Starting phenix.real_space_refine on Thu Oct 22 19:51:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nfn_49371/10_2026/9nfn_49371.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nfn_49371/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/9nfn_49371/10_2026/9nfn_49371.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nfn_49371/10_2026/9nfn_49371.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nfn_49371/10_2026/9nfn_49371.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nfn_49371/10_2026/9nfn_49371.map" } 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-2.3rc1-6221/lib/python3.11/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: 1.04, per 1000 atoms: 0.22 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: 0.36 Conformation dependent library (CDL) restraints added in 114.3 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: 0.14 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: 0.50 Time building geometry restraints manager: 0.50 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: 5.500 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: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.220 Find NCS groups from input model: 0.190 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 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/Z covalent geometry : bond 0.01098 / 0.53 ( 4560) covalent geometry : angle 1.48269 / 0.85 ( 5920) hydrogen bonds : bond 0.29574 / 19.42 ( 91) hydrogen bonds : angle 11.71117 / 7.11 ( 273) Misc. bond : bond 0.10122 / 6.03 ( 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 : 0.219 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: 0.0748 time to fit residues: 21.6725 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 : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.064999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.058859 restraints weight = 17050.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.060660 restraints weight = 6314.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.061829 restraints weight = 3256.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.062597 restraints weight = 1994.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.063105 restraints weight = 1354.182| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4640 Z= 0.147 Angle : 0.709 7.273 5920 Z= 0.358 Chirality : 0.071 0.214 720 Planarity : 0.003 0.015 560 Dihedral : 6.576 28.669 640 Min Nonbonded Distance : 2.656 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 6.25 % Allowed : 17.92 % Favored : 75.83 % 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: 3.92 (0.40), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 3.00 (0.31), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.002 TYRAc 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.15 ( 4560) covalent geometry : angle 0.70850 / 0.36 ( 5920) hydrogen bonds : bond 0.09411 / 5.93 ( 91) hydrogen bonds : angle 10.67214 / 6.56 ( 273) Misc. bond : bond 0.00026 / 0.02 ( 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 157 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 0.225 Fit side-chains REVERT: 4 4 ILE cc_start: 0.8744 (mt) cc_final: 0.8358 (mm) REVERT: 4 6 LYS cc_start: 0.9289 (pttt) cc_final: 0.8932 (pttp) REVERT: 6 6 LYS cc_start: 0.9296 (pttt) cc_final: 0.9057 (pttp) REVERT: AD 4 ILE cc_start: 0.8530 (tt) cc_final: 0.8330 (pt) REVERT: AE 1 LYS cc_start: 0.9498 (pttm) cc_final: 0.8896 (mttt) REVERT: AJ 6 LYS cc_start: 0.9309 (pttt) cc_final: 0.8992 (pttp) REVERT: AU 1 LYS cc_start: 0.9521 (pttm) cc_final: 0.8960 (mmtt) REVERT: AX 6 LYS cc_start: 0.9289 (pttt) cc_final: 0.8925 (pttp) REVERT: AZ 6 LYS cc_start: 0.9264 (pttt) cc_final: 0.8982 (pttp) REVERT: Ap 6 LYS cc_start: 0.9225 (pttt) cc_final: 0.8900 (pttp) REVERT: i 1 LYS cc_start: 0.9508 (pttm) cc_final: 0.8886 (mttt) REVERT: j 4 ILE cc_start: 0.8994 (mt) cc_final: 0.8772 (pt) REVERT: n 6 LYS cc_start: 0.9274 (pttt) cc_final: 0.9032 (pttp) REVERT: r 4 ILE cc_start: 0.8754 (tt) cc_final: 0.8543 (pt) REVERT: x 4 ILE cc_start: 0.8428 (tt) cc_final: 0.8208 (pt) REVERT: z 4 ILE cc_start: 0.8941 (tt) cc_final: 0.8685 (pt) outliers start: 30 outliers final: 16 residues processed: 150 average time/residue: 0.0560 time to fit residues: 11.3549 Evaluate side-chains 81 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 2 ILE