Starting phenix.real_space_refine on Tue Mar 3 11:59:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ngk_49387/03_2026/9ngk_49387.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ngk_49387/03_2026/9ngk_49387.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ngk_49387/03_2026/9ngk_49387.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ngk_49387/03_2026/9ngk_49387.map" model { file = "/net/cci-nas-00/data/ceres_data/9ngk_49387/03_2026/9ngk_49387.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ngk_49387/03_2026/9ngk_49387.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 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: 3 Type Number sf(0) Gaussians C 2624 2.51 5 N 576 2.21 5 O 512 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3712 Number of models: 1 Model: "" Number of chains: 128 Chain: "0" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "7" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "8" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "8" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "9" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "9" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AA" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "AA" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AB" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "AB" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AC" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "AC" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AD" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "AD" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AE" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "AE" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AF" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "AF" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AG" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "AG" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AH" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "AH" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AI" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "AI" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AJ" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "AJ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AK" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "AK" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AL" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "AL" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AM" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "AM" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AN" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "AN" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AO" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "AO" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AP" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "AP" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AQ" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "AQ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AR" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "AR" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AS" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "AS" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AT" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "AT" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AU" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "AU" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AV" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "AV" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AW" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "AW" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AX" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "AX" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AY" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "AY" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AZ" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "AZ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "Aa" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "Aa" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "Ab" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "Ab" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "Ac" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "Ac" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "Ad" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "Ad" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "Ae" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "Ae" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "Af" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "Af" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "Ag" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "Ag" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "j" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "k" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "k" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "l" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "m" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "m" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "o" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "o" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "p" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "p" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "q" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "r" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "s" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "s" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "t" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "t" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "u" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "u" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "v" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "v" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "w" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "w" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "x" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "x" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "y" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "z" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.09, per 1000 atoms: 0.29 Number of scatterers: 3712 At special positions: 0 Unit cell: (74.008, 74.849, 54.665, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 512 8.00 N 576 7.00 C 2624 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 - 3.00 Amino acid : True - 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=64, symmetry=0 Number of additional bonds: simple=64, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.44 Conformation dependent library (CDL) restraints added in 80.0 milliseconds 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 768 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 50.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing sheet with id=AA1, first strand: chain '0' and resid 2 through 5 removed outlier: 6.800A pdb=" N ILE 6 2 " --> pdb=" O ILE 8 3 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N TYR 8 5 " --> pdb=" O ILE 6 2 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE 6 4 " --> pdb=" O TYR 8 5 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE 2 2 " --> pdb=" O ILE 4 3 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N TYR 4 5 " --> pdb=" O ILE 2 2 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE 2 4 " --> pdb=" O TYR 4 5 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE x 2 " --> pdb=" O ILE z 3 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N TYR z 5 " --> pdb=" O ILE x 2 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE x 4 " --> pdb=" O TYR z 5 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE v 2 " --> pdb=" O ILE x 3 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N TYR x 5 " --> pdb=" O ILE v 2 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE v 4 " --> pdb=" O TYR x 5 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'AA' and resid 2 through 5 removed outlier: 6.576A pdb=" N ILE 1 3 " --> pdb=" O ILE y 4 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'AB' and resid 2 through 5 removed outlier: 6.611A pdb=" N ILEAB 2 " --> pdb=" O ILEAD 3 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N TYRAD 5 " --> pdb=" O ILEAB 2 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILEAB 4 " --> pdb=" O TYRAD 5 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILEAD 2 " --> pdb=" O ILEAF 3 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N TYRAF 5 " --> pdb=" O ILEAD 2 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILEAD 4 " --> pdb=" O TYRAF 5 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILEAF 2 " --> pdb=" O ILEAH 3 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N TYRAH 5 " --> pdb=" O ILEAF 2 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILEAF 4 " --> pdb=" O TYRAH 5 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILEAH 2 " --> pdb=" O ILEAJ 3 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N TYRAJ 5 " --> pdb=" O ILEAH 2 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILEAH 4 " --> pdb=" O TYRAJ 5 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILEAL 2 " --> pdb=" O ILEAN 3 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N TYRAN 5 " --> pdb=" O ILEAL 2 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILEAL 4 " --> pdb=" O TYRAN 5 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILEAN 2 " --> pdb=" O ILEAP 3 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N TYRAP 5 " --> pdb=" O ILEAN 2 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILEAN 4 " --> pdb=" O TYRAP 5 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'AC' and resid 2 through 5 Processing sheet with id=AA5, first strand: chain 'AR' and resid 2 through 5 removed outlier: 6.646A pdb=" N ILEAR 2 " --> pdb=" O ILEAT 3 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N TYRAT 5 " --> pdb=" O ILEAR 2 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILEAR 4 " --> pdb=" O TYRAT 5 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILEAT 2 " --> pdb=" O ILEAV 3 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N TYRAV 5 " --> pdb=" O ILEAT 2 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILEAT 4 " --> pdb=" O TYRAV 5 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILEAV 2 " --> pdb=" O ILEAX 3 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N TYRAX 5 " --> pdb=" O ILEAV 2 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILEAV 4 " --> pdb=" O TYRAX 5 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILEAX 2 " --> pdb=" O ILEAZ 3 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N TYRAZ 5 " --> pdb=" O ILEAX 2 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILEAX 4 " --> pdb=" O TYRAZ 5 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILEAZ 2 " --> pdb=" O ILEAb 3 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N TYRAb 5 " --> pdb=" O ILEAZ 2 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILEAZ 4 " --> pdb=" O TYRAb 5 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILEAd 2 " --> pdb=" O ILEAf 3 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N TYRAf 5 " --> pdb=" O ILEAd 2 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILEAd 4 " --> pdb=" O TYRAf 5 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'AS' and resid 2 through 5 Processing sheet with id=AA7, first strand: chain 'f' and resid 2 through 5 removed outlier: 6.638A pdb=" N ILE f 2 " --> pdb=" O ILE h 3 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N TYR h 5 " --> pdb=" O ILE f 2 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE f 4 " --> pdb=" O TYR h 5 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE h 2 " --> pdb=" O ILE j 3 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N TYR j 5 " --> pdb=" O ILE h 2 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE h 4 " --> pdb=" O TYR j 5 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE j 2 " --> pdb=" O ILE l 3 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N TYR l 5 " --> pdb=" O ILE j 2 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE j 4 " --> pdb=" O TYR l 5 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE l 2 " --> pdb=" O ILE n 3 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N TYR n 5 " --> pdb=" O ILE l 2 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE l 4 " --> pdb=" O TYR n 5 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE n 2 " --> pdb=" O ILE p 3 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N TYR p 5 " --> pdb=" O ILE n 2 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE n 4 " --> pdb=" O TYR p 5 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE p 2 " --> pdb=" O ILE r 3 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N TYR r 5 " --> pdb=" O ILE p 2 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE p 4 " --> pdb=" O TYR r 5 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE r 2 " --> pdb=" O ILE t 3 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N TYR t 5 " --> pdb=" O ILE r 2 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE r 4 " --> pdb=" O TYR t 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'g' and resid 2 through 5 removed outlier: 6.546A pdb=" N ILE s 2 " --> pdb=" O ILE u 3 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N TYR u 5 " --> pdb=" O ILE s 2 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE s 4 " --> pdb=" O TYR u 5 " (cutoff:3.500A) 93 hydrogen bonds defined for protein. 