Starting phenix.real_space_refine on Tue Mar 3 12:58:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nfn_49371/03_2026/9nfn_49371.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nfn_49371/03_2026/9nfn_49371.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nfn_49371/03_2026/9nfn_49371.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nfn_49371/03_2026/9nfn_49371.map" model { file = "/net/cci-nas-00/data/ceres_data/9nfn_49371/03_2026/9nfn_49371.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nfn_49371/03_2026/9nfn_49371.cif" } resolution = 3.66 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= -0.000 sd= 0.013 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 3280 2.51 5 N 720 2.21 5 O 640 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 4640 Number of models: 1 Model: "" Number of chains: 160 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: "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: "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: 1.17, per 1000 atoms: 0.25 Number of scatterers: 4640 At special positions: 0 Unit cell: (83.259, 83.259, 60.552, 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 640 8.00 N 720 7.00 C 3280 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=80, symmetry=0 Number of additional bonds: simple=80, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.38 Conformation dependent library (CDL) restraints added in 104.2 milliseconds 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 960 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 38.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing sheet with id=AA1, first strand: chain '0' and resid 2 through 5 removed outlier: 3.639A pdb=" N TYR 6 5 " --> pdb=" O ILE 8 4 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE 2 2 " --> pdb=" O ILE z 3 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'AA' and resid 2 through 5 removed outlier: 3.596A pdb=" N ILEAA 4 " --> pdb=" O ILE 9 3 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE 9 4 " --> pdb=" O ILE 7 3 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE 5 4 " --> pdb=" O ILE 3 3 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE 3 4 " --> pdb=" O ILE 1 3 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ILE 1 2 " --> pdb=" O ILE y 3 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE y 4 " --> pdb=" O ILE w 3 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'AB' and resid 2 through 5 removed outlier: 3.528A pdb=" N TYRAH 5 " --> pdb=" O ILEAJ 4 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYRAN 5 " --> pdb=" O ILEAP 4 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'AC' and resid 2 through 4 removed outlier: 3.558A pdb=" N ILEAE 4 " --> pdb=" O ILEAC 3 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILEAG 4 " --> pdb=" O ILEAE 3 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILEAI 4 " --> pdb=" O ILEAG 3 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILEAK 4 " --> pdb=" O ILEAI 3 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILEAM 4 " --> pdb=" O ILEAK 3 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILEAO 4 " --> pdb=" O ILEAM 3 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ILEAO 3 " --> pdb=" O ILEAQ 4 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'AR' and resid 2 through 5 removed outlier: 3.619A pdb=" N TYRAT 5 " --> pdb=" O ILEAV 4 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ILEAb 3 " --> pdb=" O ILEAd 4 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ILEAd 3 " --> pdb=" O ILEAf 4 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'AS' and resid 2 through 4 removed outlier: 3.750A pdb=" N ILEAU 4 " --> pdb=" O ILEAS 3 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILEAW 4 " --> pdb=" O ILEAU 3 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILEAY 4 " --> pdb=" O ILEAW 3 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILEAa 4 " --> pdb=" O ILEAY 3 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILEAa 3 " --> pdb=" O ILEAc 2 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILEAc 4 " --> pdb=" O ILEAa 3 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILEAe 3 " --> pdb=" O ILEAg 2 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILEAg 4 " --> pdb=" O ILEAe 3 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Ah' and resid 2 through 5 removed outlier: 3.664A pdb=" N TYRAn 5 " --> pdb=" O ILEAp 4 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYRAp 5 " --> pdb=" O ILEAr 4 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYRAr 5 " --> pdb=" O ILEAt 4 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYRAt 5 " --> pdb=" O ILEAv 4 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Ai' and resid 2 through 4 removed outlier: 3.814A pdb=" N ILEAk 4 " --> pdb=" O ILEAi 3 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILEAm 4 " --> pdb=" O ILEAk 3 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILEAm 3 " --> pdb=" O ILEAo 2 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILEAo 4 " --> pdb=" O ILEAm 3 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILEAq 4 " --> pdb=" O ILEAo 3 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILEAs 4 " --> pdb=" O ILEAq 3 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILEAu 4 " --> pdb=" O ILEAs 3 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ILEAu 3 " --> pdb=" O ILEAw 4 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'f' and resid 2 through 5 removed outlier: 6.023A pdb=" N ILE f 3 " --> pdb=" O ILE h 4 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR h 5 " --> pdb=" O ILE j 4 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR j 5 " --> pdb=" O ILE l 4 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR p 5 " --> pdb=" O ILE r 4 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR r 5 " --> pdb=" O ILE t 4 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'g' and resid 2 through 4 removed outlier: 3.688A pdb=" N ILE i 4 " --> pdb=" O ILE g 3 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE k 4 " --> pdb=" O ILE i 3 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE m 4 " --> pdb=" O ILE k 3 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE o 4 " --> pdb=" O ILE m 3 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE q 4 " --> pdb=" O ILE o 3 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE s 4 " --> pdb=" O ILE q 3 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ILE s 3 " --> pdb=" O ILE u 4 " (cutoff:3.500A) 91 hydrogen bonds defined for protein. 273 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: 0.57 Time building geometry restraints manager: 0.52 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: 560 1.28 - 1.35: 480 1.35 - 1.42: 560 1.42 - 1.48: 636 1.48 - 1.55: 2324 Bond restraints: 4560 Sorted by residual: bond pdb=" C TYRAG 5 " pdb=" O TYRAG 5 " ideal model delta sigma weight residual 1.234 1.214 0.021 1.11e-02 8.12e+03 3.41e+00 bond pdb=" C TYRAa 5 " pdb=" O TYRAa 5 " ideal model delta sigma weight residual 1.234 1.214 0.020 1.11e-02 8.12e+03 3.27e+00 bond pdb=" C TYRAk 5 " pdb=" O TYRAk 5 " ideal model delta sigma weight residual 1.234 1.215 0.020 1.11e-02 8.12e+03 3.16e+00 bond pdb=" C TYRAW 5 " pdb=" O TYRAW 5 " ideal model delta sigma weight residual 1.234 1.215 0.020 1.11e-02 8.12e+03 3.11e+00 bond pdb=" C TYRAI 5 " pdb=" O TYRAI 5 " ideal model delta sigma weight residual 1.235 1.214 0.021 1.18e-02 7.18e+03 3.03e+00 ... (remaining 4555 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 4030 1.28 - 2.56: 1373 2.56 - 3.84: 311 3.84 - 5.12: 201 5.12 - 6.40: 5 Bond angle restraints: 5920 Sorted by residual: angle pdb=" CA ILE 7 3 " pdb=" CB ILE 7 3 " pdb=" CG1 ILE 7 3 " ideal model delta sigma weight residual 110.40 116.80 -6.40 1.70e+00 3.46e-01 1.42e+01 angle pdb=" N TYR 7 5 " pdb=" CA TYR 7 5 " pdb=" C TYR 7 5 " ideal model delta sigma weight residual 108.13 114.49 -6.36 1.72e+00 3.38e-01 1.37e+01 angle pdb=" N TYRAs 5 " pdb=" CA TYRAs 5 " pdb=" C TYRAs 5 " ideal model delta sigma weight residual 108.26 113.59 -5.33 1.66e+00 3.63e-01 1.03e+01 angle pdb=" C ILEAM 3 " pdb=" CA ILEAM 3 " pdb=" CB ILEAM 3 " ideal model delta sigma weight residual 110.33 114.71 -4.38 1.46e+00 4.69e-01 8.99e+00 angle pdb=" CA ILEAo 2 " pdb=" CB ILEAo 2 " pdb=" CG1 ILEAo 2 " ideal model delta sigma weight residual 110.40 115.42 -5.02 1.70e+00 3.46e-01 8.74e+00 ... (remaining 5915 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.70: 2382 8.70 - 17.39: 363 17.39 - 26.09: 90 26.09 - 34.78: 35 34.78 - 43.48: 10 Dihedral angle restraints: 2880 sinusoidal: 1440 harmonic: 1440 Sorted by residual: dihedral pdb=" CA LYS u 1 " pdb=" C LYS u 1 " pdb=" N ILE u 2 " pdb=" CA ILE u 2 " ideal model delta harmonic sigma weight residual 180.00 152.50 27.50 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA LYSAQ 1 " pdb=" C LYSAQ 1 " pdb=" N ILEAQ 2 " pdb=" CA ILEAQ 2 " ideal model delta harmonic sigma weight residual 180.00 152.86 27.14 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA ILEAk 2 " pdb=" C ILEAk 2 " pdb=" N ILEAk 3 " pdb=" CA ILEAk 3 " ideal model delta harmonic sigma weight residual 180.00 153.17 26.83 0 5.00e+00 4.00e-02 2.88e+01 ... (remaining 2877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 208 0.046 - 0.093: 151 0.093 - 0.139: 170 0.139 - 0.185: 125 0.185 - 0.232: 66 Chirality restraints: 720 Sorted by residual: chirality pdb=" CA LYS f 1 " pdb=" N LYS f 1 " pdb=" C LYS f 1 " pdb=" CB LYS f 1 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA TYRAA 5 " pdb=" N TYRAA 5 " pdb=" C TYRAA 5 " pdb=" CB TYRAA 5 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA TYR u 5 " pdb=" N TYR u 5 " pdb=" C TYR u 5 " pdb=" CB TYR u 5 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 717 not shown) Planarity restraints: 560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ACE t 0 " -0.066 2.00e-02 2.50e+03 6.10e-02 4.65e+01 pdb=" O ACE t 0 " 0.008 2.00e-02 2.50e+03 pdb=" CH3 ACE t 0 " 0.065 2.00e-02 2.50e+03 pdb=" N LYS t 1 " -0.074 2.00e-02 2.50e+03 pdb=" CA LYS t 1 " 0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ACEAv 0 " 0.056 2.00e-02 2.50e+03 5.44e-02 3.69e+01 pdb=" O ACEAv 0 " -0.006 2.00e-02 2.50e+03 pdb=" CH3 ACEAv 0 " -0.058 2.00e-02 2.50e+03 pdb=" N LYSAv 1 " 0.068 2.00e-02 2.50e+03 pdb=" CA LYSAv 1 " -0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ACE 0 0 " -0.045 2.00e-02 2.50e+03 5.17e-02 3.35e+01 pdb=" O ACE 0 0 " 0.003 2.00e-02 2.50e+03 pdb=" CH3 ACE 0 0 " 0.054 2.00e-02 2.50e+03 pdb=" N LYS 0 1 " -0.071 2.00e-02 2.50e+03 pdb=" CA LYS 0 1 " 0.059 2.00e-02 2.50e+03 ... (remaining 557 not shown) Histogram of nonbonded interaction distances: 2.68 - 3.13: 2772 3.13 - 3.57: 4198 3.57 - 4.01: 5864 4.01 - 4.46: 5792 4.46 - 4.90: 11739 Nonbonded interactions: 30365 Sorted by model distance: nonbonded pdb=" N ILE u 2 " pdb=" O ILE u 2 " model vdw 2.684 2.496 nonbonded pdb=" N ILE 1 2 " pdb=" O ILE 1 2 " model vdw 2.685 2.496 nonbonded pdb=" N ILEAg 2 " pdb=" O ILEAg 2 " model vdw 2.690 2.496 nonbonded pdb=" N ILEAq 2 " pdb=" O ILEAq 2 " model vdw 2.691 2.496 nonbonded pdb=" N ILEAQ 2 " pdb=" O ILEAQ 2 " model vdw 2.694 2.496 ... (remaining 30360 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 '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 '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: 7.600 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 6.670 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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:1.