Chi-restraints excluded: chain 7 residue 2 ILE Chi-restraints excluded: chain AA residue 4 ILE Chi-restraints excluded: chain AB residue 4 ILE Chi-restraints excluded: chain AM residue 4 ILE Chi-restraints excluded: chain AR residue 4 ILE Chi-restraints excluded: chain AY residue 4 ILE Chi-restraints excluded: chain Ah residue 4 ILE Chi-restraints excluded: chain Ai residue 3 ILE Chi-restraints excluded: chain At residue 4 ILE Chi-restraints excluded: chain Aw residue 4 ILE Chi-restraints excluded: chain f residue 4 ILE Chi-restraints excluded: chain k residue 2 ILE Chi-restraints excluded: chain m residue 2 ILE Chi-restraints excluded: chain u residue 4 ILE Chi-restraints excluded: chain v residue 4 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 8.9990 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.057603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.051594 restraints weight = 19182.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.053063 restraints weight = 7175.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.054025 restraints weight = 3970.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.054653 restraints weight = 2660.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.055095 restraints weight = 1982.858| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.4725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.076 4640 Z= 0.588 Angle : 1.052 8.384 5920 Z= 0.533 Chirality : 0.085 0.215 720 Planarity : 0.005 0.015 560 Dihedral : 7.606 31.079 640 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 26.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 17.71 % Allowed : 14.38 % Favored : 67.92 % 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: 2.61 (0.40), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 2.00 (0.31), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.034 0.006 TYRAc 5 Details of bonding type rmsd/Z covalent geometry : bond 0.01475 / 0.59 ( 4560) covalent geometry : angle 1.05204 / 0.53 ( 5920) hydrogen bonds : bond 0.12112 / 7.82 ( 91) hydrogen bonds : angle 11.73657 / 7.23 ( 273) Misc. bond : bond 0.00232 / 0.14 ( 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 151 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 66 time to evaluate : 0.211 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: w 1 LYS cc_start: 0.9334 (pttm) cc_final: 0.8945 (mmtm) outliers start: 85 outliers final: 64 residues processed: 133 average time/residue: 0.0692 time to fit residues: 11.8597 Evaluate side-chains 114 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 50 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 2 ILE Chi-restraints excluded: chain 3 residue 2 ILE Chi-restraints excluded: chain 5 residue 4 ILE Chi-restraints excluded: chain 6 residue 4 ILE Chi-restraints excluded: chain 7 residue 2 ILE Chi-restraints excluded: chain 7 residue 4 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 3 ILE Chi-restraints excluded: chain AD residue 4 ILE Chi-restraints excluded: chain AE residue 3 ILE Chi-restraints excluded: chain AG residue 2 ILE Chi-restraints excluded: chain AH residue 4 ILE Chi-restraints excluded: chain AK residue 2 ILE Chi-restraints excluded: chain AL residue 4 ILE Chi-restraints excluded: chain AN residue 4 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 AT residue 4 ILE Chi-restraints excluded: chain AU residue 2 ILE Chi-restraints excluded: chain AV residue 4 ILE Chi-restraints excluded: chain AW residue 4 ILE Chi-restraints excluded: chain AY residue 3 ILE Chi-restraints excluded: chain AZ residue 4 ILE Chi-restraints excluded: chain Aa residue 4 ILE Chi-restraints excluded: chain Ab residue 4 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 Aj residue 4 ILE Chi-restraints excluded: chain Al residue 4 ILE Chi-restraints excluded: chain An residue 4 ILE Chi-restraints excluded: chain Ap residue 4 ILE Chi-restraints excluded: chain At residue 4 ILE Chi-restraints excluded: chain Au residue 4 ILE Chi-restraints excluded: chain Aw residue 3 ILE Chi-restraints excluded: chain f residue 4 ILE Chi-restraints excluded: chain h residue 4 ILE Chi-restraints excluded: chain i residue 2 ILE Chi-restraints excluded: chain i residue 3 ILE Chi-restraints excluded: chain i residue 4 ILE Chi-restraints excluded: chain k residue 2 ILE Chi-restraints excluded: chain l residue 