Starting phenix.real_space_refine on Thu Oct 22 18:38:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ngk_49387/10_2026/9ngk_49387.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ngk_49387/10_2026/9ngk_49387.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ngk_49387/10_2026/9ngk_49387.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ngk_49387/10_2026/9ngk_49387.map" model { file = "/net/cci-nas-00/data/ceres_data/9ngk_49387/10_2026/9ngk_49387.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ngk_49387/10_2026/9ngk_49387.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 2624 2.51 5 N 576 2.21 5 O 512 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3712 Number of models: 1 Model: "" Number of chains: 128 Chain: "0" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "7" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "8" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "8" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "9" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "9" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AA" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "AA" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AB" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "AB" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AC" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "AC" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AD" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "AD" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AE" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "AE" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AF" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "AF" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AG" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "AG" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AH" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "AH" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AI" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "AI" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AJ" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "AJ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AK" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "AK" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AL" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "AL" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AM" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "AM" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AN" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "AN" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AO" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "AO" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AP" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "AP" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AQ" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "AQ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AR" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "AR" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AS" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "AS" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AT" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "AT" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AU" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "AU" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AV" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "AV" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AW" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "AW" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AX" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "AX" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AY" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "AY" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "AZ" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "AZ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "Aa" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "Aa" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "Ab" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "Ab" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "Ac" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "Ac" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "Ad" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "Ad" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "Ae" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "Ae" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "Af" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "Af" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "Ag" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "Ag" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "j" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "k" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "k" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "l" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "m" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "m" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "o" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "o" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "p" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "p" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "q" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "r" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "s" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "s" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "t" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "t" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "u" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "u" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "v" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "v" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "w" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "w" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "x" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "x" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "y" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "z" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {'ACE': 1} Classifications: {'peptide': 6, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 5} Chain: "z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.11, per 1000 atoms: 0.30 Number of scatterers: 3712 At special positions: 0 Unit cell: (74.008, 74.849, 54.665, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 512 8.00 N 576 7.00 C 2624 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=64, symmetry=0 Number of additional bonds: simple=64, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.29 Conformation dependent library (CDL) restraints added in 80.5 milliseconds 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 768 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 50.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing sheet with id=AA1, first strand: chain '0' and resid 2 through 5 removed outlier: 6.800A pdb=" N ILE 6 2 " --> pdb=" O ILE 8 3 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N TYR 8 5 " --> pdb=" O ILE 6 2 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE 6 4 " --> pdb=" O TYR 8 5 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE 2 2 " --> pdb=" O ILE 4 3 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N TYR 4 5 " --> pdb=" O ILE 2 2 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE 2 4 " --> pdb=" O TYR 4 5 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE x 2 " --> pdb=" O ILE z 3 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N TYR z 5 " --> pdb=" O ILE x 2 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE x 4 " --> pdb=" O TYR z 5 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE v 2 " --> pdb=" O ILE x 3 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N TYR x 5 " --> pdb=" O ILE v 2 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE v 4 " --> pdb=" O TYR x 5 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'AA' and resid 2 through 5 removed outlier: 6.576A pdb=" N ILE 1 3 " --> pdb=" O ILE y 4 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'AB' and resid 2 through 5 removed outlier: 6.611A pdb=" N ILEAB 2 " --> pdb=" O ILEAD 3 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N TYRAD 5 " --> pdb=" O ILEAB 2 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILEAB 4 " --> pdb=" O TYRAD 5 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILEAD 2 " --> pdb=" O ILEAF 3 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N TYRAF 5 " --> pdb=" O ILEAD 2 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILEAD 4 " --> pdb=" O TYRAF 5 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILEAF 2 " --> pdb=" O ILEAH 3 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N TYRAH 5 " --> pdb=" O ILEAF 2 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILEAF 4 " --> pdb=" O TYRAH 5 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILEAH 2 " --> pdb=" O ILEAJ 3 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N TYRAJ 5 " --> pdb=" O ILEAH 2 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILEAH 4 " --> pdb=" O TYRAJ 5 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILEAL 2 " --> pdb=" O ILEAN 3 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N TYRAN 5 " --> pdb=" O ILEAL 2 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILEAL 4 " --> pdb=" O TYRAN 5 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILEAN 2 " --> pdb=" O ILEAP 3 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N TYRAP 5 " --> pdb=" O ILEAN 2 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILEAN 4 " --> pdb=" O TYRAP 5 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'AC' and resid 2 through 5 Processing sheet with id=AA5, first strand: chain 'AR' and resid 2 through 5 removed outlier: 6.646A pdb=" N ILEAR 2 " --> pdb=" O ILEAT 3 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N TYRAT 5 " --> pdb=" O ILEAR 2 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILEAR 4 " --> pdb=" O TYRAT 5 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILEAT 2 " --> pdb=" O