Chi-restraints excluded: chain 5M residue 61 THR Chi-restraints excluded: chain 5N residue 23 MET Chi-restraints excluded: chain 5N residue 47 LEU Chi-restraints excluded: chain 5P residue 46 LEU Chi-restraints excluded: chain 5P residue 52 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 286 optimal weight: 3.9990 chunk 184 optimal weight: 9.9990 chunk 276 optimal weight: 50.0000 chunk 139 optimal weight: 20.0000 chunk 90 optimal weight: 50.0000 chunk 89 optimal weight: 2.9990 chunk 294 optimal weight: 6.9990 chunk 315 optimal weight: 6.9990 chunk 228 optimal weight: 0.0470 chunk 43 optimal weight: 9.9990 chunk 363 optimal weight: 7.9990 overall best weight: 4.2086 ------------------------------------------------------------------------------- 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: 0.7785 moved from start: 0.7237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 41600 Z= 0.247 Angle : 0.636 11.390 55410 Z= 0.308 Chirality : 0.038 0.187 7190 Planarity : 0.002 0.038 6070 Dihedral : 14.419 78.105 8495 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 5.36 % Allowed : 29.47 % Favored : 65.17 % 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: -1.06 (0.12), residues: 4880 helix: -0.38 (0.08), residues: 3280 sheet: None (None), residues: 0 loop : -1.12 (0.17), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.017 0.001 PHE3N 15 TYR 0.023 0.002 TYR2I 37 ARG 0.008 0.000 ARG2O 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1891 residues out of total 4160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 1668 time to evaluate : 4.080 Fit side-chains REVERT: 1B 12 LYS cc_start: 0.7994 (tppt) cc_final: 0.7749 (tttp) REVERT: 1H 46 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8533 (mp) REVERT: 1I 40 THR cc_start: 0.8833 (m) cc_final: 0.8423 (p) REVERT: 1J 40 THR cc_start: 0.8510 (m) cc_final: 0.8058 (p) REVERT: 1J 61 THR cc_start: 0.8039 (p) cc_final: 0.7501 (m) REVERT: 2E 40 THR cc_start: 0.8708 (m) cc_final: 0.8488 (p) REVERT: 2H 40 THR cc_start: 0.8716 (m) cc_final: 0.8495 (p) REVERT: 2I 40 THR cc_start: 0.8943 (m) cc_final: 0.8676 (p) REVERT: 2J 26 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.8336 (tt) REVERT: 2K 29 GLU cc_start: 0.7950 (tp30) cc_final: 0.7716 (tp30) REVERT: 2L 29 GLU cc_start: 0.7496 (tp30) cc_final: 0.7117 (tp30) REVERT: 2O 29 GLU cc_start: 0.7642 (tp30) cc_final: 0.7237 (tp30) REVERT: 3B 37 TYR cc_start: 0.8769 (t80) cc_final: 0.8554 (t80) REVERT: 3C 40 THR cc_start: 0.8762 (m) cc_final: 0.8511 (p) REVERT: 3F 40 THR cc_start: 0.8556 (m) cc_final: 0.8217 (p) REVERT: 3H 40 THR cc_start: 0.8588 (m) cc_final: 0.8372 (p) REVERT: 3I 40 THR cc_start: 0.8886 (m) cc_final: 0.8560 (p) REVERT: 3L 40 THR cc_start: 0.8544 (m) cc_final: 0.8175 (p) REVERT: 4K 40 THR cc_start: 0.8663 (m) cc_final: 0.8446 (p) REVERT: 4L 40 THR cc_start: 0.8603 (m) cc_final: 0.8397 (p) REVERT: 4N 60 LEU cc_start: 0.8049 (mt) cc_final: 0.7846 (mt) REVERT: 5B 29 GLU cc_start: 0.7746 (tp30) cc_final: 0.7200 (tp30) REVERT: 5I 40 THR cc_start: 0.8782 (m) cc_final: 0.8499 (p) REVERT: 5J 40 THR cc_start: 0.8671 (m) cc_final: 0.8390 (p) REVERT: 5K 40 THR cc_start: 0.8685 (m) cc_final: 0.8481 (p) outliers start: 223 outliers final: 195 residues processed: 1750 average time/residue: 0.4992 time to fit residues: 1431.3369 Evaluate side-chains 1834 residues out of total 4160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 1637 time to evaluate : 4.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 57 THR Chi-restraints excluded: chain 1B residue 11 VAL Chi-restraints excluded: chain 1B residue 23 MET Chi-restraints excluded: chain 1B residue 25 ILE Chi-restraints excluded: chain 1B residue 26 ILE Chi-restraints excluded: chain 1B residue 29 GLU Chi-restraints excluded: chain 1C residue 21 VAL Chi-restraints excluded: chain 1C residue 23 MET Chi-restraints excluded: chain 1C residue 26 ILE Chi-restraints excluded: chain 1C residue 53 ILE Chi-restraints excluded: chain 1D residue 26 ILE Chi-restraints excluded: chain 1D residue 31 ILE Chi-restraints excluded: chain 1D residue 47 LEU Chi-restraints excluded: chain 1D residue 51 VAL Chi-restraints excluded: chain 1E residue 21 VAL Chi-restraints excluded: chain 1E residue 26 ILE Chi-restraints excluded: chain 1E residue 31 ILE Chi-restraints excluded: chain 1E residue 41 LYS Chi-restraints excluded: chain 1F residue 26 ILE Chi-restraints excluded: chain 1G residue 25 ILE Chi-restraints excluded: chain 1G residue 26 ILE Chi-restraints excluded: chain 1G residue 31 ILE Chi-restraints excluded: chain 1G residue 47 LEU Chi-restraints excluded: chain 1G residue 51 VAL Chi-restraints excluded: chain 1G residue 52 VAL Chi-restraints excluded: chain 1H residue 23 MET Chi-restraints excluded: chain 1H residue 26 ILE Chi-restraints excluded: chain 1H residue 46 LEU Chi-restraints excluded: chain 1H residue 47 LEU Chi-restraints excluded: chain 1I residue 23 MET Chi-restraints excluded: chain 1I residue 26 ILE Chi-restraints excluded: chain 1I residue 31 ILE Chi-restraints excluded: chain 1J residue 21 VAL Chi-restraints excluded: chain 1J residue 26 ILE Chi-restraints excluded: chain 1J residue 46 LEU Chi-restraints excluded: chain 1J residue 47 LEU Chi-restraints excluded: chain 1J residue 58 VAL Chi-restraints excluded: chain 1K residue 23 MET Chi-restraints excluded: chain 1L residue 21 VAL Chi-restraints excluded: chain 1L residue 26 ILE Chi-restraints excluded: chain 1L residue 41 LYS Chi-restraints excluded: chain 1L residue 49 LEU Chi-restraints excluded: chain 1L residue 53 ILE Chi-restraints excluded: chain 1M residue 11 VAL Chi-restraints excluded: chain 1N residue 11 VAL Chi-restraints excluded: chain 1N residue 23 MET Chi-restraints excluded: chain 1N residue 31 ILE Chi-restraints excluded: chain 1O residue 31 ILE Chi-restraints excluded: chain 1P residue 52 VAL Chi-restraints excluded: chain 2A residue 11 VAL Chi-restraints excluded: chain 2A residue 51 VAL Chi-restraints excluded: chain 2B residue 23 MET Chi-restraints excluded: chain 2B residue 24 CYS Chi-restraints excluded: chain 2B residue 26 ILE Chi-restraints excluded: chain 2B residue 57 THR Chi-restraints excluded: chain 2C residue 26 ILE Chi-restraints excluded: chain 2D residue 26 ILE Chi-restraints excluded: chain 2D residue 43 LEU Chi-restraints excluded: chain 2D residue 52 VAL Chi-restraints excluded: chain 2D residue 53 ILE Chi-restraints excluded: chain 2F residue 47 LEU Chi-restraints excluded: chain 2F residue 51 VAL Chi-restraints excluded: chain 2G residue 26 ILE Chi-restraints excluded: chain 2H residue 31 ILE Chi-restraints excluded: chain 2I residue 21 VAL Chi-restraints excluded: chain 2I residue 26 ILE Chi-restraints excluded: chain 2I residue 47 LEU Chi-restraints excluded: chain 2I residue 51 VAL Chi-restraints excluded: chain 2I residue 52 VAL Chi-restraints excluded: chain 2I residue 53 ILE Chi-restraints excluded: chain 2J residue 4 LEU Chi-restraints excluded: chain 2J residue 26 ILE Chi-restraints excluded: chain 2J residue 47 LEU Chi-restraints excluded: chain 2J residue 52 VAL Chi-restraints excluded: chain 2K residue 26 ILE Chi-restraints excluded: chain 2K residue 43 LEU Chi-restraints excluded: chain 2K residue 53 ILE Chi-restraints excluded: chain 2L residue 23 MET Chi-restraints excluded: chain 2M residue 11 VAL Chi-restraints excluded: chain 2M residue 31 ILE Chi-restraints excluded: chain 2M residue 47 LEU Chi-restraints excluded: chain 2M residue 50 VAL Chi-restraints excluded: chain 2N residue 23 MET Chi-restraints excluded: chain 2N residue 31 ILE Chi-restraints excluded: chain 2O residue 60 LEU Chi-restraints excluded: chain 3A residue 60 LEU Chi-restraints excluded: chain 3B residue 25 ILE Chi-restraints excluded: chain 3B residue 26 ILE Chi-restraints excluded: chain 3C residue 12 LYS Chi-restraints excluded: chain 3C residue 31 ILE Chi-restraints excluded: chain 3C residue 51 VAL Chi-restraints excluded: chain 3C residue 57 THR Chi-restraints excluded: chain 3D residue 10 ASP Chi-restraints excluded: chain 3D residue 50 VAL Chi-restraints excluded: chain 3E residue 11 VAL Chi-restraints excluded: chain 3E residue 50 VAL Chi-restraints excluded: chain 3F residue 11 VAL Chi-restraints excluded: chain 3F residue 26 ILE Chi-restraints excluded: chain 3F residue 43 LEU Chi-restraints excluded: chain 3F residue 51 VAL Chi-restraints excluded: chain 3G residue 19 SER Chi-restraints excluded: chain 3G residue 23 MET Chi-restraints excluded: chain 3G residue 31 ILE Chi-restraints excluded: chain 3G residue 51 VAL Chi-restraints excluded: chain 3G residue 58 VAL Chi-restraints excluded: chain 3H residue 21 VAL Chi-restraints excluded: chain 3H residue 23 MET Chi-restraints excluded: chain 3I residue 11 VAL Chi-restraints excluded: chain 3I residue 23 MET Chi-restraints excluded: chain 3I residue 51 VAL Chi-restraints excluded: chain 3I residue 58 VAL Chi-restraints excluded: chain 3J residue 4 LEU Chi-restraints excluded: chain 3J residue 11 VAL Chi-restraints excluded: chain 3K residue 47 LEU Chi-restraints excluded: chain 3K residue 51 VAL Chi-restraints excluded: chain 3K residue 53 ILE Chi-restraints excluded: chain 3L residue 11 VAL Chi-restraints excluded: chain 3L residue 21 VAL Chi-restraints excluded: chain 3L residue 23 MET Chi-restraints excluded: chain 3L residue 53 ILE Chi-restraints excluded: chain 3M residue 21 VAL Chi-restraints excluded: chain 3M residue 58 VAL Chi-restraints excluded: chain 3N residue 10 ASP Chi-restraints excluded: chain 3N residue 21 VAL Chi-restraints excluded: chain 3N residue 47 LEU Chi-restraints excluded: chain 3O residue 50 VAL Chi-restraints excluded: chain 3P residue 53 ILE Chi-restraints excluded: chain 4A residue 4 LEU Chi-restraints excluded: chain 4A residue 11 VAL Chi-restraints excluded: chain 4A residue 50 VAL Chi-restraints excluded: chain 4B residue 31 ILE Chi-restraints excluded: chain 4B residue 57 THR Chi-restraints excluded: chain 4C residue 26 ILE Chi-restraints excluded: chain 4D residue 31 ILE Chi-restraints excluded: chain 4D residue 41 LYS Chi-restraints