279 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: 0.39 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.28: 448 1.28 - 1.35: 385 1.35 - 1.42: 447 1.42 - 1.49: 476 1.49 - 1.55: 1892 Bond restraints: 3648 Sorted by residual: bond pdb=" N TYR m 5 " pdb=" CA TYR m 5 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.19e-02 7.06e+03 5.88e+00 bond pdb=" N TYR 3 5 " pdb=" CA TYR 3 5 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.19e-02 7.06e+03 5.73e+00 bond pdb=" N TYRAY 5 " pdb=" CA TYRAY 5 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.19e-02 7.06e+03 5.52e+00 bond pdb=" N ILE g 2 " pdb=" CA ILE g 2 " ideal model delta sigma weight residual 1.458 1.485 -0.027 1.18e-02 7.18e+03 5.42e+00 bond pdb=" N TYR w 5 " pdb=" CA TYR w 5 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.26e-02 6.30e+03 4.90e+00 ... (remaining 3643 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 3319 1.69 - 3.38: 1177 3.38 - 5.07: 175 5.07 - 6.77: 37 6.77 - 8.46: 28 Bond angle restraints: 4736 Sorted by residual: angle pdb=" CA ILE x 3 " pdb=" C ILE x 3 " pdb=" N ILE x 4 " ideal model delta sigma weight residual 116.40 119.88 -3.48 1.12e+00 7.97e-01 9.66e+00 angle pdb=" CA ILE w 3 " pdb=" CB ILE w 3 " pdb=" CG1 ILE w 3 " ideal model delta sigma weight residual 110.40 115.62 -5.22 1.70e+00 3.46e-01 9.44e+00 angle pdb=" CA ILEAD 3 " pdb=" C ILEAD 3 " pdb=" N ILEAD 4 " ideal model delta sigma weight residual 116.40 119.80 -3.40 1.12e+00 7.97e-01 9.23e+00 angle pdb=" CA TYRAe 5 " pdb=" CB TYRAe 5 " pdb=" CG TYRAe 5 " ideal model delta sigma weight residual 113.90 119.30 -5.40 1.80e+00 3.09e-01 9.00e+00 angle pdb=" CA ILEAT 3 " pdb=" C ILEAT 3 " pdb=" N ILEAT 4 " ideal model delta sigma weight residual 116.40 119.74 -3.34 1.12e+00 7.97e-01 8.89e+00 ... (remaining 4731 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 2243 35.82 - 71.63: 29 71.63 - 107.45: 0 107.45 - 143.27: 0 143.27 - 179.08: 32 Dihedral angle restraints: 2304 sinusoidal: 1152 harmonic: 1152 Sorted by residual: dihedral pdb=" CH3 ACEAY 0 " pdb=" C ACEAY 0 " pdb=" N LYSAY 1 " pdb=" CA LYSAY 1 " ideal model delta sinusoidal sigma weight residual -180.00 -0.92 -179.08 1 5.00e+00 4.00e-02 7.68e+02 dihedral pdb=" CH3 ACE g 0 " pdb=" C ACE g 0 " pdb=" N LYS g 1 " pdb=" CA LYS g 1 " ideal model delta sinusoidal sigma weight residual 180.00 1.13 178.87 1 5.00e+00 4.00e-02 7.68e+02 dihedral pdb=" CH3 ACEAE 0 " pdb=" C ACEAE 0 " pdb=" N LYSAE 1 " pdb=" CA LYSAE 1 " ideal model delta sinusoidal sigma weight residual -180.00 -1.31 -178.69 1 5.00e+00 4.00e-02 7.68e+02 ... (remaining 2301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 262 0.043 - 0.086: 212 0.086 - 0.130: 72 0.130 - 0.173: 20 0.173 - 0.216: 10 Chirality restraints: 576 Sorted by residual: chirality pdb=" CB ILEAS 3 " pdb=" CA ILEAS 3 " pdb=" CG1 ILEAS 3 " pdb=" CG2 ILEAS 3 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB ILEAd 2 " pdb=" CA ILEAd 2 " pdb=" CG1 ILEAd 2 " pdb=" CG2 ILEAd 2 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB ILE w 3 " pdb=" CA ILE w 3 " pdb=" CG1 ILE w 3 " pdb=" CG2 ILE w 3 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 573 not shown) Planarity restraints: 448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYRAR 5 " -0.102 2.00e-02 2.50e+03 5.31e-02 5.63e+01 pdb=" CG TYRAR 5 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TYRAR 5 " 0.041 2.00e-02 2.50e+03 pdb=" CD2 TYRAR 5 " 0.049 2.00e-02 2.50e+03 pdb=" CE1 TYRAR 5 " 0.027 2.00e-02 2.50e+03 pdb=" CE2 TYRAR 5 " 0.020 2.00e-02 2.50e+03 pdb=" CZ TYRAR 5 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYRAR 5 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR f 5 " 0.101 2.00e-02 2.50e+03 5.26e-02 5.53e+01 pdb=" CG TYR f 5 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR f 5 " -0.041 2.00e-02 2.50e+03 pdb=" CD2 TYR f 5 " -0.048 2.00e-02 2.50e+03 pdb=" CE1 TYR f 5 " -0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR f 5 " -0.019 2.00e-02 2.50e+03 pdb=" CZ TYR f 5 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR f 5 " 0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYRAB 5 " -0.097 2.00e-02 2.50e+03 5.01e-02 5.02e+01 pdb=" CG TYRAB 5 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYRAB 5 " 0.039 2.00e-02 2.50e+03 pdb=" CD2 TYRAB 5 " 0.042 2.00e-02 2.50e+03 pdb=" CE1 TYRAB 5 " 0.023 2.00e-02 2.50e+03 pdb=" CE2 TYRAB 5 " 0.021 2.00e-02 2.50e+03 pdb=" CZ TYRAB 5 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYRAB 5 " -0.066 2.00e-02 2.50e+03 ... (remaining 445 not shown) Histogram of nonbonded interaction distances: 2.74 - 3.17: 2349 3.17 - 3.60: 3056 3.60 - 4.04: 4799 4.04 - 4.47: 5368 4.47 - 4.90: 9946 Nonbonded interactions: 25518 Sorted by model distance: nonbonded pdb=" O ACEAD 0 " pdb=" CA LYSAD 1 " model vdw 2.741 2.776 nonbonded pdb=" N LYSAH 1 " pdb=" N ILEAH 2 " model vdw 2.743 2.560 nonbonded pdb=" N LYS 2 1 " pdb=" N ILE 2 2 " model vdw 2.744 2.560 nonbonded pdb=" O ACE h 0 " pdb=" CA LYS h 1 " model vdw 2.748 2.776 nonbonded pdb=" N LYS l 1 " pdb=" N ILE l 2 " model vdw 2.755 2.560 ... (remaining 25513 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain 'AA' selection = chain 'AB' selection = chain 'AC' selection = chain 'AD' selection = chain 'AE' selection = chain 'AF' selection = chain 'AG' selection = chain 'AH' selection = chain 'AI' selection = chain 'AJ' selection = chain 'AK' selection = chain 'AL' selection = chain 'AM' selection = chain 'AN' selection = chain 'AO' selection = chain 'AP' selection = chain 'AQ' selection = chain 'AR' selection = chain 'AS' selection = chain 'AT' selection = chain 'AU' selection = chain 'AV' selection = chain 'AW' selection = chain 'AX' selection = chain 'AY' selection = chain 'AZ' selection = chain 'Aa' selection = chain 'Ab' selection = chain 'Ac' selection = chain 'Ad' selection = chain 'Ae' selection = chain 'Af' selection = chain 'Ag' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' selection = chain 'z' } 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: 8.830 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: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.620 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 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 : 0.018 0.102 3712 Z= 1.455 Angle : 1.767 8.456 4736 Z= 1.006 Chirality : 0.066 0.216 576 Planarity : 0.014 0.056 448 Dihedral : 27.614 179.084 1536 Min Nonbonded Distance : 2.741 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.79 (0.38), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 4.43 (0.29), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.102 0.017 TYRAR 5 Details of bonding type rmsd covalent geometry : bond 0.01222 ( 3648) covalent geometry : angle 1.76705 ( 4736) hydrogen bonds : bond 0.15293 ( 93) hydrogen bonds : angle 7.09008 ( 279) Misc. bond : bond 0.10100 ( 64) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.127 Fit side-chains REVERT: 1 1 LYS cc_start: 0.7758 (tttt) cc_final: 0.7477 (tttt) REVERT: AG 1 LYS cc_start: 0.7925 (tttt) cc_final: 0.7704 (tttt) REVERT: AP 6 LYS cc_start: 0.7624 (mttt) cc_final: 0.7330 (mttt) REVERT: AW 1 LYS cc_start: 0.7941 (tttt) cc_final: 0.7668 (tttt) REVERT: t 6 LYS cc_start: 0.7627 (mttt) cc_final: 0.7331 (mttt) REVERT: u 1 LYS cc_start: 0.7195 (tttt) cc_final: 0.6835 (tttt) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.1767 time to fit residues: 3.0542 Evaluate side-chains 15 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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 = 0.2411 r_free = 0.2411 target = 0.045794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2117 r_free = 0.2117 target = 0.033610 restraints weight = 14122.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2159 r_free = 0.2159 target = 0.035241 restraints weight = 8805.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2189 r_free = 0.2189 target = 0.036358 restraints weight = 6651.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2209 r_free = 0.2209 target = 0.037175 restraints weight = 5499.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2225 r_free = 0.2225 target = 0.037794 restraints weight = 4777.163| |-----------------------------------------------------------------------------| r_work (final): 0.2238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.8060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.228 0.856 3712 Z= 9.384 Angle : 9.480 78.408 4736 Z= 4.359 Chirality : 0.736 1.551 576 Planarity : 0.037 0.159 448 Dihedral : 25.963 173.630 512 Min Nonbonded Distance : 1.538 Molprobity Statistics. All-atom Clashscore : 103.23 Ramachandran Plot: Outliers : 14.84 % Allowed : 31.25 % Favored : 53.91 % Rotamer: Outliers : 17.97 % Allowed : 16.93 % Favored : 65.10 % Cbeta Deviations : 59.90 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.88 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -9.20 (0.26), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.01 (0.20), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.186 0.038 TYRAA 5 Details of bonding type rmsd covalent geometry : bond 0.22979 ( 3648) covalent geometry : angle 9.48042 ( 4736) hydrogen bonds : bond 0.35974 ( 93) hydrogen bonds : angle 8.67664 ( 279) Misc. bond : bond 0.03426 ( 64) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 166 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 1 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8419 (mtmm) REVERT: 7 1 LYS cc_start: 0.8607 (tttt) cc_final: 0.8347 (tttt) REVERT: AB 1 LYS cc_start: 0.8271 (mttt) cc_final: 0.7657 (tptt) REVERT: AC 1 LYS cc_start: 0.8754 (tttt) cc_final: 0.8483 (tttm) REVERT: AC 6 LYS cc_start: 0.8637 (mttt) cc_final: 0.8413 (mttt) REVERT: AF 6 LYS cc_start: 0.8993 (mttt) cc_final: 0.8771 (mttp) REVERT: AH 1 LYS cc_start: 0.8793 (mttt) cc_final: 0.8364 (mtmm) REVERT: AR 1 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7266 (tptt) REVERT: AX 1 LYS cc_start: 0.8733 (mttt) cc_final: 0.8479 (mtmm) REVERT: AX 6 LYS cc_start: 0.8891 (mttt) cc_final: 0.8598 (mttp) REVERT: AZ 1 LYS cc_start: 0.9017 (mttt) cc_final: 0.8631 (mtmm) REVERT: Aa 6 LYS cc_start: 0.8772 (mttt) cc_final: 0.8507 (mtmm) REVERT: Ae 1 LYS cc_start: 0.8494 (tttt) cc_final: 0.8277 (ttmm) REVERT: f 1 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7199 (tptt) REVERT: l 1 LYS cc_start: 0.8730 (mttt) cc_final: 0.8525 (mtmm) REVERT: l 4 ILE cc_start: 0.9037 (mt) cc_final: 0.8751 (mm) REVERT: n 1 LYS cc_start: 0.8986 (mttt) cc_final: 0.8568 (mtmm) REVERT: n 6 LYS cc_start: 0.8970 (mttt) cc_final: 0.8748 (mttt) REVERT: o 6 LYS cc_start: 0.8732 (mttt) cc_final: 0.8506 (mtmm) REVERT: u 6 LYS cc_start: 0.8603 (mttt) cc_final: 0.8386 (mttt) REVERT: v 1 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.7892 (mmmt) outliers start: 69 outliers final: 58 residues processed: 206 average time/residue: 0.1436 time to fit residues: 32.7137 Evaluate side-chains 227 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 165 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 3 ILE Chi-restraints excluded: chain 2 residue 1 LYS Chi-restraints excluded: chain 2 residue 2 ILE Chi-restraints excluded: chain 5 residue 2 ILE Chi-restraints excluded: chain 5 residue 5 TYR Chi-restraints excluded: chain 8 residue 2 ILE Chi-restraints excluded: chain 8 residue 3 ILE Chi-restraints excluded: chain 9 residue 4 ILE Chi-restraints excluded: chain 9 residue 5 TYR Chi-restraints excluded: chain AA residue 3 ILE Chi-restraints excluded: chain AB residue 2 ILE Chi-restraints excluded: chain AB residue 4 ILE Chi-restraints excluded: chain AD residue 2 ILE Chi-restraints excluded: chain AD residue 3 ILE Chi-restraints excluded: chain AF residue 2 ILE Chi-restraints excluded: chain AF residue 3 ILE Chi-restraints excluded: chain AH residue 2 ILE Chi-restraints excluded: chain AJ residue 3 ILE Chi-restraints excluded: chain AK residue 2 ILE Chi-restraints excluded: chain AK residue 5 TYR Chi-restraints excluded: chain AN residue 2 ILE Chi-restraints excluded: chain AN residue 3 ILE Chi-restraints excluded: chain AO residue 5 TYR Chi-restraints excluded: chain AQ residue 3 ILE Chi-restraints excluded: chain AR residue 1 LYS Chi-restraints excluded: chain AS residue 1 LYS Chi-restraints excluded: chain AS residue 4 ILE Chi-restraints excluded: chain AT residue 2 ILE Chi-restraints excluded: chain AT residue 3 ILE Chi-restraints excluded: chain AV residue 2 ILE Chi-restraints excluded: chain AV residue 3 ILE Chi-restraints excluded: chain AX residue 2 ILE Chi-restraints excluded: chain Aa residue 2 ILE Chi-restraints excluded: chain Aa residue 5 TYR Chi-restraints excluded: chain Ac residue 5 TYR Chi-restraints excluded: chain Ad residue 3 ILE Chi-restraints excluded: chain Ae residue 5 TYR Chi-restraints excluded: chain Ag residue 3 ILE Chi-restraints excluded: chain f residue 1 LYS Chi-restraints excluded: chain f residue 2 ILE Chi-restraints excluded: chain f residue 4 ILE Chi-restraints excluded: chain g residue 2 ILE Chi-restraints excluded: chain h residue 2 ILE Chi-restraints excluded: chain h residue 3 ILE Chi-restraints excluded: chain j residue 2 ILE Chi-restraints excluded: chain j residue 3 ILE Chi-restraints excluded: chain l residue 2 ILE Chi-restraints excluded: chain o residue 2 ILE Chi-restraints excluded: chain o residue 5 TYR Chi-restraints excluded: chain r residue 2 ILE Chi-restraints excluded: chain r residue 3 ILE Chi-restraints excluded: chain s residue 5 TYR Chi-restraints excluded: chain u residue 3 ILE Chi-restraints excluded: chain v residue 1 LYS Chi-restraints excluded: chain v residue 2 ILE Chi-restraints excluded: chain w residue 1 LYS Chi-restraints excluded: chain w residue 3 ILE Chi-restraints excluded: chain w residue 4 ILE Chi-restraints excluded: chain x residue 2 ILE Chi-restraints excluded: chain x residue 3 ILE Chi-restraints excluded: chain z residue 2 ILE Chi-restraints excluded: chain z residue 3 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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 = 0.2403 r_free = 0.2403 target = 0.045788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2135 r_free = 0.2135 target = 0.035029 restraints weight = 14090.