ILEAV 3 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N TYRAV 5 " --> pdb=" O ILEAT 2 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILEAT 4 " --> pdb=" O TYRAV 5 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILEAV 2 " --> pdb=" O ILEAX 3 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N TYRAX 5 " --> pdb=" O ILEAV 2 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILEAV 4 " --> pdb=" O TYRAX 5 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILEAX 2 " --> pdb=" O ILEAZ 3 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N TYRAZ 5 " --> pdb=" O ILEAX 2 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILEAX 4 " --> pdb=" O TYRAZ 5 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILEAZ 2 " --> pdb=" O ILEAb 3 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N TYRAb 5 " --> pdb=" O ILEAZ 2 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILEAZ 4 " --> pdb=" O TYRAb 5 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILEAd 2 " --> pdb=" O ILEAf 3 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N TYRAf 5 " --> pdb=" O ILEAd 2 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILEAd 4 " --> pdb=" O TYRAf 5 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'AS' and resid 2 through 5 Processing sheet with id=AA7, first strand: chain 'f' and resid 2 through 5 removed outlier: 6.638A pdb=" N ILE f 2 " --> pdb=" O ILE h 3 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N TYR h 5 " --> pdb=" O ILE f 2 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE f 4 " --> pdb=" O TYR h 5 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE h 2 " --> pdb=" O ILE j 3 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N TYR j 5 " --> pdb=" O ILE h 2 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE h 4 " --> pdb=" O TYR j 5 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE j 2 " --> pdb=" O ILE l 3 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N TYR l 5 " --> pdb=" O ILE j 2 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE j 4 " --> pdb=" O TYR l 5 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE l 2 " --> pdb=" O ILE n 3 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N TYR n 5 " --> pdb=" O ILE l 2 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE l 4 " --> pdb=" O TYR n 5 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE n 2 " --> pdb=" O ILE p 3 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N TYR p 5 " --> pdb=" O ILE n 2 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE n 4 " --> pdb=" O TYR p 5 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE p 2 " --> pdb=" O ILE r 3 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N TYR r 5 " --> pdb=" O ILE p 2 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE p 4 " --> pdb=" O TYR r 5 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE r 2 " --> pdb=" O ILE t 3 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N TYR t 5 " --> pdb=" O ILE r 2 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE r 4 " --> pdb=" O TYR t 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'g' and resid 2 through 5 removed outlier: 6.546A pdb=" N ILE s 2 " --> pdb=" O ILE u 3 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N TYR u 5 " --> pdb=" O ILE s 2 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE s 4 " --> pdb=" O TYR u 5 " (cutoff:3.500A) 93 hydrogen bonds defined for protein. 279 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.46 Time building geometry restraints manager: 0.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.28: 448 1.28 - 1.35: 385 1.35 - 1.42: 447 1.42 - 1.49: 476 1.49 - 1.55: 1892 Bond restraints: 3648 Sorted by residual: bond pdb=" N TYR m 5 " pdb=" CA TYR m 5 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.19e-02 7.06e+03 5.88e+00 bond pdb=" N TYR 3 5 " pdb=" CA TYR 3 5 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.19e-02 7.06e+03 5.73e+00 bond pdb=" N TYRAY 5 " pdb=" CA TYRAY 5 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.19e-02 7.06e+03 5.52e+00 bond pdb=" N ILE g 2 " pdb=" CA ILE g 2 " ideal model delta sigma weight residual 1.458 1.485 -0.027 1.18e-02 7.18e+03 5.42e+00 bond pdb=" N TYR w 5 " pdb=" CA TYR w 5 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.26e-02 6.30e+03 4.90e+00 ... (remaining 3643 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 3319 1.69 - 3.38: 1177 3.38 - 5.07: 175 5.07 - 6.77: 37 6.77 - 8.46: 28 Bond angle restraints: 4736 Sorted by residual: angle pdb=" CA ILE x 3 " pdb=" C ILE x 3 " pdb=" N ILE x 4 " ideal model delta sigma weight residual 116.40 119.88 -3.48 1.12e+00 7.97e-01 9.66e+00 angle pdb=" CA ILE w 3 " pdb=" CB ILE w 3 " pdb=" CG1 ILE w 3 " ideal model delta sigma weight residual 110.40 115.62 -5.22 1.70e+00 3.46e-01 9.44e+00 angle pdb=" CA ILEAD 3 " pdb=" C ILEAD 3 " pdb=" N ILEAD 4 " ideal model delta sigma weight residual 116.40 119.80 -3.40 1.12e+00 7.97e-01 9.23e+00 angle pdb=" CA TYRAe 5 " pdb=" CB TYRAe 5 " pdb=" CG TYRAe 5 " ideal model delta sigma weight residual 113.90 119.30 -5.40 1.80e+00 3.09e-01 9.00e+00 angle pdb=" CA ILEAT 3 " pdb=" C