Starting phenix.real_space_refine on Sun Jul 5 02:40:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b3q_15833/07_2026/8b3q_15833.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b3q_15833/07_2026/8b3q_15833.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8b3q_15833/07_2026/8b3q_15833.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b3q_15833/07_2026/8b3q_15833.map" model { file = "/net/cci-nas-00/data/ceres_data/8b3q_15833/07_2026/8b3q_15833.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b3q_15833/07_2026/8b3q_15833.cif" } resolution = 2.58 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 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: 4 Type Number sf(0) Gaussians S 150 5.16 5 C 16470 2.51 5 N 3910 2.21 5 O 4565 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25095 Number of models: 1 Model: "" Number of chains: 75 Chain: "AAA" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "BBB" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "CCC" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "DDD" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "EEE" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "AaA" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "BaB" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "CaC" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "DaD" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "EaE" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "AbA" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "BbB" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "CbC" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "DbD" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "EbE" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "AcA" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "BcB" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "CcC" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "DcD" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "EcE" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "AdA" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "BdB" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "CdC" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "DdD" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "EdE" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "AeA" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "BeB" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "CeC" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "DeD" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "EeE" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "AfA" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "BfB" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "CfC" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "DfD" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "EfE" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "AgA" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 259 Classifications: {'peptide': 35} Modifications used: {'COO': 1} Link IDs: {'TRANS': 34} Chain: "BgB" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 259 Classifications: {'peptide': 35} Modifications used: {'COO': 1} Link IDs: {'TRANS': 34} Chain: "CgC" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 259 Classifications: {'peptide': 35} Modifications used: {'COO': 1} Link IDs: {'TRANS': 34} Chain: "DgD" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 259 Classifications: {'peptide': 35} Modifications used: {'COO': 1} Link IDs: {'TRANS': 34} Chain: "EgE" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 259 Classifications: {'peptide': 35} Modifications used: {'COO': 1} Link IDs: {'TRANS': 34} Chain: "AhA" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "BhB" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "ChC" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "DhD" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "EhE" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "AiA" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "BiB" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "CiC" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "DiD" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "EiE" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "AjA" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "BjB" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "CjC" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "DjD" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "EjE" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "AkA" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "BkB" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "CkC" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "DkD" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "EkE" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "AlA" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "BlB" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "ClC" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "DlD" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "ElE" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "AmA" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "BmB" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "CmC" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "DmD" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "EmE" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "AnA" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "BnB" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "CnC" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "DnD" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "EnE" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 340 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Time building chain proxies: 4.72, per 1000 atoms: 0.19 Number of scatterers: 25095 At special positions: 0 Unit cell: (82.59, 80.3876, 298.425, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 150 16.00 O 4565 8.00 N 3910 7.00 C 16470 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=0, symmetry=0 Time building additional restraints: 2.13 Conformation dependent library (CDL) restraints added in 822.4 milliseconds 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6340 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 0 sheets defined 97.