excluded: chain 4D residue 47 LEU Chi-restraints excluded: chain 4E residue 23 MET Chi-restraints excluded: chain 4E residue 50 VAL Chi-restraints excluded: chain 4F residue 3 LEU Chi-restraints excluded: chain 4F residue 4 LEU Chi-restraints excluded: chain 4F residue 11 VAL Chi-restraints excluded: chain 4F residue 26 ILE Chi-restraints excluded: chain 4H residue 21 VAL Chi-restraints excluded: chain 4I residue 4 LEU Chi-restraints excluded: chain 4I residue 21 VAL Chi-restraints excluded: chain 4I residue 23 MET Chi-restraints excluded: chain 4I residue 26 ILE Chi-restraints excluded: chain 4I residue 43 LEU Chi-restraints excluded: chain 4I residue 50 VAL Chi-restraints excluded: chain 4K residue 21 VAL Chi-restraints excluded: chain 4K residue 26 ILE Chi-restraints excluded: chain 4L residue 4 LEU Chi-restraints excluded: chain 4L residue 23 MET Chi-restraints excluded: chain 4L residue 49 LEU Chi-restraints excluded: chain 4N residue 23 MET Chi-restraints excluded: chain 4N residue 57 THR Chi-restraints excluded: chain 4O residue 27 ILE Chi-restraints excluded: chain 4O residue 31 ILE Chi-restraints excluded: chain 5B residue 11 VAL Chi-restraints excluded: chain 5B residue 26 ILE Chi-restraints excluded: chain 5B residue 47 LEU Chi-restraints excluded: chain 5B residue 53 ILE Chi-restraints excluded: chain 5C residue 11 VAL Chi-restraints excluded: chain 5C residue 23 MET Chi-restraints excluded: chain 5C residue 31 ILE Chi-restraints excluded: chain 5C residue 57 THR Chi-restraints excluded: chain 5D residue 4 LEU Chi-restraints excluded: chain 5E residue 10 ASP Chi-restraints excluded: chain 5E residue 11 VAL Chi-restraints excluded: chain 5E residue 19 SER Chi-restraints excluded: chain 5E residue 21 VAL Chi-restraints excluded: chain 5E residue 26 ILE Chi-restraints excluded: chain 5E residue 31 ILE Chi-restraints excluded: chain 5E residue 50 VAL Chi-restraints excluded: chain 5F residue 11 VAL Chi-restraints excluded: chain 5F residue 21 VAL Chi-restraints excluded: chain 5F residue 26 ILE Chi-restraints excluded: chain 5F residue 31 ILE Chi-restraints excluded: chain 5F residue 47 LEU Chi-restraints excluded: chain 5F residue 53 ILE Chi-restraints excluded: chain 5G residue 31 ILE Chi-restraints excluded: chain 5G residue 57 THR Chi-restraints excluded: chain 5H residue 11 VAL Chi-restraints excluded: chain 5H residue 26 ILE Chi-restraints excluded: chain 5I residue 31 ILE Chi-restraints excluded: chain 5I residue 53 ILE Chi-restraints excluded: chain 5I residue 61 THR Chi-restraints excluded: chain 5J residue 23 MET Chi-restraints excluded: chain 5L residue 21 VAL Chi-restraints excluded: chain 5M residue 11 VAL Chi-restraints excluded: chain 5M residue 50 VAL Chi-restraints excluded: chain 5M residue 61 THR Chi-restraints excluded: chain 5N residue 23 MET Chi-restraints excluded: chain 5N residue 47 LEU Chi-restraints excluded: chain 5O residue 21 VAL Chi-restraints excluded: chain 5O residue 50 VAL Chi-restraints excluded: chain 5P residue 52 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 420 optimal weight: 0.0040 chunk 443 optimal weight: 8.9990 chunk 404 optimal weight: 9.9990 chunk 431 optimal weight: 5.9990 chunk 259 optimal weight: 7.9990 chunk 187 optimal weight: 50.0000 chunk 338 optimal weight: 10.0000 chunk 132 optimal weight: 4.9990 chunk 389 optimal weight: 0.8980 chunk 407 optimal weight: 7.9990 chunk 429 optimal weight: 5.9990 overall best weight: 3.5798 ------------------------------------------------------------------------------- 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: 0.7764 moved from start: 0.7366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 41600 Z= 0.228 Angle : 0.635 12.007 55410 Z= 0.307 Chirality : 0.038 0.206 7190 Planarity : 0.002 0.032 6070 Dihedral : 14.182 80.076 8495 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 5.24 % Allowed : 29.81 % Favored : 64.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.12), residues: 4880 helix: -0.28 (0.08), residues: 3280 sheet: None (None), residues: 0 loop : -1.11 (0.17), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.019 0.001 PHE2D 15 TYR 0.025 0.002 TYR2I 37 ARG 0.008 0.000 ARG2O 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1874 residues out of total 4160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 1656 time to evaluate : 4.101 Fit side-chains REVERT: 1B 12 LYS cc_start: 0.7977 (tppt) cc_final: 0.7740 (tttp) REVERT: 1H 46 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8523 (mp) REVERT: 1I 40 THR cc_start: 0.8818 (m) cc_final: 0.8452 (p) REVERT: 1J 61 THR cc_start: 0.8091 (p) cc_final: 0.7524 (m) REVERT: 2A 37 TYR cc_start: 0.8800 (t80) cc_final: 0.8404 (t80) REVERT: 2D 26 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8395 (mt) REVERT: 2E 40 THR cc_start: 0.8698 (m) cc_final: 0.8486 (p) REVERT: 2H 40 THR cc_start: 0.8706 (m) cc_final: 0.8493 (p) REVERT: 2I 40 THR cc_start: 0.8940 (m) cc_final: 0.8691 (p) REVERT: 2L 29 GLU cc_start: 0.7540 (tp30) cc_final: 0.7257 (tp30) REVERT: 2O 29 GLU cc_start: 