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 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 : 0.017 0.102 4640 Z= 1.429 Angle : 1.483 6.405 5920 Z= 0.845 Chirality : 0.113 0.232 720 Planarity : 0.013 0.061 560 Dihedral : 9.236 43.475 1920 Min Nonbonded Distance : 2.684 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % 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: 3.76 (0.40), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 2.88 (0.31), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.071 0.011 TYRAv 5 Details of bonding type rmsd covalent geometry : bond 0.01098 ( 4560) covalent geometry : angle 1.48269 ( 5920) hydrogen bonds : bond 0.29574 ( 91) hydrogen bonds : angle 11.71117 ( 273) Misc. bond : bond 0.10122 ( 80) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.258 Fit side-chains REVERT: 2 6 LYS cc_start: 0.9198 (pttt) cc_final: 0.8879 (pttp) REVERT: 4 2 ILE cc_start: 0.8892 (mm) cc_final: 0.8639 (tp) REVERT: 4 4 ILE cc_start: 0.8802 (mt) cc_final: 0.8590 (tt) REVERT: 4 6 LYS cc_start: 0.9166 (pttt) cc_final: 0.8859 (pttp) REVERT: 6 6 LYS cc_start: 0.9235 (pttt) cc_final: 0.8987 (pttp) REVERT: 9 2 ILE cc_start: 0.8469 (mt) cc_final: 0.8267 (mm) REVERT: AE 1 LYS cc_start: 0.9456 (pttm) cc_final: 0.8788 (mttt) REVERT: AE 2 ILE cc_start: 0.8978 (pt) cc_final: 0.8728 (mt) REVERT: AH 6 LYS cc_start: 0.9118 (pttt) cc_final: 0.8816 (pttp) REVERT: AJ 6 LYS cc_start: 0.9253 (pttt) cc_final: 0.8952 (pttp) REVERT: AL 6 LYS cc_start: 0.9123 (pttt) cc_final: 0.8905 (pttp) REVERT: AT 2 ILE cc_start: 0.8789 (mm) cc_final: 0.8478 (tp) REVERT: AT 4 ILE cc_start: 0.8377 (mt) cc_final: 0.8166 (tt) REVERT: AU 1 LYS cc_start: 0.9484 (pttm) cc_final: 0.8762 (mttt) REVERT: AU 2 ILE cc_start: 0.9008 (pt) cc_final: 0.8586 (mt) REVERT: AV 4 ILE cc_start: 0.8574 (mt) cc_final: 0.8352 (tt) REVERT: AX 6 LYS cc_start: 0.9181 (pttt) cc_final: 0.8795 (pttp) REVERT: AZ 6 LYS cc_start: 0.9171 (pttt) cc_final: 0.8903 (pttp) REVERT: Ab 6 LYS cc_start: 0.9271 (pttt) cc_final: 0.9043 (pttp) REVERT: An 4 ILE cc_start: 0.8733 (mt) cc_final: 0.8516 (tt) REVERT: Ao 1 LYS cc_start: 0.9558 (pttm) cc_final: 0.9330 (pttp) REVERT: Ao 2 ILE cc_start: 0.9030 (pt) cc_final: 0.8491 (mt) REVERT: Ap 6 LYS cc_start: 0.9208 (pttt) cc_final: 0.8827 (pttp) REVERT: Ar 6 LYS cc_start: 0.9293 (pttt) cc_final: 0.9061 (pttp) REVERT: At 6 LYS cc_start: 0.9140 (pttt) cc_final: 0.8888 (pttp) REVERT: h 4 ILE cc_start: 0.8537 (mt) cc_final: 0.8331 (tt) REVERT: i 1 LYS cc_start: 0.9470 (pttm) cc_final: 0.8663 (mttt) REVERT: i 2 ILE cc_start: 0.9107 (pt) cc_final: 0.8733 (mt) REVERT: n 6 LYS cc_start: 0.9215 (pttt) cc_final: 0.8937 (pttp) REVERT: p 6 LYS cc_start: 0.9297 (pttt) cc_final: 0.9085 (pttp) REVERT: x 2 ILE cc_start: 0.8845 (mm) cc_final: 0.8593 (tp) REVERT: y 2 ILE cc_start: 0.9008 (pt) cc_final: 0.8735 (mt) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.0704 time to fit residues: 20.3557 Evaluate side-chains 116 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.210 ------------------------------------------------------------------------------- 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: 0.8980 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 = 0.3013 r_free = 0.3013 target = 0.050409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.044843 restraints weight = 25754.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.045900 restraints weight = 11393.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.046591 restraints weight = 7093.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.047039 restraints weight = 5235.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.047249 restraints weight = 4260.432| |-----------------------------------------------------------------------------| r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.6486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.070 0.241 4640 Z= 2.818 Angle : 3.327 17.869 5920 Z= 1.699 Chirality : 0.215 0.555 720 Planarity : 0.013 0.041 560 Dihedral : 16.395 59.318 640 Min Nonbonded Distance : 1.665 Molprobity Statistics. All-atom Clashscore : 97.65 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.19 % Favored : 92.50 % Rotamer: Outliers : 28.54 % Allowed : 16.46 % Favored : 55.00 % 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: -2.24 (0.39), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.30), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.067 0.015 TYRAB 5 Details of bonding type rmsd covalent geometry : bond 0.07025 ( 4560) covalent geometry : angle 3.32711 ( 5920) hydrogen bonds : bond 0.20314 ( 91) hydrogen bonds : angle 11.73991 ( 273) Misc. bond : bond 0.01034 ( 80) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 12 time to evaluate : 0.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 5 TYR cc_start: 0.8767 (OUTLIER) cc_final: 0.8395 (p90) REVERT: AC 5 TYR cc_start: 0.8045 (OUTLIER) cc_final: 0.4093 (m-10) REVERT: AE 5 TYR cc_start: 0.8603 (OUTLIER) cc_final: 0.7684 (p90) REVERT: AS 5 TYR cc_start: 0.7933 (OUTLIER) cc_final: 0.4244 (m-10) REVERT: AY 5 TYR cc_start: 0.8696 (OUTLIER) cc_final: 0.7594 (p90) REVERT: Ai 5 TYR cc_start: 0.8057 (OUTLIER) cc_final: 0.4283 (m-10) REVERT: Ao 5 TYR cc_start: 0.8705 (OUTLIER) cc_final: 0.8418 (p90) REVERT: w 1 LYS cc_start: 0.9413 (pttm) cc_final: 0.9000 (tptp) REVERT: w 5 TYR cc_start: 0.7886 (OUTLIER) cc_final: 0.4060 (m-10) outliers start: 137 outliers final: 88 residues processed: 149 average time/residue: 0.0474 time to fit residues: 9.7912 Evaluate side-chains 109 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 13 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 2 ILE Chi-restraints excluded: chain 1 residue 4 ILE Chi-restraints excluded: chain 2 residue 2 ILE Chi-restraints excluded: chain 3 residue 2 ILE Chi-restraints excluded: chain 3 residue 4 ILE Chi-restraints excluded: chain 5 residue 4 ILE Chi-restraints excluded: chain 5 residue 5 TYR Chi-restraints excluded: chain 7 residue 2 ILE Chi-restraints excluded: chain 7 residue 3 ILE Chi-restraints excluded: chain 7 residue 4 ILE Chi-restraints excluded: chain 8 residue 4 ILE Chi-restraints excluded: chain 9 residue 2 ILE Chi-restraints excluded: chain 9 residue 3 ILE Chi-restraints excluded: chain 9 residue 4 ILE Chi-restraints excluded: chain AA residue 2 ILE Chi-restraints excluded: chain AA residue 3 ILE Chi-restraints excluded: chain AA residue 4 ILE Chi-restraints excluded: chain AB residue 4 ILE Chi-restraints excluded: chain AC residue 5 TYR Chi-restraints excluded: chain AD residue 4 ILE Chi-restraints excluded: chain AE 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 AG residue 2 ILE Chi-restraints excluded: chain AG residue 4 ILE Chi-restraints excluded: chain AI residue 2 ILE Chi-restraints excluded: chain AI residue 3 ILE Chi-restraints excluded: chain AI residue 4 ILE Chi-restraints excluded: chain AK residue 4 ILE Chi-restraints excluded: chain AM residue 2 ILE Chi-restraints excluded: chain AN residue 2 ILE Chi-restraints excluded: chain AO residue 2 ILE Chi-restraints excluded: chain AO residue 4 ILE Chi-restraints excluded: chain AP residue 2 ILE Chi-restraints excluded: chain AR residue 4 ILE Chi-restraints excluded: chain AS residue 3 ILE Chi-restraints excluded: chain AS residue 5 TYR Chi-restraints excluded: chain AU residue 4 ILE Chi-restraints excluded: chain AV residue 2 ILE Chi-restraints excluded: chain AW residue 4 ILE Chi-restraints excluded: chain AY residue 2 ILE Chi-restraints excluded: chain AY residue 3 ILE Chi-restraints excluded: chain AY residue 5 TYR Chi-restraints excluded: chain Aa residue 3 ILE Chi-restraints excluded: chain Aa residue 5 TYR Chi-restraints excluded: chain Ab residue 4 ILE Chi-restraints excluded: chain Ac residue 4 ILE Chi-restraints excluded: chain Ac residue 5 TYR Chi-restraints excluded: chain Ad residue 2 ILE Chi-restraints excluded: chain Ae residue 2 ILE Chi-restraints excluded: chain Ae residue 4 ILE Chi-restraints excluded: chain Af residue 2 ILE Chi-restraints excluded: chain Ah residue 4 ILE Chi-restraints excluded: chain Ai residue 5 TYR Chi-restraints excluded: chain Aj residue 4 ILE Chi-restraints excluded: chain Ak residue 4 ILE Chi-restraints excluded: chain Al residue 2 ILE Chi-restraints excluded: chain Al residue 4 ILE Chi-restraints excluded: chain Am residue 4 ILE Chi-restraints excluded: chain Ao residue 5 TYR Chi-restraints excluded: chain Aq residue 3 ILE Chi-restraints excluded: chain Aq residue 4 ILE Chi-restraints excluded: chain Ar residue 4 ILE Chi-restraints excluded: chain As residue 2 ILE Chi-restraints excluded: chain As residue 4 ILE Chi-restraints excluded: chain At residue 2 ILE Chi-restraints excluded: chain At residue 4 ILE Chi-restraints excluded: chain Au residue 2 ILE Chi-restraints excluded: chain Au residue 4 ILE Chi-restraints excluded: chain Av residue 2 ILE Chi-restraints excluded: chain Av residue 4 ILE Chi-restraints excluded: chain Aw residue 3 ILE Chi-restraints excluded: chain f residue 4 ILE Chi-restraints excluded: chain i residue 4 ILE Chi-restraints excluded: chain k residue 2 ILE Chi-restraints excluded: chain k residue 4 ILE Chi-restraints excluded: chain l residue 2 ILE Chi-restraints excluded: chain m residue 2 ILE Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain m residue 4 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 p residue 4 ILE Chi-restraints excluded: chain q residue 4 ILE Chi-restraints excluded: chain r residue 4 ILE Chi-restraints excluded: chain s residue 2 ILE Chi-restraints excluded: chain s residue 3 ILE Chi-restraints excluded: chain t residue 2 ILE Chi-restraints excluded: chain u residue 3 ILE Chi-restraints excluded: chain v residue 4 ILE Chi-restraints excluded: chain w residue 5 TYR Chi-restraints excluded: chain x residue 4 ILE Chi-restraints excluded: chain y residue 3 ILE Chi-restraints excluded: chain z residue 4 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 1.9990 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 = 0.3011 r_free = 0.3011 target = 0.050798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.044753 restraints weight = 26343.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.045842 restraints weight = 11992.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.046386 restraints weight = 7564.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.046922 restraints weight = 5941.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.047219 restraints weight = 4782.300| |-----------------------------------------------------------------------------| r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.7051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.068 0.242 4640 Z= 2.766 Angle : 3.334 14.016 5920 Z= 1.677 Chirality : 0.203 0.590 720 Planarity : 0.012 0.037 560 Dihedral : 16.368 59.496 640 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 96.00 Ramachandran Plot: Outliers : 0.31 % Allowed : 17.50 % Favored : 82.19 % Rotamer: Outliers : 32.08 % Allowed : 15.21 % Favored : 52.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.00 % 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: -3.52 (0.39), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.30), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.065 0.012 TYRAo 5 Details of bonding type rmsd covalent geometry : bond 0.06891 ( 4560) covalent geometry : angle 3.33351 ( 5920) hydrogen bonds : bond 0.21098 ( 91) hydrogen bonds : angle 11.47494 ( 273) Misc. bond : bond 0.00923 ( 80) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 12 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 5 TYR cc_start: 0.8577 (OUTLIER) cc_final: 0.8307 (p90) REVERT: AC 5 TYR cc_start: 0.7669 (OUTLIER) cc_final: 0.4212 (m-10) REVERT: AO 5 TYR cc_start: 0.8450 (OUTLIER) cc_final: 0.8209 (p90) REVERT: AS 5 TYR cc_start: 0.7848 (OUTLIER) cc_final: 0.4244 (m-10) REVERT: AW 5 TYR cc_start: 0.8661 (OUTLIER) cc_final: 0.8013 (p90) REVERT: AY 5 TYR cc_start: 0.8542 (OUTLIER) cc_final: 0.7781 (p90) REVERT: Ai 5 TYR cc_start: 0.7765 (OUTLIER) cc_final: 0.4110 (m-10) REVERT: Ao 5 TYR cc_start: 0.8518 (OUTLIER) cc_final: 0.8182 (p90) REVERT: Au 5 TYR cc_start: 0.8565 (OUTLIER) cc_final: 0.7958 (p90) REVERT: Aw 5 TYR cc_start: 0.7972 (OUTLIER) cc_final: 0.7568 (p90) REVERT: g 5 TYR cc_start: 0.7628 (OUTLIER) cc_final: 0.4225 (m-10) REVERT: i 3 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8942 (pp) REVERT: w 1 LYS cc_start: 0.9412 (pttm) cc_final: 0.8903 (tptp) REVERT: w 5 TYR cc_start: 0.7810 (OUTLIER) cc_final: 0.4223 (m-10) outliers start: 154 outliers final: 113 residues processed: 166 average time/residue: 0.0478 time to fit residues: 10.9648 Evaluate side-chains 138 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 12 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 2 ILE Chi-restraints excluded: chain 1 residue 4 ILE Chi-restraints excluded: chain 1 residue 5 TYR Chi-restraints excluded: chain 2 residue 2 ILE Chi-restraints excluded: chain 3 residue 2 ILE Chi-restraints excluded: chain 3 residue 5 TYR Chi-restraints excluded: chain 5 residue 4 ILE Chi-restraints excluded: chain 5 residue 5 TYR Chi-restraints excluded: chain 6 residue 2 ILE Chi-restraints excluded: chain 7 residue 2 ILE Chi-restraints excluded: chain 7 residue 3 ILE Chi-restraints excluded: chain 7 residue 4 ILE Chi-restraints excluded: chain 8 residue 4 ILE Chi-restraints excluded: chain 9 residue 2 ILE Chi-restraints excluded: chain 9 residue 3 ILE Chi-restraints excluded: chain 9 residue 4 ILE Chi-restraints excluded: chain AA residue 2 ILE Chi-restraints excluded: chain AA residue 3 ILE Chi-restraints excluded: chain AB residue 4 ILE Chi-restraints excluded: chain AC residue 3 ILE Chi-restraints