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'AAA' and resid 5 through 50 removed outlier: 3.834A pdb=" N ALAAAA 9 " --> pdb=" O ASPAAA 5 " (cutoff:3.500A) Processing helix chain 'BBB' and resid 6 through 50 Processing helix chain 'CCC' and resid 6 through 50 Processing helix chain 'DDD' and resid 6 through 50 Processing helix chain 'EEE' and resid 6 through 50 Processing helix chain 'AaA' and resid 6 through 50 Processing helix chain 'BaB' and resid 6 through 50 Processing helix chain 'CaC' and resid 6 through 50 Processing helix chain 'DaD' and resid 6 through 50 Processing helix chain 'EaE' and resid 6 through 50 Processing helix chain 'AbA' and resid 6 through 50 Processing helix chain 'BbB' and resid 6 through 50 Processing helix chain 'CbC' and resid 6 through 50 Processing helix chain 'DbD' and resid 6 through 50 Processing helix chain 'EbE' and resid 6 through 50 Processing helix chain 'AcA' and resid 6 through 50 Processing helix chain 'BcB' and resid 6 through 50 Processing helix chain 'CcC' and resid 6 through 50 Processing helix chain 'DcD' and resid 6 through 50 Processing helix chain 'EcE' and resid 6 through 50 Processing helix chain 'AdA' and resid 6 through 50 Processing helix chain 'BdB' and resid 6 through 50 Processing helix chain 'CdC' and resid 6 through 50 Processing helix chain 'DdD' and resid 6 through 50 Processing helix chain 'EdE' and resid 6 through 50 Processing helix chain 'AeA' and resid 6 through 50 Processing helix chain 'BeB' and resid 6 through 50 Processing helix chain 'CeC' and resid 6 through 50 Processing helix chain 'DeD' and resid 6 through 50 Processing helix chain 'EeE' and resid 6 through 50 Processing helix chain 'AfA' and resid 6 through 50 Processing helix chain 'BfB' and resid 6 through 50 Processing helix chain 'CfC' and resid 6 through 50 Processing helix chain 'DfD' and resid 6 through 50 Processing helix chain 'EfE' and resid 6 through 50 Processing helix chain 'AgA' and resid 17 through 50 Processing helix chain 'BgB' and resid 17 through 50 Processing helix chain 'CgC' and resid 17 through 50 Processing helix chain 'DgD' and resid 17 through 50 Processing helix chain 'EgE' and resid 17 through 50 Processing helix chain 'AhA' and resid 6 through 50 Processing helix chain 'BhB' and resid 6 through 50 Processing helix chain 'ChC' and resid 6 through 50 Processing helix chain 'DhD' and resid 6 through 50 Processing helix chain 'EhE' and resid 6 through 50 Processing helix chain 'AiA' and resid 6 through 50 Processing helix chain 'BiB' and resid 6 through 50 Processing helix chain 'CiC' and resid 6 through 50 Processing helix chain 'DiD' and resid 6 through 50 Processing helix chain 'EiE' and resid 6 through 50 Processing helix chain 'AjA' and resid 6 through 50 Processing helix chain 'BjB' and resid 6 through 50 Processing helix chain 'CjC' and resid 6 through 50 Processing helix chain 'DjD' and resid 6 through 50 Processing helix chain 'EjE' and resid 6 through 50 Processing helix chain 'AkA' and resid 6 through 50 Processing helix chain 'BkB' and resid 6 through 50 Processing helix chain 'CkC' and resid 6 through 50 Processing helix chain 'DkD' and resid 6 through 50 Processing helix chain 'EkE' and resid 6 through 50 Processing helix chain 'AlA' and resid 6 through 50 Processing helix chain 'BlB' and resid 6 through 50 Processing helix chain 'ClC' and resid 6 through 50 Processing helix chain 'DlD' and resid 6 through 50 Processing helix chain 'ElE' and resid 6 through 50 Processing helix chain 'AmA' and resid 6 through 50 Processing helix chain 'BmB' and resid 6 through 50 Processing helix chain 'CmC' and resid 6 through 50 Processing helix chain 'DmD' and resid 6 through 50 Processing helix chain 'EmE' and resid 6 through 50 Processing helix chain 'AnA' and resid 6 through 50 Processing helix chain 'BnB' and resid 6 through 50 Processing helix chain 'CnC' and resid 6 through 50 Processing helix chain 'DnD' and resid 6 through 50 Processing helix chain 'EnE' and resid 6 through 50 3020 hydrogen bonds defined for protein. 9060 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: 4.41 Time building geometry restraints manager: 2.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4952 1.33 - 1.45: 7494 1.45 - 1.57: 12789 1.57 - 1.69: 0 1.69 - 1.81: 300 Bond restraints: 25535 Sorted by residual: bond pdb=" N ALADgD 16 " pdb=" CA ALADgD 16 " ideal model delta sigma weight residual 1.458 1.533 -0.075 1.90e-02 2.77e+03 1.54e+01 bond pdb=" N ALAAgA 16 " pdb=" CA ALAAgA 16 " ideal model delta sigma weight residual 1.458 1.532 -0.074 1.90e-02 2.77e+03 1.53e+01 bond pdb=" CA SERCbC 47 " pdb=" CB SERCbC 47 " ideal model delta sigma weight residual 1.529 1.469 0.060 1.55e-02 4.16e+03 1.51e+01 bond pdb=" CA SEREaE 47 " pdb=" CB SEREaE 47 " ideal model delta sigma weight residual 1.529 1.470 0.059 1.55e-02 4.16e+03 1.47e+01 bond pdb=" CA SEREcE 47 " pdb=" CB SEREcE 47 " ideal model delta sigma weight residual 1.529 1.470 0.059 1.55e-02 4.16e+03 1.47e+01 ... (remaining 25530 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 27427 1.73 - 3.46: 5663 3.46 - 5.18: 1065 5.18 - 6.91: 188 6.91 - 8.64: 117 Bond angle restraints: 34460 Sorted by residual: angle pdb=" CA PHEAcA 45 " pdb=" CB PHEAcA 45 " pdb=" CG PHEAcA 45 " ideal model delta sigma weight residual 113.80 107.56 6.24 1.00e+00 1.00e+00 3.89e+01 angle pdb=" CA PHEAbA 45 " pdb=" CB PHEAbA 45 " pdb=" CG PHEAbA 45 " ideal model delta sigma weight residual 113.80 107.57 6.23 1.00e+00 1.00e+00 3.88e+01 angle pdb=" CA PHECaC 45 " pdb=" CB PHECaC 45 " pdb=" CG PHECaC 45 " ideal model delta sigma weight residual 113.80 107.63 6.17 1.00e+00 1.00e+00 3.80e+01 angle pdb=" CA PHEEbE 45 " pdb=" CB PHEEbE 45 " pdb=" CG PHEEbE 45 " ideal model delta sigma weight residual 113.80 107.66 6.14 1.00e+00 1.00e+00 3.78e+01 angle pdb=" CA PHEDcD 45 " pdb=" CB PHEDcD 45 " pdb=" CG PHEDcD 45 " ideal model delta sigma weight residual 113.80 107.68 6.12 1.00e+00 1.00e+00 3.75e+01 ... (remaining 34455 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.80: 12575 11.80 - 23.60: 1346 23.60 - 35.40: 835 35.40 - 47.20: 278 47.20 - 59.01: 81 Dihedral angle restraints: 15115 sinusoidal: 5380 harmonic: 9735 Sorted by residual: dihedral pdb=" C THREgE 19 " pdb=" N THREgE 19 " pdb=" CA THREgE 19 " pdb=" CB THREgE 19 " ideal model delta harmonic sigma weight residual -122.00 -130.66 8.66 0 2.50e+00 1.60e-01 1.20e+01 dihedral pdb=" CB METEjE 28 " pdb=" CG METEjE 28 " pdb=" SD METEjE 28 " pdb=" CE METEjE 28 " ideal model delta sinusoidal sigma weight residual -60.00 -119.01 59.01 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N SERCkC 13 " pdb=" CA SERCkC 13 " pdb=" CB SERCkC 13 " pdb=" OG SERCkC 13 " ideal model delta sinusoidal sigma weight residual -60.00 -1.23 -58.77 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 15112 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2265 0.064 - 0.128: 1281 0.128 - 0.192: 355 0.192 - 0.257: 180 0.257 - 0.321: 59 Chirality restraints: 4140 Sorted by residual: chirality pdb=" CA PHEDaD 45 " pdb=" N PHEDaD 45 " pdb=" C PHEDaD 45 " pdb=" CB PHEDaD 45 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CA PHEEhE 45 " pdb=" N PHEEhE 45 " pdb=" C PHEEhE 45 " pdb=" CB PHEEhE 45 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CA PHEAaA 45 " pdb=" N PHEAaA 45 " pdb=" C PHEAaA 45 " pdb=" CB PHEAaA 45 