4 ILE 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 p residue 4 ILE Chi-restraints excluded: chain p residue 6 LYS Chi-restraints excluded: chain q residue 2 ILE Chi-restraints excluded: chain q residue 4 ILE Chi-restraints excluded: chain r residue 4 ILE Chi-restraints excluded: chain t residue 2 ILE Chi-restraints excluded: chain u residue 3 ILE Chi-restraints excluded: chain u residue 4 ILE Chi-restraints excluded: chain v residue 4 ILE Chi-restraints excluded: chain w residue 3 ILE Chi-restraints excluded: chain x residue 4 ILE Chi-restraints excluded: chain y residue 4 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: [0] chunk 0 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.065726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.059258 restraints weight = 17438.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.060991 restraints weight = 6621.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.062107 restraints weight = 3499.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.062844 restraints weight = 2222.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.063345 restraints weight = 1581.239| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.4990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4640 Z= 0.128 Angle : 0.688 9.162 5920 Z= 0.338 Chirality : 0.072 0.224 720 Planarity : 0.003 0.011 560 Dihedral : 6.557 33.177 640 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 6.88 % Allowed : 25.62 % Favored : 67.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.62 (0.42), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 2.01 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYRAT 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 ( 4560) covalent geometry : angle 0.68775 / 0.34 ( 5920) hydrogen bonds : bond 0.08388 / 5.21 ( 91) hydrogen bonds : angle 10.44785 / 6.42 ( 273) Misc. bond : bond 0.00028 / 0.02 ( 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 129 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 96 time to evaluate : 0.219 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: Af 4 ILE cc_start: 0.8960 (mt) cc_final: 0.8731 (tt) REVERT: h 4 ILE cc_start: 0.8874 (OUTLIER) cc_final: 0.8580 (pt) REVERT: h 6 LYS cc_start: 0.9190 (pttt) cc_final: 0.8939 (pttp) REVERT: s 3 ILE cc_start: 0.9389 (mp) cc_final: 0.9122 (mp) REVERT: w 1 LYS cc_start: 0.9427 (pttm) cc_final: 0.9056 (mmtm) REVERT: x 4 ILE cc_start: 0.8521 (tt) cc_final: 0.8260 (pt) outliers start: 33 outliers final: 15 residues processed: 118 average time/residue: 0.0625 time to fit residues: 9.7775 Evaluate side-chains 73 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 4 ILE Chi-restraints excluded: chain 6 residue 4 ILE Chi-restraints excluded: chain AB residue 4 ILE Chi-restraints excluded: chain AR residue 4 ILE Chi-restraints excluded: chain AY residue 4 ILE Chi-restraints excluded: chain Ac residue 2 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 An residue 4 ILE Chi-restraints excluded: chain As residue 2 ILE Chi-restraints excluded: chain f residue 4 ILE Chi-restraints excluded: chain h residue 4 ILE Chi-restraints excluded: chain p residue 6 LYS Chi-restraints excluded: chain v residue 4 ILE Chi-restraints excluded: chain y residue 3 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 8.9990 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.059612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.053773 restraints weight = 19276.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.055222 restraints weight = 7798.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.056182 restraints weight = 4413.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.056804 restraints weight = 2941.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.057183 restraints weight = 2173.354| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.5309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.097 4640 Z= 0.583 Angle : 1.059 9.736 5920 Z= 0.535 Chirality : 0.084 0.223 720 Planarity : 0.005 0.014 560 Dihedral : 7.481 31.352 640 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 28.