0.7625 (tp30) cc_final: 0.7209 (tp30) REVERT: 3B 37 TYR cc_start: 0.8766 (t80) cc_final: 0.8558 (t80) REVERT: 3C 40 THR cc_start: 0.8734 (m) cc_final: 0.8452 (p) REVERT: 3F 40 THR cc_start: 0.8550 (m) cc_final: 0.8210 (p) REVERT: 3I 40 THR cc_start: 0.8885 (m) cc_final: 0.8566 (p) REVERT: 3L 40 THR cc_start: 0.8515 (m) cc_final: 0.8154 (p) REVERT: 4N 60 LEU cc_start: 0.8028 (mt) cc_final: 0.7806 (mt) REVERT: 5B 29 GLU cc_start: 0.7769 (tp30) cc_final: 0.7222 (tp30) REVERT: 5E 40 THR cc_start: 0.8846 (m) cc_final: 0.8508 (p) REVERT: 5I 40 THR cc_start: 0.8754 (m) cc_final: 0.8474 (p) REVERT: 5J 40 THR cc_start: 0.8645 (m) cc_final: 0.8368 (p) REVERT: 5K 40 THR cc_start: 0.8685 (m) cc_final: 0.8465 (p) REVERT: 5P 47 LEU cc_start: 0.8754 (tp) cc_final: 0.8479 (tp) outliers start: 218 outliers final: 192 residues processed: 1727 average time/residue: 0.5076 time to fit residues: 1436.5333 Evaluate side-chains 1818 residues out of total 4160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 1624 time to evaluate : 4.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 51 VAL Chi-restraints excluded: chain 1A residue 57 THR Chi-restraints excluded: chain 1B residue 23 MET Chi-restraints excluded: chain 1B residue 25 ILE Chi-restraints excluded: chain 1B residue 26 ILE Chi-restraints excluded: chain 1B residue 29 GLU Chi-restraints excluded: chain 1C residue 21 VAL Chi-restraints excluded: chain 1C residue 23 MET Chi-restraints excluded: chain 1C residue 26 ILE Chi-restraints excluded: chain 1C residue 53 ILE Chi-restraints excluded: chain 1D residue 26 ILE Chi-restraints excluded: chain 1D residue 31 ILE Chi-restraints excluded: chain 1D residue 47 LEU Chi-restraints excluded: chain 1D residue 51 VAL Chi-restraints excluded: chain 1E residue 21 VAL Chi-restraints excluded: chain 1E residue 23 MET Chi-restraints excluded: chain 1E residue 26 ILE Chi-restraints excluded: chain 1E residue 31 ILE Chi-restraints excluded: chain 1E residue 41 LYS Chi-restraints excluded: chain 1F residue 26 ILE Chi-restraints excluded: chain 1G residue 25 ILE Chi-restraints excluded: chain 1G residue 26 ILE Chi-restraints excluded: chain 1G residue 47 LEU Chi-restraints excluded: chain 1G residue 51 VAL Chi-restraints excluded: chain 1G residue 52 VAL Chi-restraints excluded: chain 1H residue 23 MET Chi-restraints excluded: chain 1H residue 26 ILE Chi-restraints excluded: chain 1H residue 46 LEU Chi-restraints excluded: chain 1H residue 47 LEU Chi-restraints excluded: chain 1I residue 23 MET Chi-restraints excluded: chain 1I residue 26 ILE Chi-restraints excluded: chain 1I residue 31 ILE Chi-restraints excluded: chain 1J residue 21 VAL Chi-restraints excluded: chain 1J residue 23 MET Chi-restraints excluded: chain 1J residue 26 ILE Chi-restraints excluded: chain 1J residue 46 LEU Chi-restraints excluded: chain 1J residue 47 LEU Chi-restraints excluded: chain 1K residue 23 MET Chi-restraints excluded: chain 1L residue 21 VAL Chi-restraints excluded: chain 1L residue 23 MET Chi-restraints excluded: chain 1L residue 26 ILE Chi-restraints excluded: chain 1L residue 41 LYS Chi-restraints excluded: chain 1L residue 49 LEU Chi-restraints excluded: chain 1L residue 53 ILE Chi-restraints excluded: chain 1M residue 11 VAL Chi-restraints excluded: chain 1N residue 23 MET Chi-restraints excluded: chain 1P residue 52 VAL Chi-restraints excluded: chain 2A residue 11 VAL Chi-restraints excluded: chain 2A residue 51 VAL Chi-restraints excluded: chain 2B residue 23 MET Chi-restraints excluded: chain 2B residue 24 CYS Chi-restraints excluded: chain 2B residue 26 ILE Chi-restraints excluded: chain 2B residue 57 THR Chi-restraints excluded: chain 2C residue 26 ILE Chi-restraints excluded: chain 2D residue 26 ILE Chi-restraints excluded: chain 2D residue 52 VAL Chi-restraints excluded: chain 2D residue 53 ILE Chi-restraints excluded: chain 2F residue 47 LEU Chi-restraints excluded: chain 2F residue 51 VAL Chi-restraints excluded: chain 2G residue 26 ILE Chi-restraints excluded: chain 2H residue 31 ILE Chi-restraints excluded: chain 2I residue 4 LEU Chi-restraints excluded: chain 2I residue 21 VAL Chi-restraints excluded: chain 2I residue 26 ILE Chi-restraints excluded: chain 2I residue 47 LEU Chi-restraints excluded: chain 2I residue 51 VAL Chi-restraints excluded: chain 2I residue 52 VAL Chi-restraints excluded: chain 2J residue 4 LEU Chi-restraints excluded: chain 2J residue 47 LEU Chi-restraints excluded: chain 2K residue 26 ILE Chi-restraints excluded: chain 2K residue 53 ILE Chi-restraints excluded: chain 2L residue 23 MET Chi-restraints excluded: chain 2M residue 31 ILE Chi-restraints excluded: chain 2M residue 47 LEU Chi-restraints excluded: chain 2M residue 50 VAL Chi-restraints excluded: chain 2N residue 31 ILE Chi-restraints excluded: chain 2O residue 23 MET Chi-restraints excluded: chain 2O residue 60 LEU Chi-restraints excluded: chain 3A residue 60 LEU Chi-restraints excluded: chain 3B residue 22 MET Chi-restraints excluded: chain 3B residue 23 MET Chi-restraints excluded: chain 