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.40e+00 ... (remaining 4137 not shown) Planarity restraints: 4120 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYRDhD 24 " 0.049 2.00e-02 2.50e+03 3.14e-02 1.97e+01 pdb=" CG TYRDhD 24 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYRDhD 24 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 TYRDhD 24 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYRDhD 24 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYRDhD 24 " -0.039 2.00e-02 2.50e+03 pdb=" CZ TYRDhD 24 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYRDhD 24 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYREiE 24 " 0.050 2.00e-02 2.50e+03 3.10e-02 1.92e+01 pdb=" CG TYREiE 24 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYREiE 24 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TYREiE 24 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYREiE 24 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYREiE 24 " -0.037 2.00e-02 2.50e+03 pdb=" CZ TYREiE 24 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYREiE 24 " 0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYRBBB 24 " -0.048 2.00e-02 2.50e+03 3.08e-02 1.90e+01 pdb=" CG TYRBBB 24 " 0.009 2.00e-02 2.50e+03 pdb=" CD1 TYRBBB 24 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TYRBBB 24 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYRBBB 24 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TYRBBB 24 " 0.036 2.00e-02 2.50e+03 pdb=" CZ TYRBBB 24 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYRBBB 24 " -0.051 2.00e-02 2.50e+03 ... (remaining 4117 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 8202 2.86 - 3.37: 27971 3.37 - 3.88: 40893 3.88 - 4.39: 41548 4.39 - 4.90: 73798 Nonbonded interactions: 192412 Sorted by model distance: nonbonded pdb=" NZ LYSEdE 40 " pdb=" OXT SEREeE 50 " model vdw 2.348 3.120 nonbonded pdb=" NZ LYSEbE 40 " pdb=" OXT SEREcE 50 " model vdw 2.348 3.120 nonbonded pdb=" NZ LYSDdD 40 " pdb=" OXT SERDeD 50 " model vdw 2.350 3.120 nonbonded pdb=" NZ LYSBdB 40 " pdb=" OXT SERBeB 50 " model vdw 2.350 3.120 nonbonded pdb=" NZ LYSCdC 40 " pdb=" OXT SERCeC 50 " model vdw 2.351 3.120 ... (remaining 192407 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: 0.07 Found NCS groups: ncs_group { reference = chain 'AAA' selection = chain 'BBB' selection = chain 'CCC' selection = chain 'DDD' selection = chain 'EEE' selection = chain 'AaA' selection = chain 'BaB' selection = chain 'CaC' selection = chain 'DaD' selection = chain 'EaE' selection = chain 'AbA' selection = chain 'BbB' selection = chain 'CbC' selection = chain 'DbD' selection = chain 'EbE' selection = chain 'AcA' selection = chain 'BcB' selection = chain 'CcC' selection = chain 'DcD' selection = chain 'EcE' selection = chain 'AdA' selection = chain 'BdB' selection = chain 'CdC' selection = chain 'DdD' selection = chain 'EdE' selection = chain 'AeA' selection = chain 'BeB' selection = chain 'CeC' selection = chain 'DeD' selection = chain 'EeE' selection = chain 'AfA' selection = chain 'BfB' selection = chain 'CfC' selection = chain 'DfD' selection = chain 'EfE' selection = chain 'AhA' selection = chain 'BhB' selection = chain 'ChC' selection = chain 'DhD' selection = chain 'EhE' selection = chain 'AiA' selection = chain 'BiB' selection = chain 'CiC' selection = chain 'DiD' selection = chain 'EiE' selection = chain 'AjA' selection = chain 'BjB' selection = chain 'CjC' selection = chain 'DjD' selection = chain 'EjE' selection = chain 'AkA' selection = chain 'BkB' selection = chain 'CkC' selection = chain 'DkD' selection = chain 'EkE' selection = chain 'AlA' selection = chain 'BlB' selection = chain 'ClC' selection = chain 'DlD' selection = chain 'ElE' selection = chain 'AmA' selection = chain 'BmB' selection = chain 'CmC' selection = chain 'DmD' selection = chain 'EmE' selection = chain 'AnA' selection = chain 'BnB' selection = chain 'CnC' selection = chain 'DnD' selection = chain 'EnE' } ncs_group { reference = chain 'AgA' selection = chain 'BgB' selection = chain 'CgC' selection = chain 'DgD' selection = chain 'EgE' } 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 individual isotropic 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: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.230 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.120 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:6.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9393 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 : 0.011 0.075 25535 Z= 0.684 Angle : 1.554 8.640 34460 Z= 1.083 Chirality : 0.093 0.321 4140 Planarity : 0.007 0.031 4120 Dihedral : 14.854 59.006 8775 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.20 % Allowed : 13.59 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.12), residues: 3245 helix: -0.53 (0.07), residues: 3245 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.051 0.016 TYRBBB 24 PHE 0.034 0.008 PHEEeE 45 TRP 0.034 0.009 TRPEhE 26 Details of bonding type rmsd/Z covalent geometry : bond 0.01105 / 0.68 (25535) covalent geometry : angle 1.55429 / 1.08 (34460) hydrogen bonds : bond 0.23965 / 16.18 ( 3020) hydrogen bonds : angle 6.89042 / 5.20 ( 9060) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1035 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 1030 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: BBB 46 THR cc_start: 0.9501 (m) cc_final: 0.9295 (p) REVERT: DDD 46 THR cc_start: 0.9470 (m) cc_final: 0.9215 (p) REVERT: EEE 46 THR cc_start: 0.9498 (m) cc_final: 0.9280 (p) REVERT: DaD 46 THR cc_start: 0.9446 (m) cc_final: 0.9216 (p) REVERT: EaE 46 THR cc_start: 0.9438 (m) cc_final: 0.9153 (p) REVERT: AbA 46 THR cc_start: 0.9458 (m) cc_final: 0.9189 (p) REVERT: BbB 46 THR cc_start: 0.9488 (m) cc_final: 0.9263 (p) REVERT: CbC 46 THR cc_start: 0.9429 (m) cc_final: 0.9216 (p) REVERT: EbE 46 THR cc_start: 0.9453 (m) cc_final: 0.9193 (p) REVERT: AcA 46 THR cc_start: 0.9486 (m) cc_final: 0.9244 (p) REVERT: CcC 46 THR cc_start: 0.9484 (m) cc_final: 0.9249 (p) REVERT: DcD 46 THR cc_start: 0.9474 (m) cc_final: 0.9213 (p) REVERT: EcE 46 THR cc_start: 0.9495 (m) cc_final: 0.9265 (p) REVERT: AdA 12 ASP cc_start: 0.9756 (m-30) cc_final: 0.9501 (m-30) REVERT: CdC 46 THR cc_start: 0.9480 (m) cc_final: 0.9265 (p) REVERT: DdD 12 ASP cc_start: 0.9728 (m-30) cc_final: 0.9503 (m-30) REVERT: EdE 12 ASP cc_start: 0.9743 (m-30) cc_final: 0.9517 (m-30) REVERT: AeA 8 LYS cc_start: 0.9724 (tttt) cc_final: 0.9515 (ttmm) REVERT: BeB 12 ASP cc_start: 0.9745 (m-30) cc_final: 0.9484 (m-30) REVERT: DeD 46 THR cc_start: 0.9641 (m) cc_final: 0.9429 (p) REVERT: EeE 22 ILE cc_start: 0.9750 (mt) cc_final: 0.9505 (mp) REVERT: AfA 12 ASP cc_start: 0.9592 (m-30) cc_final: 0.9377 (m-30) REVERT: BfB 12 ASP cc_start: 0.9628 (m-30) cc_final: 0.9368 (m-30) REVERT: DfD 12 ASP cc_start: 0.9620 (m-30) cc_final: 0.9370 (m-30) REVERT: EfE 36 THR cc_start: 