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2178 r_free = 0.2178 target = 0.036596 restraints weight = 8318.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2207 r_free = 0.2207 target = 0.037696 restraints weight = 6067.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2228 r_free = 0.2228 target = 0.038510 restraints weight = 4860.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2245 r_free = 0.2245 target = 0.039154 restraints weight = 4109.348| |-----------------------------------------------------------------------------| r_work (final): 0.2229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.8474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.228 0.873 3712 Z= 9.385 Angle : 9.656 82.281 4736 Z= 4.407 Chirality : 0.739 1.582 576 Planarity : 0.034 0.120 448 Dihedral : 22.204 170.805 512 Min Nonbonded Distance : 1.534 Molprobity Statistics. All-atom Clashscore : 93.57 Ramachandran Plot: Outliers : 10.94 % Allowed : 39.84 % Favored : 49.22 % Rotamer: Outliers : 30.21 % Allowed : 26.04 % Favored : 43.75 % Cbeta Deviations : 60.42 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.75 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -9.87 (0.22), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.52 (0.17), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.177 0.038 TYRAA 5 Details of bonding type rmsd covalent geometry : bond 0.23002 ( 3648) covalent geometry : angle 9.65606 ( 4736) hydrogen bonds : bond 0.37902 ( 93) hydrogen bonds : angle 9.00797 ( 279) Misc. bond : bond 0.03465 ( 64) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 166 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 1 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8165 (ptpp) REVERT: 3 1 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8569 (tmtt) REVERT: 7 1 LYS cc_start: 0.8610 (tttt) cc_final: 0.8338 (tttt) REVERT: AB 1 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.7182 (tptt) REVERT: AC 1 LYS cc_start: 0.8794 (mttt) cc_final: 0.8559 (mtpp) REVERT: AC 6 LYS cc_start: 0.8740 (mttt) cc_final: 0.8464 (mttt) REVERT: AF 6 LYS cc_start: 0.8997 (mttt) cc_final: 0.8768 (mttp) REVERT: AH 1 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8528 (mtmm) REVERT: AP 1 LYS cc_start: 0.8780 (mttt) cc_final: 0.8530 (mtmm) REVERT: AR 1 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7332 (tptt) REVERT: AX 1 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8367 (mtmm) REVERT: AX 6 LYS cc_start: 0.8903 (mttt) cc_final: 0.8612 (mttp) REVERT: AZ 1 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8624 (mtmm) REVERT: Aa 6 LYS cc_start: 0.8776 (mttt) cc_final: 0.8507 (mtmm) REVERT: f 1 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7274 (mmtt) REVERT: n 1 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8679 (mtmm) REVERT: n 6 LYS cc_start: 0.8960 (mttt) cc_final: 0.8745 (mttt) REVERT: o 6 LYS cc_start: 0.8784 (mttt) cc_final: 0.8582 (mtmm) REVERT: v 1 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.7857 (mmmt) REVERT: v 6 LYS cc_start: 0.8948 (mttt) cc_final: 0.8634 (mtmm) outliers start: 116 outliers final: 89 residues processed: 237 average time/residue: 0.1253 time to fit residues: 33.4986 Evaluate side-chains 262 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 163 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 3 ILE Chi-restraints excluded: chain 0 residue 4 ILE Chi-restraints excluded: chain 2 residue 1 LYS Chi-restraints excluded: chain 2 residue 2 ILE Chi-restraints excluded: chain 3 residue 1 LYS Chi-restraints excluded: chain 4 residue 3 ILE Chi-restraints excluded: chain 5 residue 1 LYS Chi-restraints excluded: chain 5 residue 2 ILE Chi-restraints excluded: chain 5 residue 4 ILE Chi-restraints excluded: chain 8 residue 2 ILE Chi-restraints excluded: chain 8 residue 3 ILE Chi-restraints excluded: chain 9 residue 4 ILE Chi-restraints excluded: chain 9 residue 5 TYR Chi-restraints excluded: chain AA residue 3 ILE Chi-restraints excluded: chain AB residue 1 LYS Chi-restraints excluded: chain AB residue 2 ILE Chi-restraints excluded: chain AB residue 4 ILE Chi-restraints excluded: chain AC residue 2 ILE Chi-restraints excluded: chain AD residue 2 ILE Chi-restraints excluded: chain AD residue 3 ILE Chi-restraints excluded: chain AE residue 2 ILE Chi-restraints excluded: chain AE residue 3 ILE Chi-restraints excluded: chain AF residue 1 LYS Chi-restraints excluded: chain AF residue 2 ILE Chi-restraints excluded: chain AF residue 3 ILE Chi-restraints excluded: chain AF residue 4 ILE Chi-restraints excluded: chain AH residue 1 LYS Chi-restraints excluded: chain AJ residue 3 ILE Chi-restraints excluded: chain AK residue 1 LYS Chi-restraints excluded: chain AK residue 2 ILE Chi-restraints excluded: chain AK residue 4 ILE Chi-restraints excluded: chain AK residue 5 TYR Chi-restraints excluded: chain AL residue 2 ILE Chi-restraints excluded: chain AN residue 2 ILE Chi-restraints excluded: chain AN residue 3 ILE Chi-restraints excluded: chain AN residue 5 TYR Chi-restraints excluded: chain AO residue 4 ILE Chi-restraints excluded: chain AO residue 5 TYR Chi-restraints excluded: chain AP residue 2 ILE Chi-restraints excluded: chain AP residue 5 TYR Chi-restraints excluded: chain AQ residue 3 ILE Chi-restraints excluded: chain AR residue 1 LYS Chi-restraints excluded: chain AR residue 2 ILE Chi-restraints excluded: chain AR residue 4 ILE Chi-restraints excluded: chain AS residue 1 LYS Chi-restraints excluded: chain AS residue 2 ILE Chi-restraints excluded: chain AT residue 2 ILE Chi-restraints excluded: chain AT residue 3 ILE Chi-restraints excluded: chain AU residue 2 ILE Chi-restraints excluded: chain AV residue 2 ILE Chi-restraints excluded: chain AV residue 3 ILE Chi-restraints excluded: chain AX residue 1 LYS Chi-restraints excluded: chain AX residue 2 ILE Chi-restraints excluded: chain AZ residue 1 LYS Chi-restraints excluded: chain AZ residue 3 ILE Chi-restraints excluded: chain Aa residue 2 ILE Chi-restraints excluded: chain Aa residue 5 TYR Chi-restraints excluded: chain Ac residue 5 TYR Chi-restraints excluded: chain Ad residue 3 ILE Chi-restraints excluded: chain Ae residue 4 ILE Chi-restraints excluded: chain Ae residue 5 TYR Chi-restraints excluded: chain Af residue 5 TYR Chi-restraints excluded: chain Ag residue 3 ILE Chi-restraints excluded: chain Ag residue 5 TYR Chi-restraints excluded: chain f residue 1 LYS Chi-restraints excluded: chain f residue 2 ILE Chi-restraints excluded: chain f residue 3 ILE Chi-restraints excluded: chain f residue 4 ILE Chi-restraints excluded: chain h residue 1 LYS Chi-restraints excluded: chain h residue 2 ILE Chi-restraints excluded: chain h residue 3 ILE Chi-restraints excluded: chain i residue 2 ILE Chi-restraints excluded: chain j residue 1 LYS Chi-restraints excluded: chain j residue 2 ILE Chi-restraints excluded: chain j residue 3 ILE Chi-restraints excluded: chain k residue 2 ILE Chi-restraints excluded: chain l residue 2 ILE Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain n residue 1 LYS Chi-restraints excluded: chain n residue 2 ILE Chi-restraints excluded: chain o residue 2 ILE Chi-restraints excluded: chain o residue 5 TYR Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain r residue 2 ILE Chi-restraints excluded: chain r residue 3 ILE Chi-restraints excluded: chain s residue 5 TYR Chi-restraints excluded: chain u residue 3 ILE Chi-restraints excluded: chain v residue 1 LYS Chi-restraints excluded: chain v residue 2 ILE Chi-restraints excluded: chain v residue 3 ILE Chi-restraints excluded: chain w residue 1 LYS Chi-restraints excluded: chain w residue 3 ILE Chi-restraints excluded: chain w residue 4 ILE Chi-restraints excluded: chain x residue 2 ILE Chi-restraints excluded: chain x residue 3 ILE Chi-restraints excluded: chain y residue 2 ILE Chi-restraints excluded: chain y residue 3 ILE Chi-restraints excluded: chain z residue 2 ILE Chi-restraints excluded: chain z residue 3 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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 = 0.2394 r_free = 0.2394 target = 0.045292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2119 r_free = 0.2119 target = 0.034302 restraints weight = 14255.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2163 r_free = 0.2163 target = 0.035906 restraints weight = 8369.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2192 r_free = 0.2192 target = 0.037022 restraints weight = 6087.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2213 r_free = 0.2213 target = 0.037836 restraints weight = 4876.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2230 r_free = 0.2230 target = 0.038481 restraints weight = 4129.672| |-----------------------------------------------------------------------------| r_work (final): 0.2215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.8601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.228 0.856 3712 Z= 9.383 Angle : 9.647 84.006 4736 Z= 4.405 Chirality : 0.744 1.678 576 Planarity : 0.034 0.087 448 Dihedral : 21.525 169.739 512 Min Nonbonded Distance : 1.546 Molprobity Statistics. All-atom Clashscore : 100.57 Ramachandran Plot: Outliers : 10.55 % Allowed : 42.97 % Favored : 46.48 % Rotamer: Outliers : 37.76 % Allowed : 24.22 % Favored : 38.02 % Cbeta Deviations : 59.64 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.75 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -10.02 (0.21), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.63 (0.16), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.176 0.038 TYRAA 5 Details of bonding type rmsd covalent geometry : bond 0.23003 ( 3648) covalent geometry : angle 9.64718 ( 4736) hydrogen bonds : bond 0.38383 ( 93) hydrogen bonds : angle 9.00790 ( 279) Misc. bond : bond 0.03496 ( 64) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 165 time to evaluate : 0.