ILEAT 3 " pdb=" N ILEAT 4 " ideal model delta sigma weight residual 116.40 119.74 -3.34 1.12e+00 7.97e-01 8.89e+00 ... (remaining 4731 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 2243 35.82 - 71.63: 29 71.63 - 107.45: 0 107.45 - 143.27: 0 143.27 - 179.08: 32 Dihedral angle restraints: 2304 sinusoidal: 1152 harmonic: 1152 Sorted by residual: dihedral pdb=" CH3 ACEAY 0 " pdb=" C ACEAY 0 " pdb=" N LYSAY 1 " pdb=" CA LYSAY 1 " ideal model delta sinusoidal sigma weight residual -180.00 -0.92 -179.08 1 5.00e+00 4.00e-02 7.68e+02 dihedral pdb=" CH3 ACE g 0 " pdb=" C ACE g 0 " pdb=" N LYS g 1 " pdb=" CA LYS g 1 " ideal model delta sinusoidal sigma weight residual 180.00 1.13 178.87 1 5.00e+00 4.00e-02 7.68e+02 dihedral pdb=" CH3 ACEAE 0 " pdb=" C ACEAE 0 " pdb=" N LYSAE 1 " pdb=" CA LYSAE 1 " ideal model delta sinusoidal sigma weight residual -180.00 -1.31 -178.69 1 5.00e+00 4.00e-02 7.68e+02 ... (remaining 2301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 262 0.043 - 0.086: 212 0.086 - 0.130: 72 0.130 - 0.173: 20 0.173 - 0.216: 10 Chirality restraints: 576 Sorted by residual: chirality pdb=" CB ILEAS 3 " pdb=" CA ILEAS 3 " pdb=" CG1 ILEAS 3 " pdb=" CG2 ILEAS 3 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB ILEAd 2 " pdb=" CA ILEAd 2 " pdb=" CG1 ILEAd 2 " pdb=" CG2 ILEAd 2 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB ILE w 3 " pdb=" CA ILE w 3 " pdb=" CG1 ILE w 3 " pdb=" CG2 ILE w 3 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 573 not shown) Planarity restraints: 448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYRAR 5 " -0.102 2.00e-02 2.50e+03 5.31e-02 5.63e+01 pdb=" CG TYRAR 5 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TYRAR 5 " 0.041 2.00e-02 2.50e+03 pdb=" CD2 TYRAR 5 " 0.049 2.00e-02 2.50e+03 pdb=" CE1 TYRAR 5 " 0.027 2.00e-02 2.50e+03 pdb=" CE2 TYRAR 5 " 0.020 2.00e-02 2.50e+03 pdb=" CZ TYRAR 5 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYRAR 5 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR f 5 " 0.101 2.00e-02 2.50e+03 5.26e-02 5.53e+01 pdb=" CG TYR f 5 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR f 5 " -0.041 2.00e-02 2.50e+03 pdb=" CD2 TYR f 5 " -0.048 2.00e-02 2.50e+03 pdb=" CE1 TYR f 5 " -0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR f 5 " -0.019 2.00e-02 2.50e+03 pdb=" CZ TYR f 5 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR f 5 " 0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYRAB 5 " -0.097 2.00e-02 2.50e+03 5.01e-02 5.02e+01 pdb=" CG TYRAB 5 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYRAB 5 " 0.039 2.00e-02 2.50e+03 pdb=" CD2 TYRAB 5 " 0.042 2.00e-02 2.50e+03 pdb=" CE1 TYRAB 5 " 0.023 2.00e-02 2.50e+03 pdb=" CE2 TYRAB 5 " 0.021 2.00e-02 2.50e+03 pdb=" CZ TYRAB 5 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYRAB 5 " -0.066 2.00e-02 2.50e+03 ... (remaining 445 not shown) Histogram of nonbonded interaction distances: 2.74 - 3.17: 2349 3.17 - 3.60: 3056 3.60 - 4.04: 4799 4.04 - 4.47: 5368 4.47 - 4.90: 9946 Nonbonded interactions: 25518 Sorted by model distance: nonbonded pdb=" O ACEAD 0 " pdb=" CA LYSAD 1 " model vdw 2.741 2.776 nonbonded pdb=" N LYSAH 1 " pdb=" N ILEAH 2 " model vdw 2.743 2.560 nonbonded pdb=" N LYS 2 1 " pdb=" N ILE 2 2 " model vdw 2.744 2.560 nonbonded pdb=" O ACE h 0 " pdb=" CA LYS h 1 " model vdw 2.748 2.776 nonbonded pdb=" N LYS l 1 " pdb=" N ILE l 2 " model vdw 2.755 2.560 ... (remaining 25513 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain 'AA' selection = chain 'AB' selection = chain 'AC' selection = chain 'AD' selection = chain 'AE' selection = chain 'AF' selection = chain 'AG' selection = chain 'AH' selection = chain 'AI' selection = chain 'AJ' selection = chain 'AK' selection = chain 'AL' selection = chain 'AM' selection = chain 'AN' selection = chain 'AO' selection = chain 'AP' selection = chain 'AQ' selection = chain 'AR' selection = chain 'AS' selection = chain 'AT' selection = chain 'AU' selection = chain 'AV' selection = chain 'AW' selection = chain 'AX' selection = chain 'AY' selection = chain 'AZ' selection = chain 'Aa' selection = chain 'Ab' selection = chain 'Ac' selection = chain 'Ad' selection = chain 'Ae' selection = chain 'Af' selection = chain 'Ag' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.000 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.018 0.102 3712 Z= 1.455 Angle : 1.767 8.456 4736 Z= 1.006 Chirality : 0.066 0.216 576 Planarity : 0.014 0.056 448 Dihedral : 27.614 179.084 1536 Min Nonbonded Distance : 2.741 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.79 (0.38), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 4.43 (0.29), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.102 0.017 TYRAR 5 Details of bonding type rmsd/Z covalent geometry : bond 0.01222 / 0.60 ( 3648) covalent geometry : angle 1.76705 / 1.01 ( 4736) hydrogen bonds : bond 0.15293 / 8.80 ( 93) hydrogen bonds : angle 7.09008 / 4.45 ( 279) Misc. bond : bond 0.10100 / 5.92 ( 64) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.154 Fit side-chains REVERT: 1 1 LYS cc_start: 0.7758 (tttt) cc_final: 0.7477 (tttt) REVERT: AG 1 LYS cc_start: 0.7925 (tttt) cc_final: 0.7704 (tttt) REVERT: AP 6 LYS cc_start: 0.7624 (mttt) cc_final: 0.7330 (mttt) REVERT: AW 1 LYS cc_start: 0.7941 (tttt) cc_final: 0.7668 (tttt) REVERT: t 6 LYS cc_start: 0.7627 (mttt) cc_final: 0.7331 (mttt) REVERT: u 1 LYS cc_start: 0.7195 (tttt) cc_final: 0.6835 (tttt) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.1808 time to fit residues: 3.1671 Evaluate side-chains 15 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.095 ------------------------------------------------------------------------------- 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: 0.9990 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 = 0.3371 r_free = 0.3371 target = 0.091499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.084416 restraints weight = 5751.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.087391 restraints weight = 2258.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.089014 restraints weight = 1085.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.089921 restraints weight = 582.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.090423 restraints weight = 330.972| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 3712 Z= 0.179 Angle : 0.654 5.473 4736 Z= 0.289 Chirality : 0.066 0.141 576 Planarity : 0.003 0.010 448 Dihedral : 46.026 179.963 512 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 6.91 (0.38), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 5.28 (0.29), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.021 0.003 TYRAR 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 ( 3648) covalent geometry : angle 0.65366 / 0.29 ( 4736) hydrogen bonds : bond 0.05962 / 3.50 ( 93) hydrogen bonds : angle 5.88587 / 3.69 ( 279) Misc. bond : bond 0.00057 / 0.03 ( 64) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.109 Fit side-chains REVERT: 5 6 LYS cc_start: 0.8075 (mttt) cc_final: 0.7712 (mttt) REVERT: AG 1 LYS cc_start: 0.7772 (tttt) cc_final: 0.7565 (tttt) REVERT: Aa 6 LYS cc_start: 0.8100 (mttt) cc_final: 0.7536 (ttmm) REVERT: u 1 LYS cc_start: 0.7123 (tttt) cc_final: 0.6828 (tttt) outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.1787 time to fit residues: 2.7074 Evaluate side-chains 13 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.3174 r_free = 0.3174 target = 0.077791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.069561 restraints weight = 6671.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.072214 restraints weight = 3163.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.073947 restraints weight = 1806.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.075060 restraints weight = 1124.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.075805 restraints weight = 743.093| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.052 3712 Z= 0.521 Angle : 0.894 7.812 4736 Z= 0.419 Chirality : 0.068 0.158 576 Planarity : 0.004 0.013 448 Dihedral : 45.485 179.574 512 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 0.26 % Allowed : 2.86 % Favored : 96.88 % 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: 4.48 (0.44), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 3.43 (0.34), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.029 0.005 TYRAR 5 Details of bonding type rmsd/Z covalent geometry : bond 0.01212 / 0.52 ( 3648) covalent geometry : angle 0.89378 / 0.42 ( 4736) hydrogen bonds : bond 0.07967 / 4.66 ( 93) hydrogen bonds : angle 6.51472 / 4.12 ( 279) Misc. bond : bond 0.00326 / 0.19 ( 64) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 1 LYS cc_start: 0.7799 (tttt) cc_final: 0.7482 (tttt) REVERT: Aa 6 LYS cc_start: 0.8337 (mttt) cc_final: 0.7765 (ttmm) REVERT: l 6 LYS cc_start: 0.7993 (mttt) cc_final: 0.7711 (mttt) REVERT: o 1 LYS cc_start: 0.7617 (tttt) cc_final: 0.7178 (tttt) REVERT: t 6 LYS cc_start: 0.7643 (mttt) cc_final: 0.7356 (mttt) outliers start: 1 outliers final: 0 residues processed: 32 average time/residue: 0.1995 time to fit residues: 7.0236 Evaluate side-chains 32 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- 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 = 0.3222 r_free = 0.3222 target = 0.080158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.071885 restraints weight = 6532.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.074627 restraints weight = 3051.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.076401 restraints weight = 1712.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.077502 restraints weight = 1048.