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 16.25 % Allowed : 17.50 % Favored : 66.25 % 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: 2.21 (0.40), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 1.70 (0.31), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.034 0.006 TYRAc 5 Details of bonding type rmsd/Z covalent geometry : bond 0.01474 / 0.59 ( 4560) covalent geometry : angle 1.05905 / 0.54 ( 5920) hydrogen bonds : bond 0.11952 / 7.61 ( 91) hydrogen bonds : angle 11.20923 / 6.90 ( 273) Misc. bond : bond 0.00205 / 0.12 ( 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 138 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 60 time to evaluate : 0.220 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ai 1 LYS cc_start: 0.9312 (pttm) cc_final: 0.9024 (tptp) REVERT: w 1 LYS cc_start: 0.9426 (pttm) cc_final: 0.9090 (tptp) outliers start: 78 outliers final: 56 residues processed: 121 average time/residue: 0.0751 time to fit residues: 11.5018 Evaluate side-chains 112 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 56 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 4 ILE Chi-restraints excluded: chain 3 residue 2 ILE Chi-restraints excluded: chain 5 residue 4 ILE Chi-restraints excluded: chain 6 residue 4 ILE Chi-restraints excluded: chain 7 residue 4 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 4 ILE Chi-restraints excluded: chain AB residue 4 ILE Chi-restraints excluded: chain AC residue 3 ILE Chi-restraints excluded: chain AG residue 2 ILE Chi-restraints excluded: chain AH residue 4 ILE Chi-restraints excluded: chain AJ residue 4 ILE Chi-restraints excluded: chain AL residue 4 ILE Chi-restraints excluded: chain AN residue 4 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 AT residue 4 ILE Chi-restraints excluded: chain AU residue 2 ILE Chi-restraints excluded: chain AW residue 4 ILE Chi-restraints excluded: chain AX residue 4 ILE Chi-restraints excluded: chain AZ residue 4 ILE Chi-restraints excluded: chain Aa residue 4 ILE Chi-restraints excluded: chain Ab residue 4 ILE Chi-restraints excluded: chain Ad residue 4 ILE Chi-restraints excluded: chain Ae residue 4 ILE Chi-restraints excluded: chain Ah residue 4 ILE Chi-restraints excluded: chain Ah residue 6 LYS Chi-restraints excluded: chain Aj residue 4 ILE Chi-restraints excluded: chain Al residue 4 ILE Chi-restraints excluded: chain Am residue 3 ILE Chi-restraints excluded: chain An residue 4 ILE Chi-restraints excluded: chain Ap residue 4 ILE Chi-restraints excluded: chain At residue 4 ILE Chi-restraints excluded: chain Av residue 2 ILE Chi-restraints excluded: chain f residue 4 ILE Chi-restraints excluded: chain h residue 4 ILE Chi-restraints excluded: chain i residue 2 ILE Chi-restraints excluded: chain i residue 3 ILE Chi-restraints excluded: chain j residue 4 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 p residue 4 ILE Chi-restraints excluded: chain p residue 6 LYS Chi-restraints excluded: chain q residue 2 ILE Chi-restraints excluded: chain u residue 4 ILE 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 x residue 4 ILE Chi-restraints excluded: chain y residue 4 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: [0] chunk 0 optimal weight: 0.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.067107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.061101 restraints weight = 18117.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.062775 restraints weight = 7555.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.063843 restraints weight = 4125.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.064514 restraints weight = 2658.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.064997 restraints weight = 1894.985| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.5439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4640 Z= 0.141 Angle : 0.708 9.194 5920 Z= 0.352 Chirality : 0.073 0.222 720 Planarity : 0.003 0.010 560 Dihedral : 6.669 30.153 640 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 8.12 % Allowed : 25.83 % Favored : 66.