3B residue 25 ILE Chi-restraints excluded: chain 3B residue 26 ILE Chi-restraints excluded: chain 3C residue 12 LYS Chi-restraints excluded: chain 3C residue 31 ILE Chi-restraints excluded: chain 3C residue 47 LEU Chi-restraints excluded: chain 3C residue 51 VAL Chi-restraints excluded: chain 3C residue 57 THR Chi-restraints excluded: chain 3D residue 10 ASP Chi-restraints excluded: chain 3D residue 50 VAL Chi-restraints excluded: chain 3E residue 50 VAL Chi-restraints excluded: chain 3F residue 11 VAL Chi-restraints excluded: chain 3F residue 26 ILE Chi-restraints excluded: chain 3F residue 43 LEU Chi-restraints excluded: chain 3F residue 50 VAL Chi-restraints excluded: chain 3G residue 23 MET Chi-restraints excluded: chain 3G residue 31 ILE Chi-restraints excluded: chain 3G residue 51 VAL Chi-restraints excluded: chain 3G residue 58 VAL Chi-restraints excluded: chain 3H residue 21 VAL Chi-restraints excluded: chain 3H residue 23 MET Chi-restraints excluded: chain 3H residue 49 LEU Chi-restraints excluded: chain 3I residue 11 VAL Chi-restraints excluded: chain 3I residue 23 MET Chi-restraints excluded: chain 3I residue 41 LYS Chi-restraints excluded: chain 3I residue 51 VAL Chi-restraints excluded: chain 3I residue 58 VAL Chi-restraints excluded: chain 3J residue 4 LEU Chi-restraints excluded: chain 3J residue 23 MET Chi-restraints excluded: chain 3J residue 50 VAL Chi-restraints excluded: chain 3K residue 47 LEU Chi-restraints excluded: chain 3K residue 51 VAL Chi-restraints excluded: chain 3K residue 53 ILE Chi-restraints excluded: chain 3L residue 11 VAL Chi-restraints excluded: chain 3L residue 21 VAL Chi-restraints excluded: chain 3L residue 23 MET Chi-restraints excluded: chain 3M residue 21 VAL Chi-restraints excluded: chain 3M residue 58 VAL Chi-restraints excluded: chain 3N residue 10 ASP Chi-restraints excluded: chain 3N residue 21 VAL Chi-restraints excluded: chain 3N residue 47 LEU Chi-restraints excluded: chain 3O residue 50 VAL Chi-restraints excluded: chain 3P residue 53 ILE Chi-restraints excluded: chain 4A residue 4 LEU Chi-restraints excluded: chain 4A residue 11 VAL Chi-restraints excluded: chain 4A residue 50 VAL Chi-restraints excluded: chain 4B residue 31 ILE Chi-restraints excluded: chain 4C residue 26 ILE Chi-restraints excluded: chain 4D residue 31 ILE Chi-restraints excluded: chain 4D residue 41 LYS Chi-restraints excluded: chain 4D residue 47 LEU Chi-restraints excluded: chain 4E residue 23 MET Chi-restraints excluded: chain 4E residue 50 VAL Chi-restraints excluded: chain 4F residue 3 LEU Chi-restraints excluded: chain 4F residue 4 LEU Chi-restraints excluded: chain 4F residue 11 VAL Chi-restraints excluded: chain 4F residue 19 SER Chi-restraints excluded: chain 4F residue 26 ILE Chi-restraints excluded: chain 4H residue 21 VAL Chi-restraints excluded: chain 4I residue 4 LEU Chi-restraints excluded: chain 4I residue 21 VAL Chi-restraints excluded: chain 4I residue 23 MET Chi-restraints excluded: chain 4I residue 26 ILE Chi-restraints excluded: chain 4I residue 43 LEU Chi-restraints excluded: chain 4K residue 21 VAL Chi-restraints excluded: chain 4K residue 26 ILE Chi-restraints excluded: chain 4L residue 4 LEU Chi-restraints excluded: chain 4L residue 23 MET Chi-restraints excluded: chain 4L residue 49 LEU Chi-restraints excluded: chain 4N residue 57 THR Chi-restraints excluded: chain 4O residue 31 ILE Chi-restraints excluded: chain 5A residue 22 MET Chi-restraints excluded: chain 5B residue 11 VAL Chi-restraints excluded: chain 5B residue 25 ILE Chi-restraints excluded: chain 5B residue 26 ILE Chi-restraints excluded: chain 5B residue 47 LEU Chi-restraints excluded: chain 5B residue 53 ILE Chi-restraints excluded: chain 5C residue 11 VAL Chi-restraints excluded: chain 5C residue 23 MET Chi-restraints excluded: chain 5C residue 31 ILE Chi-restraints excluded: chain 5C residue 57 THR Chi-restraints excluded: chain 5C residue 61 THR Chi-restraints excluded: chain 5D residue 4 LEU Chi-restraints excluded: chain 5E residue 10 ASP Chi-restraints excluded: chain 5E residue 11 VAL Chi-restraints excluded: chain 5E residue 19 SER Chi-restraints excluded: chain 5E residue 21 VAL Chi-restraints excluded: chain 5E residue 26 ILE Chi-restraints excluded: chain 5E residue 31 ILE Chi-restraints excluded: chain 5E residue 50 VAL Chi-restraints excluded: chain 5F residue 11 VAL Chi-restraints excluded: chain 5F residue 21 VAL Chi-restraints excluded: chain 5F residue 26 ILE Chi-restraints excluded: chain 5F residue 31 ILE Chi-restraints excluded: chain 5F residue 53 ILE Chi-restraints excluded: chain 5G residue 23 MET Chi-restraints excluded: chain 5G residue 31 ILE Chi-restraints excluded: chain 5G residue 57 THR Chi-restraints excluded: chain 5H residue 26 ILE Chi-restraints excluded: chain 5H residue 46 LEU Chi-restraints excluded: chain 5I residue 31 ILE Chi-restraints excluded: chain 5I residue 53 ILE Chi-restraints excluded: chain 5I residue 61 THR Chi-restraints excluded: chain 5J residue 23 MET Chi-restraints excluded: chain 