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.078245 restraints weight = 682.142| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 3712 Z= 0.177 Angle : 0.632 5.918 4736 Z= 0.275 Chirality : 0.065 0.140 576 Planarity : 0.002 0.009 448 Dihedral : 45.735 179.168 512 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.26 % Allowed : 2.86 % Favored : 96.88 % 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: 5.50 (0.44), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 4.20 (0.33), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.002 TYR f 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 ( 3648) covalent geometry : angle 0.63167 / 0.28 ( 4736) hydrogen bonds : bond 0.05666 / 3.33 ( 93) hydrogen bonds : angle 6.01696 / 3.80 ( 279) Misc. bond : bond 0.00067 / 0.04 ( 64) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 1 LYS cc_start: 0.7657 (tttt) cc_final: 0.7380 (tttt) REVERT: 5 6 LYS cc_start: 0.8215 (mttt) cc_final: 0.8002 (mttt) REVERT: AD 6 LYS cc_start: 0.7798 (mttt) cc_final: 0.7204 (mtpp) REVERT: Aa 6 LYS cc_start: 0.8204 (mttt) cc_final: 0.7673 (ttmm) REVERT: l 6 LYS cc_start: 0.8015 (mttt) cc_final: 0.7683 (mttt) REVERT: t 6 LYS cc_start: 0.7472 (mttt) cc_final: 0.7239 (mttt) outliers start: 1 outliers final: 1 residues processed: 30 average time/residue: 0.1764 time to fit residues: 5.8219 Evaluate side-chains 31 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 6 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.3190 r_free = 0.3190 target = 0.077837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.068973 restraints weight = 6717.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.071696 restraints weight = 3277.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.073488 restraints weight = 1909.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.074700 restraints weight = 1217.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.075507 restraints weight = 816.717| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.053 3712 Z= 0.528 Angle : 0.886 7.474 4736 Z= 0.416 Chirality : 0.067 0.156 576 Planarity : 0.004 0.012 448 Dihedral : 45.511 179.176 512 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.52 % Allowed : 4.95 % Favored : 94.53 % 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: 3.30 (0.47), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 2.53 (0.36), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.027 0.005 TYR v 5 Details of bonding type rmsd/Z covalent geometry : bond 0.01233 / 0.53 ( 3648) covalent geometry : angle 0.88630 / 0.42 ( 4736) hydrogen bonds : bond 0.08258 / 4.78 ( 93) hydrogen bonds : angle 6.30487 / 3.99 ( 279) Misc. bond : bond 0.00238 / 0.15 ( 64) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 47 time to evaluate : 0.102 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: 3 1 LYS cc_start: 0.8106 (tttt) cc_final: 0.7775 (tttt) REVERT: 3 6 LYS cc_start: 0.8195 (mttt) cc_final: 0.7982 (mttt) REVERT: 5 6 LYS cc_start: 0.8454 (mttt) cc_final: 0.7966 (ttmm) REVERT: AB 6 LYS cc_start: 0.7880 (mttt) cc_final: 0.7584 (mttt) REVERT: AD 6 LYS cc_start: 0.8103 (mttt) cc_final: 0.7450 (mtpp) REVERT: Aa 6 LYS cc_start: 0.8414 (mttt) cc_final: 0.7850 (ttmm) REVERT: k 1 LYS cc_start: 0.7761 (tttt) cc_final: 0.7429 (tttt) REVERT: l 6 LYS cc_start: 0.8308 (mttt) cc_final: 0.7936 (mttt) REVERT: o 1 LYS cc_start: 0.7587 (tttt) cc_final: 0.7161 (tttt) REVERT: t 6 LYS cc_start: 0.7653 (mttt) cc_final: 0.7400 (mttt) outliers start: 2 outliers final: 0 residues processed: 47 average time/residue: 0.2024 time to fit residues: 10.3703 Evaluate side-chains 47 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 = 0.3251 r_free = 0.3251 target = 0.081414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.072795 restraints weight = 6868.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.075677 restraints weight = 3104.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.077531 restraints weight = 1717.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.078703 restraints weight = 1045.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.079479 restraints weight = 684.106| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 3712 Z= 0.176 Angle : 0.626 5.824 4736 Z= 0.275 Chirality : 0.065 0.140 576 Planarity : 0.002 0.010 448 Dihedral : 45.791 179.180 512 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 0.26 % Allowed : 4.95 % Favored : 94.79 % 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: 4.33 (0.48), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 3.32 (0.36), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.002 TYR x 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 ( 3648) covalent geometry : angle 0.62575 / 0.28 ( 4736) hydrogen bonds : bond 0.05717 / 3.35 ( 93) hydrogen bonds : angle 5.99724 / 3.80 ( 279) Misc. bond : bond 0.00077 / 0.05 ( 64) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 6 LYS cc_start: 0.8334 (mttt) cc_final: 0.7886 (mttt) REVERT: 3 6 LYS cc_start: 0.8157 (mttt) cc_final: 0.7947 (mttt) REVERT: AE 6 LYS cc_start: 0.7941 (mttt) cc_final: 0.7715 (mttt) REVERT: Aa 6 LYS cc_start: 0.8309 (mttt) cc_final: 0.7813 (ttmm) REVERT: k 1 LYS cc_start: 0.7709 (tttt) cc_final: 0.7346 (tttt) REVERT: l 6 LYS cc_start: 0.8167 (mttt) cc_final: 0.7791 (mttt) REVERT: o 1 LYS cc_start: 0.7559 (tttt) cc_final: 0.7150 (tttt) REVERT: t 6 LYS cc_start: 0.7520 (mttt) cc_final: 0.7267 (mttt) outliers start: 1 outliers final: 0 residues processed: 41 average time/residue: 0.2055 time to fit residues: 9.2322 Evaluate side-chains 41 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.3189 r_free = 0.3189 target = 0.078061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.068797 restraints weight = 6806.