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.42 (0.42), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 1.86 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYRAc 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.14 ( 4560) covalent geometry : angle 0.70815 / 0.35 ( 5920) hydrogen bonds : bond 0.08652 / 5.35 ( 91) hydrogen bonds : angle 10.34331 / 6.39 ( 273) Misc. bond : bond 0.00030 / 0.02 ( 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 115 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 76 time to evaluate : 0.210 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: symmetry clash REVERT: AF 4 ILE cc_start: 0.8934 (mt) cc_final: 0.8678 (mt) REVERT: Ai 1 LYS cc_start: 0.9268 (pttm) cc_final: 0.9055 (tptp) REVERT: n 4 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8759 (pt) REVERT: w 1 LYS cc_start: 0.9406 (pttm) cc_final: 0.9090 (mmtt) REVERT: x 4 ILE cc_start: 0.8843 (tt) cc_final: 0.8582 (pt) outliers start: 39 outliers final: 28 residues processed: 109 average time/residue: 0.0688 time to fit residues: 9.5136 Evaluate side-chains 90 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 61 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 2 ILE Chi-restraints excluded: chain 2 residue 4 ILE Chi-restraints excluded: chain 6 residue 4 ILE Chi-restraints excluded: chain 9 residue 3 ILE Chi-restraints excluded: chain AB residue 4 ILE Chi-restraints excluded: chain AE residue 3 ILE Chi-restraints excluded: chain AG residue 2 ILE Chi-restraints excluded: chain AL residue 4 ILE Chi-restraints excluded: chain AN residue 4 ILE Chi-restraints excluded: chain AR residue 4 ILE Chi-restraints excluded: chain AT residue 4 ILE Chi-restraints excluded: chain AV residue 4 ILE Chi-restraints excluded: chain AY residue 4 ILE Chi-restraints excluded: chain Ac residue 2 ILE Chi-restraints excluded: chain Ad 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 An residue 4 ILE Chi-restraints excluded: chain Ap residue 4 ILE Chi-restraints excluded: chain Aq residue 2 ILE Chi-restraints excluded: chain As residue 2 ILE Chi-restraints excluded: chain f residue 4 ILE Chi-restraints excluded: chain h residue 4 ILE Chi-restraints excluded: chain n residue 4 ILE Chi-restraints excluded: chain p residue 6 LYS Chi-restraints excluded: chain v residue 2 ILE Chi-restraints excluded: chain v residue 4 ILE Chi-restraints excluded: chain y residue 3 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 8.9990 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.059578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.053894 restraints weight = 19706.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.055317 restraints weight = 7817.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.056243 restraints weight = 4356.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.056864 restraints weight = 2904.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.057280 restraints weight = 2136.933| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.5599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.091 4640 Z= 0.589 Angle : 1.081 9.345 5920 Z= 0.545 Chirality : 0.084 0.221 720 Planarity : 0.005 0.014 560 Dihedral : 7.479 30.860 640 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 29.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 13.12 % Allowed : 20.21 % Favored : 66.67 % 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: 1.86 (0.41), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 1.43 (0.31), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.033 0.006 TYRAc 5 Details of bonding type rmsd/Z covalent geometry : bond 0.01487 / 0.59 ( 4560) covalent geometry : angle 1.08089 / 0.55 ( 5920) hydrogen bonds : bond 0.11949 / 7.58 ( 91) hydrogen bonds : angle 11.19594 / 6.94 ( 273) Misc. bond : bond 0.00183 / 0.11 ( 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 120 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 57 time to evaluate : 0.269 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ai 1 LYS cc_start: 0.9316 (pttm) cc_final: 0.9037 (tptp) REVERT: w 1 LYS cc_start: 0.9396 (pttm) cc_final: 0.9107 (mmtt) outliers start: 63 outliers final: 51 residues processed: 104 average time/residue: 0.0870 time to fit residues: 11.1330 Evaluate side-chains 108 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 57 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 4 ILE Chi-restraints excluded: chain 4 residue 2 ILE Chi-restraints excluded: chain 4 residue 4 ILE Chi-restraints excluded: chain 5 residue 4 ILE Chi-restraints excluded: chain 6 residue 4 ILE Chi-restraints excluded: chain 7 residue 4 ILE Chi-restraints excluded: chain 9 residue 3 ILE Chi-restraints excluded: chain 9 residue 4 ILE Chi-restraints excluded: chain AB residue 4 ILE Chi-restraints excluded: chain AC residue 3 ILE Chi-restraints