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 1 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.7978 (ptpp) REVERT: 7 1 LYS cc_start: 0.8590 (tttt) cc_final: 0.8346 (tttt) REVERT: AB 1 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7269 (mmtt) REVERT: AC 6 LYS cc_start: 0.8719 (mttt) cc_final: 0.8482 (mttt) REVERT: AF 6 LYS cc_start: 0.8994 (mttt) cc_final: 0.8773 (mttp) REVERT: AH 1 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8391 (ptpp) REVERT: AP 1 LYS cc_start: 0.8785 (mttt) cc_final: 0.8539 (mtmm) REVERT: AR 1 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7293 (tptt) REVERT: AT 1 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8394 (mtmm) REVERT: AX 1 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8445 (mtmm) REVERT: AX 6 LYS cc_start: 0.8886 (mttt) cc_final: 0.8543 (mttp) REVERT: AZ 1 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8549 (mtmm) REVERT: f 1 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7238 (mmtt) REVERT: g 1 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8544 (mmtt) REVERT: n 1 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8632 (mtmm) REVERT: n 6 LYS cc_start: 0.8933 (mttt) cc_final: 0.8706 (mttt) REVERT: o 6 LYS cc_start: 0.8754 (mttt) cc_final: 0.8545 (mtmm) REVERT: v 1 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.7845 (mmmt) REVERT: v 6 LYS cc_start: 0.8957 (mttt) cc_final: 0.8680 (mtmm) outliers start: 145 outliers final: 111 residues processed: 253 average time/residue: 0.1124 time to fit residues: 32.1216 Evaluate side-chains 288 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 166 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 2 ILE Chi-restraints excluded: chain 0 residue 3 ILE Chi-restraints excluded: chain 0 residue 4 ILE Chi-restraints excluded: chain 0 residue 5 TYR Chi-restraints excluded: chain 2 residue 1 LYS Chi-restraints excluded: chain 2 residue 2 ILE Chi-restraints excluded: chain 3 residue 1 LYS Chi-restraints excluded: chain 4 residue 1 LYS Chi-restraints excluded: chain 5 residue 1 LYS Chi-restraints excluded: chain 5 residue 2 ILE Chi-restraints excluded: chain 5 residue 4 ILE Chi-restraints excluded: chain 5 residue 5 TYR Chi-restraints excluded: chain 7 residue 4 ILE Chi-restraints excluded: chain 8 residue 2 ILE Chi-restraints excluded: chain 8 residue 3 ILE Chi-restraints excluded: chain 8 residue 5 TYR Chi-restraints excluded: chain 9 residue 4 ILE Chi-restraints excluded: chain 9 residue 5 TYR Chi-restraints excluded: chain AA residue 3 ILE Chi-restraints excluded: chain AA residue 4 ILE Chi-restraints excluded: chain AB residue 1 LYS Chi-restraints excluded: chain AB residue 2 ILE Chi-restraints excluded: chain AB residue 3 ILE Chi-restraints excluded: chain AB residue 4 ILE Chi-restraints excluded: chain AC residue 1 LYS Chi-restraints excluded: chain AC residue 2 ILE Chi-restraints excluded: chain AD residue 2 ILE Chi-restraints excluded: chain AD residue 3 ILE Chi-restraints excluded: chain AE residue 2 ILE Chi-restraints excluded: chain AE residue 3 ILE Chi-restraints excluded: chain AF residue 1 LYS Chi-restraints excluded: chain AF residue 2 ILE Chi-restraints excluded: chain AF residue 3 ILE Chi-restraints excluded: chain AF residue 4 ILE Chi-restraints excluded: chain AH residue 1 LYS Chi-restraints excluded: chain AJ residue 3 ILE Chi-restraints excluded: chain AK residue 1 LYS Chi-restraints excluded: chain AK residue 2 ILE Chi-restraints excluded: chain AK residue 4 ILE Chi-restraints excluded: chain AK residue 5 TYR Chi-restraints excluded: chain AL residue 2 ILE Chi-restraints excluded: chain AN residue 2 ILE Chi-restraints excluded: chain AN residue 3 ILE Chi-restraints excluded: chain AN residue 5 TYR Chi-restraints excluded: chain AO residue 4 ILE Chi-restraints excluded: chain AO residue 5 TYR Chi-restraints excluded: chain AP residue 2 ILE Chi-restraints excluded: chain AP residue 5 TYR Chi-restraints excluded: chain AQ residue 3 ILE Chi-restraints excluded: chain AR residue 1 LYS Chi-restraints excluded: chain AR residue 2 ILE Chi-restraints excluded: chain AR residue 3 ILE Chi-restraints excluded: chain AR residue 4 ILE Chi-restraints excluded: chain AS residue 1 LYS Chi-restraints excluded: chain AS residue 2 ILE Chi-restraints excluded: chain AS residue 3 ILE Chi-restraints excluded: chain AT residue 1 LYS Chi-restraints excluded: chain AT residue 2 ILE Chi-restraints excluded: chain AT residue 3 ILE Chi-restraints excluded: chain AU residue 2 ILE Chi-restraints excluded: chain AV residue 2 ILE Chi-restraints excluded: chain AV residue 3 ILE Chi-restraints excluded: chain AV residue 4 ILE Chi-restraints excluded: chain AW residue 2 ILE Chi-restraints excluded: chain AX residue 1 LYS Chi-restraints excluded: chain AX residue 2 ILE Chi-restraints excluded: chain AY residue 3 ILE Chi-restraints excluded: chain AZ residue 1 LYS Chi-restraints excluded: chain AZ residue 3 ILE Chi-restraints excluded: chain Aa residue 2 ILE Chi-restraints excluded: chain Aa residue 4 ILE Chi-restraints excluded: chain Aa residue 5 TYR Chi-restraints excluded: chain Ac residue 5 TYR Chi-restraints excluded: chain Ac residue 6 LYS Chi-restraints excluded: chain Ad residue 3 ILE Chi-restraints excluded: chain Ae residue 5 TYR Chi-restraints excluded: chain Af residue 2 ILE Chi-restraints excluded: chain Af residue 3 ILE Chi-restraints excluded: chain Af residue 5 TYR Chi-restraints excluded: chain Ag residue 3 ILE Chi-restraints excluded: chain f residue 1 LYS Chi-restraints excluded: chain f residue 2 ILE Chi-restraints excluded: chain f residue 3 ILE Chi-restraints excluded: chain f residue 4 ILE Chi-restraints excluded: chain g residue 1 LYS Chi-restraints excluded: chain g residue 2 ILE Chi-restraints excluded: chain h residue 1 LYS Chi-restraints excluded: chain h residue 2 ILE Chi-restraints excluded: chain h residue 3 ILE Chi-restraints excluded: chain i residue 2 ILE Chi-restraints excluded: chain j residue 1 LYS Chi-restraints excluded: chain j residue 3 ILE Chi-restraints excluded: chain j residue 4 ILE Chi-restraints excluded: chain k residue 2 ILE Chi-restraints excluded: chain l residue 2 ILE Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain n residue 1 LYS Chi-restraints excluded: chain o residue 2 ILE Chi-restraints excluded: chain o residue 4 ILE Chi-restraints excluded: chain o residue 5 TYR Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain q residue 6 LYS Chi-restraints excluded: chain r residue 2 ILE Chi-restraints excluded: chain r residue 3 ILE Chi-restraints excluded: chain s residue 5 TYR Chi-restraints excluded: chain t residue 2 ILE Chi-restraints excluded: chain t residue 6 LYS Chi-restraints excluded: chain u residue 3 ILE Chi-restraints excluded: chain v residue 1 LYS Chi-restraints excluded: chain v residue 2 ILE Chi-restraints excluded: chain v residue 3 ILE Chi-restraints excluded: chain w residue 1 LYS Chi-restraints excluded: chain w residue 2 ILE Chi-restraints excluded: chain w residue 3 ILE Chi-restraints excluded: chain w residue 4 ILE Chi-restraints excluded: chain x residue 2 ILE Chi-restraints excluded: chain x residue 3 ILE Chi-restraints excluded: chain y residue 2 ILE Chi-restraints excluded: chain y residue 3 ILE Chi-restraints excluded: chain z residue 2 ILE Chi-restraints excluded: chain z residue 3 ILE Chi-restraints excluded: chain z residue 4 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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 = 0.2414 r_free = 0.2414 target = 0.046075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2154 r_free = 0.2154 target = 0.035625 restraints weight = 13150.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2194 r_free = 0.2194 target = 0.037181 restraints weight = 7992.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2223 r_free = 0.2223 target = 0.038272 restraints weight = 5868.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2244 r_free = 0.2244 target = 0.039103 restraints weight = 4706.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2259 r_free = 0.2259 target = 0.039715 restraints weight = 3973.072| |-----------------------------------------------------------------------------| r_work (final): 0.2233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.8651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.228 0.858 3712 Z= 9.382 Angle : 9.633 82.063 4736 Z= 4.397 Chirality : 0.745 1.771 576 Planarity : 0.034 0.088 448 Dihedral : 21.611 168.146 512 Min Nonbonded Distance : 1.534 Molprobity Statistics. All-atom Clashscore : 104.11 Ramachandran Plot: Outliers : 10.55 % Allowed : 44.53 % Favored : 44.92 % Rotamer: Outliers : 37.50 % Allowed : 25.52 % Favored : 36.98 % Cbeta Deviations : 60.42 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.75 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -10.08 (0.21), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.68 (0.16), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.175 0.037 TYRAA 5 Details of bonding type rmsd covalent geometry : bond 0.23008 ( 3648) covalent geometry : angle 9.63304 ( 4736) hydrogen bonds : bond 0.38427 ( 93) hydrogen bonds : angle 9.00104 ( 279) Misc. bond : bond 0.03507 ( 64) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 165 time to evaluate : 0.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 1 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8110 (ptpp) REVERT: AB 1 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7292 (mmtt) REVERT: AG 1 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8201 (mttt) REVERT: AH 1 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8415 (ptpp) REVERT: AJ 6 LYS cc_start: 0.9051 (tttt) cc_final: 0.8760 (tttt) REVERT: AP 1 LYS cc_start: 0.8773 (mttt) cc_final: 0.8528 (mtmm) REVERT: AR 1 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7385 (tptp) REVERT: AX 6 LYS cc_start: 0.8886 (mttt) cc_final: 0.8540 (mttp) REVERT: AZ 1 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8560 (mtmm) REVERT: f 1 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7208 (mmtt) REVERT: g 1 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8552 (mmtt) REVERT: j 5 TYR cc_start: 0.8877 (OUTLIER) cc_final: 0.8394 (m-80) REVERT: n 1 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8644 (mtmm) REVERT: n 6 LYS cc_start: 0.8968 (mttt) cc_final: 0.8741 (mttt) REVERT: v 1 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.7860 (mmmt) outliers start: 144 outliers final: 116 residues processed: 251 average time/residue: 0.1167 time to fit residues: 32.8340 Evaluate side-chains 292 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 165 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 2 ILE Chi-restraints excluded: chain 0 residue 3 ILE Chi-restraints excluded: chain 0 residue 4 ILE Chi-restraints excluded: chain 0 residue 5 TYR Chi-restraints excluded: chain 2 residue 1 LYS Chi-restraints excluded: chain 2 residue 2 ILE Chi-restraints excluded: chain 4 residue 1 LYS Chi-restraints excluded: chain 4 residue 3 ILE Chi-restraints excluded: chain 5 residue 1 LYS Chi-restraints excluded: chain 5 residue 2 ILE Chi-restraints excluded: chain 5 residue 4 ILE Chi-restraints excluded: chain 5 residue 5 TYR Chi-restraints excluded: chain 7 residue 4 ILE Chi-restraints excluded: chain 8 residue 2 ILE Chi-restraints excluded: chain 8 residue 3 ILE Chi-restraints excluded: chain 8 residue 5 TYR Chi-restraints excluded: chain 9 residue 4 ILE Chi-restraints excluded: chain 9 residue 5 TYR Chi-restraints excluded: chain AA residue 3 ILE Chi-restraints excluded: chain AA residue 4 ILE Chi-restraints excluded: chain AB residue 1 LYS Chi-restraints excluded: chain AB residue 2 ILE Chi-restraints excluded: chain AB residue 3 ILE Chi-restraints excluded: chain AB residue 4 ILE Chi-restraints excluded: chain AC residue 1 LYS Chi-restraints excluded: chain AC residue 2 ILE Chi-restraints excluded: chain AD residue 2 ILE Chi-restraints excluded: chain AD residue 3 ILE Chi-restraints excluded: chain AE residue 2 ILE Chi-restraints excluded: chain AE residue 3 ILE Chi-restraints excluded: chain AF residue 1 LYS Chi-restraints excluded: chain AF residue 2 ILE Chi-restraints excluded: chain AF residue 3 ILE Chi-restraints excluded: chain AF residue 4 ILE Chi-restraints excluded: chain AG residue 1 LYS Chi-restraints excluded: chain AH residue 1 LYS Chi-restraints excluded: chain AH residue 2 ILE Chi-restraints excluded: chain AJ residue 3 ILE Chi-restraints excluded: chain AK residue 2 ILE Chi-restraints excluded: chain AK residue 4 ILE Chi-restraints excluded: chain AK residue 5 TYR Chi-restraints excluded: chain AL residue 2 ILE Chi-restraints excluded: chain AN residue 2 ILE Chi-restraints excluded: chain AN residue 3 ILE Chi-restraints excluded: chain AN residue 5 TYR Chi-restraints excluded: chain AO residue 4 ILE Chi-restraints excluded: chain AO residue 5 TYR Chi-restraints excluded: chain AP residue 2 ILE Chi-restraints excluded: chain AP residue 5 TYR Chi-restraints excluded: chain AQ residue 3 ILE Chi-restraints excluded: chain AQ residue 6 LYS Chi-restraints excluded: chain AR residue 1 LYS Chi-restraints excluded: chain AR residue 2 ILE Chi-restraints excluded: chain AR residue 3 ILE Chi-restraints excluded: chain AR residue 4 ILE Chi-restraints excluded: chain AS residue 1 LYS Chi-restraints excluded: chain AS residue 2 ILE Chi-restraints excluded: chain AT residue 2 ILE Chi-restraints excluded: chain AT residue 3 ILE Chi-restraints excluded: chain AU residue 2 ILE Chi-restraints excluded: chain AU residue 3 ILE Chi-restraints excluded: chain AV residue 2 ILE Chi-restraints excluded: chain AV residue 3 ILE Chi-restraints excluded: chain AV residue 4 ILE Chi-restraints excluded: chain AW residue 2 ILE Chi-restraints excluded: chain AX residue 2 ILE Chi-restraints excluded: chain AY residue 3 ILE Chi-restraints excluded: chain AZ residue 1 LYS Chi-restraints excluded: chain AZ residue 3 ILE Chi-restraints excluded: chain Aa residue 2 ILE Chi-restraints excluded: chain Aa residue 4 ILE Chi-restraints excluded: chain Aa residue 5 TYR Chi-restraints excluded: chain Ac residue 5 TYR Chi-restraints excluded: chain Ac residue 6 LYS Chi-restraints excluded: chain Ad residue 2 ILE Chi-restraints excluded: chain Ad residue 3 ILE Chi-restraints excluded: chain Ae residue 3 ILE Chi-restraints excluded: chain Ae residue 5 TYR Chi-restraints excluded: chain