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.071638 restraints weight = 3282.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.073518 restraints weight = 1909.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.074748 restraints weight = 1220.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.075595 restraints weight = 829.078| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.054 3712 Z= 0.519 Angle : 0.877 7.330 4736 Z= 0.412 Chirality : 0.067 0.158 576 Planarity : 0.004 0.011 448 Dihedral : 45.564 178.801 512 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.52 % Allowed : 5.99 % Favored : 93.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.55 (0.48), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 1.95 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.026 0.004 TYRAb 5 Details of bonding type rmsd/Z covalent geometry : bond 0.01212 / 0.52 ( 3648) covalent geometry : angle 0.87721 / 0.41 ( 4736) hydrogen bonds : bond 0.08330 / 4.85 ( 93) hydrogen bonds : angle 6.26507 / 3.98 ( 279) Misc. bond : bond 0.00236 / 0.14 ( 64) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.158 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: 1 6 LYS cc_start: 0.8196 (mttt) cc_final: 0.7980 (mttt) REVERT: 2 6 LYS cc_start: 0.8460 (mttt) cc_final: 0.8049 (mttt) REVERT: 3 1 LYS cc_start: 0.8142 (tttt) cc_final: 0.7776 (tttt) REVERT: 3 5 TYR cc_start: 0.8571 (t80) cc_final: 0.8274 (t80) REVERT: 3 6 LYS cc_start: 0.8298 (mttt) cc_final: 0.8076 (mttt) REVERT: AF 6 LYS cc_start: 0.8468 (tttt) cc_final: 0.7934 (ttmm) REVERT: AI 6 LYS cc_start: 0.8083 (mttt) cc_final: 0.7881 (mttt) REVERT: Aa 6 LYS cc_start: 0.8438 (mttt) cc_final: 0.7922 (ttmm) REVERT: k 1 LYS cc_start: 0.7759 (tttt) cc_final: 0.7389 (tttt) REVERT: l 6 LYS cc_start: 0.8342 (mttt) cc_final: 0.7953 (mttt) REVERT: o 1 LYS cc_start: 0.7613 (tttt) cc_final: 0.7204 (tttt) REVERT: t 6 LYS cc_start: 0.7749 (mttt) cc_final: 0.7532 (mttt) outliers start: 2 outliers final: 0 residues processed: 51 average time/residue: 0.1946 time to fit residues: 10.8733 Evaluate side-chains 51 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 = 0.3252 r_free = 0.3252 target = 0.081239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.072339 restraints weight = 6811.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.075250 restraints weight = 3137.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.077167 restraints weight = 1763.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.078390 restraints weight = 1086.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.079177 restraints weight = 709.572| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 3712 Z= 0.177 Angle : 0.624 5.815 4736 Z= 0.276 Chirality : 0.065 0.140 576 Planarity : 0.002 0.009 448 Dihedral : 45.904 179.186 512 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 0.26 % Allowed : 7.55 % Favored : 92.19 % 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: 3.80 (0.49), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 2.91 (0.38), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.002 TYR x 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 ( 3648) covalent geometry : angle 0.62446 / 0.28 ( 4736) hydrogen bonds : bond 0.05791 / 3.42 ( 93) hydrogen bonds : angle 5.95115 / 3.79 ( 279) Misc. bond : bond 0.00079 / 0.05 ( 64) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 6 LYS cc_start: 0.8064 (mttt) cc_final: 0.7827 (mttt) REVERT: 2 6 LYS cc_start: 0.8387 (mttt) cc_final: 0.7931 (mttt) REVERT: 3 1 LYS cc_start: 0.7987 (tttt) cc_final: 0.7662 (tttt) REVERT: AE 6 LYS cc_start: 0.7909 (mttt) cc_final: 0.7632 (mttt) REVERT: AF 6 LYS cc_start: 0.8378 (tttt) cc_final: 0.7834 (ttmm) REVERT: Aa 6 LYS cc_start: 0.8330 (mttt) cc_final: 0.7797 (ttmm) REVERT: k 1 LYS cc_start: 0.7715 (tttt) cc_final: 0.7329 (tttt) REVERT: l 6 LYS cc_start: 0.8253 (mttt) cc_final: 0.7859 (mttt) REVERT: o 1 LYS cc_start: 0.7584 (tttt) cc_final: 0.7183 (tttt) REVERT: t 6 LYS cc_start: 0.7520 (mttt) cc_final: 0.7272 (mttt) outliers start: 1 outliers final: 0 residues processed: 47 average time/residue: 0.1991 time to fit residues: 10.2529 Evaluate side-chains 47 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.3185 r_free = 0.3185 target = 0.077626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.068383 restraints weight = 7115.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.071147 restraints weight = 3476.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.073024 restraints weight = 2028.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.074241 restraints weight = 1305.