excluded: chain AE residue 3 ILE Chi-restraints excluded: chain AG residue 2 ILE Chi-restraints excluded: chain AJ residue 4 ILE Chi-restraints excluded: chain AL residue 4 ILE Chi-restraints excluded: chain AN residue 4 ILE Chi-restraints excluded: chain AO residue 4 ILE Chi-restraints excluded: chain AR residue 4 ILE Chi-restraints excluded: chain AT residue 4 ILE Chi-restraints excluded: chain AV residue 4 ILE Chi-restraints excluded: chain AW residue 4 ILE Chi-restraints excluded: chain AX residue 4 ILE Chi-restraints excluded: chain AY residue 3 ILE Chi-restraints excluded: chain AZ residue 4 ILE Chi-restraints excluded: chain Aa residue 4 ILE Chi-restraints excluded: chain Ad residue 4 ILE Chi-restraints excluded: chain Ae residue 4 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 Am residue 3 ILE Chi-restraints excluded: chain An residue 4 ILE Chi-restraints excluded: chain Ao residue 3 ILE Chi-restraints excluded: chain Ap residue 4 ILE Chi-restraints excluded: chain At residue 4 ILE Chi-restraints excluded: chain Av residue 2 ILE Chi-restraints excluded: chain f residue 4 ILE Chi-restraints excluded: chain h residue 4 ILE Chi-restraints excluded: chain i residue 3 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 p residue 4 ILE Chi-restraints excluded: chain p residue 6 LYS Chi-restraints excluded: chain q residue 2 ILE Chi-restraints excluded: chain t residue 2 ILE Chi-restraints excluded: chain u residue 4 ILE Chi-restraints excluded: chain v residue 2 ILE Chi-restraints excluded: chain v 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 4 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.066205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.060158 restraints weight = 17915.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.061862 restraints weight = 6786.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.062934 restraints weight = 3528.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.063638 restraints weight = 2193.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.064126 restraints weight = 1516.970| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.5683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 4640 Z= 0.145 Angle : 0.722 9.406 5920 Z= 0.358 Chirality : 0.073 0.213 720 Planarity : 0.003 0.012 560 Dihedral : 6.751 29.548 640 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 7.29 % Allowed : 26.04 % Favored : 66.67 % 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: 2.05 (0.42), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 1.57 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.002 TYRAc 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.15 ( 4560) covalent geometry : angle 0.72236 / 0.36 ( 5920) hydrogen bonds : bond 0.08965 / 5.57 ( 91) hydrogen bonds : angle 10.28178 / 6.36 ( 273) Misc. bond : bond 0.00026 / 0.02 ( 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 108 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 73 time to evaluate : 0.224 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ai 1 LYS cc_start: 0.9330 (pttm) cc_final: 0.9050 (tptp) REVERT: w 1 LYS cc_start: 0.9391 (pttm) cc_final: 0.8974 (mmtt) outliers start: 35 outliers final: 30 residues processed: 101 average time/residue: 0.0944 time to fit residues: 11.7936 Evaluate side-chains 98 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 68 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 4 ILE Chi-restraints excluded: chain 6 residue 4 ILE Chi-restraints excluded: chain 9 residue 3 ILE Chi-restraints excluded: chain AB residue 4 ILE Chi-restraints excluded: chain AG residue 2 ILE Chi-restraints excluded: chain AJ residue 4 ILE Chi-restraints excluded: chain AL residue 4 ILE Chi-restraints excluded: chain AM residue 4 ILE Chi-restraints excluded: chain AN residue 4 ILE Chi-restraints excluded: chain AR residue 2 ILE Chi-restraints excluded: chain AR residue 4 ILE Chi-restraints excluded: chain AT residue 4 ILE Chi-restraints excluded: chain AV residue 4 ILE Chi-restraints excluded: chain Ac residue 2 ILE Chi-restraints excluded: chain Ad residue 4 ILE Chi-restraints excluded: chain Ah residue 4 ILE Chi-restraints excluded: chain Ah residue 6 LYS Chi-restraints excluded: chain An residue 4 ILE Chi-restraints excluded: chain Ap residue 4 ILE Chi-restraints excluded: chain Aq residue 2 ILE