5L residue 21 VAL Chi-restraints excluded: chain 5M residue 11 VAL Chi-restraints excluded: chain 5M residue 50 VAL Chi-restraints excluded: chain 5M residue 61 THR Chi-restraints excluded: chain 5N residue 23 MET Chi-restraints excluded: chain 5N residue 47 LEU Chi-restraints excluded: chain 5O residue 21 VAL Chi-restraints excluded: chain 5O residue 50 VAL Chi-restraints excluded: chain 5P residue 46 LEU Chi-restraints excluded: chain 5P residue 52 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 283 optimal weight: 50.0000 chunk 455 optimal weight: 7.9990 chunk 278 optimal weight: 20.0000 chunk 216 optimal weight: 40.0000 chunk 316 optimal weight: 4.9990 chunk 478 optimal weight: 8.9990 chunk 440 optimal weight: 2.9990 chunk 380 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 294 optimal weight: 20.0000 chunk 233 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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: 0.7826 moved from start: 0.7331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 41600 Z= 0.319 Angle : 0.701 13.711 55410 Z= 0.336 Chirality : 0.040 0.246 7190 Planarity : 0.002 0.039 6070 Dihedral : 14.760 79.367 8495 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 5.36 % Allowed : 30.29 % Favored : 64.35 % 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: -1.17 (0.12), residues: 4880 helix: -0.46 (0.08), residues: 3280 sheet: None (None), residues: 0 loop : -1.15 (0.17), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.022 0.001 PHE2D 15 TYR 0.028 0.002 TYR2I 37 ARG 0.008 0.000 ARG2O 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9760 Ramachandran restraints generated. 4880 Oldfield, 0 Emsley, 4880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1850 residues out of total 4160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 1627 time to evaluate : 4.174 Fit side-chains REVERT: 1B 12 LYS cc_start: 0.8058 (tppt) cc_final: 0.7812 (tttp) REVERT: 1D 40 THR cc_start: 0.8617 (m) cc_final: 0.8289 (p) REVERT: 1H 46 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8544 (mp) REVERT: 1I 40 THR cc_start: 0.8805 (m) cc_final: 0.8437 (p) REVERT: 1J 40 THR cc_start: 0.8606 (m) cc_final: 0.8171 (p) REVERT: 1J 61 THR cc_start: 0.8147 (p) cc_final: 0.7584 (m) REVERT: 2A 37 TYR cc_start: 0.8837 (t80) cc_final: 0.8432 (t80) REVERT: 2H 40 THR cc_start: 0.8710 (m) cc_final: 0.8496 (p) REVERT: 2I 40 THR cc_start: 0.8839 (m) cc_final: 0.8627 (p) REVERT: 2L 29 GLU cc_start: 0.7521 (tp30) cc_final: 0.7152 (tp30) REVERT: 2P 39 ARG cc_start: 0.5848 (mmt180) cc_final: 0.5391 (mmt180) REVERT: 3C 40 THR cc_start: 0.8854 (m) cc_final: 0.8597 (p) REVERT: 3F 40 THR cc_start: 0.8556 (m) cc_final: 0.8243 (p) REVERT: 3I 40 THR cc_start: 0.8976 (m) cc_final: 0.8658 (p) REVERT: 3L 40 THR cc_start: 0.8567 (m) cc_final: 0.8303 (p) REVERT: 4M 10 ASP cc_start: 0.7394 (OUTLIER) cc_final: 0.7170 (p0) REVERT: 5B 12 LYS cc_start: 0.8005 (tttt) cc_final: 0.7803 (tttp) REVERT: 5B 29 GLU cc_start: 0.7785 (tp30) cc_final: 0.7262 (tp30) REVERT: 5E 40 THR cc_start: 0.8862 (m) cc_final: 0.8536 (p) REVERT: 5H 40 THR cc_start: 0.8792 (m) cc_final: 0.8463 (p) REVERT: 5I 12 LYS cc_start: 0.8235 (ttmt) cc_final: 0.7989 (tttp) REVERT: 5I 40 THR cc_start: 0.8769 (m) cc_final: 0.8498 (p) REVERT: 5J 40 THR cc_start: 0.8654 (m) cc_final: 0.8405 (p) REVERT: 5O 40 THR cc_start: 0.8828 (m) cc_final: 0.8387 (p) REVERT: 5P 47 LEU cc_start: 0.8740 (tp) cc_final: 0.8505 (tp) outliers start: 223 outliers final: 200 residues processed: 1711 average time/residue: 0.5060 time to fit residues: 1413.4144 Evaluate side-chains 1805 residues out of total 4160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 1603 time to evaluate : 5.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1A residue 11 VAL Chi-restraints excluded: chain 1A residue 51 VAL Chi-restraints excluded: chain 1A residue 57 THR Chi-restraints excluded: chain 1B residue 11 VAL Chi-restraints excluded: chain 1B residue 23 MET Chi-restraints excluded: chain 1B residue 25 ILE Chi-restraints excluded: chain 1B residue 26 ILE Chi-restraints excluded: chain 1B residue 29 GLU Chi-restraints excluded: chain 1C residue 21 VAL Chi-restraints excluded: chain 1C residue 23 MET Chi-restraints excluded: chain 1C residue 26 ILE Chi-restraints excluded: chain 1C residue 43 LEU Chi-restraints excluded: chain 1C residue 53 ILE Chi-restraints excluded: chain 1D residue 26 ILE Chi-restraints excluded: chain 1D residue 31 ILE Chi-restraints excluded: chain 1D residue 47 LEU Chi-restraints excluded: chain 1D residue 51 VAL Chi-restraints excluded: chain 1E residue 21 VAL Chi-restraints excluded: chain 1E residue 23 MET Chi-restraints excluded: chain 1E residue 26 ILE Chi-restraints excluded: chain 1E residue 31 ILE Chi-restraints excluded: chain 1F residue 26 ILE Chi-restraints excluded: chain 1F residue 47 LEU Chi-restraints excluded: chain 1G residue 26 ILE Chi-restraints excluded: chain 1G residue 47 LEU Chi-restraints excluded: chain 1G residue 51 VAL Chi-restraints excluded: chain 1H residue 23 MET