excluded: chain AC residue 5 TYR Chi-restraints excluded: chain AD residue 4 ILE Chi-restraints excluded: chain AE 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 AG residue 2 ILE Chi-restraints excluded: chain AG residue 4 ILE Chi-restraints excluded: chain AG residue 5 TYR Chi-restraints excluded: chain AH residue 2 ILE Chi-restraints excluded: chain AI residue 2 ILE Chi-restraints excluded: chain AI residue 3 ILE Chi-restraints excluded: chain AI residue 4 ILE Chi-restraints excluded: chain AK residue 4 ILE Chi-restraints excluded: chain AK residue 5 TYR Chi-restraints excluded: chain AL residue 4 ILE Chi-restraints excluded: chain AM residue 2 ILE Chi-restraints excluded: chain AN residue 2 ILE Chi-restraints excluded: chain AO residue 2 ILE 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 AQ residue 5 TYR Chi-restraints excluded: chain AR residue 2 ILE Chi-restraints excluded: chain AR residue 4 ILE Chi-restraints excluded: chain AS residue 5 TYR Chi-restraints excluded: chain AT residue 2 ILE Chi-restraints excluded: chain AU residue 3 ILE Chi-restraints excluded: chain AU residue 4 ILE Chi-restraints excluded: chain AU residue 5 TYR Chi-restraints excluded: chain AV residue 2 ILE Chi-restraints excluded: chain AW residue 5 TYR Chi-restraints excluded: chain AY residue 2 ILE Chi-restraints excluded: chain AY residue 3 ILE Chi-restraints excluded: chain AY residue 5 TYR Chi-restraints excluded: chain Aa residue 3 ILE Chi-restraints excluded: chain Aa residue 5 TYR Chi-restraints excluded: chain Ab residue 4 ILE Chi-restraints excluded: chain Ac residue 4 ILE Chi-restraints excluded: chain Ac residue 5 TYR Chi-restraints excluded: chain Ad residue 2 ILE Chi-restraints excluded: chain Ae residue 2 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 4 ILE Chi-restraints excluded: chain Ah residue 4 ILE Chi-restraints excluded: chain Ai residue 5 TYR Chi-restraints excluded: chain Aj residue 4 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 Al residue 4 ILE Chi-restraints excluded: chain Am residue 4 ILE Chi-restraints excluded: chain Am residue 5 TYR Chi-restraints excluded: chain An residue 2 ILE Chi-restraints excluded: chain Ao residue 3 ILE Chi-restraints excluded: chain Ao residue 5 TYR Chi-restraints excluded: chain Aq residue 3 ILE Chi-restraints excluded: chain Aq residue 4 ILE Chi-restraints excluded: chain Ar residue 2 ILE Chi-restraints excluded: chain Ar residue 4 ILE Chi-restraints excluded: chain As residue 2 ILE Chi-restraints excluded: chain As residue 4 ILE Chi-restraints excluded: chain At residue 2 ILE Chi-restraints excluded: chain At residue 4 ILE Chi-restraints excluded: chain Au residue 2 ILE Chi-restraints excluded: chain Au residue 4 ILE Chi-restraints excluded: chain Au residue 5 TYR Chi-restraints excluded: chain Av residue 2 ILE Chi-restraints excluded: chain Av residue 4 ILE Chi-restraints excluded: chain Aw residue 3 ILE Chi-restraints excluded: chain Aw residue 5 TYR Chi-restraints excluded: chain f residue 4 ILE Chi-restraints excluded: chain g residue 5 TYR Chi-restraints excluded: chain h residue 2 ILE Chi-restraints excluded: chain i residue 3 ILE Chi-restraints excluded: chain i residue 4 ILE Chi-restraints excluded: chain j residue 2 ILE Chi-restraints excluded: chain k residue 2 ILE Chi-restraints excluded: chain k residue 4 ILE Chi-restraints excluded: chain k residue 5 TYR Chi-restraints excluded: chain m residue 2 ILE Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain m residue 4 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 p residue 4 ILE Chi-restraints excluded: chain q residue 4 ILE Chi-restraints excluded: chain r residue 4 ILE Chi-restraints excluded: chain s residue 2 ILE Chi-restraints excluded: chain s residue 3 ILE Chi-restraints excluded: chain s residue 5 TYR Chi-restraints excluded: chain t residue 2 ILE Chi-restraints excluded: chain u residue 3 ILE Chi-restraints excluded: chain u residue 5 TYR Chi-restraints excluded: chain v residue 2 ILE Chi-restraints excluded: chain v residue 4 ILE Chi-restraints excluded: chain w residue 3 ILE Chi-restraints excluded: chain w residue 5 TYR Chi-restraints excluded: chain x residue 4 ILE Chi-restraints excluded: chain y residue 3 ILE Chi-restraints excluded: chain y residue 4 ILE Chi-restraints excluded: chain z residue 2 ILE Chi-restraints excluded: chain z residue 4 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- 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 = 0.3012 r_free = 0.3012 target = 0.050960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.045036 restraints weight = 26226.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.046124 restraints weight = 11837.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.046846 restraints weight = 7411.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.047317 restraints weight = 5463.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.047644 restraints weight = 4431.023| |-----------------------------------------------------------------------------| r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.7207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.068 0.240 4640 Z= 2.761 Angle : 3.332 14.241 5920 Z= 1.676 Chirality : 0.199 0.597 720 Planarity : 0.013 0.036 560 Dihedral : 16.781 58.820 640 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 98.17 Ramachandran Plot: Outliers : 0.31 % Allowed : 21.56 % Favored : 78.12 % Rotamer: Outliers : 33.75 % Allowed : 17.50 % Favored : 48.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.50 % 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: -4.01 (0.39), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.05 (0.30), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.066 0.011 TYRAo 5 Details of bonding type rmsd covalent geometry : bond 0.06881 ( 4560) covalent geometry : angle 3.33246 ( 5920) hydrogen bonds : bond 0.21933 ( 91) hydrogen bonds : angle 11.24386 ( 273) Misc. bond : bond 0.00911 ( 80) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 12 time to evaluate : 0.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 5 TYR cc_start: 0.8510 (OUTLIER) cc_final: 0.8244 (p90) REVERT: 7 6 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8168 (pttt) REVERT: AC 5 TYR cc_start: 0.7636 (OUTLIER) cc_final: 0.4269 (m-10) REVERT: AO 5 TYR cc_start: 0.8418 (OUTLIER) cc_final: 0.8182 (p90) REVERT: AS 5 TYR cc_start: 0.7791 (OUTLIER) cc_final: 0.4282 (m-10) REVERT: AW 5 TYR cc_start: 0.8651 (OUTLIER) cc_final: 0.8032 (p90) REVERT: AY 5 TYR cc_start: 0.8508 (OUTLIER) cc_final: 0.7883 (p90) REVERT: Ai 5 TYR cc_start: 0.7796 (OUTLIER) cc_final: 0.4170 (m-10) REVERT: Ao 5 TYR cc_start: 0.8461 (OUTLIER) cc_final: 0.8129 (p90) REVERT: Au 5 TYR cc_start: 0.8514 (OUTLIER) cc_final: 0.7981 (p90) REVERT: Aw 5 TYR cc_start: 0.7951 (OUTLIER) cc_final: 0.7625 (p90) REVERT: g 5 TYR cc_start: 0.7543 (OUTLIER) cc_final: 0.4178 (m-10) REVERT: w 1 LYS cc_start: 0.9404 (pttm) cc_final: 0.8904 (tptp) REVERT: w 5 TYR cc_start: 0.7825 (OUTLIER) cc_final: 0.4186 (m-10) outliers start: 162 outliers final: 123 residues processed: 174 average time/residue: 0.0460 time to fit residues: 10.9303 Evaluate side-chains 148 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 12 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 2 ILE Chi-restraints excluded: chain 1 residue 4 ILE Chi-restraints excluded: chain 1 residue 5 TYR Chi-restraints excluded: chain 2 residue 2 ILE Chi-restraints excluded: chain 3 residue 2 ILE Chi-restraints excluded: chain 3 residue 5 TYR Chi-restraints excluded: chain 4 residue 4 ILE Chi-restraints excluded: chain 5 residue 3 ILE Chi-restraints excluded: chain 5 residue 4 ILE Chi-restraints excluded: chain 5 residue 5 TYR Chi-restraints excluded: chain 6 residue 4 ILE Chi-restraints excluded: chain 7 residue 2 ILE Chi-restraints excluded: chain 7 residue 3 ILE Chi-restraints excluded: chain 7 residue 4 ILE Chi-restraints excluded: chain 7 residue 6 LYS Chi-restraints excluded: chain 8 residue 4 ILE Chi-restraints excluded: chain 9 residue 2 ILE Chi-restraints excluded: chain 9 residue 3 ILE Chi-restraints excluded: chain 9 residue 5 TYR Chi-restraints excluded: chain AA residue 2 ILE Chi-restraints excluded: chain AA residue 3 ILE Chi-restraints excluded: chain AA residue 5 TYR Chi-restraints excluded: chain AB residue 4 ILE Chi-restraints excluded: chain AC residue 3 ILE Chi-restraints excluded: chain AC residue 5 TYR Chi-restraints excluded: chain AD residue 2 ILE Chi-restraints excluded: chain AD residue 4 ILE Chi-restraints excluded: chain AE 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 AG residue 2 ILE Chi-restraints excluded: chain AG residue 4 ILE Chi-restraints excluded: chain AG residue 5 TYR Chi-restraints excluded: chain AI residue 2 ILE Chi-restraints excluded: chain AI residue 3 ILE Chi-restraints excluded: chain AI residue 4 ILE Chi-restraints excluded: chain AJ residue 4 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 AM residue 2 ILE Chi-restraints excluded: chain AN residue 2 ILE Chi-restraints excluded: chain AO residue 2 ILE 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 4 ILE Chi-restraints excluded: chain AQ residue 3 ILE Chi-restraints excluded: chain AQ residue 5 TYR Chi-restraints excluded: chain AR residue 2 ILE Chi-restraints excluded: chain AR residue 4 ILE Chi-restraints excluded: chain AS residue 5 TYR Chi-restraints excluded: chain AU residue 3 ILE Chi-restraints excluded: chain AU residue 4 ILE Chi-restraints excluded: chain AU residue 5 TYR Chi-restraints excluded: chain AV residue 2 ILE Chi-restraints excluded: chain AW residue 5 TYR Chi-restraints excluded: chain AY residue 2 ILE Chi-restraints excluded: chain AY residue 3 ILE Chi-restraints excluded: chain AY residue 5 TYR Chi-restraints excluded: chain AZ residue 2 ILE Chi-restraints excluded: chain AZ residue 4 ILE Chi-restraints excluded: chain Aa residue 3 ILE Chi-restraints excluded: chain Aa residue 5 TYR Chi-restraints excluded: chain Ab residue 4 ILE Chi-restraints excluded: chain Ac residue 2 ILE Chi-restraints excluded: chain Ac residue 4 ILE Chi-restraints excluded: chain Ac residue 5 TYR Chi-restraints excluded: chain Ad residue 2 ILE Chi-restraints excluded: chain Ae residue 2 ILE Chi-restraints excluded: chain Ae 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 4 ILE Chi-restraints excluded: chain Ag residue 5 TYR Chi-restraints excluded: chain Ah residue 4 ILE Chi-restraints excluded: chain Ai residue 3 ILE Chi-restraints excluded: chain Ai residue 5 TYR Chi-restraints excluded: chain Aj residue 4 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 Al residue 4 ILE Chi-restraints excluded: chain Am residue 4 ILE Chi-restraints excluded: chain Am residue 5 TYR Chi-restraints excluded: chain An residue 2 ILE Chi-restraints excluded: chain Ao residue 3 ILE Chi-restraints excluded: chain Ao residue 5 TYR Chi-restraints excluded: chain Aq residue 3 ILE Chi-restraints excluded: chain Aq residue 4 ILE Chi-restraints excluded: chain Ar residue 4 ILE Chi-restraints excluded: chain As residue 4 ILE Chi-restraints excluded: chain At residue 2 ILE Chi-restraints excluded: chain At residue 4 ILE Chi-restraints excluded: chain Au residue 2 ILE Chi-restraints excluded: chain Au residue 3 ILE Chi-restraints excluded: chain Au residue 4 ILE Chi-restraints excluded: chain Au residue 5 TYR Chi-restraints excluded: chain Av residue 2 ILE Chi-restraints excluded: chain Av residue 4 ILE Chi-restraints excluded: chain Aw residue 3 ILE Chi-restraints excluded: chain Aw residue 5 TYR Chi-restraints excluded: chain f residue 4 ILE Chi-restraints excluded: chain g residue 5 TYR Chi-restraints excluded: chain h residue 2 ILE Chi-restraints excluded: chain i residue 4 ILE Chi-restraints excluded: chain j residue 2 ILE Chi-restraints excluded: chain k residue 2 ILE Chi-restraints excluded: chain k residue 4 ILE Chi-restraints excluded: chain k residue 5 TYR Chi-restraints excluded: chain m residue 2 ILE Chi-restraints excluded: chain m residue 4 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 p residue 4 ILE Chi-restraints excluded: chain q residue 4 ILE Chi-restraints excluded: chain r residue 2 ILE Chi-restraints excluded: chain r residue 4 ILE Chi-restraints excluded: chain s residue 2 ILE Chi-restraints excluded: chain s 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 4 ILE Chi-restraints excluded: chain u residue 3 ILE Chi-restraints excluded: chain u residue 5 TYR Chi-restraints excluded: chain v residue 2 ILE Chi-restraints excluded: chain v residue 4 ILE Chi-restraints excluded: chain w residue 3 ILE Chi-restraints excluded: chain w residue 5 TYR Chi-restraints excluded: chain x residue 2 ILE Chi-restraints excluded: chain x residue 4 ILE Chi-restraints excluded: chain z residue 2 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: 0.9990 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 = 0.3014 r_free = 0.3014 target = 0.050959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.045046 restraints weight = 26194.