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.075044 restraints weight = 893.355| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.053 3712 Z= 0.514 Angle : 0.862 6.935 4736 Z= 0.404 Chirality : 0.068 0.160 576 Planarity : 0.004 0.011 448 Dihedral : 45.617 178.777 512 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % 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: 2.33 (0.49), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 1.79 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.026 0.004 TYRAb 5 Details of bonding type rmsd/Z covalent geometry : bond 0.01198 / 0.52 ( 3648) covalent geometry : angle 0.86220 / 0.40 ( 4736) hydrogen bonds : bond 0.08229 / 4.81 ( 93) hydrogen bonds : angle 6.24725 / 3.98 ( 279) Misc. bond : bond 0.00240 / 0.14 ( 64) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 6 LYS cc_start: 0.8297 (mttt) cc_final: 0.7946 (mttt) REVERT: 2 6 LYS cc_start: 0.8482 (mttt) cc_final: 0.8058 (mttt) REVERT: 3 1 LYS cc_start: 0.8152 (tttt) cc_final: 0.7798 (tttt) REVERT: AE 6 LYS cc_start: 0.8043 (mttt) cc_final: 0.7777 (mttt) REVERT: AF 6 LYS cc_start: 0.8582 (tttt) cc_final: 0.7989 (ttmm) REVERT: AW 6 LYS cc_start: 0.8182 (mttt) cc_final: 0.7860 (mttt) REVERT: Aa 6 LYS cc_start: 0.8436 (mttt) cc_final: 0.7891 (ttmm) REVERT: h 6 LYS cc_start: 0.8174 (mttt) cc_final: 0.7888 (mttt) REVERT: k 1 LYS cc_start: 0.7815 (tttt) cc_final: 0.7395 (tttt) REVERT: l 6 LYS cc_start: 0.8391 (mttt) cc_final: 0.8165 (mttt) REVERT: o 1 LYS cc_start: 0.7618 (tttt) cc_final: 0.7232 (tttt) REVERT: t 6 LYS cc_start: 0.7797 (mttt) cc_final: 0.7561 (mttt) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1965 time to fit residues: 11.4027 Evaluate side-chains 53 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- 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 = 0.3276 r_free = 0.3276 target = 0.082807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.074190 restraints weight = 6766.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.077063 restraints weight = 3079.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.078964 restraints weight = 1691.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.080147 restraints weight = 1036.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.080937 restraints weight = 667.573| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 3712 Z= 0.175 Angle : 0.623 5.764 4736 Z= 0.277 Chirality : 0.065 0.142 576 Planarity : 0.002 0.009 448 Dihedral : 45.964 179.129 512 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 0.26 % Allowed : 8.33 % Favored : 91.41 % 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: 3.51 (0.50), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 2.69 (0.38), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.002 TYRAa 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 ( 3648) covalent geometry : angle 0.62318 / 0.28 ( 4736) hydrogen bonds : bond 0.05832 / 3.45 ( 93) hydrogen bonds : angle 5.94466 / 3.79 ( 279) Misc. bond : bond 0.00079 / 0.05 ( 64) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 512 Ramachandran restraints generated. 256 Oldfield, 0 Emsley, 256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 6 LYS cc_start: 0.8117 (mttt) cc_final: 0.7912 (mttt) REVERT: 2 6 LYS cc_start: 0.8425 (mttt) cc_final: 0.7999 (mttt) REVERT: 3 1 LYS cc_start: 0.7982 (tttt) cc_final: 0.7642 (tttt) REVERT: AE 6 LYS cc_start: 0.7877 (mttt) cc_final: 0.7625 (mttt) REVERT: AF 6 LYS cc_start: 0.8468 (tttt) cc_final: 0.7901 (ttmm) REVERT: AW 6 LYS cc_start: 0.8101 (mttt) cc_final: 0.7795 (mttt) REVERT: Aa 6 LYS cc_start: 0.8352 (mttt) cc_final: 0.7839 (ttmm) REVERT: h 6 LYS cc_start: 0.8077 (mttt) cc_final: 0.7749 (mttt) REVERT: k 1 LYS cc_start: 0.7714 (tttt) cc_final: 0.7307 (tttt) REVERT: l 6 LYS cc_start: 0.8281 (mttt) cc_final: 0.7941 (mttt) REVERT: o 1 LYS cc_start: 0.7564 (tttt) cc_final: 0.7182 (tttt) REVERT: t 6 LYS cc_start: 0.7525 (mttt) cc_final: 0.7271 (mttt) outliers start: 1 outliers final: 0 residues processed: 49 average time/residue: 0.1917 time to fit residues: 10.2271 Evaluate side-chains 49 residues out of total 384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: [0] chunk 0 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.3192 r_free = 0.3192 target = 0.077718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.068334 restraints weight = 7025.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.071151 restraints weight = 3371.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.073018 restraints weight = 1970.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.074261 restraints weight = 1279.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.075099 restraints weight = 875.304| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.054 3712 Z= 0.515 Angle : 0.870 6.850 4736 Z= 0.408 Chirality : 0.068 0.161 576 Planarity : 0.004 0.011 448 Dihedral : 45.619 178.795 512 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.26 % Allowed : 8.33 % Favored : 91.41 % 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: 2.15 (0.49), residues: 256 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 1.65 (0.38), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.028 0.004 TYR j 5 Details of bonding type rmsd/Z covalent geometry : bond 0.01202 / 0.52 ( 3648) covalent geometry : angle 0.86983 / 0.41 ( 4736) hydrogen bonds : bond 0.08293 / 4.85 ( 93) hydrogen bonds : angle 6.23640 / 3.97 ( 279) Misc. bond : bond 0.00242 / 0.14 ( 64) =============================================================================== Job complete usr+sys time: 518.66 seconds wall clock time: 9 minutes 39.13 seconds (579.13 seconds total)