Chi-restraints excluded: chain 1H residue 26 ILE Chi-restraints excluded: chain 1H residue 46 LEU Chi-restraints excluded: chain 1H residue 47 LEU Chi-restraints excluded: chain 1I residue 23 MET Chi-restraints excluded: chain 1I residue 26 ILE Chi-restraints excluded: chain 1I residue 31 ILE Chi-restraints excluded: chain 1J residue 21 VAL Chi-restraints excluded: chain 1J residue 26 ILE Chi-restraints excluded: chain 1J residue 46 LEU Chi-restraints excluded: chain 1J residue 47 LEU Chi-restraints excluded: chain 1K residue 23 MET Chi-restraints excluded: chain 1L residue 21 VAL Chi-restraints excluded: chain 1L residue 26 ILE Chi-restraints excluded: chain 1L residue 41 LYS Chi-restraints excluded: chain 1L residue 49 LEU Chi-restraints excluded: chain 1L residue 53 ILE Chi-restraints excluded: chain 1M residue 11 VAL Chi-restraints excluded: chain 1N residue 11 VAL Chi-restraints excluded: chain 1N residue 23 MET Chi-restraints excluded: chain 1O residue 23 MET Chi-restraints excluded: chain 1O residue 52 VAL Chi-restraints excluded: chain 1P residue 52 VAL Chi-restraints excluded: chain 2A residue 11 VAL Chi-restraints excluded: chain 2A residue 51 VAL Chi-restraints excluded: chain 2B residue 23 MET Chi-restraints excluded: chain 2B residue 24 CYS Chi-restraints excluded: chain 2B residue 26 ILE Chi-restraints excluded: chain 2B residue 57 THR Chi-restraints excluded: chain 2C residue 11 VAL Chi-restraints excluded: chain 2C residue 26 ILE Chi-restraints excluded: chain 2D residue 26 ILE Chi-restraints excluded: chain 2D residue 47 LEU Chi-restraints excluded: chain 2D residue 52 VAL Chi-restraints excluded: chain 2D residue 53 ILE Chi-restraints excluded: chain 2F residue 47 LEU Chi-restraints excluded: chain 2F residue 51 VAL Chi-restraints excluded: chain 2G residue 26 ILE Chi-restraints excluded: chain 2H residue 31 ILE Chi-restraints excluded: chain 2I residue 4 LEU Chi-restraints excluded: chain 2I residue 21 VAL Chi-restraints excluded: chain 2I residue 26 ILE Chi-restraints excluded: chain 2I residue 47 LEU Chi-restraints excluded: chain 2I residue 51 VAL Chi-restraints excluded: chain 2I residue 52 VAL Chi-restraints excluded: chain 2I residue 53 ILE Chi-restraints excluded: chain 2J residue 4 LEU Chi-restraints excluded: chain 2J residue 47 LEU Chi-restraints excluded: chain 2J residue 52 VAL Chi-restraints excluded: chain 2K residue 26 ILE Chi-restraints excluded: chain 2K residue 51 VAL Chi-restraints excluded: chain 2K residue 53 ILE Chi-restraints excluded: chain 2L residue 23 MET Chi-restraints excluded: chain 2M residue 31 ILE Chi-restraints excluded: chain 2M residue 47 LEU Chi-restraints excluded: chain 2M residue 50 VAL Chi-restraints excluded: chain 2N residue 31 ILE Chi-restraints excluded: chain 2O residue 23 MET Chi-restraints excluded: chain 2O residue 60 LEU Chi-restraints excluded: chain 3A residue 4 LEU Chi-restraints excluded: chain 3B residue 22 MET Chi-restraints excluded: chain 3B residue 23 MET Chi-restraints excluded: chain 3B residue 25 ILE Chi-restraints excluded: chain 3B residue 26 ILE Chi-restraints excluded: chain 3C residue 12 LYS Chi-restraints excluded: chain 3C residue 51 VAL Chi-restraints excluded: chain 3C residue 57 THR Chi-restraints excluded: chain 3D residue 10 ASP Chi-restraints excluded: chain 3D residue 50 VAL Chi-restraints excluded: chain 3E residue 50 VAL Chi-restraints excluded: chain 3F residue 11 VAL Chi-restraints excluded: chain 3F residue 26 ILE Chi-restraints excluded: chain 3F residue 43 LEU Chi-restraints excluded: chain 3F residue 50 VAL Chi-restraints excluded: chain 3F residue 51 VAL Chi-restraints excluded: chain 3G residue 23 MET Chi-restraints excluded: chain 3G residue 31 ILE Chi-restraints excluded: chain 3G residue 51 VAL Chi-restraints excluded: chain 3G residue 57 THR Chi-restraints excluded: chain 3G residue 58 VAL Chi-restraints excluded: chain 3H residue 21 VAL Chi-restraints excluded: chain 3H residue 23 MET Chi-restraints excluded: chain 3H residue 49 LEU Chi-restraints excluded: chain 3I residue 11 VAL Chi-restraints excluded: chain 3I residue 41 LYS Chi-restraints excluded: chain 3I residue 51 VAL Chi-restraints excluded: chain 3I residue 58 VAL Chi-restraints excluded: chain 3J residue 4 LEU Chi-restraints excluded: chain 3J residue 11 VAL Chi-restraints excluded: chain 3J residue 23 MET Chi-restraints excluded: chain 3J residue 50 VAL Chi-restraints excluded: chain 3K residue 51 VAL Chi-restraints excluded: chain 3L residue 11 VAL Chi-restraints excluded: chain 3L residue 21 VAL Chi-restraints excluded: chain 3L residue 23 MET Chi-restraints excluded: chain 3M residue 21 VAL Chi-restraints excluded: chain 3M residue 58 VAL Chi-restraints excluded: chain 3N residue 10 ASP Chi-restraints excluded: chain 3N residue 21 VAL Chi-restraints excluded: chain 3N residue 47 LEU Chi-restraints excluded: chain 3P residue 53 ILE Chi-restraints excluded: chain 4A residue 11 VAL Chi-restraints excluded: chain 4A residue 50 VAL Chi-restraints excluded: chain 4B residue 31 ILE