Chi-restraints excluded: chain As residue 2 ILE Chi-restraints excluded: chain f residue 4 ILE Chi-restraints excluded: chain h residue 4 ILE Chi-restraints excluded: chain p residue 6 LYS Chi-restraints excluded: chain q residue 2 ILE Chi-restraints excluded: chain u residue 4 ILE Chi-restraints excluded: chain v residue 2 ILE Chi-restraints excluded: chain v residue 4 ILE Chi-restraints excluded: chain y residue 3 ILE Chi-restraints excluded: chain y residue 4 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 8.9990 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.058333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.052650 restraints weight = 19555.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.054090 restraints weight = 7333.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.055028 restraints weight = 3945.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.055655 restraints weight = 2575.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.056077 restraints weight = 1869.166| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.5650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.088 4640 Z= 0.588 Angle : 1.075 10.210 5920 Z= 0.542 Chirality : 0.083 0.224 720 Planarity : 0.005 0.014 560 Dihedral : 7.411 30.027 640 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 29.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 11.04 % Allowed : 22.08 % Favored : 66.88 % 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: 1.73 (0.41), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 1.33 (0.31), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.034 0.006 TYRAc 5 Details of bonding type rmsd/Z covalent geometry : bond 0.01481 / 0.59 ( 4560) covalent geometry : angle 1.07464 / 0.54 ( 5920) hydrogen bonds : bond 0.11879 / 7.53 ( 91) hydrogen bonds : angle 11.09151 / 6.88 ( 273) Misc. bond : bond 0.00202 / 0.12 ( 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 109 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 56 time to evaluate : 0.150 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ai 1 LYS cc_start: 0.9355 (pttm) cc_final: 0.9070 (tptp) REVERT: w 1 LYS cc_start: 0.9372 (pttm) cc_final: 0.9044 (mmtt) outliers start: 53 outliers final: 40 residues processed: 98 average time/residue: 0.0889 time to fit residues: 10.6472 Evaluate side-chains 96 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 56 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 2 ILE Chi-restraints excluded: chain 2 residue 4 ILE Chi-restraints excluded: chain 6 residue 4 ILE Chi-restraints excluded: chain 7 residue 4 ILE Chi-restraints excluded: chain 9 residue 3 ILE Chi-restraints excluded: chain 9 residue 4 ILE Chi-restraints excluded: chain AB residue 4 ILE Chi-restraints excluded: chain AJ residue 4 ILE Chi-restraints excluded: chain AL residue 4 ILE Chi-restraints excluded: chain AN residue 4 ILE Chi-restraints excluded: chain AP residue 2 ILE Chi-restraints excluded: chain AR residue 2 ILE Chi-restraints excluded: chain AR residue 4 ILE Chi-restraints excluded: chain AT residue 4 ILE Chi-restraints excluded: chain AV residue 4 ILE Chi-restraints excluded: chain AW residue 4 ILE Chi-restraints excluded: chain AX residue 4 ILE Chi-restraints excluded: chain Aa residue 4 ILE Chi-restraints excluded: chain Ad residue 4 ILE Chi-restraints excluded: chain Ae residue 4 ILE Chi-restraints excluded: chain Ah residue 4 ILE Chi-restraints excluded: chain Ah residue 6 LYS Chi-restraints excluded: chain An residue 4 ILE Chi-restraints excluded: chain Ap residue 4 ILE Chi-restraints excluded: chain Au residue 4 ILE Chi-restraints excluded: chain f residue 4 ILE Chi-restraints excluded: chain g residue 3 ILE Chi-restraints excluded: chain h residue 4 ILE Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain m residue 4 ILE Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 6 LYS Chi-restraints excluded: chain q residue 2 ILE Chi-restraints excluded: chain u residue 4 ILE 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 x residue 4 ILE Chi-restraints excluded: chain y residue 3 ILE Chi-restraints excluded: chain y residue 4 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.067350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.061214 restraints weight = 18230.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.062933 restraints weight = 7073.