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.046134 restraints weight = 11764.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.046862 restraints weight = 7372.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.047341 restraints weight = 5417.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.047667 restraints weight = 4370.435| |-----------------------------------------------------------------------------| r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.7282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.068 0.242 4640 Z= 2.760 Angle : 3.336 15.152 5920 Z= 1.672 Chirality : 0.198 0.599 720 Planarity : 0.013 0.036 560 Dihedral : 17.051 58.787 640 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 99.53 Ramachandran Plot: Outliers : 0.31 % Allowed : 22.81 % Favored : 76.88 % Rotamer: Outliers : 37.08 % Allowed : 18.96 % Favored : 43.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.75 % 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: -4.05 (0.40), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.08 (0.31), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.069 0.011 TYRAM 5 Details of bonding type rmsd covalent geometry : bond 0.06879 ( 4560) covalent geometry : angle 3.33630 ( 5920) hydrogen bonds : bond 0.22048 ( 91) hydrogen bonds : angle 11.23106 ( 273) Misc. bond : bond 0.00909 ( 80) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 13 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 5 TYR cc_start: 0.8563 (OUTLIER) cc_final: 0.8239 (p90) REVERT: 7 5 TYR cc_start: 0.8505 (OUTLIER) cc_final: 0.7813 (p90) REVERT: 7 6 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8218 (pttt) REVERT: AC 5 TYR cc_start: 0.7659 (OUTLIER) cc_final: 0.4281 (m-10) REVERT: AM 5 TYR cc_start: 0.8437 (OUTLIER) cc_final: 0.8123 (p90) REVERT: AS 5 TYR cc_start: 0.7833 (OUTLIER) cc_final: 0.4325 (m-10) REVERT: AW 5 TYR cc_start: 0.8657 (OUTLIER) cc_final: 0.8049 (p90) REVERT: AY 5 TYR cc_start: 0.8553 (OUTLIER) cc_final: 0.8021 (p90) REVERT: Ai 1 LYS cc_start: 0.9485 (pttm) cc_final: 0.9026 (tptp) REVERT: Ai 5 TYR cc_start: 0.7791 (OUTLIER) cc_final: 0.4131 (m-10) REVERT: Ao 5 TYR cc_start: 0.8528 (OUTLIER) cc_final: 0.8201 (p90) REVERT: Aq 5 TYR cc_start: 0.8591 (OUTLIER) cc_final: 0.8249 (p90) REVERT: Au 5 TYR cc_start: 0.8573 (OUTLIER) cc_final: 0.8105 (p90) REVERT: Aw 5 TYR cc_start: 0.8009 (OUTLIER) cc_final: 0.7656 (p90) REVERT: g 5 TYR cc_start: 0.7598 (OUTLIER) cc_final: 0.4316 (m-10) REVERT: q 5 TYR cc_start: 0.8539 (OUTLIER) cc_final: 0.8027 (p90) REVERT: w 1 LYS cc_start: 0.9406 (pttm) cc_final: 0.8907 (tptp) REVERT: w 5 TYR cc_start: 0.7890 (OUTLIER) cc_final: 0.4227 (m-10) outliers start: 178 outliers final: 133 residues processed: 191 average time/residue: 0.0502 time to fit residues: 13.0126 Evaluate side-chains 162 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 13 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 2 ILE Chi-restraints excluded: chain 1 residue 3 ILE Chi-restraints excluded: chain 1 residue 4 ILE Chi-restraints excluded: chain 1 residue 5 TYR Chi-restraints excluded: chain 2 residue 2 ILE Chi-restraints excluded: chain 3 residue 2 ILE Chi-restraints excluded: chain 3 residue 5 TYR Chi-restraints excluded: chain 5 residue 4 ILE Chi-restraints excluded: chain 5 residue 5 TYR Chi-restraints excluded: chain 6 residue 2 ILE Chi-restraints excluded: chain 6 residue 4 ILE Chi-restraints excluded: chain 7 residue 2 ILE Chi-restraints excluded: chain 7 residue 3 ILE Chi-restraints excluded: chain 7 residue 4 ILE Chi-restraints excluded: chain 7 residue 5 TYR Chi-restraints excluded: chain 7 residue 6 LYS Chi-restraints excluded: chain 8 residue 4 ILE Chi-restraints excluded: chain 9 residue 2 ILE Chi-restraints excluded: chain 9 residue 3 ILE Chi-restraints excluded: chain 9 residue 5 TYR Chi-restraints excluded: chain AA residue 2 ILE Chi-restraints excluded: chain AA residue 3 ILE Chi-restraints excluded: chain AA residue 5 TYR Chi-restraints excluded: chain AB residue 4 ILE Chi-restraints excluded: chain AC residue 3 ILE Chi-restraints excluded: chain AC residue 5 TYR Chi-restraints excluded: chain AD residue 2 ILE Chi-restraints excluded: chain AD residue 4 ILE Chi-restraints excluded: chain AE 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 AG residue 2 ILE Chi-restraints excluded: chain AG residue 4 ILE Chi-restraints excluded: chain AG residue 5 TYR Chi-restraints excluded: chain AI residue 2 ILE Chi-restraints excluded: chain AI residue 3 ILE Chi-restraints excluded: chain AI residue 4 ILE Chi-restraints excluded: chain AJ residue 4 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 AL residue 4 ILE Chi-restraints excluded: chain AM residue 2 ILE Chi-restraints excluded: chain AM residue 5 TYR Chi-restraints excluded: chain AN residue 2 ILE Chi-restraints excluded: chain AN residue 4 ILE Chi-restraints excluded: chain AO residue 2 ILE Chi-restraints excluded: chain AO residue 4 ILE Chi-restraints excluded: chain AP residue 2 ILE Chi-restraints excluded: chain AP residue 4 ILE Chi-restraints excluded: chain AQ residue 3 ILE Chi-restraints excluded: chain AQ residue 5 TYR Chi-restraints excluded: chain AR residue 2 ILE Chi-restraints excluded: chain AR residue 4 ILE Chi-restraints excluded: chain AR residue 6 LYS Chi-restraints excluded: chain AS residue 5 TYR Chi-restraints excluded: chain AT residue 2 ILE Chi-restraints excluded: chain AU residue 3 ILE Chi-restraints excluded: chain AU residue 4 ILE Chi-restraints excluded: chain AU residue 5 TYR Chi-restraints excluded: chain AV residue 2 ILE Chi-restraints excluded: chain AW residue 4 ILE Chi-restraints excluded: chain AW residue 5 TYR Chi-restraints excluded: chain AY residue 2 ILE Chi-restraints excluded: chain AY residue 3 ILE Chi-restraints excluded: chain AY residue 5 TYR Chi-restraints excluded: chain AZ residue 2 ILE Chi-restraints excluded: chain AZ residue 4 ILE Chi-restraints excluded: chain Aa residue 3 ILE Chi-restraints excluded: chain Ab residue 4 ILE Chi-restraints excluded: chain Ac residue 2 ILE Chi-restraints excluded: chain Ac residue 4 ILE Chi-restraints excluded: chain Ac residue 5 TYR Chi-restraints excluded: chain Ad residue 2 ILE Chi-restraints excluded: chain Ae residue 2 ILE Chi-restraints excluded: chain Ae 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 4 ILE Chi-restraints excluded: chain Ag residue 5 TYR Chi-restraints excluded: chain Ah residue 4 ILE Chi-restraints excluded: chain Ah residue 6 LYS Chi-restraints excluded: chain Ai residue 3 ILE Chi-restraints excluded: chain Ai residue 5 TYR Chi-restraints excluded: chain Aj residue 2 ILE Chi-restraints excluded: chain Aj residue 4 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 Al residue 4 ILE Chi-restraints excluded: chain Am residue 4 ILE Chi-restraints excluded: chain Am residue 5 TYR Chi-restraints excluded: chain An residue 2 ILE Chi-restraints excluded: chain Ao residue 3 ILE Chi-restraints excluded: chain Ao residue 5 TYR Chi-restraints excluded: chain Ap residue 4 ILE Chi-restraints excluded: chain Aq residue 3 ILE Chi-restraints excluded: chain Aq residue 4 ILE Chi-restraints excluded: chain Aq residue 5 TYR Chi-restraints excluded: chain Ar residue 2 ILE Chi-restraints excluded: chain Ar residue 4 ILE Chi-restraints excluded: chain As residue 4 ILE Chi-restraints excluded: chain At residue 2 ILE Chi-restraints excluded: chain At residue 4 ILE Chi-restraints excluded: chain Au residue 2 ILE Chi-restraints excluded: chain Au residue 4 ILE Chi-restraints excluded: chain Au residue 5 TYR Chi-restraints excluded: chain Av residue 2 ILE Chi-restraints excluded: chain Av residue 4 ILE Chi-restraints excluded: chain Aw residue 3 ILE Chi-restraints excluded: chain Aw residue 5 TYR Chi-restraints excluded: chain f residue 4 ILE Chi-restraints excluded: chain g residue 5 TYR Chi-restraints excluded: chain h residue 2 ILE Chi-restraints excluded: chain i residue 4 ILE Chi-restraints excluded: chain i residue 5 TYR Chi-restraints excluded: chain j residue 2 ILE Chi-restraints excluded: chain k residue 2 ILE Chi-restraints excluded: chain k residue 4 ILE Chi-restraints excluded: chain k residue 5 TYR Chi-restraints excluded: chain m residue 2 ILE Chi-restraints excluded: chain m residue 4 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 p residue 4 ILE Chi-restraints excluded: chain q residue 4 ILE Chi-restraints excluded: chain q residue 5 TYR Chi-restraints excluded: chain r residue 2 ILE Chi-restraints excluded: chain r residue 4 ILE Chi-restraints excluded: chain s residue 2 ILE Chi-restraints excluded: chain s 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 4 ILE Chi-restraints excluded: chain u residue 3 ILE Chi-restraints excluded: chain u residue 5 TYR Chi-restraints excluded: chain v residue 2 ILE Chi-restraints excluded: chain v residue 4 ILE Chi-restraints excluded: chain v residue 6 LYS Chi-restraints excluded: chain w residue 3 ILE Chi-restraints excluded: chain w residue 4 ILE Chi-restraints excluded: chain w residue 5 TYR Chi-restraints excluded: chain x residue 2 ILE Chi-restraints excluded: chain x residue 4 ILE Chi-restraints excluded: chain z residue 2 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: 0.9990 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 = 0.3013 r_free = 0.3013 target = 0.050896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.044978 restraints weight = 26529.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.046085 restraints weight = 11965.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.046837 restraints weight = 7474.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.047337 restraints weight = 5464.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.047648 restraints weight = 4365.438| |-----------------------------------------------------------------------------| r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.7321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.068 0.256 4640 Z= 2.762 Angle : 3.349 13.592 5920 Z= 1.677 Chirality : 0.198 0.598 720 Planarity : 0.013 0.036 560 Dihedral : 17.248 59.109 640 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 101.45 Ramachandran Plot: Outliers : 0.62 % Allowed : 24.69 % Favored : 74.69 % Rotamer: Outliers : 37.29 % Allowed : 21.67 % Favored : 41.