Chi-restraints excluded: chain 4B residue 57 THR Chi-restraints excluded: chain 4C residue 26 ILE Chi-restraints excluded: chain 4D residue 31 ILE Chi-restraints excluded: chain 4D residue 41 LYS Chi-restraints excluded: chain 4D residue 47 LEU Chi-restraints excluded: chain 4E residue 23 MET Chi-restraints excluded: chain 4E residue 50 VAL Chi-restraints excluded: chain 4F residue 3 LEU Chi-restraints excluded: chain 4F residue 4 LEU Chi-restraints excluded: chain 4F residue 11 VAL Chi-restraints excluded: chain 4F residue 19 SER Chi-restraints excluded: chain 4F residue 26 ILE Chi-restraints excluded: chain 4H residue 21 VAL Chi-restraints excluded: chain 4H residue 57 THR Chi-restraints excluded: chain 4I residue 4 LEU Chi-restraints excluded: chain 4I residue 21 VAL Chi-restraints excluded: chain 4I residue 23 MET Chi-restraints excluded: chain 4I residue 26 ILE Chi-restraints excluded: chain 4I residue 43 LEU Chi-restraints excluded: chain 4I residue 61 THR Chi-restraints excluded: chain 4J residue 51 VAL Chi-restraints excluded: chain 4K residue 21 VAL Chi-restraints excluded: chain 4K residue 26 ILE Chi-restraints excluded: chain 4K residue 57 THR Chi-restraints excluded: chain 4L residue 49 LEU Chi-restraints excluded: chain 4M residue 10 ASP Chi-restraints excluded: chain 4N residue 23 MET Chi-restraints excluded: chain 4N residue 57 THR Chi-restraints excluded: chain 4O residue 31 ILE Chi-restraints excluded: chain 5A residue 22 MET Chi-restraints excluded: chain 5B residue 11 VAL Chi-restraints excluded: chain 5B residue 26 ILE Chi-restraints excluded: chain 5B residue 47 LEU Chi-restraints excluded: chain 5B residue 53 ILE Chi-restraints excluded: chain 5C residue 11 VAL Chi-restraints excluded: chain 5C residue 23 MET Chi-restraints excluded: chain 5C residue 31 ILE Chi-restraints excluded: chain 5C residue 57 THR Chi-restraints excluded: chain 5C residue 61 THR Chi-restraints excluded: chain 5D residue 4 LEU Chi-restraints excluded: chain 5D residue 23 MET Chi-restraints excluded: chain 5E residue 10 ASP Chi-restraints excluded: chain 5E residue 11 VAL Chi-restraints excluded: chain 5E residue 19 SER Chi-restraints excluded: chain 5E residue 21 VAL Chi-restraints excluded: chain 5E residue 26 ILE Chi-restraints excluded: chain 5E residue 31 ILE Chi-restraints excluded: chain 5E residue 50 VAL Chi-restraints excluded: chain 5F residue 11 VAL Chi-restraints excluded: chain 5F residue 26 ILE Chi-restraints excluded: chain 5F residue 31 ILE Chi-restraints excluded: chain 5F residue 47 LEU Chi-restraints excluded: chain 5F residue 53 ILE Chi-restraints excluded: chain 5G residue 23 MET Chi-restraints excluded: chain 5G residue 31 ILE Chi-restraints excluded: chain 5G residue 57 THR Chi-restraints excluded: chain 5H residue 11 VAL Chi-restraints excluded: chain 5H residue 26 ILE Chi-restraints excluded: chain 5H residue 46 LEU Chi-restraints excluded: chain 5I residue 31 ILE Chi-restraints excluded: chain 5I residue 53 ILE Chi-restraints excluded: chain 5I residue 61 THR Chi-restraints excluded: chain 5J residue 23 MET Chi-restraints excluded: chain 5K residue 46 LEU Chi-restraints excluded: chain 5L residue 21 VAL Chi-restraints excluded: chain 5M residue 11 VAL Chi-restraints excluded: chain 5M residue 50 VAL Chi-restraints excluded: chain 5M residue 61 THR Chi-restraints excluded: chain 5N residue 23 MET Chi-restraints excluded: chain 5N residue 47 LEU Chi-restraints excluded: chain 5O residue 21 VAL Chi-restraints excluded: chain 5P residue 52 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 302 optimal weight: 4.9990 chunk 405 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 351 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 105 optimal weight: 9.9990 chunk 381 optimal weight: 3.9990 chunk 159 optimal weight: 6.9990 chunk 391 optimal weight: 0.0980 chunk 48 optimal weight: 30.0000 chunk 70 optimal weight: 10.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 = 0.3688 r_free = 0.3688 target = 0.126374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.101705 restraints weight = 58241.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.105961 restraints weight = 29420.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.108824 restraints weight = 18134.290| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.7652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 41600 Z= 0.184 Angle : 0.642 12.754 55410 Z= 0.307 Chirality : 0.038 0.227 7190 Planarity : 0.002 0.029 6070 Dihedral : 13.631 76.674 8495 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.89 % Allowed : 32.24 % Favored : 63.87 % 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: -0.68 (0.12), residues: 4880 helix: -0.06 (0.09), residues: 3280 sheet: None (None), residues: 0 loop : -1.04 (0.17), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.017 0.001 PHE2B 15 TYR 0.031 0.002 TYR1J 37 ARG 0.007 0.000 ARG2O 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18500.21 seconds wall clock time: 325 minutes 36.14 seconds (19536.14 seconds total)