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.064024 restraints weight = 3719.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.064756 restraints weight = 2316.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.065247 restraints weight = 1601.342| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.5806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 4640 Z= 0.143 Angle : 0.719 7.504 5920 Z= 0.357 Chirality : 0.074 0.226 720 Planarity : 0.003 0.011 560 Dihedral : 6.766 28.444 640 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 5.83 % Allowed : 27.08 % Favored : 67.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.93 (0.43), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 1.48 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.002 TYRAk 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.14 ( 4560) covalent geometry : angle 0.71869 / 0.36 ( 5920) hydrogen bonds : bond 0.08859 / 5.48 ( 91) hydrogen bonds : angle 10.20649 / 6.31 ( 273) Misc. bond : bond 0.00028 / 0.02 ( 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 102 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 74 time to evaluate : 0.201 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ai 1 LYS cc_start: 0.9330 (pttm) cc_final: 0.9052 (tptp) REVERT: w 1 LYS cc_start: 0.9393 (pttm) cc_final: 0.8978 (mmtt) outliers start: 28 outliers final: 24 residues processed: 97 average time/residue: 0.0887 time to fit residues: 10.5456 Evaluate side-chains 94 residues out of total 480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 70 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 4 ILE Chi-restraints excluded: chain 6 residue 4 ILE Chi-restraints excluded: chain AB residue 4 ILE Chi-restraints excluded: chain AJ residue 4 ILE Chi-restraints excluded: chain AL residue 4 ILE Chi-restraints excluded: chain AN residue 4 ILE Chi-restraints excluded: chain AR residue 2 ILE Chi-restraints excluded: chain AR residue 4 ILE Chi-restraints excluded: chain AT residue 4 ILE Chi-restraints excluded: chain AV residue 4 ILE Chi-restraints excluded: chain Ad residue 4 ILE Chi-restraints excluded: chain Ah residue 4 ILE Chi-restraints excluded: chain Ah residue 6 LYS Chi-restraints excluded: chain An residue 4 ILE Chi-restraints excluded: chain Ap residue 4 ILE Chi-restraints excluded: chain Aq residue 2 ILE Chi-restraints excluded: chain As residue 2 ILE Chi-restraints excluded: chain f residue 4 ILE Chi-restraints excluded: chain h residue 4 ILE Chi-restraints excluded: chain p residue 6 LYS Chi-restraints excluded: chain u residue 4 ILE Chi-restraints excluded: chain v residue 2 ILE Chi-restraints excluded: chain v residue 4 ILE Chi-restraints excluded: chain x residue 4 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 7.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.059094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.053378 restraints weight = 19460.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.054824 restraints weight = 7338.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.055781 restraints weight = 3961.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.056412 restraints weight = 2579.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.056849 restraints weight = 1869.512| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.5662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.081 4640 Z= 0.521 Angle : 1.034 10.928 5920 Z= 0.523 Chirality : 0.081 0.251 720 Planarity : 0.004 0.013 560 Dihedral : 7.392 30.179 640 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 28.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 8.75 % Allowed : 23.75 % Favored : 67.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.86 (0.42), residues: 320 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 1.43 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.032 0.005 TYRAc 5 Details of bonding type rmsd/Z covalent geometry : bond 0.01314 / 0.52 ( 4560) covalent geometry : angle 1.03357 / 0.52 ( 5920) hydrogen bonds : bond 0.11748 / 7.46 ( 91) hydrogen bonds : angle 11.01477 / 6.82 ( 273) Misc. bond : bond 0.00162 / 0.10 ( 80) =============================================================================== Job complete usr+sys time: 676.41 seconds wall clock time: 12 minutes 34.01 seconds (754.01 seconds total)