Af residue 2 ILE Chi-restraints excluded: chain Af residue 3 ILE Chi-restraints excluded: chain Af residue 5 TYR Chi-restraints excluded: chain Ag residue 3 ILE Chi-restraints excluded: chain f residue 1 LYS Chi-restraints excluded: chain f residue 2 ILE Chi-restraints excluded: chain f residue 3 ILE Chi-restraints excluded: chain f residue 4 ILE Chi-restraints excluded: chain g residue 1 LYS Chi-restraints excluded: chain g residue 2 ILE Chi-restraints excluded: chain h residue 1 LYS Chi-restraints excluded: chain h residue 2 ILE Chi-restraints excluded: chain h residue 3 ILE Chi-restraints excluded: chain i residue 2 ILE Chi-restraints excluded: chain j residue 1 LYS Chi-restraints excluded: chain j residue 2 ILE Chi-restraints excluded: chain j residue 3 ILE Chi-restraints excluded: chain j residue 4 ILE Chi-restraints excluded: chain j residue 5 TYR Chi-restraints excluded: chain k residue 2 ILE Chi-restraints excluded: chain l residue 2 ILE Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain n residue 1 LYS Chi-restraints excluded: chain n residue 3 ILE Chi-restraints excluded: chain n residue 4 ILE Chi-restraints excluded: chain o residue 2 ILE Chi-restraints excluded: chain o residue 4 ILE Chi-restraints excluded: chain o residue 5 TYR Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain r residue 2 ILE Chi-restraints excluded: chain r residue 3 ILE Chi-restraints excluded: chain s residue 5 TYR Chi-restraints excluded: chain t residue 2 ILE Chi-restraints excluded: chain t residue 6 LYS Chi-restraints excluded: chain u residue 3 ILE Chi-restraints excluded: chain v residue 1 LYS Chi-restraints excluded: chain v residue 2 ILE Chi-restraints excluded: chain v residue 3 ILE Chi-restraints excluded: chain w residue 1 LYS Chi-restraints excluded: chain w residue 2 ILE Chi-restraints excluded: chain w residue 3 ILE Chi-restraints excluded: chain w residue 4 ILE Chi-restraints excluded: chain x residue 2 ILE Chi-restraints excluded: chain x residue 3 ILE Chi-restraints excluded: chain y residue 2 ILE Chi-restraints excluded: chain y residue 3 ILE Chi-restraints excluded: chain z residue 2 ILE Chi-restraints excluded: chain z residue 3 ILE Chi-restraints excluded: chain z residue 4 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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 = 0.2408 r_free = 0.2408 target = 0.045805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2144 r_free = 0.2144 target = 0.035177 restraints weight = 14344.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2188 r_free = 0.2188 target = 0.036794 restraints weight = 8411.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2216 r_free = 0.2216 target = 0.037893 restraints weight = 6107.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2237 r_free = 0.2237 target = 0.038721 restraints weight = 4869.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2253 r_free = 0.2253 target = 0.039361 restraints weight = 4101.798| |-----------------------------------------------------------------------------| r_work (final): 0.2230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.8696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.228 0.861 3712 Z= 9.386 Angle : 9.657 81.761 4736 Z= 4.406 Chirality : 0.746 1.752 576 Planarity : 0.033 0.088 448 Dihedral : 21.623 168.160 512 Min Nonbonded Distance : 1.538 Molprobity Statistics. All-atom Clashscore : 103.63 Ramachandran Plot: Outliers : 10.94 % Allowed : 43.75 % Favored : 45.31 % Rotamer: Outliers : 38.54 % Allowed : 26.56 % Favored : 34.90 % Cbeta Deviations : 60.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.75 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -10.13 (0.20), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.72 (0.15), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.173 0.037 TYRAA 5 Details of bonding type rmsd covalent geometry : bond 0.23025 ( 3648) covalent geometry : angle 9.65724 ( 4736) hydrogen bonds : bond 0.38551 ( 93) hydrogen bonds : angle 9.06644 ( 279) Misc. bond : bond 0.03518 ( 64) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 165 time to evaluate : 0.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 1 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8106 (ptpp) REVERT: AB 1 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7250 (mmtt) REVERT: AG 1 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8213 (mttt) REVERT: AH 1 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8400 (ptpp) REVERT: AP 1 LYS cc_start: 0.8775 (mttt) cc_final: 0.8527 (mtmm) REVERT: AR 1 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7392 (tptp) REVERT: AT 1 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8500 (ptpp) REVERT: AZ 1 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8773 (mtmm) REVERT: f 1 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7213 (mmtt) REVERT: g 1 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8521 (mmtt) REVERT: j 5 TYR cc_start: 0.8876 (OUTLIER) cc_final: 0.8392 (m-80) REVERT: n 1 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8654 (mtmm) REVERT: n 6 LYS cc_start: 0.8975 (mttt) cc_final: 0.8735 (mttt) REVERT: v 1 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.7866 (mmmt) outliers start: 148 outliers final: 117 residues processed: 255 average time/residue: 0.1158 time to fit residues: 33.1985 Evaluate side-chains 292 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 163 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 2 ILE Chi-restraints excluded: chain 0 residue 3 ILE Chi-restraints excluded: chain 0 residue 4 ILE Chi-restraints excluded: chain 0 residue 5 TYR Chi-restraints excluded: chain 2 residue 1 LYS Chi-restraints excluded: chain 2 residue 2 ILE Chi-restraints excluded: chain 3 residue 1 LYS Chi-restraints excluded: chain 4 residue 1 LYS Chi-restraints excluded: chain 4 residue 3 ILE Chi-restraints excluded: chain 5 residue 1 LYS Chi-restraints excluded: chain 5 residue 2 ILE Chi-restraints excluded: chain 5 residue 4 ILE Chi-restraints excluded: chain 7 residue 4 ILE Chi-restraints excluded: chain 7 residue 6 LYS Chi-restraints excluded: chain 8 residue 2 ILE Chi-restraints excluded: chain 8 residue 3 ILE Chi-restraints excluded: chain 8 residue 5 TYR Chi-restraints excluded: chain 9 residue 4 ILE Chi-restraints excluded: chain 9 residue 5 TYR Chi-restraints excluded: chain AA residue 3 ILE Chi-restraints excluded: chain AA residue 4 ILE Chi-restraints excluded: chain AB residue 1 LYS Chi-restraints excluded: chain AB residue 2 ILE Chi-restraints excluded: chain AB residue 3 ILE Chi-restraints excluded: chain AB residue 4 ILE Chi-restraints excluded: chain AC residue 1 LYS Chi-restraints excluded: chain AC residue 2 ILE Chi-restraints excluded: chain AD residue 2 ILE Chi-restraints excluded: chain AD residue 3 ILE Chi-restraints excluded: chain AE residue 2 ILE Chi-restraints excluded: chain AE residue 3 ILE Chi-restraints excluded: chain AF residue 1 LYS Chi-restraints excluded: chain AF residue 2 ILE Chi-restraints excluded: chain AF residue 3 ILE Chi-restraints excluded: chain AF residue 4 ILE Chi-restraints excluded: chain AG residue 1 LYS Chi-restraints excluded: chain AH residue 1 LYS Chi-restraints excluded: chain AI residue 1 LYS Chi-restraints excluded: chain AJ residue 3 ILE Chi-restraints excluded: chain AK residue 2 ILE Chi-restraints excluded: chain AK residue 4 ILE Chi-restraints excluded: chain AK residue 5 TYR Chi-restraints excluded: chain AL residue 2 ILE Chi-restraints excluded: chain AN residue 2 ILE Chi-restraints excluded: chain AN residue 3 ILE Chi-restraints excluded: chain AN residue 5 TYR Chi-restraints excluded: chain AO residue 4 ILE Chi-restraints excluded: chain AO residue 5 TYR Chi-restraints excluded: chain AP residue 2 ILE Chi-restraints excluded: chain AP residue 5 TYR Chi-restraints excluded: chain AQ residue 3 ILE Chi-restraints excluded: chain AQ residue 6 LYS Chi-restraints excluded: chain AR residue 1 LYS Chi-restraints excluded: chain AR residue 2 ILE Chi-restraints excluded: chain AR residue 3 ILE Chi-restraints excluded: chain AR residue 4 ILE Chi-restraints excluded: chain AS residue 1 LYS Chi-restraints excluded: chain AS residue 2 ILE Chi-restraints excluded: chain AT residue 1 LYS Chi-restraints excluded: chain AT residue 2 ILE Chi-restraints excluded: chain AT residue 3 ILE Chi-restraints excluded: chain AU residue 2 ILE Chi-restraints excluded: chain AU residue 3 ILE Chi-restraints excluded: chain AV residue 2 ILE Chi-restraints excluded: chain AV residue 3 ILE Chi-restraints excluded: chain AV residue 4 ILE Chi-restraints excluded: chain AW residue 2 ILE Chi-restraints excluded: chain AX residue 2 ILE Chi-restraints excluded: chain AY residue 3 ILE Chi-restraints excluded: chain AZ residue 1 LYS Chi-restraints excluded: chain AZ residue 3 ILE Chi-restraints excluded: chain Aa residue 2 ILE Chi-restraints excluded: chain Aa residue 4 ILE Chi-restraints excluded: chain Aa residue 5 TYR Chi-restraints excluded: chain Ac residue 5 TYR Chi-restraints excluded: chain Ac residue 6 LYS Chi-restraints excluded: chain Ad residue 2 ILE Chi-restraints excluded: chain Ad residue 3 ILE Chi-restraints excluded: chain Ae residue 5 TYR Chi-restraints excluded: chain Af residue 2 ILE Chi-restraints excluded: chain Af residue 3 ILE Chi-restraints excluded: chain Af residue 5 TYR Chi-restraints excluded: chain Ag residue 3 ILE Chi-restraints excluded: chain f residue 1 LYS Chi-restraints excluded: chain f residue 2 ILE Chi-restraints excluded: chain f residue 3 ILE Chi-restraints excluded: chain f residue 4 ILE Chi-restraints excluded: chain g residue 1 LYS Chi-restraints excluded: chain g residue 2 ILE Chi-restraints excluded: chain h residue 1 LYS Chi-restraints excluded: chain h residue 2 ILE Chi-restraints excluded: chain h residue 3 ILE Chi-restraints excluded: chain h residue 6 LYS Chi-restraints excluded: chain i residue 2 ILE Chi-restraints excluded: chain j residue 1 LYS Chi-restraints excluded: chain j residue 2 ILE Chi-restraints excluded: chain j residue 3 ILE Chi-restraints excluded: chain j residue 4 ILE Chi-restraints excluded: chain j residue 5 TYR Chi-restraints excluded: chain k residue 2 ILE Chi-restraints excluded: chain l residue 2 ILE Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain n residue 1 LYS Chi-restraints excluded: chain n residue 4 ILE Chi-restraints excluded: chain o residue 2 ILE Chi-restraints excluded: chain o residue 4 ILE Chi-restraints excluded: chain o residue 5 TYR Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain q residue 6 LYS Chi-restraints excluded: chain r residue 2 ILE Chi-restraints excluded: chain r residue 3 ILE Chi-restraints excluded: chain s residue 5 TYR Chi-restraints excluded: chain t residue 2 ILE Chi-restraints excluded: chain t residue 6 LYS Chi-restraints excluded: chain u residue 3 ILE Chi-restraints excluded: chain v residue 1 LYS Chi-restraints excluded: chain v residue 2 ILE Chi-restraints excluded: chain v residue 3 ILE Chi-restraints excluded: chain w residue 1 LYS Chi-restraints excluded: chain w residue 2 ILE Chi-restraints excluded: chain w residue 3 ILE Chi-restraints excluded: chain w residue 4 ILE Chi-restraints excluded: chain x residue 2 ILE Chi-restraints excluded: chain x residue 3 ILE Chi-restraints excluded: chain y residue 2 ILE Chi-restraints excluded: chain y residue 3 ILE Chi-restraints excluded: chain z residue 2 ILE Chi-restraints excluded: chain z residue 3 ILE Chi-restraints excluded: chain z residue 4 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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 = 0.2407 r_free = 0.2407 target = 0.045480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2144 r_free = 0.2144 target = 0.034917 restraints weight = 13535.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2185 r_free = 0.2185 target = 0.036423 restraints weight = 8096.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2213 r_free = 0.2213 target = 0.037516 restraints weight = 5913.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2234 r_free = 0.2234 target = 0.038338 restraints weight = 4737.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2249 r_free = 0.2249 target = 0.038919 restraints weight = 4002.299| |-----------------------------------------------------------------------------| r_work (final): 0.2228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.8708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.228 0.873 3712 Z= 9.386 Angle : 9.659 81.847 4736 Z= 4.408 Chirality : 0.746 1.755 576 Planarity : 0.033 0.088 448 Dihedral : 21.590 168.054 512 Min Nonbonded Distance : 1.538 Molprobity Statistics. All-atom Clashscore : 104.12 Ramachandran Plot: Outliers : 10.55 % Allowed : 44.14 % Favored : 45.31 % Rotamer: Outliers : 37.50 % Allowed : 27.86 % Favored : 34.64 % Cbeta Deviations : 61.