0.9866 (m) cc_final: 0.9625 (p) REVERT: AgA 20 GLU cc_start: 0.9651 (mt-10) cc_final: 0.9433 (mp0) REVERT: AgA 36 THR cc_start: 0.9884 (m) cc_final: 0.9672 (p) REVERT: DgD 36 THR cc_start: 0.9890 (m) cc_final: 0.9669 (p) REVERT: EgE 36 THR cc_start: 0.9894 (m) cc_final: 0.9691 (p) REVERT: AlA 36 THR cc_start: 0.9814 (m) cc_final: 0.9568 (p) REVERT: ClC 36 THR cc_start: 0.9824 (m) cc_final: 0.9600 (p) REVERT: ElE 36 THR cc_start: 0.9832 (m) cc_final: 0.9622 (p) REVERT: CmC 12 ASP cc_start: 0.9733 (m-30) cc_final: 0.9512 (m-30) REVERT: BnB 33 VAL cc_start: 0.9631 (t) cc_final: 0.9425 (p) REVERT: CnC 36 THR cc_start: 0.9541 (m) cc_final: 0.9334 (p) outliers start: 5 outliers final: 5 residues processed: 1035 average time/residue: 0.5376 time to fit residues: 645.0447 Evaluate side-chains 726 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 721 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BdB residue 5 ASP Chi-restraints excluded: chain DdD residue 5 ASP Chi-restraints excluded: chain BeB residue 5 ASP Chi-restraints excluded: chain CeC residue 5 ASP Chi-restraints excluded: chain CeC residue 14 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.3980 chunk 111 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.063860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.043589 restraints weight = 66045.396| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 2.59 r_work: 0.2779 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.4715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 25535 Z= 0.181 Angle : 0.463 4.567 34460 Z= 0.267 Chirality : 0.036 0.122 4140 Planarity : 0.003 0.016 4120 Dihedral : 5.937 97.650 3480 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.78 % Allowed : 22.87 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 5.05 (0.10), residues: 3245 helix: 3.29 (0.07), residues: 3095 sheet: None (None), residues: 0 loop : 3.19 (0.12), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYRBgB 24 PHE 0.009 0.001 PHEBiB 45 TRP 0.010 0.002 TRPDDD 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.18 (25535) covalent geometry : angle 0.46342 / 0.27 (34460) hydrogen bonds : bond 0.08347 / 5.65 ( 3020) hydrogen bonds : angle 3.91958 / 2.93 ( 9060) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1012 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 917 time to evaluate : 1.111 Fit side-chains REVERT: EEE 5 ASP cc_start: 0.7383 (t0) cc_final: 0.7099 (t0) REVERT: BaB 5 ASP cc_start: 0.7228 (t0) cc_final: 0.6825 (t0) REVERT: DaD 5 ASP cc_start: 0.7316 (t0) cc_final: 0.6978 (t0) REVERT: EaE 5 ASP cc_start: 0.7569 (t0) cc_final: 0.7237 (t0) REVERT: BbB 5 ASP cc_start: 0.7643 (t0) cc_final: 0.7406 (t0) REVERT: CbC 5 ASP cc_start: 0.7633 (t0) cc_final: 0.7430 (t0) REVERT: DbD 5 ASP cc_start: 0.7641 (t0) cc_final: 0.7298 (t0) REVERT: EbE 5 ASP cc_start: 0.7774 (t0) cc_final: 0.7513 (t0) REVERT: CcC 5 ASP cc_start: 0.7759 (t0) cc_final: 0.7530 (t0) REVERT: DcD 5 ASP cc_start: 0.7791 (t0) cc_final: 0.7550 (t0) REVERT: EcE 21 MET cc_start: 0.9227 (OUTLIER) cc_final: 0.9013 (mmm) REVERT: AdA 5 ASP cc_start: 0.7846 (t0) cc_final: 0.7609 (t0) REVERT: BdB 12 ASP cc_start: 0.9537 (m-30) cc_final: 0.9323 (m-30) REVERT: CdC 5 ASP cc_start: 0.7868 (t0) cc_final: 0.7666 (t0) REVERT: DdD 5 ASP cc_start: 0.7922 (t0) cc_final: 0.7708 (t0) REVERT: AeA 5 ASP cc_start: 0.7800 (t0) cc_final: 0.7564 (t0) REVERT: AeA 20 GLU cc_start: 0.9106 (mt-10) cc_final: 0.8763 (mt-10) REVERT: BeB 20 GLU cc_start: 0.9091 (mt-10) cc_final: 0.8825 (mt-10) REVERT: CeC 20 GLU cc_start: 0.9146 (mt-10) cc_final: 0.8828 (mt-10) REVERT: DeD 5 ASP cc_start: 0.7797 (t0) cc_final: 0.7556 (t0) REVERT: DeD 20 GLU cc_start: 0.9131 (mt-10) cc_final: 0.8845 (mt-10) REVERT: EeE 22 ILE cc_start: 0.9250 (mt) cc_final: 0.8978 (mp) REVERT: AfA 20 GLU cc_start: 0.9406 (mt-10) cc_final: 0.9184 (mt-10) REVERT: BfB 20 GLU cc_start: 0.9218 (mt-10) cc_final: 0.8973 (mt-10) REVERT: CfC 20 GLU cc_start: 0.9210 (mt-10) cc_final: 0.8993 (mt-10) REVERT: DfD 15 GLN cc_start: 0.9112 (tt0) cc_final: 0.8863 (mt0) REVERT: DfD 20 GLU cc_start: 0.9204 (mt-10) cc_final: 0.8857 (mt-10) REVERT: EfE 20 GLU cc_start: 0.9156 (mt-10) cc_final: 0.8889 (mt-10) REVERT: DgD 17 SER cc_start: 0.8975 (p) cc_final: 0.8552 (p) REVERT: AkA 8 LYS cc_start: 0.8211 (tttp) cc_final: 0.7855 (mtpp) REVERT: AkA 12 ASP cc_start: 0.9109 (m-30) cc_final: 0.8839 (m-30) REVERT: BkB 12 ASP cc_start: 0.9149 (m-30) cc_final: 0.8923 (m-30) REVERT: CkC 12 ASP cc_start: 0.9137 (m-30) cc_final: 0.8912 (m-30) REVERT: BlB 8 LYS cc_start: 0.8508 (tttm) cc_final: 0.8128 (ttmm) REVERT: ClC 22 ILE cc_start: 0.9363 (mt) cc_final: 0.9143 (mp) REVERT: DlD 8 LYS cc_start: 0.8402 (tttm) cc_final: 0.8031 (tttm) REVERT: DlD 22 ILE cc_start: 0.9263 (OUTLIER) cc_final: 0.9042 (mp) REVERT: AmA 20 GLU cc_start: 0.8931 (mt-10) cc_final: 0.8712 (mt-10) REVERT: AmA 48 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8565 (tppp) REVERT: CmC 20 GLU cc_start: 0.8966 (mt-10) cc_final: 0.8653 (mt-10) REVERT: CmC 40 LYS cc_start: 0.9231 (tttt) cc_final: 0.9026 (ttmt) REVERT: DmD 20 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8652 (mt-10) REVERT: DmD 22 ILE cc_start: 0.9223 (mt) cc_final: 0.8993 (mp) REVERT: EmE 20 GLU cc_start: 0.8935 (mt-10) cc_final: 0.8663 (mt-10) REVERT: EmE 22 ILE cc_start: 0.9299 (mt) cc_final: 0.9074 (mp) REVERT: AnA 20 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8716 (mt-10) REVERT: BnB 20 GLU cc_start: 0.8957 (mt-10) cc_final: 0.8730 (mt-10) REVERT: CnC 20 GLU cc_start: 0.9032 (mt-10) cc_final: 0.8797 (mt-10) REVERT: CnC 36 THR cc_start: 0.8957 (m) cc_final: 0.8690 (p) REVERT: CnC 44 LYS cc_start: 0.8851 (ttmm) cc_final: 0.8591 (tppt) REVERT: DnD 20 GLU cc_start: 0.9174 (mt-10) cc_final: 0.8901 (mt-10) REVERT: DnD 21 MET cc_start: 0.9277 (mmm) cc_final: 0.8957 (ttm) REVERT: DnD 22 ILE cc_start: 0.9164 (mt) cc_final: 0.8921 (mp) REVERT: DnD 44 LYS cc_start: 0.8824 (ttmm) cc_final: 0.8528 (tppt) outliers start: 95 outliers final: 2 residues processed: 937 average time/residue: 0.5423 time to fit residues: 588.4594 Evaluate side-chains 717 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 712 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain EcE residue 21 MET Chi-restraints excluded: chain BgB residue 36 THR Chi-restraints excluded: chain DlD residue 22 ILE Chi-restraints excluded: chain AmA residue 48 LYS Chi-restraints excluded: chain AnA residue 36 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 87 optimal weight: 1.9990 chunk 219 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 205 optimal weight: 4.9990 chunk 178 optimal weight: 0.6980 chunk 143 optimal weight: 9.9990 chunk 209 optimal weight: 0.9990 chunk 287 optimal weight: 3.9990 chunk 192 optimal weight: 0.7980 chunk 294 optimal weight: 0.9990 chunk 235 optimal weight: 4.