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.25 % 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: -4.07 (0.41), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.10 (0.31), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.070 0.011 TYRAM 5 Details of bonding type rmsd covalent geometry : bond 0.06889 ( 4560) covalent geometry : angle 3.34931 ( 5920) hydrogen bonds : bond 0.22106 ( 91) hydrogen bonds : angle 11.18069 ( 273) Misc. bond : bond 0.00904 ( 80) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 13 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 5 TYR cc_start: 0.8519 (OUTLIER) cc_final: 0.8198 (p90) REVERT: 7 5 TYR cc_start: 0.8460 (OUTLIER) cc_final: 0.7769 (p90) REVERT: 7 6 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8173 (pttt) REVERT: AC 5 TYR cc_start: 0.7662 (OUTLIER) cc_final: 0.4220 (m-10) REVERT: AM 5 TYR cc_start: 0.8419 (OUTLIER) cc_final: 0.8154 (p90) REVERT: AS 5 TYR cc_start: 0.7766 (OUTLIER) cc_final: 0.4292 (m-10) REVERT: AW 5 TYR cc_start: 0.8632 (OUTLIER) cc_final: 0.8021 (p90) REVERT: AY 5 TYR cc_start: 0.8494 (OUTLIER) cc_final: 0.7958 (p90) REVERT: Ai 1 LYS cc_start: 0.9487 (pttm) cc_final: 0.9030 (tptp) REVERT: Ai 5 TYR cc_start: 0.7740 (OUTLIER) cc_final: 0.4122 (m-10) REVERT: Ao 5 TYR cc_start: 0.8470 (OUTLIER) cc_final: 0.8146 (p90) REVERT: Aq 5 TYR cc_start: 0.8528 (OUTLIER) cc_final: 0.8192 (p90) REVERT: Au 5 TYR cc_start: 0.8529 (OUTLIER) cc_final: 0.8059 (p90) REVERT: Aw 5 TYR cc_start: 0.7962 (OUTLIER) cc_final: 0.7619 (p90) REVERT: g 5 TYR cc_start: 0.7628 (OUTLIER) cc_final: 0.4308 (m-10) REVERT: q 5 TYR cc_start: 0.8496 (OUTLIER) cc_final: 0.7923 (p90) REVERT: w 1 LYS cc_start: 0.9398 (pttm) cc_final: 0.8895 (tptp) REVERT: w 5 TYR cc_start: 0.7841 (OUTLIER) cc_final: 0.4147 (m-10) REVERT: y 5 TYR cc_start: 0.8317 (OUTLIER) cc_final: 0.6902 (p90) outliers start: 179 outliers final: 141 residues processed: 192 average time/residue: 0.0546 time to fit residues: 13.7747 Evaluate side-chains 171 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 13 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 2 ILE Chi-restraints excluded: chain 1 residue 3 ILE Chi-restraints excluded: chain 1 residue 4 ILE Chi-restraints excluded: chain 1 residue 5 TYR Chi-restraints excluded: chain 2 residue 2 ILE Chi-restraints excluded: chain 3 residue 2 ILE Chi-restraints excluded: chain 3 residue 5 TYR Chi-restraints excluded: chain 4 residue 4 ILE Chi-restraints excluded: chain 5 residue 3 ILE Chi-restraints excluded: chain 5 residue 4 ILE Chi-restraints excluded: chain 5 residue 5 TYR Chi-restraints excluded: chain 6 residue 2 ILE Chi-restraints excluded: chain 6 residue 4 ILE Chi-restraints excluded: chain 7 residue 2 ILE Chi-restraints excluded: chain 7 residue 3 ILE Chi-restraints excluded: chain 7 residue 4 ILE Chi-restraints excluded: chain 7 residue 5 TYR Chi-restraints excluded: chain 7 residue 6 LYS Chi-restraints excluded: chain 8 residue 4 ILE Chi-restraints excluded: chain 9 residue 2 ILE Chi-restraints excluded: chain 9 residue 3 ILE Chi-restraints excluded: chain 9 residue 5 TYR Chi-restraints excluded: chain AA residue 2 ILE Chi-restraints excluded: chain AA residue 3 ILE Chi-restraints excluded: chain AA residue 5 TYR Chi-restraints excluded: chain AB residue 4 ILE Chi-restraints excluded: chain AC residue 3 ILE Chi-restraints excluded: chain AC residue 5 TYR Chi-restraints excluded: chain AD residue 2 ILE Chi-restraints excluded: chain AD residue 4 ILE Chi-restraints excluded: chain AE 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 AG residue 2 ILE Chi-restraints excluded: chain AG residue 4 ILE Chi-restraints excluded: chain AG residue 5 TYR Chi-restraints excluded: chain AI residue 2 ILE Chi-restraints excluded: chain AI residue 3 ILE Chi-restraints excluded: chain AI residue 4 ILE Chi-restraints excluded: chain AI residue 6 LYS Chi-restraints excluded: chain AJ residue 4 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 AL residue 4 ILE Chi-restraints excluded: chain AM residue 2 ILE Chi-restraints excluded: chain AM residue 5 TYR Chi-restraints excluded: chain AN residue 2 ILE Chi-restraints excluded: chain AN residue 4 ILE Chi-restraints excluded: chain AO residue 2 ILE Chi-restraints excluded: chain AO residue 4 ILE Chi-restraints excluded: chain AP residue 2 ILE Chi-restraints excluded: chain AP residue 4 ILE Chi-restraints excluded: chain AQ residue 3 ILE Chi-restraints excluded: chain AQ residue 5 TYR Chi-restraints excluded: chain AR residue 2 ILE Chi-restraints excluded: chain AR residue 4 ILE Chi-restraints excluded: chain AR residue 6 LYS Chi-restraints excluded: chain AS residue 3 ILE Chi-restraints excluded: chain AS residue 5 TYR Chi-restraints excluded: chain AT residue 2 ILE Chi-restraints excluded: chain AU residue 3 ILE Chi-restraints excluded: chain AU residue 4 ILE Chi-restraints excluded: chain AU residue 5 TYR Chi-restraints excluded: chain AV residue 2 ILE Chi-restraints excluded: chain AW residue 4 ILE Chi-restraints excluded: chain AW residue 5 TYR Chi-restraints excluded: chain AY residue 2 ILE Chi-restraints excluded: chain AY residue 3 ILE Chi-restraints excluded: chain AY residue 5 TYR Chi-restraints excluded: chain AZ residue 2 ILE Chi-restraints excluded: chain AZ residue 4 ILE Chi-restraints excluded: chain Aa residue 3 ILE Chi-restraints excluded: chain Ab residue 4 ILE Chi-restraints excluded: chain Ac residue 2 ILE Chi-restraints excluded: chain Ac residue 4 ILE Chi-restraints excluded: chain Ac residue 5 TYR Chi-restraints excluded: chain Ad residue 2 ILE Chi-restraints excluded: chain Ad residue 4 ILE Chi-restraints excluded: chain Ae residue 2 ILE Chi-restraints excluded: chain Ae 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 4 ILE Chi-restraints excluded: chain Ah residue 4 ILE Chi-restraints excluded: chain Ah residue 6 LYS Chi-restraints excluded: chain Ai residue 3 ILE Chi-restraints excluded: chain Ai residue 5 TYR Chi-restraints excluded: chain Aj residue 2 ILE Chi-restraints excluded: chain Aj residue 4 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 Al residue 4 ILE Chi-restraints excluded: chain Am residue 4 ILE Chi-restraints excluded: chain Am residue 5 TYR Chi-restraints excluded: chain An residue 2 ILE Chi-restraints excluded: chain Ao residue 3 ILE Chi-restraints excluded: chain Ao residue 5 TYR Chi-restraints excluded: chain Ap residue 4 ILE Chi-restraints excluded: chain Aq residue 3 ILE Chi-restraints excluded: chain Aq residue 4 ILE Chi-restraints excluded: chain Aq residue 5 TYR 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 3 ILE Chi-restraints excluded: chain As residue 4 ILE Chi-restraints excluded: chain At residue 2 ILE Chi-restraints excluded: chain At residue 4 ILE Chi-restraints excluded: chain Au residue 2 ILE Chi-restraints excluded: chain Au residue 3 ILE Chi-restraints excluded: chain Au residue 4 ILE Chi-restraints excluded: chain Au residue 5 TYR Chi-restraints excluded: chain Av residue 2 ILE Chi-restraints excluded: chain Av residue 4 ILE Chi-restraints excluded: chain Aw residue 3 ILE Chi-restraints excluded: chain Aw residue 5 TYR Chi-restraints excluded: chain f residue 4 ILE Chi-restraints excluded: chain g residue 5 TYR Chi-restraints excluded: chain h residue 2 ILE Chi-restraints excluded: chain h residue 4 ILE Chi-restraints excluded: chain i residue 4 ILE Chi-restraints excluded: chain j residue 2 ILE Chi-restraints excluded: chain k residue 2 ILE Chi-restraints excluded: chain k residue 4 ILE Chi-restraints excluded: chain k residue 5 TYR Chi-restraints excluded: chain m residue 2 ILE Chi-restraints excluded: chain m residue 4 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 p residue 4 ILE Chi-restraints excluded: chain q residue 4 ILE Chi-restraints excluded: chain q residue 5 TYR Chi-restraints excluded: chain r residue 2 ILE Chi-restraints excluded: chain r residue 4 ILE Chi-restraints excluded: chain s residue 2 ILE Chi-restraints excluded: chain s 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 4 ILE Chi-restraints excluded: chain u residue 3 ILE Chi-restraints excluded: chain u residue 5 TYR Chi-restraints excluded: chain v residue 2 ILE Chi-restraints excluded: chain v residue 4 ILE Chi-restraints excluded: chain v residue 6 LYS Chi-restraints excluded: chain w residue 3 ILE Chi-restraints excluded: chain w residue 4 ILE Chi-restraints excluded: chain w residue 5 TYR Chi-restraints excluded: chain x residue 2 ILE Chi-restraints excluded: chain x residue 4 ILE Chi-restraints excluded: chain y residue 1 LYS Chi-restraints excluded: chain y residue 5 TYR Chi-restraints excluded: chain z residue 2 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: 1.9990 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 = 0.3011 r_free = 0.3011 target = 0.050896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.044970 restraints weight = 26497.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.046082 restraints weight = 11827.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.046825 restraints weight = 7362.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.047300 restraints weight = 5388.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.047624 restraints weight = 4341.116| |-----------------------------------------------------------------------------| r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.7342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.068 0.248 4640 Z= 2.761 Angle : 3.352 14.692 5920 Z= 1.676 Chirality : 0.197 0.602 720 Planarity : 0.014 0.039 560 Dihedral : 17.332 59.208 640 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 101.74 Ramachandran Plot: Outliers : 0.62 % Allowed : 25.00 % Favored : 74.38 % Rotamer: Outliers : 39.58 % Allowed : 22.92 % Favored : 37.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.25 % 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: -4.02 (0.41), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.05 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.080 0.011 TYRAI 5 Details of bonding type rmsd covalent geometry : bond 0.06885 ( 4560) covalent geometry : angle 3.35216 ( 5920) hydrogen bonds : bond 0.22139 ( 91) hydrogen bonds : angle 11.16100 ( 273) Misc. bond : bond 0.00902 ( 80) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 13 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 5 TYR cc_start: 0.8579 (OUTLIER) cc_final: 0.8259 (p90) REVERT: 7 5 TYR cc_start: 0.8514 (OUTLIER) cc_final: 0.7814 (p90) REVERT: 7 6 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8227 (pttt) REVERT: AC 5 TYR cc_start: 0.7710 (OUTLIER) cc_final: 0.4244 (m-10) REVERT: AM 5 TYR cc_start: 0.8487 (OUTLIER) cc_final: 0.8177 (p90) REVERT: AS 5 TYR cc_start: 0.7774 (OUTLIER) cc_final: 0.4286 (m-10) REVERT: AW 5 TYR cc_start: 0.8678 (OUTLIER) cc_final: 0.8074 (p90) REVERT: AY 5 TYR cc_start: 0.8553 (OUTLIER) cc_final: 0.7985 (p90) REVERT: Ai 1 LYS cc_start: 0.9499 (pttm) cc_final: 0.9078 (tptp) REVERT: Ai 5 TYR cc_start: 0.7784 (OUTLIER) cc_final: 0.4145 (m-10) REVERT: Ao 5 TYR cc_start: 0.8527 (OUTLIER) cc_final: 0.8206 (p90) REVERT: Ao 6 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8540 (pttt) REVERT: Aq 5 TYR cc_start: 0.8573 (OUTLIER) cc_final: 0.8228 (p90) REVERT: Au 5 TYR cc_start: 0.8576 (OUTLIER) cc_final: 0.8098 (p90) REVERT: Aw 5 TYR cc_start: 0.7882 (OUTLIER) cc_final: 0.7564 (p90) REVERT: g 5 TYR cc_start: 0.7568 (OUTLIER) cc_final: 0.4196 (m-10) REVERT: i 5 TYR cc_start: 0.8462 (OUTLIER) cc_final: 0.7119 (p90) REVERT: q 5 TYR cc_start: 0.8540 (OUTLIER) cc_final: 0.8020 (p90) REVERT: w 1 LYS cc_start: 0.9416 (pttm) cc_final: 0.8912 (tptp) REVERT: w 5 TYR cc_start: 0.7890 (OUTLIER) cc_final: 0.4186 (m-10) REVERT: y 5 TYR cc_start: 0.8388 (OUTLIER) cc_final: 0.6949 (p90) outliers start: 190 outliers final: 147 residues processed: 203 average time/residue: 0.0611 time to fit residues: 15.9132 Evaluate side-chains 179 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 13 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 2 ILE Chi-restraints excluded: chain 1 residue 3 ILE Chi-restraints excluded: chain 1 residue 4 ILE Chi-restraints excluded: chain 1 residue 5 TYR Chi-restraints excluded: chain 2 residue 2 ILE Chi-restraints excluded: chain 3 residue 2 ILE Chi-restraints excluded: chain 3 residue 5 TYR Chi-restraints excluded: chain 3 residue 6 LYS Chi-restraints excluded: chain 4 residue 4 ILE Chi-restraints excluded: chain 5 residue 3 ILE Chi-restraints excluded: chain 5 residue 4 ILE Chi-restraints excluded: chain 5 residue 5 TYR Chi-restraints excluded: chain 6 residue 2 ILE Chi-restraints excluded: chain 6 residue 4 ILE Chi-restraints excluded: chain 7 residue 2 ILE Chi-restraints excluded: chain 7 residue 3 ILE Chi-restraints excluded: chain 7 residue 4 ILE Chi-restraints excluded: chain 7 residue 5 TYR Chi-restraints excluded: chain 7 residue 6 LYS Chi-restraints excluded: chain 8 residue 4 ILE Chi-restraints excluded: chain 9 residue 2 ILE Chi-restraints excluded: chain 9 residue 3 ILE Chi-restraints excluded: chain 9 residue 5 TYR Chi-restraints excluded: chain AA residue 2 ILE Chi-restraints excluded: chain AA residue 3 ILE Chi-restraints excluded: chain AA residue 5 TYR Chi-restraints excluded: chain AB residue 4 ILE Chi-restraints excluded: chain AB residue 6 LYS Chi-restraints excluded: chain AC residue 3 ILE Chi-restraints excluded: chain AC residue 5 TYR Chi-restraints excluded: chain AD residue 2 ILE Chi-restraints excluded: chain AD residue 4 ILE Chi-restraints excluded: chain AE 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 AG residue 2 ILE Chi-restraints excluded: chain AG residue 4 ILE Chi-restraints excluded: chain AG residue 5 TYR Chi-restraints excluded: chain AI residue 2 ILE Chi-restraints excluded: chain AI residue 3 ILE Chi-restraints excluded: chain AI residue 4 ILE Chi-restraints excluded: chain AI residue 6 LYS Chi-restraints excluded: chain AJ residue 4 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 AL residue 4 ILE Chi-restraints excluded: chain AM residue 2 ILE Chi-restraints excluded: chain AM residue 5 TYR Chi-restraints excluded: chain AN residue 2 ILE Chi-restraints excluded: chain AN residue 4 ILE Chi-restraints excluded: chain AO residue 2 ILE Chi-restraints excluded: chain AO residue 4 ILE Chi-restraints excluded: chain AP residue 2 ILE Chi-restraints excluded: chain AP residue 4 ILE Chi-restraints excluded: chain AQ residue 3 ILE Chi-restraints excluded: chain AR residue 2 ILE Chi-restraints excluded: chain AR residue 4 ILE Chi-restraints excluded: chain AR residue 6 LYS Chi-restraints excluded: chain AS residue 3 ILE Chi-restraints excluded: chain AS residue 5 TYR Chi-restraints excluded: chain AT residue 2 ILE Chi-restraints excluded: chain AU residue 3 ILE Chi-restraints excluded: chain AU residue 4 ILE Chi-restraints excluded: chain AU residue 5 TYR Chi-restraints excluded: chain AV residue 2 ILE Chi-restraints excluded: chain AW residue 4 ILE Chi-restraints excluded: chain AW residue 5 TYR Chi-restraints excluded: chain AY residue 2 ILE Chi-restraints excluded: chain AY residue 3 ILE Chi-restraints excluded: chain AY residue 5 TYR Chi-restraints excluded: chain AZ residue 2 ILE Chi-restraints excluded: chain AZ residue 4 ILE Chi-restraints excluded: chain Aa residue 3 ILE Chi-restraints excluded: chain Aa residue 5 TYR Chi-restraints excluded: chain Ab residue 4 ILE Chi-restraints excluded: chain Ac residue 2 ILE Chi-restraints excluded: chain Ac residue 4 ILE Chi-restraints excluded: chain Ac residue 5 TYR Chi-restraints excluded: chain Ad residue 2 ILE Chi-restraints excluded: chain Ad residue 4 ILE Chi-restraints excluded: chain Ae residue 2 ILE Chi-restraints excluded: chain Ae 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 4 ILE Chi-restraints excluded: chain Ah residue 4 ILE Chi-restraints excluded: chain Ah residue 6 LYS Chi-restraints excluded: chain Ai residue 3 ILE Chi-restraints excluded: chain Ai residue 5 TYR Chi-restraints excluded: chain Aj residue 2 ILE Chi-restraints excluded: chain Aj residue 4 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 Al residue 4 ILE Chi-restraints excluded: chain Am residue 4 ILE Chi-restraints excluded: chain Am residue 5 TYR Chi-restraints excluded: chain An residue 2 ILE Chi-restraints excluded: chain Ao residue 3 ILE Chi-restraints excluded: chain Ao residue 5 TYR Chi-restraints excluded: chain Ao residue 6 LYS Chi-restraints excluded: chain Ap residue 4 ILE Chi-restraints excluded: chain Aq residue 3 ILE Chi-restraints excluded: chain Aq residue 4 ILE Chi-restraints excluded: chain Aq residue 5 TYR 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 3 ILE Chi-restraints excluded: chain As residue 4 ILE Chi-restraints excluded: chain At residue 2 ILE Chi-restraints excluded: chain At residue 4 ILE Chi-restraints excluded: chain Au residue 2 ILE Chi-restraints excluded: chain Au residue 3 ILE Chi-restraints excluded: chain Au residue 4 ILE Chi-restraints excluded: chain Au residue 5 TYR Chi-restraints excluded: chain Av residue 2 ILE Chi-restraints excluded: chain Av residue 4 ILE Chi-restraints excluded: chain Aw residue 3 ILE Chi-restraints excluded: chain Aw residue 5 TYR Chi-restraints excluded: chain f residue 4 ILE Chi-restraints excluded: chain f residue 6 LYS Chi-restraints excluded: chain g residue 5 TYR Chi-restraints excluded: chain h residue 2 ILE Chi-restraints excluded: chain h residue 4 ILE Chi-restraints excluded: chain i residue 4 ILE Chi-restraints excluded: chain i residue 5 TYR Chi-restraints excluded: chain j residue 2 ILE Chi-restraints excluded: chain k residue 2 ILE Chi-restraints excluded: chain k residue 4 ILE Chi-restraints excluded: chain k residue 5 TYR Chi-restraints excluded: chain m residue 2 ILE Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain m residue 4 ILE Chi-restraints excluded: chain n residue 2 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 p residue 4 ILE Chi-restraints excluded: chain q residue 4 ILE Chi-restraints excluded: chain q residue 5 TYR Chi-restraints excluded: chain r residue 2 ILE Chi-restraints excluded: chain r residue 4 ILE Chi-restraints excluded: chain s residue 2 ILE Chi-restraints excluded: chain s 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 4 ILE Chi-restraints excluded: chain u residue 1 LYS Chi-restraints excluded: chain u residue 3 ILE Chi-restraints excluded: chain u residue 5 TYR Chi-restraints excluded: chain v residue 2 ILE Chi-restraints excluded: chain v residue 4 ILE Chi-restraints excluded: chain v residue 6 LYS Chi-restraints excluded: chain w residue 3 ILE Chi-restraints excluded: chain w residue 4 ILE Chi-restraints excluded: chain w residue 5 TYR Chi-restraints excluded: chain x residue 2 ILE Chi-restraints excluded: chain x residue 4 ILE Chi-restraints excluded: chain y residue 1 LYS Chi-restraints excluded: chain y residue 5 TYR Chi-restraints excluded: chain z residue 2 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: 0.9990 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 = 0.3009 r_free = 0.3009 target = 0.050857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.044941 restraints weight = 26248.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.046046 restraints weight = 11766.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.046785 restraints weight = 7338.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.047290 restraints weight = 5381.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.047598 restraints weight = 4297.516| |-----------------------------------------------------------------------------| r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.7347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.068 0.248 4640 Z= 2.762 Angle : 3.355 15.028 5920 Z= 1.678 Chirality : 0.198 0.603 720 Planarity : 0.014 0.041 560 Dihedral : 17.370 59.369 640 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 102.03 Ramachandran Plot: Outliers : 0.62 % Allowed : 25.62 % Favored : 73.75 % Rotamer: Outliers : 38.75 % Allowed : 25.42 % Favored : 35.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.25 % 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: -3.99 (0.42), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.03 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.076 0.011 TYRAs 5 Details of bonding type rmsd covalent geometry : bond 0.06886 ( 4560) covalent geometry : angle 3.35517 ( 5920) hydrogen bonds : bond 0.22119 ( 91) hydrogen bonds : angle 11.14266 ( 273) Misc. bond : bond 0.00903 ( 80) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 13 time to evaluate : 0.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 5 TYR cc_start: 0.8585 (OUTLIER) cc_final: 0.8268 (p90) REVERT: 7 5 TYR cc_start: 0.8510 (OUTLIER) cc_final: 0.7819 (p90) REVERT: 7 6 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8234 (pttt) REVERT: AC 5 TYR cc_start: 0.7717 (OUTLIER) cc_final: 0.4249 (m-10) REVERT: AM 5 TYR cc_start: 0.8484 (OUTLIER) cc_final: 0.8212 (p90) REVERT: AS 5 TYR cc_start: 0.7773 (OUTLIER) cc_final: 0.4269 (m-10) REVERT: AW 5 TYR cc_start: 0.8690 (OUTLIER) cc_final: 0.8085 (p90) REVERT: AY 5 TYR cc_start: 0.8558 (OUTLIER) cc_final: 0.7996 (p90) REVERT: Ai 1 LYS cc_start: 0.9499 (pttm) cc_final: 0.9080 (tptp) REVERT: Ai 5 TYR cc_start: 0.7792 (OUTLIER) cc_final: 0.4158 (m-10) REVERT: Ao 5 TYR cc_start: 0.8532 (OUTLIER) cc_final: 0.8211 (p90) REVERT: Ao 6 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8548 (pttt) REVERT: Aq 5 TYR cc_start: 0.8579 (OUTLIER) cc_final: 0.8235 (p90) REVERT: Au 5 TYR cc_start: 0.8581 (OUTLIER) cc_final: 0.8104 (p90) REVERT: Aw 5 TYR cc_start: 0.7957 (OUTLIER) cc_final: 0.7618 (p90) REVERT: g 5 TYR cc_start: 0.7641 (OUTLIER) cc_final: 0.4200 (m-10) REVERT: i 5 TYR cc_start: 0.8456 (OUTLIER) cc_final: 0.7101 (p90) REVERT: q 5 TYR cc_start: 0.8544 (OUTLIER) cc_final: 0.7996 (p90) REVERT: w 1 LYS cc_start: 0.9416 (pttm) cc_final: 0.8911 (tptp) REVERT: w 5 TYR cc_start: 0.7888 (OUTLIER) cc_final: 0.4178 (m-10) REVERT: y 5 TYR cc_start: 0.8395 (OUTLIER) cc_final: 0.6890 (p90) outliers start: 186 outliers final: 150 residues processed: 199 average time/residue: 0.0624 time to fit residues: 15.9862 Evaluate side-chains 182 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 13 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 2 ILE Chi-restraints excluded: chain 1 residue 3 ILE Chi-restraints excluded: chain 1 residue 4 ILE Chi-restraints excluded: chain 1 residue 5 TYR Chi-restraints excluded: chain 2 residue 2 ILE Chi-restraints excluded: chain 3 residue 2 ILE Chi-restraints excluded: chain 3 residue 5 TYR Chi-restraints excluded: chain 3 residue 6 LYS Chi-restraints excluded: chain 4 residue 4 ILE Chi-restraints excluded: chain 5 residue 3 ILE Chi-restraints excluded: chain 5 residue 4 ILE Chi-restraints excluded: chain 5 residue 5 TYR Chi-restraints excluded: chain 6 residue 2 ILE Chi-restraints excluded: chain 6 residue 4 ILE Chi-restraints excluded: chain 7 residue 2 ILE Chi-restraints excluded: chain 7 residue 3 ILE Chi-restraints excluded: chain 7 residue 4 ILE Chi-restraints excluded: chain 7 residue 5 TYR Chi-restraints excluded: chain 7 residue 6 LYS Chi-restraints excluded: chain 8 residue 4 ILE Chi-restraints excluded: chain 9 residue 2 ILE Chi-restraints excluded: chain 9 residue 3 ILE Chi-restraints excluded: chain 9 residue 5 TYR Chi-restraints excluded: chain AA residue 2 ILE Chi-restraints excluded: chain AA residue 3 ILE Chi-restraints excluded: chain AA residue 5 TYR Chi-restraints excluded: chain AB residue 4 ILE Chi-restraints excluded: chain AB residue 6 LYS Chi-restraints excluded: chain AC residue 3 ILE Chi-restraints excluded: chain AC residue 5 TYR Chi-restraints excluded: chain AD residue 2 ILE Chi-restraints excluded: chain AD residue 4 ILE Chi-restraints excluded: chain AE 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 AG residue 2 ILE Chi-restraints excluded: chain AG residue 4 ILE Chi-restraints excluded: chain AG residue 5 TYR Chi-restraints excluded: chain AI residue 2 ILE Chi-restraints excluded: chain AI residue 3 ILE Chi-restraints excluded: chain AI residue 4 ILE Chi-restraints excluded: chain AI residue 6 LYS Chi-restraints excluded: chain AJ residue 4 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 AL residue 4 ILE Chi-restraints excluded: chain AM residue 2 ILE Chi-restraints excluded: chain AM residue 5 TYR Chi-restraints excluded: chain AN residue 2 ILE Chi-restraints excluded: chain AN residue 4 ILE Chi-restraints excluded: chain AN residue 6 LYS Chi-restraints excluded: chain AO residue 2 ILE Chi-restraints excluded: chain AO residue 4 ILE Chi-restraints excluded: chain AP residue 2 ILE Chi-restraints excluded: chain AP residue 4 ILE Chi-restraints excluded: chain AQ residue 3 ILE Chi-restraints excluded: chain AQ residue 5 TYR Chi-restraints excluded: chain AR residue 2 ILE Chi-restraints excluded: chain AR residue 4 ILE Chi-restraints excluded: chain AR residue 6 LYS Chi-restraints excluded: chain AS residue 3 ILE Chi-restraints excluded: chain AS residue 5 TYR Chi-restraints excluded: chain AT residue 2 ILE Chi-restraints excluded: chain AU residue 3 ILE Chi-restraints excluded: chain AU residue 4 ILE Chi-restraints excluded: chain AU residue 5 TYR Chi-restraints excluded: chain AV residue 2 ILE Chi-restraints excluded: chain AW residue 4 ILE Chi-restraints excluded: chain AW residue 5 TYR Chi-restraints excluded: chain AY residue 2 ILE Chi-restraints excluded: chain AY residue 3 ILE Chi-restraints excluded: chain AY residue 5 TYR Chi-restraints excluded: chain AZ residue 2 ILE Chi-restraints excluded: chain AZ residue 4 ILE Chi-restraints excluded: chain Aa residue 3 ILE Chi-restraints excluded: chain Aa residue 5 TYR Chi-restraints excluded: chain Ab residue 4 ILE Chi-restraints excluded: chain Ac residue 2 ILE Chi-restraints excluded: chain Ac residue 4 ILE Chi-restraints excluded: chain Ac residue 5 TYR Chi-restraints excluded: chain Ad residue 2 ILE Chi-restraints excluded: chain Ad residue 4 ILE Chi-restraints excluded: chain Ae residue 2 ILE Chi-restraints excluded: chain Ae 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 4 ILE Chi-restraints excluded: chain Ah residue 4 ILE Chi-restraints excluded: chain Ah residue 6 LYS Chi-restraints excluded: chain Ai residue 3 ILE Chi-restraints excluded: chain Ai residue 5 TYR Chi-restraints excluded: chain Aj residue 2 ILE Chi-restraints excluded: chain Aj residue 4 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 Al residue 4 ILE Chi-restraints excluded: chain Am residue 3 ILE Chi-restraints excluded: chain Am residue 4 ILE Chi-restraints excluded: chain Am residue 5 TYR Chi-restraints excluded: chain An residue 2 ILE Chi-restraints excluded: chain Ao residue 3 ILE Chi-restraints excluded: chain Ao residue 5 TYR Chi-restraints excluded: chain Ao residue 6 LYS Chi-restraints excluded: chain Ap residue 4 ILE Chi-restraints excluded: chain Aq residue 3 ILE Chi-restraints excluded: chain Aq residue 4 ILE Chi-restraints