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.75 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -10.12 (0.21), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.71 (0.16), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.170 0.037 TYRAA 5 Details of bonding type rmsd covalent geometry : bond 0.23033 ( 3648) covalent geometry : angle 9.65932 ( 4736) hydrogen bonds : bond 0.38559 ( 93) hydrogen bonds : angle 9.08841 ( 279) Misc. bond : bond 0.03504 ( 64) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 164 time to evaluate : 0.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 1 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8124 (ptpp) REVERT: AB 1 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7220 (mmtt) REVERT: AG 1 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8252 (mttt) REVERT: AH 1 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8405 (ptpp) REVERT: AP 1 LYS cc_start: 0.8764 (mttt) cc_final: 0.8511 (mtmm) REVERT: AR 1 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7217 (tptt) REVERT: AT 1 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8343 (mtmm) REVERT: AZ 1 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8549 (mtmm) REVERT: f 1 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7198 (mmtt) REVERT: g 1 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8489 (mmtt) REVERT: j 5 TYR cc_start: 0.8876 (OUTLIER) cc_final: 0.8463 (m-80) REVERT: n 1 LYS cc_start: 0.8995 (OUTLIER) cc_final: 0.8645 (mtmm) REVERT: n 6 LYS cc_start: 0.8964 (mttt) cc_final: 0.8731 (mttt) REVERT: v 1 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.7864 (mmmt) outliers start: 144 outliers final: 121 residues processed: 251 average time/residue: 0.1183 time to fit residues: 33.2907 Evaluate side-chains 297 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 164 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 2 ILE Chi-restraints excluded: chain 0 residue 3 ILE Chi-restraints excluded: chain 0 residue 4 ILE Chi-restraints excluded: chain 0 residue 5 TYR Chi-restraints excluded: chain 2 residue 1 LYS Chi-restraints excluded: chain 2 residue 2 ILE Chi-restraints excluded: chain 3 residue 1 LYS Chi-restraints excluded: chain 4 residue 1 LYS Chi-restraints excluded: chain 4 residue 3 ILE Chi-restraints excluded: chain 5 residue 1 LYS Chi-restraints excluded: chain 5 residue 2 ILE Chi-restraints excluded: chain 5 residue 4 ILE Chi-restraints excluded: chain 7 residue 4 ILE Chi-restraints excluded: chain 7 residue 6 LYS Chi-restraints excluded: chain 8 residue 2 ILE Chi-restraints excluded: chain 8 residue 3 ILE Chi-restraints excluded: chain 8 residue 5 TYR Chi-restraints excluded: chain 9 residue 4 ILE Chi-restraints excluded: chain 9 residue 5 TYR Chi-restraints excluded: chain AA residue 3 ILE Chi-restraints excluded: chain AA residue 4 ILE Chi-restraints excluded: chain AB residue 1 LYS Chi-restraints excluded: chain AB residue 2 ILE Chi-restraints excluded: chain AB residue 3 ILE Chi-restraints excluded: chain AB residue 4 ILE Chi-restraints excluded: chain AC residue 1 LYS Chi-restraints excluded: chain AC residue 2 ILE Chi-restraints excluded: chain AD residue 2 ILE Chi-restraints excluded: chain AD residue 3 ILE Chi-restraints excluded: chain AE residue 2 ILE Chi-restraints excluded: chain AE residue 3 ILE Chi-restraints excluded: chain AF residue 1 LYS Chi-restraints excluded: chain AF residue 2 ILE Chi-restraints excluded: chain AF residue 3 ILE Chi-restraints excluded: chain AF residue 4 ILE Chi-restraints excluded: chain AG residue 1 LYS Chi-restraints excluded: chain AH residue 1 LYS Chi-restraints excluded: chain AJ residue 3 ILE Chi-restraints excluded: chain AK residue 2 ILE Chi-restraints excluded: chain AK residue 4 ILE Chi-restraints excluded: chain AK residue 5 TYR Chi-restraints excluded: chain AL residue 2 ILE Chi-restraints excluded: chain AN residue 2 ILE Chi-restraints excluded: chain AN residue 3 ILE Chi-restraints excluded: chain AN residue 5 TYR Chi-restraints excluded: chain AO residue 4 ILE Chi-restraints excluded: chain AO residue 5 TYR Chi-restraints excluded: chain AP residue 2 ILE Chi-restraints excluded: chain AP residue 5 TYR Chi-restraints excluded: chain AQ residue 3 ILE Chi-restraints excluded: chain AQ residue 6 LYS Chi-restraints excluded: chain AR residue 1 LYS Chi-restraints excluded: chain AR residue 2 ILE Chi-restraints excluded: chain AR residue 3 ILE Chi-restraints excluded: chain AR residue 4 ILE Chi-restraints excluded: chain AS residue 1 LYS Chi-restraints excluded: chain AS residue 2 ILE Chi-restraints excluded: chain AT residue 1 LYS Chi-restraints excluded: chain AT residue 2 ILE Chi-restraints excluded: chain AT residue 3 ILE Chi-restraints excluded: chain AU residue 2 ILE Chi-restraints excluded: chain AU residue 3 ILE Chi-restraints excluded: chain AV residue 2 ILE Chi-restraints excluded: chain AV residue 3 ILE Chi-restraints excluded: chain AV residue 4 ILE Chi-restraints excluded: chain AW residue 2 ILE Chi-restraints excluded: chain AX residue 2 ILE Chi-restraints excluded: chain AY residue 1 LYS Chi-restraints excluded: chain AY residue 3 ILE Chi-restraints excluded: chain AZ residue 1 LYS Chi-restraints excluded: chain AZ residue 3 ILE Chi-restraints excluded: chain Aa residue 2 ILE Chi-restraints excluded: chain Aa residue 4 ILE Chi-restraints excluded: chain Aa residue 5 TYR Chi-restraints excluded: chain Ac residue 5 TYR Chi-restraints excluded: chain Ac residue 6 LYS Chi-restraints excluded: chain Ad residue 2 ILE Chi-restraints excluded: chain Ad residue 3 ILE Chi-restraints excluded: chain Ae residue 3 ILE Chi-restraints excluded: chain Ae residue 5 TYR Chi-restraints excluded: chain Af residue 2 ILE Chi-restraints excluded: chain Af residue 3 ILE Chi-restraints excluded: chain Af residue 5 TYR Chi-restraints excluded: chain Ag residue 3 ILE Chi-restraints excluded: chain f residue 1 LYS Chi-restraints excluded: chain f residue 2 ILE Chi-restraints excluded: chain f residue 3 ILE Chi-restraints excluded: chain f residue 4 ILE Chi-restraints excluded: chain g residue 1 LYS Chi-restraints excluded: chain g residue 2 ILE Chi-restraints excluded: chain g residue 3 ILE Chi-restraints excluded: chain h residue 1 LYS Chi-restraints excluded: chain h residue 2 ILE Chi-restraints excluded: chain h residue 3 ILE Chi-restraints excluded: chain h residue 6 LYS Chi-restraints excluded: chain i residue 2 ILE Chi-restraints excluded: chain j residue 1 LYS Chi-restraints excluded: chain j residue 2 ILE Chi-restraints excluded: chain j residue 3 ILE Chi-restraints excluded: chain j residue 4 ILE Chi-restraints excluded: chain j residue 5 TYR Chi-restraints excluded: chain k residue 2 ILE Chi-restraints excluded: chain l residue 2 ILE Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain n residue 1 LYS Chi-restraints excluded: chain n residue 3 ILE Chi-restraints excluded: chain n residue 4 ILE Chi-restraints excluded: chain o residue 2 ILE Chi-restraints excluded: chain o residue 4 ILE Chi-restraints excluded: chain o residue 5 TYR Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain q residue 6 LYS Chi-restraints excluded: chain r residue 2 ILE Chi-restraints excluded: chain r residue 3 ILE Chi-restraints excluded: chain s residue 5 TYR Chi-restraints excluded: chain t residue 2 ILE Chi-restraints excluded: chain t residue 6 LYS Chi-restraints excluded: chain u residue 3 ILE Chi-restraints excluded: chain v residue 1 LYS Chi-restraints excluded: chain v residue 2 ILE Chi-restraints excluded: chain v residue 3 ILE Chi-restraints excluded: chain v residue 6 LYS Chi-restraints excluded: chain w residue 1 LYS Chi-restraints excluded: chain w residue 2 ILE Chi-restraints excluded: chain w residue 3 ILE Chi-restraints excluded: chain w residue 4 ILE Chi-restraints excluded: chain x residue 2 ILE Chi-restraints excluded: chain x residue 3 ILE Chi-restraints excluded: chain y residue 2 ILE Chi-restraints excluded: chain y residue 3 ILE Chi-restraints excluded: chain z residue 2 ILE Chi-restraints excluded: chain z residue 3 ILE Chi-restraints excluded: chain z residue 4 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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 = 0.2409 r_free = 0.2409 target = 0.045513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2142 r_free = 0.2142 target = 0.034780 restraints weight = 14198.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2185 r_free = 0.2185 target = 0.036365 restraints weight = 8286.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2214 r_free = 0.2214 target = 0.037472 restraints weight = 6000.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2236 r_free = 0.2236 target = 0.038333 restraints weight = 4786.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2250 r_free = 0.2250 target = 0.038873 restraints weight = 4030.231| |-----------------------------------------------------------------------------| r_work (final): 0.2236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.8725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.228 0.857 3712 Z= 9.381 Angle : 9.674 81.796 4736 Z= 4.410 Chirality : 0.746 1.753 576 Planarity : 0.033 0.088 448 Dihedral : 21.620 168.241 512 Min Nonbonded Distance : 1.538 Molprobity Statistics. All-atom Clashscore : 97.54 Ramachandran Plot: Outliers : 10.55 % Allowed : 44.92 % Favored : 44.53 % Rotamer: Outliers : 38.28 % Allowed : 28.39 % Favored : 33.33 % Cbeta Deviations : 61.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.75 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -10.09 (0.21), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.69 (0.16), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.170 0.037 TYRAA 5 Details of bonding type rmsd covalent geometry : bond 0.23024 ( 3648) covalent geometry : angle 9.67420 ( 4736) hydrogen bonds : bond 0.38461 ( 93) hydrogen bonds : angle 9.07470 ( 279) Misc. bond : bond 0.03514 ( 64) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 164 time to evaluate : 0.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 1 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8145 (ptpp) REVERT: 4 1 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8679 (mtmm) REVERT: AB 1 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7165 (mmtt) REVERT: AG 1 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8253 (mttt) REVERT: AH 1 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8391 (ptpp) REVERT: AP 1 LYS cc_start: 0.8766 (mttt) cc_final: 0.8311 (mtmm) REVERT: AR 1 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7228 (tptt) REVERT: AT 1 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8346 (mtmm) REVERT: AZ 1 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8787 (mtmm) REVERT: f 1 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7208 (mmtt) REVERT: g 1 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8496 (mmtt) REVERT: j 5 TYR cc_start: 0.8879 (OUTLIER) cc_final: 0.8397 (m-80) REVERT: n 1 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8659 (mtmm) REVERT: n 6 LYS cc_start: 0.8963 (mttt) cc_final: 0.8739 (mttt) REVERT: u 6 LYS cc_start: 0.8621 (tttt) cc_final: 0.8409 (tttt) REVERT: v 1 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.7874 (mmmt) outliers start: 147 outliers final: 123 residues processed: 251 average time/residue: 0.1126 time to fit residues: 31.7882 Evaluate side-chains 300 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 164 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 2 ILE Chi-restraints excluded: chain 0 residue 3 ILE Chi-restraints excluded: chain 0 residue 4 ILE Chi-restraints excluded: chain 0 residue 5 TYR Chi-restraints excluded: chain 2 residue 1 LYS Chi-restraints excluded: chain 2 residue 2 ILE Chi-restraints excluded: chain 3 residue 1 LYS Chi-restraints excluded: chain 3 residue 3 ILE Chi-restraints excluded: chain 4 residue 1 LYS Chi-restraints excluded: chain 4 residue 3 ILE Chi-restraints excluded: chain 5 residue 1 LYS Chi-restraints excluded: chain 5 residue 2 ILE Chi-restraints excluded: chain 5 residue 4 ILE Chi-restraints excluded: chain 7 residue 4 ILE Chi-restraints excluded: chain 7 residue 6 LYS Chi-restraints excluded: chain 8 residue 2 ILE Chi-restraints excluded: chain 8 residue 3 ILE Chi-restraints excluded: chain 8 residue 5 TYR Chi-restraints excluded: chain 9 residue 4 ILE Chi-restraints excluded: chain 9 residue 5 TYR Chi-restraints excluded: chain AA residue 3 ILE Chi-restraints excluded: chain AA residue 4 ILE Chi-restraints excluded: chain AB residue 1 LYS Chi-restraints excluded: chain AB residue 2 ILE Chi-restraints excluded: chain AB residue 3 ILE Chi-restraints excluded: chain AB residue 4 ILE Chi-restraints excluded: chain AC residue 1 LYS Chi-restraints excluded: chain AC residue 2 ILE Chi-restraints excluded: chain AD residue 2 ILE Chi-restraints excluded: chain AD residue 3 ILE Chi-restraints excluded: chain AE residue 2 ILE Chi-restraints excluded: chain AE residue 3 ILE Chi-restraints excluded: chain AF residue 1 LYS Chi-restraints excluded: chain AF residue 2 ILE Chi-restraints excluded: chain AF residue 3 ILE Chi-restraints excluded: chain AF residue 4 ILE Chi-restraints excluded: chain AG residue 1 LYS Chi-restraints excluded: chain AH residue 1 LYS Chi-restraints excluded: chain AI residue 1 LYS Chi-restraints excluded: chain AJ residue 3 ILE Chi-restraints excluded: chain AK residue 2 ILE Chi-restraints excluded: chain AK residue 4 ILE Chi-restraints excluded: chain AK residue 5 TYR Chi-restraints excluded: chain AL residue 2 ILE Chi-restraints excluded: chain AN residue 2 ILE Chi-restraints excluded: chain AN residue 3 ILE Chi-restraints excluded: chain AN residue 5 TYR Chi-restraints excluded: chain AO residue 4 ILE Chi-restraints excluded: chain AO residue 5 TYR Chi-restraints excluded: chain AP residue 2 ILE Chi-restraints excluded: chain AP residue 5 TYR Chi-restraints excluded: chain AQ residue 3 ILE Chi-restraints excluded: chain AQ residue 6 LYS Chi-restraints excluded: chain AR residue 1 LYS Chi-restraints excluded: chain AR residue 2 ILE Chi-restraints excluded: chain AR residue 3 ILE Chi-restraints excluded: chain AR residue 4 ILE Chi-restraints excluded: chain AS residue 1 LYS Chi-restraints excluded: chain AS residue 2 ILE Chi-restraints excluded: chain AT residue 1 LYS Chi-restraints excluded: chain AT residue 2 ILE Chi-restraints excluded: chain AT residue 3 ILE Chi-restraints excluded: chain AU residue 2 ILE Chi-restraints excluded: chain AU residue 3 ILE Chi-restraints excluded: chain AV residue 2 ILE Chi-restraints excluded: chain AV residue 3 ILE Chi-restraints excluded: chain AV residue 4 ILE Chi-restraints excluded: chain AW residue 2 ILE Chi-restraints excluded: chain AX residue 2 ILE Chi-restraints excluded: chain AY residue 1 LYS Chi-restraints excluded: chain AY residue 3 ILE Chi-restraints excluded: chain AZ residue 1 LYS Chi-restraints excluded: chain AZ residue 3 ILE Chi-restraints excluded: chain Aa residue 2 ILE Chi-restraints excluded: chain Aa residue 4 ILE Chi-restraints excluded: chain Aa residue 5 TYR Chi-restraints excluded: chain Ac residue 5 TYR Chi-restraints excluded: chain Ac residue 6 LYS Chi-restraints excluded: chain Ad residue 2 ILE Chi-restraints excluded: chain Ad residue 3 ILE Chi-restraints excluded: chain Ae residue 5 TYR Chi-restraints excluded: chain Af residue 2 ILE Chi-restraints excluded: chain Af residue 3 ILE Chi-restraints excluded: chain Af residue 5 TYR Chi-restraints excluded: chain Ag residue 3 ILE Chi-restraints excluded: chain f residue 1 LYS Chi-restraints excluded: chain f residue 2 ILE Chi-restraints excluded: chain f residue 3 ILE Chi-restraints excluded: chain f residue 4 ILE Chi-restraints excluded: chain g residue 1 LYS Chi-restraints excluded: chain g residue 2 ILE Chi-restraints excluded: chain g residue 3 ILE Chi-restraints excluded: chain h residue 1 LYS Chi-restraints excluded: chain h residue 2 ILE Chi-restraints excluded: chain h residue 3 ILE Chi-restraints excluded: chain h residue 6 LYS Chi-restraints excluded: chain i residue 2 ILE Chi-restraints excluded: chain j residue 1 LYS Chi-restraints excluded: chain j residue 2 ILE Chi-restraints excluded: chain j residue 3 ILE Chi-restraints excluded: chain j residue 4 ILE Chi-restraints excluded: chain j residue 5 TYR Chi-restraints excluded: chain k residue 2 ILE Chi-restraints excluded: chain l residue 2 ILE Chi-restraints excluded: chain l residue 4 ILE Chi-restraints excluded: chain m residue 1 LYS Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain n residue 1 LYS Chi-restraints excluded: chain n residue 3 ILE Chi-restraints excluded: chain n residue 4 ILE Chi-restraints excluded: chain o residue 2 ILE Chi-restraints excluded: chain o residue 4 ILE Chi-restraints excluded: chain o residue 5 TYR Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain q residue 6 LYS Chi-restraints excluded: chain r residue 2 ILE Chi-restraints excluded: chain r residue 3 ILE Chi-restraints excluded: chain s residue 5 TYR Chi-restraints excluded: chain t residue 2 ILE Chi-restraints excluded: chain t residue 6 LYS Chi-restraints excluded: chain u residue 3 ILE Chi-restraints excluded: chain v residue 1 LYS Chi-restraints excluded: chain v residue 2 ILE Chi-restraints excluded: chain v residue 3 ILE Chi-restraints excluded: chain v residue 6 LYS Chi-restraints excluded: chain w residue 1 LYS Chi-restraints excluded: chain w residue 2 ILE Chi-restraints excluded: chain w residue 3 ILE Chi-restraints excluded: chain w residue 4 ILE Chi-restraints excluded: chain x residue 2 ILE Chi-restraints excluded: chain x residue 3 ILE Chi-restraints excluded: chain y residue 2 ILE Chi-restraints excluded: chain y residue 3 ILE Chi-restraints excluded: chain z residue 2 ILE Chi-restraints excluded: chain z residue 3 ILE Chi-restraints excluded: chain z residue 4 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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 = 0.2412 r_free = 0.2412 target = 0.045876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2143 r_free = 0.2143 target = 0.035102 restraints weight = 14528.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2188 r_free = 0.2188 target = 0.036772 restraints weight = 8317.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2218 r_free = 0.2218 target = 0.037926 restraints weight = 5975.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2241 r_free = 0.2241 target = 0.038804 restraints weight = 4743.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2258 r_free = 0.2258 target = 0.039488 restraints weight = 3980.122| |-----------------------------------------------------------------------------| r_work (final): 0.2258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.8736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.228 0.855 3712 Z= 9.380 Angle : 9.670 81.834 4736 Z= 4.411 Chirality : 0.746 1.755 576 Planarity : 0.034 0.088 448 Dihedral : 21.612 168.317 512 Min Nonbonded Distance : 1.537 Molprobity Statistics. All-atom Clashscore : 98.02 Ramachandran Plot: Outliers : 10.55 % Allowed : 44.14 % Favored : 45.31 % Rotamer: Outliers : 37.50 % Allowed : 29.43 % Favored : 33.07 % Cbeta Deviations : 61.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -10.08 (0.21), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.68 (0.16), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.171 0.037 TYRAA 5 Details of bonding type rmsd covalent geometry : bond 0.23025 ( 3648) covalent geometry : angle 9.67040 ( 4736) hydrogen bonds : bond 0.38529 ( 93) hydrogen bonds : angle 9.08972 ( 279) Misc. bond : bond 0.03540 ( 64) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 164 time to evaluate : 0.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 1 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8146 (ptpp) REVERT: AB 1 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7190 (mmtt) REVERT: AG 1 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8233 (mttt) REVERT: AH 1 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8412 (ptpp) REVERT: AJ 6 LYS cc_start: 0.9050 (tttt) cc_final: 0.8722 (tttt) REVERT: AP 1 LYS cc_start: 0.8765 (mttt) cc_final: 0.8320 (mtmm) REVERT: AR 1 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7229 (tptt) REVERT: AT 1 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8370 (mtmm) REVERT: AZ 1 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8804 (mtmm) REVERT: f 1 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7212 (mmtt) REVERT: g 1 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8514 (mmtt) REVERT: j 5 TYR cc_start: 0.8882 (OUTLIER) cc_final: 0.8401 (m-80) REVERT: n 1 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8663 (mtmm) REVERT: n 6 LYS cc_start: 0.8962 (mttt) cc_final: 0.8742 (mttt) REVERT: u 6 LYS cc_start: 0.8627 (tttt) cc_final: 0.8409 (tttt) REVERT: v 1 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.7883 (mmmt) outliers start: 144 outliers final: 124 residues processed: 249 average time/residue: 0.1228 time to fit residues: 34.3548 Evaluate side-chains 299 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 163 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 2 ILE Chi-restraints excluded: chain 0 residue 3 ILE Chi-restraints excluded: chain 0 residue 4 ILE Chi-restraints excluded: chain 0 residue 5 TYR Chi-restraints excluded: chain 2 residue 1 LYS Chi-restraints excluded: chain 2 residue 2 ILE Chi-restraints excluded: chain 3 residue 1 LYS Chi-restraints excluded: chain 4 residue 1 LYS Chi-restraints excluded: chain 4 residue 3 ILE Chi-restraints excluded: chain 5 residue 1 LYS Chi-restraints excluded: chain 5 residue 2 ILE Chi-restraints excluded: chain 5 residue 4 ILE Chi-restraints excluded: chain 7 residue 4 ILE Chi-restraints excluded: chain 7 residue 6 LYS Chi-restraints excluded: chain 8 residue 2 ILE Chi-restraints excluded: chain 8 residue 3 ILE Chi-restraints excluded: chain 8 residue 5 TYR Chi-restraints excluded: chain 9 residue 4 ILE Chi-restraints excluded: chain 9 residue 5 TYR Chi-restraints excluded: chain AA residue 3 ILE Chi-restraints excluded: chain AA residue 4 ILE Chi-restraints excluded: chain AB residue 1 LYS Chi-restraints excluded: chain AB residue 2 ILE Chi-restraints excluded: chain AB residue 3 ILE Chi-restraints excluded: chain AB residue 4 ILE Chi-restraints excluded: chain AC residue 1 LYS Chi-restraints excluded: chain AC residue 2 ILE Chi-restraints excluded: chain AD residue 2 ILE Chi-restraints excluded: chain AD residue 3 ILE Chi-restraints excluded: chain AE residue 2 ILE Chi-restraints excluded: chain AE residue 3 ILE Chi-restraints excluded: chain AF residue 1 LYS Chi-restraints excluded: chain AF residue 2 ILE Chi-restraints excluded: chain AF residue 3 ILE Chi-restraints excluded: chain AF residue 4 ILE Chi-restraints excluded: chain AG residue 1 LYS Chi-restraints excluded: chain AH residue 1 LYS Chi-restraints excluded: chain AH residue 2 ILE Chi-restraints excluded: chain AI residue 1 LYS Chi-restraints excluded: chain AJ residue 3 ILE Chi-restraints excluded: chain AK residue 2 ILE Chi-restraints excluded: chain AK residue 4 ILE Chi-restraints excluded: chain AK residue 5 TYR Chi-restraints excluded: chain AL residue 2 ILE Chi-restraints excluded: chain AN residue 2 ILE Chi-restraints excluded: chain AN residue 3 ILE Chi-restraints excluded: chain AN residue 5 TYR Chi-restraints excluded: chain AO residue 4 ILE Chi-restraints excluded: chain AO residue 5 TYR Chi-restraints excluded: chain AP residue 2 ILE Chi-restraints excluded: chain AP residue 5 TYR Chi-restraints excluded: chain AQ residue 3 ILE Chi-restraints excluded: chain AQ residue 6 LYS Chi-restraints excluded: chain AR residue 1 LYS Chi-restraints excluded: chain AR residue 2 ILE Chi-restraints excluded: chain AR residue 3 ILE Chi-restraints excluded: chain AR residue 4 ILE Chi-restraints excluded: chain AS residue 1 LYS Chi-restraints excluded: chain AS residue 2 ILE Chi-restraints excluded: chain AT residue 1 LYS Chi-restraints excluded: chain AT residue 2 ILE Chi-restraints excluded: chain AT residue 3 ILE Chi-restraints excluded: chain AU residue 2 ILE Chi-restraints excluded: chain AU residue 3 ILE Chi-restraints excluded: chain AV residue 2 ILE Chi-restraints excluded: chain AV residue 3 ILE Chi-restraints excluded: chain AV residue 4 ILE Chi-restraints excluded: chain AW residue 2 ILE Chi-restraints excluded: chain AX residue 2 ILE Chi-restraints excluded: chain AY residue 1 LYS Chi-restraints excluded: chain AY residue 3 ILE Chi-restraints excluded: chain AZ residue 1 LYS Chi-restraints excluded: chain AZ residue 3 ILE Chi-restraints excluded: chain Aa residue 2 ILE Chi-restraints excluded: chain Aa residue 4 ILE Chi-restraints excluded: chain Aa residue 5 TYR Chi-restraints excluded: chain Ac residue 5 TYR Chi-restraints excluded: chain Ac residue 6 LYS Chi-restraints excluded: chain Ad residue 3 ILE Chi-restraints excluded: chain Ae residue 4 ILE Chi-restraints excluded: chain Ae residue 5 TYR Chi-restraints excluded: chain Af residue 2 ILE Chi-restraints excluded: chain Af residue 3 ILE Chi-restraints excluded: chain Af residue 5 TYR Chi-restraints excluded: chain Ag residue 3 ILE Chi-restraints excluded: chain f residue 1 LYS Chi-restraints excluded: chain f residue 2 ILE Chi-restraints excluded: chain f residue 3 ILE Chi-restraints excluded: chain f residue 4 ILE Chi-restraints excluded: chain g residue 1 LYS Chi-restraints excluded: chain g residue 2 ILE Chi-restraints excluded: chain g residue 3 ILE Chi-restraints excluded: chain h residue 1 LYS Chi-restraints excluded: chain h residue 2 ILE Chi-restraints excluded: chain h residue 3 ILE Chi-restraints excluded: chain h residue 6 LYS Chi-restraints excluded: chain i residue 2 ILE Chi-restraints excluded: chain j residue 1 LYS Chi-restraints excluded: chain j residue 2 ILE Chi-restraints excluded: chain j residue 3 ILE Chi-restraints excluded: chain j residue 4 ILE Chi-restraints excluded: chain j residue 5 TYR Chi-restraints excluded: chain k residue 2 ILE Chi-restraints excluded: chain l residue 2 ILE Chi-restraints excluded: chain m residue 1 LYS Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain n residue 1 LYS Chi-restraints excluded: chain n residue 3 ILE Chi-restraints excluded: chain n residue 4 ILE Chi-restraints excluded: chain o residue 1 LYS Chi-restraints excluded: chain o residue 2 ILE Chi-restraints excluded: chain o residue 4 ILE Chi-restraints excluded: chain o residue 5 TYR Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain q residue 6 LYS Chi-restraints excluded: chain r residue 2 ILE Chi-restraints excluded: chain r residue 3 ILE Chi-restraints excluded: chain s residue 5 TYR Chi-restraints excluded: chain t residue 2 ILE Chi-restraints excluded: chain t residue 6 LYS Chi-restraints excluded: chain u residue 3 ILE Chi-restraints excluded: chain v residue 1 LYS Chi-restraints excluded: chain v residue 2 ILE Chi-restraints excluded: chain v residue 3 ILE Chi-restraints excluded: chain v residue 6 LYS Chi-restraints excluded: chain w residue 1 LYS Chi-restraints excluded: chain w residue 2 ILE Chi-restraints excluded: chain w residue 3 ILE Chi-restraints excluded: chain w residue 4 ILE Chi-restraints excluded: chain x residue 2 ILE Chi-restraints excluded: chain x residue 3 ILE Chi-restraints excluded: chain y residue 2 ILE Chi-restraints excluded: chain y residue 3 ILE Chi-restraints excluded: chain z residue 2 ILE Chi-restraints excluded: chain z residue 3 ILE Chi-restraints excluded: chain z residue 4 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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 = 0.2425 r_free = 0.2425 target = 0.046038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2169 r_free = 0.2169 target = 0.035646 restraints weight = 14383.