excluded: chain Aq residue 5 TYR 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 3 ILE Chi-restraints excluded: chain As residue 4 ILE Chi-restraints excluded: chain At residue 2 ILE Chi-restraints excluded: chain At residue 4 ILE Chi-restraints excluded: chain Au residue 2 ILE Chi-restraints excluded: chain Au residue 3 ILE Chi-restraints excluded: chain Au residue 4 ILE Chi-restraints excluded: chain Au residue 5 TYR Chi-restraints excluded: chain Av residue 2 ILE Chi-restraints excluded: chain Av residue 4 ILE Chi-restraints excluded: chain Aw residue 3 ILE Chi-restraints excluded: chain Aw residue 5 TYR Chi-restraints excluded: chain f residue 4 ILE Chi-restraints excluded: chain f residue 6 LYS Chi-restraints excluded: chain g residue 5 TYR Chi-restraints excluded: chain h residue 2 ILE Chi-restraints excluded: chain h residue 4 ILE Chi-restraints excluded: chain i residue 4 ILE Chi-restraints excluded: chain i residue 5 TYR Chi-restraints excluded: chain j residue 2 ILE Chi-restraints excluded: chain k residue 2 ILE Chi-restraints excluded: chain k residue 4 ILE Chi-restraints excluded: chain k residue 5 TYR Chi-restraints excluded: chain m residue 2 ILE Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain m residue 4 ILE Chi-restraints excluded: chain n residue 2 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 p residue 4 ILE Chi-restraints excluded: chain q residue 4 ILE Chi-restraints excluded: chain q residue 5 TYR Chi-restraints excluded: chain r residue 2 ILE Chi-restraints excluded: chain r residue 4 ILE Chi-restraints excluded: chain s residue 2 ILE Chi-restraints excluded: chain s 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 4 ILE Chi-restraints excluded: chain u residue 1 LYS Chi-restraints excluded: chain u residue 3 ILE Chi-restraints excluded: chain u residue 5 TYR Chi-restraints excluded: chain v residue 2 ILE Chi-restraints excluded: chain v residue 4 ILE Chi-restraints excluded: chain v residue 6 LYS Chi-restraints excluded: chain w residue 3 ILE Chi-restraints excluded: chain w residue 4 ILE Chi-restraints excluded: chain w residue 5 TYR Chi-restraints excluded: chain x residue 2 ILE Chi-restraints excluded: chain x residue 4 ILE Chi-restraints excluded: chain y residue 1 LYS Chi-restraints excluded: chain y residue 5 TYR Chi-restraints excluded: chain z residue 2 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: 1.9990 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 = 0.3008 r_free = 0.3008 target = 0.050831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.044920 restraints weight = 26044.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.046022 restraints weight = 11722.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.046760 restraints weight = 7318.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.047255 restraints weight = 5364.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.047570 restraints weight = 4296.149| |-----------------------------------------------------------------------------| r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.7351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.068 0.250 4640 Z= 2.762 Angle : 3.356 15.149 5920 Z= 1.678 Chirality : 0.198 0.603 720 Planarity : 0.014 0.041 560 Dihedral : 17.367 59.411 640 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 101.65 Ramachandran Plot: Outliers : 0.62 % Allowed : 25.00 % Favored : 74.38 % Rotamer: Outliers : 38.54 % Allowed : 26.04 % Favored : 35.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.25 % 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: -3.95 (0.42), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.088 0.011 TYRAs 5 Details of bonding type rmsd covalent geometry : bond 0.06887 ( 4560) covalent geometry : angle 3.35586 ( 5920) hydrogen bonds : bond 0.22118 ( 91) hydrogen bonds : angle 11.15380 ( 273) Misc. bond : bond 0.00903 ( 80) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 13 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 5 TYR cc_start: 0.8639 (OUTLIER) cc_final: 0.8326 (p90) REVERT: 7 5 TYR cc_start: 0.8560 (OUTLIER) cc_final: 0.7867 (p90) REVERT: 7 6 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8286 (pttt) REVERT: AC 5 TYR cc_start: 0.7765 (OUTLIER) cc_final: 0.4273 (m-10) REVERT: AM 5 TYR cc_start: 0.8524 (OUTLIER) cc_final: 0.8213 (p90) REVERT: AS 5 TYR cc_start: 0.7822 (OUTLIER) cc_final: 0.4294 (m-10) REVERT: AW 5 TYR cc_start: 0.8735 (OUTLIER) cc_final: 0.8134 (p90) REVERT: AY 5 TYR cc_start: 0.8608 (OUTLIER) cc_final: 0.8048 (p90) REVERT: Ai 1 LYS cc_start: 0.9500 (pttm) cc_final: 0.9076 (tptp) REVERT: Ai 5 TYR cc_start: 0.7839 (OUTLIER) cc_final: 0.4177 (m-10) REVERT: Ao 5 TYR cc_start: 0.8584 (OUTLIER) cc_final: 0.8265 (p90) REVERT: Ao 6 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8596 (pttt) REVERT: Aq 5 TYR cc_start: 0.8626 (OUTLIER) cc_final: 0.8293 (p90) REVERT: Au 5 TYR cc_start: 0.8629 (OUTLIER) cc_final: 0.8154 (p90) REVERT: Aw 5 TYR cc_start: 0.7993 (OUTLIER) cc_final: 0.7652 (p90) REVERT: g 5 TYR cc_start: 0.7683 (OUTLIER) cc_final: 0.4221 (m-10) REVERT: i 5 TYR cc_start: 0.8512 (OUTLIER) cc_final: 0.7148 (p90) REVERT: q 5 TYR cc_start: 0.8593 (OUTLIER) cc_final: 0.8043 (p90) REVERT: w 1 LYS cc_start: 0.9428 (pttm) cc_final: 0.8927 (tptp) REVERT: w 5 TYR cc_start: 0.7931 (OUTLIER) cc_final: 0.4202 (m-10) REVERT: y 5 TYR cc_start: 0.8450 (OUTLIER) cc_final: 0.6935 (p90) outliers start: 185 outliers final: 152 residues processed: 198 average time/residue: 0.0635 time to fit residues: 16.1080 Evaluate side-chains 184 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 13 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 2 ILE Chi-restraints excluded: chain 1 residue 3 ILE Chi-restraints excluded: chain 1 residue 4 ILE Chi-restraints excluded: chain 1 residue 5 TYR Chi-restraints excluded: chain 2 residue 2 ILE Chi-restraints excluded: chain 3 residue 2 ILE Chi-restraints excluded: chain 3 residue 5 TYR Chi-restraints excluded: chain 3 residue 6 LYS Chi-restraints excluded: chain 4 residue 4 ILE Chi-restraints excluded: chain 5 residue 3 ILE Chi-restraints excluded: chain 5 residue 4 ILE Chi-restraints excluded: chain 5 residue 5 TYR Chi-restraints excluded: chain 6 residue 2 ILE Chi-restraints excluded: chain 6 residue 4 ILE Chi-restraints excluded: chain 7 residue 2 ILE Chi-restraints excluded: chain 7 residue 3 ILE Chi-restraints excluded: chain 7 residue 4 ILE Chi-restraints excluded: chain 7 residue 5 TYR Chi-restraints excluded: chain 7 residue 6 LYS Chi-restraints excluded: chain 8 residue 4 ILE Chi-restraints excluded: chain 9 residue 2 ILE Chi-restraints excluded: chain 9 residue 3 ILE Chi-restraints excluded: chain 9 residue 5 TYR Chi-restraints excluded: chain AA residue 2 ILE Chi-restraints excluded: chain AA residue 3 ILE Chi-restraints excluded: chain AA residue 5 TYR Chi-restraints excluded: chain AB residue 4 ILE Chi-restraints excluded: chain AB residue 6 LYS Chi-restraints excluded: chain AC residue 3 ILE Chi-restraints excluded: chain AC residue 5 TYR Chi-restraints excluded: chain AD residue 2 ILE Chi-restraints excluded: chain AD residue 4 ILE Chi-restraints excluded: chain AE 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 AG residue 2 ILE Chi-restraints excluded: chain AG residue 4 ILE Chi-restraints excluded: chain AG residue 5 TYR Chi-restraints excluded: chain AI residue 2 ILE Chi-restraints excluded: chain AI residue 3 ILE Chi-restraints excluded: chain AI residue 4 ILE Chi-restraints excluded: chain AI residue 6 LYS Chi-restraints excluded: chain AJ residue 4 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 AL residue 4 ILE Chi-restraints excluded: chain AM residue 2 ILE Chi-restraints excluded: chain AM residue 5 TYR Chi-restraints excluded: chain AN residue 2 ILE Chi-restraints excluded: chain AN residue 4 ILE Chi-restraints excluded: chain AN residue 6 LYS Chi-restraints excluded: chain AO residue 2 ILE Chi-restraints excluded: chain AO residue 4 ILE Chi-restraints excluded: chain AP residue 2 ILE Chi-restraints excluded: chain AP residue 4 ILE Chi-restraints excluded: chain AQ residue 1 LYS Chi-restraints excluded: chain AQ residue 3 ILE Chi-restraints excluded: chain AQ residue 5 TYR Chi-restraints excluded: chain AR residue 2 ILE Chi-restraints excluded: chain AR residue 4 ILE Chi-restraints excluded: chain AR residue 6 LYS Chi-restraints excluded: chain AS residue 3 ILE Chi-restraints excluded: chain AS residue 5 TYR Chi-restraints excluded: chain AT residue 2 ILE Chi-restraints excluded: chain AU residue 3 ILE Chi-restraints excluded: chain AU residue 4 ILE Chi-restraints excluded: chain AU residue 5 TYR Chi-restraints excluded: chain AV residue 2 ILE Chi-restraints excluded: chain AW residue 4 ILE Chi-restraints excluded: chain AW residue 5 TYR Chi-restraints excluded: chain AY residue 2 ILE Chi-restraints excluded: chain AY residue 3 ILE Chi-restraints excluded: chain AY residue 5 TYR Chi-restraints excluded: chain AZ residue 2 ILE Chi-restraints excluded: chain AZ residue 4 ILE Chi-restraints excluded: chain Aa residue 3 ILE Chi-restraints excluded: chain Aa residue 5 TYR Chi-restraints excluded: chain Ab residue 4 ILE Chi-restraints excluded: chain Ac residue 2 ILE Chi-restraints excluded: chain Ac residue 4 ILE Chi-restraints excluded: chain Ac residue 5 TYR Chi-restraints excluded: chain Ad residue 2 ILE Chi-restraints excluded: chain Ad residue 4 ILE Chi-restraints excluded: chain Ae residue 2 ILE Chi-restraints excluded: chain Ae 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 4 ILE Chi-restraints excluded: chain Ah residue 4 ILE Chi-restraints excluded: chain Ah residue 6 LYS Chi-restraints excluded: chain Ai residue 3 ILE Chi-restraints excluded: chain Ai residue 5 TYR Chi-restraints excluded: chain Aj residue 2 ILE Chi-restraints excluded: chain Aj residue 4 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 Al residue 4 ILE Chi-restraints excluded: chain Am residue 3 ILE Chi-restraints excluded: chain Am residue 4 ILE Chi-restraints excluded: chain Am residue 5 TYR Chi-restraints excluded: chain An residue 2 ILE Chi-restraints excluded: chain Ao residue 3 ILE Chi-restraints excluded: chain Ao residue 5 TYR Chi-restraints excluded: chain Ao residue 6 LYS Chi-restraints excluded: chain Ap residue 4 ILE Chi-restraints excluded: chain Aq residue 3 ILE Chi-restraints excluded: chain Aq residue 4 ILE Chi-restraints excluded: chain Aq residue 5 TYR 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 As residue 3 ILE Chi-restraints excluded: chain As residue 4 ILE Chi-restraints excluded: chain At residue 2 ILE Chi-restraints excluded: chain At residue 4 ILE Chi-restraints excluded: chain Au residue 2 ILE Chi-restraints excluded: chain Au residue 3 ILE Chi-restraints excluded: chain Au residue 4 ILE Chi-restraints excluded: chain Au residue 5 TYR Chi-restraints excluded: chain Av residue 2 ILE Chi-restraints excluded: chain Av residue 4 ILE Chi-restraints excluded: chain Aw residue 3 ILE Chi-restraints excluded: chain Aw residue 5 TYR Chi-restraints excluded: chain f residue 4 ILE Chi-restraints excluded: chain f residue 6 LYS Chi-restraints excluded: chain g residue 5 TYR Chi-restraints excluded: chain h residue 2 ILE Chi-restraints excluded: chain h residue 4 ILE Chi-restraints excluded: chain i residue 4 ILE Chi-restraints excluded: chain i residue 5 TYR Chi-restraints excluded: chain j residue 2 ILE Chi-restraints excluded: chain k residue 2 ILE Chi-restraints excluded: chain k residue 4 ILE Chi-restraints excluded: chain k residue 5 TYR Chi-restraints excluded: chain m residue 2 ILE Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain m residue 4 ILE Chi-restraints excluded: chain n residue 2 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 p residue 4 ILE Chi-restraints excluded: chain q residue 4 ILE Chi-restraints excluded: chain q residue 5 TYR Chi-restraints excluded: chain r residue 2 ILE Chi-restraints excluded: chain r residue 4 ILE Chi-restraints excluded: chain s residue 2 ILE Chi-restraints excluded: chain s 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 4 ILE Chi-restraints excluded: chain u residue 1 LYS Chi-restraints excluded: chain u residue 3 ILE Chi-restraints excluded: chain u residue 5 TYR Chi-restraints excluded: chain v residue 2 ILE Chi-restraints excluded: chain v residue 4 ILE Chi-restraints excluded: chain v residue 6 LYS Chi-restraints excluded: chain w residue 3 ILE Chi-restraints excluded: chain w residue 4 ILE Chi-restraints excluded: chain w residue 5 TYR Chi-restraints excluded: chain x residue 2 ILE Chi-restraints excluded: chain x residue 4 ILE Chi-restraints excluded: chain y residue 1 LYS Chi-restraints excluded: chain y residue 5 TYR Chi-restraints excluded: chain z residue 2 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: 1.9990 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 = 0.3007 r_free = 0.3007 target = 0.050826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.044936 restraints weight = 26277.