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2214 r_free = 0.2214 target = 0.037319 restraints weight = 8045.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2244 r_free = 0.2244 target = 0.038473 restraints weight = 5702.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2267 r_free = 0.2267 target = 0.039335 restraints weight = 4485.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2283 r_free = 0.2283 target = 0.039982 restraints weight = 3747.163| |-----------------------------------------------------------------------------| r_work (final): 0.2254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.8744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.228 0.881 3712 Z= 9.379 Angle : 9.686 81.848 4736 Z= 4.415 Chirality : 0.747 1.756 576 Planarity : 0.033 0.088 448 Dihedral : 21.616 168.479 512 Min Nonbonded Distance : 1.538 Molprobity Statistics. All-atom Clashscore : 98.43 Ramachandran Plot: Outliers : 10.55 % Allowed : 44.53 % Favored : 44.92 % Rotamer: Outliers : 36.72 % Allowed : 30.99 % Favored : 32.29 % Cbeta Deviations : 59.90 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.75 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -10.08 (0.21), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.68 (0.16), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.169 0.037 TYRAA 5 Details of bonding type rmsd covalent geometry : bond 0.23029 ( 3648) covalent geometry : angle 9.68595 ( 4736) hydrogen bonds : bond 0.38501 ( 93) hydrogen bonds : angle 9.07268 ( 279) Misc. bond : bond 0.03520 ( 64) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 163 time to evaluate : 0.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 1 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8102 (ptpp) REVERT: 4 1 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8638 (mtmm) REVERT: AB 1 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7173 (mmtt) REVERT: AG 1 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8233 (mttt) REVERT: AH 1 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8401 (ptpp) REVERT: AP 1 LYS cc_start: 0.8768 (mttt) cc_final: 0.8332 (mtmm) REVERT: AR 1 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7237 (tptt) REVERT: AT 1 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8368 (mtmm) REVERT: AZ 1 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8796 (mtmm) REVERT: f 1 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7205 (mmtt) REVERT: g 1 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8507 (mmtt) REVERT: j 5 TYR cc_start: 0.8877 (OUTLIER) cc_final: 0.8468 (m-80) REVERT: n 1 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8663 (mtmm) outliers start: 141 outliers final: 124 residues processed: 245 average time/residue: 0.1190 time to fit residues: 32.6761 Evaluate side-chains 299 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 163 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 2 ILE Chi-restraints excluded: chain 0 residue 3 ILE Chi-restraints excluded: chain 0 residue 4 ILE Chi-restraints excluded: chain 0 residue 5 TYR Chi-restraints excluded: chain 2 residue 1 LYS Chi-restraints excluded: chain 2 residue 2 ILE Chi-restraints excluded: chain 3 residue 1 LYS Chi-restraints excluded: chain 4 residue 1 LYS Chi-restraints excluded: chain 4 residue 3 ILE Chi-restraints excluded: chain 5 residue 1 LYS Chi-restraints excluded: chain 5 residue 2 ILE Chi-restraints excluded: chain 5 residue 4 ILE Chi-restraints excluded: chain 7 residue 4 ILE Chi-restraints excluded: chain 7 residue 6 LYS Chi-restraints excluded: chain 8 residue 2 ILE Chi-restraints excluded: chain 8 residue 3 ILE Chi-restraints excluded: chain 8 residue 5 TYR Chi-restraints excluded: chain 9 residue 4 ILE Chi-restraints excluded: chain 9 residue 5 TYR Chi-restraints excluded: chain AA residue 3 ILE Chi-restraints excluded: chain AA residue 4 ILE Chi-restraints excluded: chain AB residue 1 LYS Chi-restraints excluded: chain AB residue 2 ILE Chi-restraints excluded: chain AB residue 3 ILE Chi-restraints excluded: chain AB residue 4 ILE Chi-restraints excluded: chain AC residue 1 LYS Chi-restraints excluded: chain AC residue 2 ILE Chi-restraints excluded: chain AD residue 2 ILE Chi-restraints excluded: chain AD residue 3 ILE Chi-restraints excluded: chain AE residue 2 ILE Chi-restraints excluded: chain AE residue 3 ILE Chi-restraints excluded: chain AF residue 1 LYS Chi-restraints excluded: chain AF residue 2 ILE Chi-restraints excluded: chain AF residue 3 ILE Chi-restraints excluded: chain AF residue 4 ILE Chi-restraints excluded: chain AG residue 1 LYS Chi-restraints excluded: chain AH residue 1 LYS Chi-restraints excluded: chain AI residue 1 LYS Chi-restraints excluded: chain AJ residue 2 ILE Chi-restraints excluded: chain AJ residue 3 ILE Chi-restraints excluded: chain AK residue 2 ILE Chi-restraints excluded: chain AK residue 4 ILE Chi-restraints excluded: chain AK residue 5 TYR Chi-restraints excluded: chain AL residue 2 ILE Chi-restraints excluded: chain AN residue 2 ILE Chi-restraints excluded: chain AN residue 3 ILE Chi-restraints excluded: chain AN residue 5 TYR Chi-restraints excluded: chain AO residue 4 ILE Chi-restraints excluded: chain AO residue 5 TYR Chi-restraints excluded: chain AP residue 2 ILE Chi-restraints excluded: chain AP residue 5 TYR Chi-restraints excluded: chain AQ residue 3 ILE Chi-restraints excluded: chain AQ residue 6 LYS Chi-restraints excluded: chain AR residue 1 LYS Chi-restraints excluded: chain AR residue 2 ILE Chi-restraints excluded: chain AR residue 3 ILE Chi-restraints excluded: chain AR residue 4 ILE Chi-restraints excluded: chain AS residue 1 LYS Chi-restraints excluded: chain AS residue 2 ILE Chi-restraints excluded: chain AT residue 1 LYS Chi-restraints excluded: chain AT residue 2 ILE Chi-restraints excluded: chain AT residue 3 ILE Chi-restraints excluded: chain AU residue 2 ILE Chi-restraints excluded: chain AU residue 3 ILE Chi-restraints excluded: chain AV residue 2 ILE Chi-restraints excluded: chain AV residue 3 ILE Chi-restraints excluded: chain AV residue 4 ILE Chi-restraints excluded: chain AW residue 2 ILE Chi-restraints excluded: chain AX residue 2 ILE Chi-restraints excluded: chain AY residue 1 LYS Chi-restraints excluded: chain AY residue 3 ILE Chi-restraints excluded: chain AZ residue 1 LYS Chi-restraints excluded: chain AZ residue 3 ILE Chi-restraints excluded: chain Aa residue 2 ILE Chi-restraints excluded: chain Aa residue 4 ILE Chi-restraints excluded: chain Aa residue 5 TYR Chi-restraints excluded: chain Ac residue 5 TYR Chi-restraints excluded: chain Ac residue 6 LYS Chi-restraints excluded: chain Ad residue 2 ILE Chi-restraints excluded: chain Ad residue 3 ILE Chi-restraints excluded: chain Ae residue 5 TYR Chi-restraints excluded: chain Ae residue 6 LYS Chi-restraints excluded: chain Af residue 2 ILE Chi-restraints excluded: chain Af residue 3 ILE Chi-restraints excluded: chain Af residue 5 TYR Chi-restraints excluded: chain Ag residue 3 ILE Chi-restraints excluded: chain f residue 1 LYS Chi-restraints excluded: chain f residue 2 ILE Chi-restraints excluded: chain f residue 3 ILE Chi-restraints excluded: chain f residue 4 ILE Chi-restraints excluded: chain g residue 1 LYS Chi-restraints excluded: chain g residue 2 ILE Chi-restraints excluded: chain h residue 1 LYS Chi-restraints excluded: chain h residue 2 ILE Chi-restraints excluded: chain h residue 3 ILE Chi-restraints excluded: chain h residue 6 LYS Chi-restraints excluded: chain i residue 2 ILE Chi-restraints excluded: chain j residue 1 LYS Chi-restraints excluded: chain j residue 2 ILE Chi-restraints excluded: chain j residue 3 ILE Chi-restraints excluded: chain j residue 4 ILE Chi-restraints excluded: chain j residue 5 TYR Chi-restraints excluded: chain k residue 2 ILE Chi-restraints excluded: chain l residue 2 ILE Chi-restraints excluded: chain m residue 1 LYS Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain n residue 1 LYS Chi-restraints excluded: chain n residue 2 ILE Chi-restraints excluded: chain n residue 3 ILE Chi-restraints excluded: chain n residue 4 ILE Chi-restraints excluded: chain o residue 2 ILE Chi-restraints excluded: chain o residue 4 ILE Chi-restraints excluded: chain o residue 5 TYR Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain q residue 6 LYS Chi-restraints excluded: chain r residue 2 ILE Chi-restraints excluded: chain r residue 3 ILE Chi-restraints excluded: chain s residue 5 TYR Chi-restraints excluded: chain t residue 2 ILE Chi-restraints excluded: chain t residue 6 LYS Chi-restraints excluded: chain u residue 3 ILE Chi-restraints excluded: chain v residue 1 LYS Chi-restraints excluded: chain v residue 2 ILE Chi-restraints excluded: chain v residue 3 ILE Chi-restraints excluded: chain v residue 6 LYS Chi-restraints excluded: chain w residue 1 LYS Chi-restraints excluded: chain w residue 2 ILE Chi-restraints excluded: chain w residue 3 ILE Chi-restraints excluded: chain w residue 4 ILE Chi-restraints excluded: chain x residue 2 ILE Chi-restraints excluded: chain x residue 3 ILE Chi-restraints excluded: chain y residue 2 ILE Chi-restraints excluded: chain y residue 3 ILE Chi-restraints excluded: chain z residue 2 ILE Chi-restraints excluded: chain z residue 3 ILE Chi-restraints excluded: chain z residue 4 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.8980 overall best weight: 50.0000 ------------------------------------------------------------------------------- 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 = 0.2428 r_free = 0.2428 target = 0.046088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2173 r_free = 0.2173 target = 0.035769 restraints weight = 14639.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2218 r_free = 0.2218 target = 0.037437 restraints weight = 8087.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2249 r_free = 0.2249 target = 0.038611 restraints weight = 5715.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2271 r_free = 0.2271 target = 0.039473 restraints weight = 4482.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2289 r_free = 0.2289 target = 0.040149 restraints weight = 3722.725| |-----------------------------------------------------------------------------| r_work (final): 0.2246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.8754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.228 0.872 3712 Z= 9.380 Angle : 9.678 81.849 4736 Z= 4.413 Chirality : 0.747 1.756 576 Planarity : 0.033 0.088 448 Dihedral : 21.632 169.085 512 Min Nonbonded Distance : 1.537 Molprobity Statistics. All-atom Clashscore : 98.18 Ramachandran Plot: Outliers : 10.55 % Allowed : 44.53 % Favored : 44.92 % Rotamer: Outliers : 37.24 % Allowed : 30.99 % Favored : 31.77 % Cbeta Deviations : 60.68 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -10.08 (0.21), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -7.68 (0.16), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.169 0.037 TYRAA 5 Details of bonding type rmsd covalent geometry : bond 0.23030 ( 3648) covalent geometry : angle 9.67761 ( 4736) hydrogen bonds : bond 0.38531 ( 93) hydrogen bonds : angle 9.09574 ( 279) Misc. bond : bond 0.03544 ( 64) =============================================================================== Job complete usr+sys time: 767.77 seconds wall clock time: 14 minutes 0.00 seconds (840.00 seconds total)