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.046039 restraints weight = 11732.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.046773 restraints weight = 7316.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.047256 restraints weight = 5357.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.047589 restraints weight = 4309.548| |-----------------------------------------------------------------------------| r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.7350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.068 0.251 4640 Z= 2.762 Angle : 3.356 15.299 5920 Z= 1.678 Chirality : 0.198 0.603 720 Planarity : 0.014 0.041 560 Dihedral : 17.382 59.430 640 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 102.23 Ramachandran Plot: Outliers : 0.62 % Allowed : 25.62 % Favored : 73.75 % Rotamer: Outliers : 36.88 % Allowed : 27.71 % Favored : 35.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.25 % 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: -3.97 (0.42), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.093 0.011 TYRAs 5 Details of bonding type rmsd covalent geometry : bond 0.06886 ( 4560) covalent geometry : angle 3.35573 ( 5920) hydrogen bonds : bond 0.22134 ( 91) hydrogen bonds : angle 11.16369 ( 273) Misc. bond : bond 0.00900 ( 80) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 640 Ramachandran restraints generated. 320 Oldfield, 0 Emsley, 320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 13 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 5 TYR cc_start: 0.8642 (OUTLIER) cc_final: 0.8330 (p90) REVERT: 7 5 TYR cc_start: 0.8561 (OUTLIER) cc_final: 0.7868 (p90) REVERT: 7 6 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8287 (pttt) REVERT: AC 5 TYR cc_start: 0.7766 (OUTLIER) cc_final: 0.4274 (m-10) REVERT: AM 5 TYR cc_start: 0.8543 (OUTLIER) cc_final: 0.8184 (p90) REVERT: AS 5 TYR cc_start: 0.7824 (OUTLIER) cc_final: 0.4318 (m-10) REVERT: AW 5 TYR cc_start: 0.8736 (OUTLIER) cc_final: 0.8133 (p90) REVERT: AY 5 TYR cc_start: 0.8610 (OUTLIER) cc_final: 0.8048 (p90) REVERT: Ai 1 LYS cc_start: 0.9483 (pttm) cc_final: 0.9045 (tptp) REVERT: Ai 5 TYR cc_start: 0.7840 (OUTLIER) cc_final: 0.4181 (m-10) REVERT: Ao 5 TYR cc_start: 0.8587 (OUTLIER) cc_final: 0.8268 (p90) REVERT: Ao 6 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8598 (pttt) REVERT: Aq 5 TYR cc_start: 0.8626 (OUTLIER) cc_final: 0.8291 (p90) REVERT: Au 5 TYR cc_start: 0.8631 (OUTLIER) cc_final: 0.8158 (p90) REVERT: Aw 5 TYR cc_start: 0.7900 (OUTLIER) cc_final: 0.7579 (p90) REVERT: g 5 TYR cc_start: 0.7683 (OUTLIER) cc_final: 0.4221 (m-10) REVERT: i 5 TYR cc_start: 0.8516 (OUTLIER) cc_final: 0.7147 (p90) REVERT: q 5 TYR cc_start: 0.8598 (OUTLIER) cc_final: 0.8053 (p90) REVERT: w 1 LYS cc_start: 0.9427 (pttm) cc_final: 0.8925 (tptp) REVERT: w 5 TYR cc_start: 0.7928 (OUTLIER) cc_final: 0.4200 (m-10) REVERT: y 5 TYR cc_start: 0.8452 (OUTLIER) cc_final: 0.6967 (p90) outliers start: 177 outliers final: 153 residues processed: 190 average time/residue: 0.0639 time to fit residues: 15.5544 Evaluate side-chains 185 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 13 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 2 ILE Chi-restraints excluded: chain 1 residue 3 ILE Chi-restraints excluded: chain 1 residue 4 ILE Chi-restraints excluded: chain 1 residue 5 TYR Chi-restraints excluded: chain 2 residue 2 ILE Chi-restraints excluded: chain 3 residue 2 ILE Chi-restraints excluded: chain 3 residue 5 TYR Chi-restraints excluded: chain 3 residue 6 LYS Chi-restraints excluded: chain 4 residue 4 ILE Chi-restraints excluded: chain 5 residue 3 ILE Chi-restraints excluded: chain 5 residue 4 ILE Chi-restraints excluded: chain 5 residue 5 TYR Chi-restraints excluded: chain 6 residue 2 ILE Chi-restraints excluded: chain 6 residue 4 ILE Chi-restraints excluded: chain 7 residue 2 ILE Chi-restraints excluded: chain 7 residue 3 ILE Chi-restraints excluded: chain 7 residue 4 ILE Chi-restraints excluded: chain 7 residue 5 TYR Chi-restraints excluded: chain 7 residue 6 LYS Chi-restraints excluded: chain 8 residue 4 ILE Chi-restraints excluded: chain 9 residue 2 ILE Chi-restraints excluded: chain 9 residue 3 ILE Chi-restraints excluded: chain 9 residue 5 TYR Chi-restraints excluded: chain AA residue 2 ILE Chi-restraints excluded: chain AA residue 3 ILE Chi-restraints excluded: chain AA residue 5 TYR Chi-restraints excluded: chain AB residue 4 ILE Chi-restraints excluded: chain AB residue 6 LYS Chi-restraints excluded: chain AC residue 3 ILE Chi-restraints excluded: chain AC residue 5 TYR Chi-restraints excluded: chain AD residue 2 ILE Chi-restraints excluded: chain AD residue 4 ILE Chi-restraints excluded: chain AE 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 AG residue 2 ILE Chi-restraints excluded: chain AG residue 4 ILE Chi-restraints excluded: chain AG residue 5 TYR Chi-restraints excluded: chain AG residue 6 LYS Chi-restraints excluded: chain AI residue 2 ILE Chi-restraints excluded: chain AI residue 3 ILE Chi-restraints excluded: chain AI residue 4 ILE Chi-restraints excluded: chain AI residue 6 LYS Chi-restraints excluded: chain AJ residue 4 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 AL residue 4 ILE Chi-restraints excluded: chain AM residue 2 ILE Chi-restraints excluded: chain AM residue 5 TYR Chi-restraints excluded: chain AN residue 2 ILE Chi-restraints excluded: chain AN residue 4 ILE Chi-restraints excluded: chain AN residue 6 LYS Chi-restraints excluded: chain AO residue 2 ILE Chi-restraints excluded: chain AO residue 4 ILE Chi-restraints excluded: chain AP residue 2 ILE Chi-restraints excluded: chain AP residue 4 ILE Chi-restraints excluded: chain AQ residue 1 LYS Chi-restraints excluded: chain AQ residue 3 ILE Chi-restraints excluded: chain AQ residue 5 TYR Chi-restraints excluded: chain AR residue 2 ILE Chi-restraints excluded: chain AR residue 4 ILE Chi-restraints excluded: chain AR residue 6 LYS Chi-restraints excluded: chain AS residue 5 TYR Chi-restraints excluded: chain AT residue 2 ILE Chi-restraints excluded: chain AU residue 3 ILE Chi-restraints excluded: chain AU residue 4 ILE Chi-restraints excluded: chain AU residue 5 TYR Chi-restraints excluded: chain AV residue 2 ILE Chi-restraints excluded: chain AW residue 4 ILE Chi-restraints excluded: chain AW residue 5 TYR Chi-restraints excluded: chain AY residue 2 ILE Chi-restraints excluded: chain AY residue 3 ILE Chi-restraints excluded: chain AY residue 5 TYR Chi-restraints excluded: chain AZ residue 2 ILE Chi-restraints excluded: chain AZ residue 4 ILE Chi-restraints excluded: chain Aa residue 3 ILE Chi-restraints excluded: chain Aa residue 5 TYR Chi-restraints excluded: chain Ab residue 4 ILE Chi-restraints excluded: chain Ac residue 2 ILE Chi-restraints excluded: chain Ac residue 4 ILE Chi-restraints excluded: chain Ac residue 5 TYR Chi-restraints excluded: chain Ad residue 2 ILE Chi-restraints excluded: chain Ad residue 4 ILE Chi-restraints excluded: chain Ae residue 2 ILE Chi-restraints excluded: chain Ae 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 4 ILE Chi-restraints excluded: chain Ah residue 4 ILE Chi-restraints excluded: chain Ah residue 6 LYS Chi-restraints excluded: chain Ai residue 3 ILE Chi-restraints excluded: chain Ai residue 5 TYR Chi-restraints excluded: chain Aj residue 2 ILE Chi-restraints excluded: chain Aj residue 4 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 Al residue 4 ILE Chi-restraints excluded: chain Am residue 3 ILE Chi-restraints excluded: chain Am residue 4 ILE Chi-restraints excluded: chain Am residue 5 TYR Chi-restraints excluded: chain An residue 2 ILE Chi-restraints excluded: chain Ao residue 3 ILE Chi-restraints excluded: chain Ao residue 5 TYR Chi-restraints excluded: chain Ao residue 6 LYS Chi-restraints excluded: chain Ap residue 4 ILE Chi-restraints excluded: chain Aq residue 3 ILE Chi-restraints excluded: chain Aq residue 4 ILE Chi-restraints excluded: chain Aq residue 5 TYR 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 3 ILE Chi-restraints excluded: chain As residue 4 ILE Chi-restraints excluded: chain At residue 2 ILE Chi-restraints excluded: chain At residue 4 ILE Chi-restraints excluded: chain Au residue 2 ILE Chi-restraints excluded: chain Au residue 3 ILE Chi-restraints excluded: chain Au residue 4 ILE Chi-restraints excluded: chain Au residue 5 TYR Chi-restraints excluded: chain Av residue 2 ILE Chi-restraints excluded: chain Av residue 4 ILE Chi-restraints excluded: chain Aw residue 3 ILE Chi-restraints excluded: chain Aw residue 5 TYR Chi-restraints excluded: chain f residue 4 ILE Chi-restraints excluded: chain f residue 6 LYS Chi-restraints excluded: chain g residue 5 TYR Chi-restraints excluded: chain h residue 2 ILE Chi-restraints excluded: chain h residue 4 ILE Chi-restraints excluded: chain i residue 4 ILE Chi-restraints excluded: chain i residue 5 TYR Chi-restraints excluded: chain j residue 2 ILE Chi-restraints excluded: chain k residue 2 ILE Chi-restraints excluded: chain k residue 4 ILE Chi-restraints excluded: chain k residue 5 TYR Chi-restraints excluded: chain m residue 2 ILE Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain m residue 4 ILE Chi-restraints excluded: chain n residue 2 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 p residue 4 ILE Chi-restraints excluded: chain q residue 4 ILE Chi-restraints excluded: chain q residue 5 TYR Chi-restraints excluded: chain r residue 2 ILE Chi-restraints excluded: chain r residue 4 ILE Chi-restraints excluded: chain s residue 2 ILE Chi-restraints excluded: chain s 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 4 ILE Chi-restraints excluded: chain u residue 1 LYS Chi-restraints excluded: chain u residue 3 ILE Chi-restraints excluded: chain u residue 5 TYR Chi-restraints excluded: chain v residue 2 ILE Chi-restraints excluded: chain v residue 4 ILE Chi-restraints excluded: chain v residue 6 LYS Chi-restraints excluded: chain w residue 3 ILE Chi-restraints excluded: chain w residue 4 ILE Chi-restraints excluded: chain w residue 5 TYR Chi-restraints excluded: chain x residue 2 ILE Chi-restraints excluded: chain x residue 4 ILE Chi-restraints excluded: chain y residue 1 LYS Chi-restraints excluded: chain y residue 3 ILE Chi-restraints excluded: chain y residue 4 ILE Chi-restraints excluded: chain y residue 5 TYR Chi-restraints excluded: chain z residue 2 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: 1.9990 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 = 0.3004 r_free = 0.3004 target = 0.050705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.044848 restraints weight = 26004.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.045945 restraints weight = 11699.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.046691 restraints weight = 7303.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.047158 restraints weight = 5341.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.047485 restraints weight = 4301.341| |-----------------------------------------------------------------------------| r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.7352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.068 0.250 4640 Z= 2.763 Angle : 3.356 15.352 5920 Z= 1.679 Chirality : 0.198 0.604 720 Planarity : 0.014 0.041 560 Dihedral : 17.381 59.451 640 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 102.62 Ramachandran Plot: Outliers : 0.62 % Allowed : 25.62 % Favored : 73.75 % Rotamer: Outliers : 37.50 % Allowed : 27.29 % Favored : 35.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 3.25 % 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: -3.95 (0.42), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.00 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.095 0.011 TYRAs 5 Details of bonding type rmsd covalent geometry : bond 0.06888 ( 4560) covalent geometry : angle 3.35596 ( 5920) hydrogen bonds : bond 0.22125 ( 91) hydrogen bonds : angle 11.17306 ( 273) Misc. bond : bond 0.00903 ( 80) =============================================================================== Job complete usr+sys time: 679.24 seconds wall clock time: 12 minutes 44.58 seconds (764.58 seconds total)