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 = 0.3543 r_free = 0.3543 target = 0.063847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.043077 restraints weight = 66971.988| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 2.62 r_work: 0.2792 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.5141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 25535 Z= 0.167 Angle : 0.419 5.236 34460 Z= 0.239 Chirality : 0.032 0.117 4140 Planarity : 0.002 0.013 4120 Dihedral : 3.634 36.425 3470 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.47 % Allowed : 27.73 % Favored : 69.80 % 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: 6.88 (0.10), residues: 3245 helix: 4.45 (0.06), residues: 3105 sheet: None (None), residues: 0 loop : 3.82 (0.15), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYREgE 24 PHE 0.019 0.001 PHECnC 42 TRP 0.007 0.001 TRPElE 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.17 (25535) covalent geometry : angle 0.41866 / 0.24 (34460) hydrogen bonds : bond 0.07781 / 5.27 ( 3020) hydrogen bonds : angle 3.63325 / 2.73 ( 9060) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 815 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 753 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BBB 5 ASP cc_start: 0.7580 (t0) cc_final: 0.7083 (t0) REVERT: EEE 5 ASP cc_start: 0.7265 (t0) cc_final: 0.6700 (t0) REVERT: AaA 5 ASP cc_start: 0.7690 (t0) cc_final: 0.7168 (t0) REVERT: BaB 5 ASP cc_start: 0.7113 (t0) cc_final: 0.6774 (t0) REVERT: CaC 5 ASP cc_start: 0.7613 (t0) cc_final: 0.7183 (t0) REVERT: DaD 5 ASP cc_start: 0.7174 (t0) cc_final: 0.6882 (t0) REVERT: EaE 5 ASP cc_start: 0.7381 (t0) cc_final: 0.7027 (t0) REVERT: BbB 5 ASP cc_start: 0.7497 (t0) cc_final: 0.7251 (t0) REVERT: DbD 5 ASP cc_start: 0.7433 (t0) cc_final: 0.7155 (t0) REVERT: EbE 5 ASP cc_start: 0.7557 (t0) cc_final: 0.7349 (t0) REVERT: BdB 28 MET cc_start: 0.9410 (ttm) cc_final: 0.9177 (ttp) REVERT: CdC 20 GLU cc_start: 0.9321 (mt-10) cc_final: 0.9087 (mt-10) REVERT: CeC 5 ASP cc_start: 0.7539 (t0) cc_final: 0.7222 (t0) REVERT: CeC 20 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8778 (mt-10) REVERT: DeD 20 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8821 (mt-10) REVERT: EeE 20 GLU cc_start: 0.9234 (mt-10) cc_final: 0.9008 (mt-10) REVERT: EeE 22 ILE cc_start: 0.9238 (mt) cc_final: 0.9019 (mp) REVERT: BfB 20 GLU cc_start: 0.9231 (mt-10) cc_final: 0.8937 (mt-10) REVERT: CfC 20 GLU cc_start: 0.9192 (mt-10) cc_final: 0.8725 (mp0) REVERT: DfD 20 GLU cc_start: 0.9224 (mt-10) cc_final: 0.8862 (mt-10) REVERT: EfE 20 GLU cc_start: 0.9112 (mt-10) cc_final: 0.8805 (mt-10) REVERT: BgB 20 GLU cc_start: 0.9053 (pt0) cc_final: 0.8841 (pp20) REVERT: BgB 28 MET cc_start: 0.9290 (ttm) cc_final: 0.9081 (ttm) REVERT: DgD 17 SER cc_start: 0.8771 (p) cc_final: 0.8232 (p) REVERT: EgE 20 GLU cc_start: 0.9322 (pt0) cc_final: 0.9083 (pp20) REVERT: AiA 48 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8629 (mptt) REVERT: BiB 29 VAL cc_start: 0.9285 (OUTLIER) cc_final: 0.9084 (p) REVERT: BjB 8 LYS cc_start: 0.8160 (ttpp) cc_final: 0.7647 (ttpp) REVERT: CjC 12 ASP cc_start: 0.9179 (m-30) cc_final: 0.8969 (m-30) REVERT: CjC 48 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8743 (mptt) REVERT: DjD 12 ASP cc_start: 0.9138 (m-30) cc_final: 0.8932 (m-30) REVERT: BkB 12 ASP cc_start: 0.9223 (m-30) cc_final: 0.9023 (m-30) REVERT: CkC 12 ASP cc_start: 0.9233 (m-30) cc_final: 0.9026 (m-30) REVERT: CkC 20 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8736 (mt-10) REVERT: EkE 20 GLU cc_start: 0.9043 (mt-10) cc_final: 0.8782 (mt-10) REVERT: BlB 47 SER cc_start: 0.9128 (t) cc_final: 0.8718 (p) REVERT: ClC 20 GLU cc_start: 0.9146 (mt-10) cc_final: 0.8931 (mt-10) REVERT: ClC 47 SER cc_start: 0.8997 (t) cc_final: 0.8628 (p) REVERT: DlD 47 SER cc_start: 0.8997 (t) cc_final: 0.8614 (p) REVERT: ElE 5 ASP cc_start: 0.8001 (t0) cc_final: 0.7473 (t70) REVERT: ElE 47 SER cc_start: 0.9135 (t) cc_final: 0.8707 (p) REVERT: AmA 5 ASP cc_start: 0.7344 (t0) cc_final: 0.7139 (t0) REVERT: AmA 20 GLU cc_start: 0.8941 (mt-10) cc_final: 0.8705 (mt-10) REVERT: BmB 47 SER cc_start: 0.8832 (t) cc_final: 0.8501 (p) REVERT: CmC 48 LYS cc_start: 0.8911 (mptt) cc_final: 0.8693 (tppp) REVERT: DmD 22 ILE cc_start: 0.9286 (mt) cc_final: 0.9022 (mp) REVERT: EmE 20 GLU cc_start: 0.8945 (mt-10) cc_final: 0.8624 (mt-10) REVERT: CnC 20 GLU cc_start: 0.9060 (mt-10) cc_final: 0.8805 (mt-10) REVERT: CnC 22 ILE cc_start: 0.8997 (pp) cc_final: 0.8750 (pp) REVERT: CnC 44 LYS cc_start: 0.8932 (ttmm) cc_final: 0.8725 (tppt) REVERT: DnD 5 ASP cc_start: 0.7982 (t0) cc_final: 0.7700 (t0) REVERT: DnD 20 GLU cc_start: 0.9202 (mt-10) cc_final: 0.8926 (mt-10) REVERT: DnD 22 ILE cc_start: 0.9172 (mt) cc_final: 0.8901 (mp) REVERT: DnD 44 LYS cc_start: 0.8878 (ttmm) cc_final: 0.8658 (tppt) REVERT: EnE 22 ILE cc_start: 0.9078 (pp) cc_final: 0.8851 (pp) REVERT: EnE 44 LYS cc_start: 0.8754 (ttmm) cc_final: 0.8492 (tppt) outliers start: 62 outliers final: 8 residues processed: 764 average time/residue: 0.5803 time to fit residues: 511.8932 Evaluate side-chains 655 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 644 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BBB residue 21 MET Chi-restraints excluded: chain BBB residue 28 MET Chi-restraints excluded: chain CaC residue 48 LYS Chi-restraints excluded: chain EaE residue 40 LYS Chi-restraints excluded: chain AbA residue 21 MET Chi-restraints excluded: chain DfD residue 5 ASP Chi-restraints excluded: chain CgC residue 17 SER Chi-restraints excluded: chain DgD residue 39 ILE Chi-restraints excluded: chain AiA residue 48 LYS Chi-restraints excluded: chain BiB residue 29 VAL Chi-restraints excluded: chain CjC residue 48 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 88 optimal weight: 10.0000 chunk 226 optimal weight: 2.9990 chunk 117 optimal weight: 7.9990 chunk 267 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 284 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 171 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 238 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.3479 r_free = 0.3479 target = 0.060034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.039172 restraints weight = 66764.738| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 2.57 r_work: 0.2690 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.4884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 25535 Z= 0.192 Angle : 0.458 5.542 34460 Z= 0.261 Chirality : 0.032 0.119 4140 Planarity : 0.002 0.013 4120 Dihedral : 3.281 35.689 3470 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.39 % Allowed : 28.33 % Favored : 69.28 % 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: 6.61 (0.10), residues: 3245 helix: 4.31 (0.07), residues: 3105 sheet: None (None), residues: 0 loop : 2.97 (0.18), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYRClC 24 PHE 0.013 0.001 PHEDlD 45 TRP 0.007 0.001 TRPAbA 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.19 (25535) covalent geometry : angle 0.45776 / 0.26 (34460) hydrogen bonds : bond 0.08686 / 5.89 ( 3020) hydrogen bonds : angle 3.75793 / 2.82 ( 9060) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 677 time to evaluate : 2.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BBB 5 ASP cc_start: 0.7691 (t0) cc_final: 0.7122 (t0) REVERT: EEE 5 ASP cc_start: 0.7434 (t0) cc_final: 0.6938 (t0) REVERT: AaA 5 ASP cc_start: 0.7943 (t0) cc_final: 0.7349 (t0) REVERT: BaB 5 ASP cc_start: 0.7551 (t0) cc_final: 0.7181 (t0) REVERT: CaC 5 ASP cc_start: 0.7915 (t0) cc_final: 0.7402 (t0) REVERT: DaD 5 ASP cc_start: 0.7538 (t0) cc_final: 0.7232 (t0) REVERT: EaE 5 ASP cc_start: 0.7514 (t0) cc_final: 0.7071 (t0) REVERT: BbB 5 ASP cc_start: 0.7714 (t0) cc_final: 0.7420 (t0) REVERT: CbC 5 ASP cc_start: 0.7424 (t0) cc_final: 0.7209 (t0) REVERT: DbD 5 ASP cc_start: 0.7578 (t0) cc_final: 0.7297 (t0) REVERT: EbE 5 ASP cc_start: 0.7640 (t0) cc_final: 0.7354 (t0) REVERT: BdB 28 MET cc_start: 0.9472 (ttm) cc_final: 0.9250 (ttp) REVERT: BeB 5 ASP cc_start: 0.7546 (t0) cc_final: 0.7269 (t0) REVERT: CeC 5 ASP cc_start: 0.7380 (t0) cc_final: 0.7129 (t0) REVERT: CeC 20 GLU cc_start: 0.9142 (mt-10) cc_final: 0.8779 (mt-10) REVERT: DeD 20 GLU cc_start: 0.9181 (mt-10) cc_final: 0.8856 (mt-10) REVERT: EeE 20 GLU cc_start: 0.9266 (mt-10) cc_final: 0.9043 (mt-10) REVERT: AfA 5 ASP cc_start: 0.8442 (t0) cc_final: 0.7338 (t0) REVERT: AfA 8 LYS cc_start: 0.9084 (mtpp) cc_final: 0.8838 (mmtt) REVERT: BfB 20 GLU cc_start: 0.9267 (mt-10) cc_final: 0.8991 (mt-10) REVERT: CfC 20 GLU cc_start: 0.9248 (mt-10) cc_final: 0.8971 (mt-10) REVERT: DfD 20 GLU cc_start: 0.9235 (mt-10) cc_final: 0.8836 (mt-10) REVERT: EfE 20 GLU cc_start: 0.9178 (mt-10) cc_final: 0.8884 (mt-10) REVERT: BgB 20 GLU cc_start: 0.9120 (pt0) cc_final: 0.8821 (pp20) REVERT: EgE 20 GLU cc_start: 0.9368 (pt0) cc_final: 0.8971 (pp20) REVERT: AiA 48 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8550 (mptt) REVERT: BkB 8 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.8120 (mtpp) REVERT: BkB 12 ASP cc_start: 0.9261 (m-30) cc_final: 0.9045 (m-30) REVERT: CkC 12 ASP cc_start: 0.9245 (m-30) cc_final: 0.8990 (m-30) REVERT: CkC 40 LYS cc_start: 0.9240 (tttt) cc_final: 0.9035 (tttt) REVERT: EkE 20 GLU cc_start: 0.9064 (mt-10) cc_final: 0.8832 (mt-10) REVERT: AlA 20 GLU cc_start: 0.8977 (mt-10) cc_final: 0.8660 (mt-10) REVERT: BlB 47 SER cc_start: 0.9177 (t) cc_final: 0.8752 (p) REVERT: ClC 20 GLU cc_start: 0.9141 (mt-10) cc_final: 0.8900 (mt-10) REVERT: DlD 20 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8640 (mt-10) REVERT: DlD 22 ILE cc_start: 0.9362 (OUTLIER) cc_final: 0.9153 (mp) REVERT: ElE 5 ASP cc_start: 0.7886 (t0) cc_final: 0.7439 (t70) REVERT: AmA 20 GLU cc_start: 0.9014 (mt-10) cc_final: 0.8709 (mt-10) REVERT: BmB 47 SER cc_start: 0.8813 (t) cc_final: 0.8481 (p) REVERT: CmC 5 ASP cc_start: 0.7672 (t0) cc_final: 0.7428 (t0) REVERT: CmC 20 GLU cc_start: 0.9117 (mt-10) cc_final: 0.8885 (mt-10) REVERT: DmD 20 GLU cc_start: 0.9126 (mt-10) cc_final: 0.8887 (mt-10) REVERT: DmD 22 ILE cc_start: 0.9365 (mt) cc_final: 0.9131 (mp) REVERT: CnC 20 GLU cc_start: 0.9127 (mt-10) cc_final: 0.8849 (mt-10) REVERT: DnD 20 GLU cc_start: 0.9169 (mt-10) cc_final: 0.8853 (mt-10) REVERT: DnD 44 LYS cc_start: 0.8864 (ttmm) cc_final: 0.8657 (tppt) REVERT: EnE 44 LYS cc_start: 0.8809 (ttmm) cc_final: 0.8592 (tppt) outliers start: 60 outliers final: 11 residues processed: 694 average time/residue: 0.6049 time to fit residues: 481.2180 Evaluate side-chains 646 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 632 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BBB residue 21 MET Chi-restraints excluded: chain BaB residue 48 LYS Chi-restraints excluded: chain CaC residue 48 LYS Chi-restraints excluded: chain EaE residue 40 LYS Chi-restraints excluded: chain AbA residue 21 MET Chi-restraints excluded: chain AcA residue 21 MET Chi-restraints excluded: chain BhB residue 28 MET Chi-restraints excluded: chain ChC residue 8 LYS Chi-restraints excluded: chain AiA residue 48 LYS Chi-restraints excluded: chain BiB residue 29 VAL Chi-restraints excluded: chain BkB residue 8 LYS Chi-restraints excluded: chain CkC residue 8 LYS Chi-restraints excluded: chain ClC residue 21 MET Chi-restraints excluded: chain DlD residue 22 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 199 optimal weight: 2.9990 chunk 253 optimal weight: 0.8980 chunk 285 optimal weight: 0.9990 chunk 226 optimal weight: 0.9990 chunk 274 optimal weight: 0.9980 chunk 156 optimal weight: 6.9990 chunk 194 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 161 optimal weight: 0.7980 chunk 235 optimal weight: 3.9990 chunk 121 optimal weight: 10.0000 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3585 r_free = 0.3585 target = 0.065578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.044880 restraints weight = 66799.509| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.61 r_work: 0.2824 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.5660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 25535 Z= 0.158 Angle : 0.452 6.398 34460 Z= 0.250 Chirality : 0.032 0.111 4140 Planarity : 0.002 0.019 4120 Dihedral : 2.914 28.032 3470 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.95 % Allowed : 28.49 % Favored : 69.56 % 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: 7.08 (0.10), residues: 3245 helix: 4.59 (0.07), residues: 3105 sheet: None (None), residues: 0 loop : 3.49 (0.18), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.001 TYREgE 24 PHE 0.023 0.001 PHECnC 42 TRP 0.005 0.000 TRPEfE 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.16 (25535) covalent geometry : angle 0.45182 / 0.25 (34460) hydrogen bonds : bond 0.07071 / 4.80 ( 3020) hydrogen bonds : angle 3.50810 / 2.64 ( 9060) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 709 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BBB 5 ASP cc_start: 0.7627 (t0) cc_final: 0.7054 (t0) REVERT: EEE 5 ASP cc_start: 0.7296 (t0) cc_final: 0.6762 (t0) REVERT: AaA 5 ASP cc_start: 0.7703 (t0) cc_final: 0.7147 (t0) REVERT: BaB 5 ASP cc_start: 0.7382 (t0) cc_final: 0.6951 (t0) REVERT: DaD 5 ASP cc_start: 0.7383 (t0) cc_final: 0.7043 (t0) REVERT: EaE 5 ASP cc_start: 0.7480 (t0) cc_final: 0.7014 (t0) REVERT: AbA 5 ASP cc_start: 0.7623 (t0) cc_final: 0.7210 (t0) REVERT: BbB 5 ASP cc_start: 0.7675 (t0) cc_final: 0.7315 (t0) REVERT: DbD 5 ASP cc_start: 0.7626 (t0) cc_final: 0.7286 (t0) REVERT: EbE 5 ASP cc_start: 0.7440 (t0) cc_final: 0.7122 (t0) REVERT: BdB 20 GLU cc_start: 0.9317 (mt-10) cc_final: 0.9096 (mt-10) REVERT: BdB 28 MET cc_start: 0.9442 (ttm) cc_final: 0.9210 (ttp) REVERT: CdC 20 GLU cc_start: 0.9293 (mt-10) cc_final: 0.9013 (mt-10) REVERT: DdD 20 GLU cc_start: 0.8973 (mt-10) cc_final: 0.8664 (mt-10) REVERT: AeA 5 ASP cc_start: 0.7683 (t0) cc_final: 0.7361 (t0) REVERT: BeB 8 LYS cc_start: 0.9039 (mtpp) cc_final: 0.8834 (mtpp) REVERT: CeC 5 ASP cc_start: 0.7499 (t0) cc_final: 0.7264 (t0) REVERT: CeC 20 GLU cc_start: 0.9153 (mt-10) cc_final: 0.8783 (mt-10) REVERT: DeD 20 GLU cc_start: 0.9130 (mt-10) cc_final: 0.8847 (mt-10) REVERT: EeE 20 GLU cc_start: 0.9245 (mt-10) cc_final: 0.8890 (mt-10) REVERT: AfA 20 GLU cc_start: 0.9198 (mt-10) cc_final: 0.8961 (mt-10) REVERT: BfB 5 ASP cc_start: 0.8327 (t0) cc_final: 0.7925 (t0) REVERT: BfB 8 LYS cc_start: 0.8913 (mtpp) cc_final: 0.8540 (mmtt) REVERT: BfB 20 GLU cc_start: 0.9225 (mt-10) cc_final: 0.8937 (mt-10) REVERT: CfC 20 GLU cc_start: 0.9268 (mt-10) cc_final: 0.9029 (mt-10) REVERT: DfD 5 ASP cc_start: 0.8372 (t0) cc_final: 0.7735 (t0) REVERT: DfD 8 LYS cc_start: 0.9145 (mtpp) cc_final: 0.8871 (mptt) REVERT: DfD 20 GLU cc_start: 0.9255 (mt-10) cc_final: 0.8863 (mt-10) REVERT: EfE 5 ASP cc_start: 0.8593 (t0) cc_final: 0.8212 (p0) REVERT: EfE 20 GLU cc_start: 0.9183 (mt-10) cc_final: 0.8960 (mt-10) REVERT: DgD 20 GLU cc_start: 0.8451 (pp20) cc_final: 0.7804 (pp20) REVERT: DgD 24 TYR cc_start: 0.9244 (m-10) cc_final: 0.8744 (m-10) REVERT: EgE 20 GLU cc_start: 0.9390 (pt0) cc_final: 0.9148 (pp20) REVERT: CjC 8 LYS cc_start: 0.7822 (tttp) cc_final: 0.7371 (mtpp) REVERT: BkB 8 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7908 (mtpp) REVERT: CkC 8 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7847 (mtpp) REVERT: CkC 20 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8774 (mt-10) REVERT: CkC 40 LYS cc_start: 0.9271 (tttt) cc_final: 0.9046 (tttm) REVERT: EkE 20 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8812 (mt-10) REVERT: AlA 20 GLU cc_start: 0.8962 (mt-10) cc_final: 0.8651 (mt-10) REVERT: BlB 47 SER cc_start: 0.9196 (t) cc_final: 0.8754 (p) REVERT: ClC 20 GLU cc_start: 0.9216 (mt-10) cc_final: 0.9012 (mt-10) REVERT: ClC 47 SER cc_start: 0.9004 (t) cc_final: 0.8592 (p) REVERT: DlD 22 ILE cc_start: 0.9308 (OUTLIER) cc_final: 0.9077 (mp) REVERT: DlD 47 SER cc_start: 0.9037 (t) cc_final: 0.8664 (p) REVERT: ElE 47 SER cc_start: 0.9185 (t) cc_final: 0.8755 (p) REVERT: AmA 20 GLU cc_start: 0.8963 (mt-10) cc_final: 0.8644 (mt-10) REVERT: BmB 47 SER cc_start: 0.8943 (t) cc_final: 0.8602 (p) REVERT: CmC 20 GLU cc_start: 0.9034 (mt-10) cc_final: 0.8803 (mt-10) REVERT: DmD 5 ASP cc_start: 0.7771 (t0) cc_final: 0.7533 (t0) REVERT: DmD 20 GLU cc_start: 0.9115 (mt-10) cc_final: 0.8859 (mt-10) REVERT: DmD 22 ILE cc_start: 0.9306 (mt) cc_final: 0.9071 (mp) REVERT: AnA 5 ASP cc_start: 0.7699 (t0) cc_final: 0.7422 (t0) REVERT: BnB 5 ASP cc_start: 0.7800 (t0) cc_final: 0.7484 (t0) REVERT: BnB 40 LYS cc_start: 0.8875 (tttt) cc_final: 0.8628 (tmtt) REVERT: DnD 20 GLU cc_start: 0.9220 (mt-10) cc_final: 0.8833 (mt-10) REVERT: EnE 40 LYS cc_start: 0.8577 (tttt) cc_final: 0.8361 (tmtt) outliers start: 49 outliers final: 10 residues processed: 719 average time/residue: 0.5745 time to fit residues: 474.7085 Evaluate side-chains 619 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 606 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BBB residue 21 MET Chi-restraints excluded: chain AaA residue 21 MET Chi-restraints excluded: chain CaC residue 21 MET Chi-restraints excluded: chain AbA residue 21 MET Chi-restraints excluded: chain DfD residue 37 ILE Chi-restraints excluded: chain CgC residue 39 ILE Chi-restraints excluded: chain DgD residue 17 SER Chi-restraints excluded: chain DgD residue 39 ILE Chi-restraints excluded: chain BhB residue 28 MET Chi-restraints excluded: chain BiB residue 29 VAL Chi-restraints excluded: chain BkB residue 8 LYS Chi-restraints excluded: chain CkC residue 8 LYS Chi-restraints excluded: chain DlD residue 22 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 26 optimal weight: 0.9990 chunk 253 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 211 optimal weight: 0.9990 chunk 141 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 270 optimal weight: 0.9990 chunk 113 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 chunk 158 optimal weight: 0.7980 chunk 220 optimal weight: 1.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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 = 0.3600 r_free = 0.3600 target = 0.066233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.045679 restraints weight = 66891.133| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.62 r_work: 0.2844 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.5826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25535 Z= 0.157 Angle : 0.471 7.147 34460 Z= 0.258 Chirality : 0.032 0.116 4140 Planarity : 0.002 0.016 4120 Dihedral : 2.722 21.892 3470 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.27 % Allowed : 31.00 % Favored : 67.73 % 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: 7.01 (0.11), residues: 3245 helix: 4.55 (0.07), residues: 3105 sheet: None (None), residues: 0 loop : 3.31 (0.19), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYRCfC 24 PHE 0.015 0.001 PHEDlD 45 TRP 0.005 0.000 TRPDkD 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.16 (25535) covalent geometry : angle 0.47069 / 0.26 (34460) hydrogen bonds : bond 0.06902 / 4.69 ( 3020) hydrogen bonds : angle 3.47554 / 2.62 ( 9060) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 658 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: EEE 5 ASP cc_start: 0.7282 (t0) cc_final: 0.6747 (t0) REVERT: AaA 5 ASP cc_start: 0.7701 (t0) cc_final: 0.7153 (t0) REVERT: BaB 5 ASP cc_start: 0.7443 (t0) cc_final: 0.7007 (t0) REVERT: DaD 5 ASP cc_start: 0.7361 (t0) cc_final: 0.7012 (t0) REVERT: EaE 5 ASP cc_start: 0.7468 (t0) cc_final: 0.6978 (t0) REVERT: BbB 5 ASP cc_start: 0.7559 (t0) cc_final: 0.7166 (t0) REVERT: DbD 5 ASP cc_start: 0.7588 (t0) cc_final: 0.7235 (t0) REVERT: EbE 5 ASP cc_start: 0.7335 (t0) cc_final: 0.7005 (t0) REVERT: BdB 28 MET cc_start: 0.9444 (ttm) cc_final: 0.9198 (ttp) REVERT: CdC 20 GLU cc_start: 0.9263 (mt-10) cc_final: 0.9028 (mt-10) REVERT: DdD 20 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8602 (mt-10) REVERT: EeE 20 GLU cc_start: 0.9243 (mt-10) cc_final: 0.8940 (mt-10) REVERT: AfA 5 ASP cc_start: 0.8419 (t0) cc_final: 0.7741 (t0) REVERT: AfA 20 GLU cc_start: 0.9231 (mt-10) cc_final: 0.9027 (mt-10) REVERT: CgC 24 TYR cc_start: 0.9282 (m-10) cc_final: 0.9054 (m-80) REVERT: BjB 21 MET cc_start: 0.9148 (mtp) cc_final: 0.8926 (tpp) REVERT: CkC 20 GLU cc_start: 0.8976 (mt-10) cc_final: 0.8748 (mt-10) REVERT: AlA 20 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8676 (mt-10) REVERT: BlB 47 SER cc_start: 0.9153 (t) cc_final: 0.8683 (p) REVERT: ClC 47 SER cc_start: 0.8991 (t) cc_final: 0.8587 (p) REVERT: DlD 22 ILE cc_start: 0.9284 (OUTLIER) cc_final: 0.9040 (mp) REVERT: DlD 47 SER cc_start: 0.9016 (t) cc_final: 0.8641 (p) REVERT: ElE 47 SER cc_start: 0.9151 (t) cc_final: 0.8736 (p) REVERT: AmA 20 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8612 (mt-10) REVERT: BmB 47 SER cc_start: 0.8955 (t) cc_final: 0.8607 (p) REVERT: DmD 20 GLU cc_start: 0.9167 (mt-10) cc_final: 0.8911 (mt-10) REVERT: DmD 22 ILE cc_start: 0.9309 (mt) cc_final: 0.9086 (mp) REVERT: EmE 20 GLU cc_start: 0.8976 (mt-10) cc_final: 0.8726 (mt-10) REVERT: BnB 40 LYS cc_start: 0.8747 (tttt) cc_final: 0.8490 (tmtt) REVERT: DnD 20 GLU cc_start: 0.9211 (mt-10) cc_final: 0.8877 (mt-10) outliers start: 32 outliers final: 8 residues processed: 670 average time/residue: 0.5857 time to fit residues: 451.0569 Evaluate side-chains 618 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 609 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AAA residue 21 MET Chi-restraints excluded: chain AaA residue 21 MET Chi-restraints excluded: chain AbA residue 21 MET Chi-restraints excluded: chain DfD residue 37 ILE Chi-restraints excluded: chain CgC residue 39 ILE Chi-restraints excluded: chain DgD residue 39 ILE Chi-restraints excluded: chain BhB residue 28 MET Chi-restraints excluded: chain EhE residue 21 MET Chi-restraints excluded: chain DlD residue 22 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 102 optimal weight: 0.7980 chunk 273 optimal weight: 0.9980 chunk 149 optimal weight: 7.9990 chunk 128 optimal weight: 30.0000 chunk 290 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 216 optimal weight: 0.9980 chunk 144 optimal weight: 0.9980 chunk 76 optimal weight: 10.0000 chunk 185 optimal weight: 0.6980 chunk 36 optimal weight: 8.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3626 r_free = 0.3626 target = 0.067136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.046678 restraints weight = 66762.202| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.59 r_work: 0.2880 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.6006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 25535 Z= 0.157 Angle : 0.502 7.838 34460 Z= 0.273 Chirality : 0.032 0.131 4140 Planarity : 0.002 0.017 4120 Dihedral : 2.646 16.709 3470 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.00 % Allowed : 31.31 % Favored : 67.69 % 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: 6.97 (0.11), residues: 3245 helix: 4.52 (0.07), residues: 3105 sheet: None (None), residues: 0 loop : 3.30 (0.19), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.001 TYRBfB 24 PHE 0.014 0.001 PHEDlD 45 TRP 0.003 0.000 TRPCCC 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.16 (25535) covalent geometry : angle 0.50174 / 0.27 (34460) hydrogen bonds : bond 0.06726 / 4.56 ( 3020) hydrogen bonds : angle 3.47315 / 2.62 ( 9060) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 651 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: EEE 5 ASP cc_start: 0.7273 (t0) cc_final: 0.6728 (t0) REVERT: AaA 5 ASP cc_start: 0.7618 (t0) cc_final: 0.7052 (t0) REVERT: BaB 5 ASP cc_start: 0.7395 (t0) cc_final: 0.6913 (t0) REVERT: DaD 5 ASP cc_start: 0.7342 (t0) cc_final: 0.6972 (t0) REVERT: EaE 5 ASP cc_start: 0.7407 (t0) cc_final: 0.6914 (t0) REVERT: BbB 5 ASP cc_start: 0.7540 (t0) cc_final: 0.7149 (t0) REVERT: DbD 5 ASP cc_start: 0.7549 (t0) cc_final: 0.7188 (t0) REVERT: DbD 44 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8826 (ttmt) REVERT: EbE 5 ASP cc_start: 0.7345 (t0) cc_final: 0.6995 (t0) REVERT: DcD 5 ASP cc_start: 0.7901 (t0) cc_final: 0.7452 (t0) REVERT: BdB 28 MET cc_start: 0.9435 (ttm) cc_final: 0.9178 (ttp) REVERT: CdC 20 GLU cc_start: 0.9274 (mt-10) cc_final: 0.9058 (mt-10) REVERT: AeA 5 ASP cc_start: 0.7740 (t0) cc_final: 0.7396 (t0) REVERT: AfA 20 GLU cc_start: 0.9222 (mt-10) cc_final: 0.8995 (mt-10) REVERT: BfB 8 LYS cc_start: 0.9027 (mtpp) cc_final: 0.8765 (mmtt) REVERT: DfD 5 ASP cc_start: 0.8440 (t0) cc_final: 0.8040 (t0) REVERT: DfD 8 LYS cc_start: 0.9121 (mtpp) cc_final: 0.8865 (mptt) REVERT: CgC 20 GLU cc_start: 0.9169 (pm20) cc_final: 0.8882 (pm20) REVERT: CgC 24 TYR cc_start: 0.9283 (m-10) cc_final: 0.9033 (m-10) REVERT: DgD 24 TYR cc_start: 0.9222 (m-10) cc_final: 0.8930 (m-10) REVERT: CkC 20 GLU cc_start: 0.8970 (mt-10) cc_final: 0.8729 (mt-10) REVERT: AlA 20 GLU cc_start: 0.8973 (mt-10) cc_final: 0.8682 (mt-10) REVERT: BlB 47 SER cc_start: 0.9148 (t) cc_final: 0.8671 (p) REVERT: ClC 47 SER cc_start: 0.9012 (t) cc_final: 0.8584 (p) REVERT: DlD 22 ILE cc_start: 0.9252 (OUTLIER) cc_final: 0.9014 (mp) REVERT: DlD 47 SER cc_start: 0.9006 (t) cc_final: 0.8637 (p) REVERT: ElE 47 SER cc_start: 0.9190 (t) cc_final: 0.8782 (p) REVERT: ElE 48 LYS cc_start: 0.9263 (tppt) cc_final: 0.9046 (tppp) REVERT: AmA 20 GLU cc_start: 0.8941 (mt-10) cc_final: 0.8651 (mt-10) REVERT: BmB 47 SER cc_start: 0.8867 (t) cc_final: 0.8493 (p) REVERT: CmC 20 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8681 (mt-10) REVERT: DmD 20 GLU cc_start: 0.9169 (mt-10) cc_final: 0.8947 (mt-10) REVERT: DmD 22 ILE cc_start: 0.9289 (mt) cc_final: 0.9071 (mp) REVERT: EmE 20 GLU cc_start: 0.8946 (mt-10) cc_final: 0.8672 (mt-10) REVERT: BnB 40 LYS cc_start: 0.8693 (tttt) cc_final: 0.8449 (tmtt) REVERT: EnE 5 ASP cc_start: 0.7935 (t0) cc_final: 0.7723 (t0) outliers start: 25 outliers final: 9 residues processed: 663 average time/residue: 0.6118 time to fit residues: 465.5763 Evaluate side-chains 626 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 615 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AAA residue 21 MET Chi-restraints excluded: chain AAA residue 48 LYS Chi-restraints excluded: chain BBB residue 21 MET Chi-restraints excluded: chain AaA residue 21 MET Chi-restraints excluded: chain DbD residue 44 LYS Chi-restraints excluded: chain DfD residue 37 ILE Chi-restraints excluded: chain DgD residue 39 ILE Chi-restraints excluded: chain BhB residue 28 MET Chi-restraints excluded: chain AjA residue 21 MET Chi-restraints excluded: chain DjD residue 44 LYS Chi-restraints excluded: chain DlD residue 22 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 249 optimal weight: 0.7980 chunk 89 optimal weight: 6.9990 chunk 138 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 283 optimal weight: 3.9990 chunk 214 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 201 optimal weight: 0.9980 chunk 68 optimal weight: 10.0000 chunk 146 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3632 r_free = 0.3632 target = 0.067164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.046671 restraints weight = 66770.395| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.61 r_work: 0.2896 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.6074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 25535 Z= 0.157 Angle : 0.513 8.517 34460 Z= 0.281 Chirality : 0.033 0.157 4140 Planarity : 0.002 0.027 4120 Dihedral : 2.609 13.094 3470 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.96 % Allowed : 31.31 % Favored : 67.73 % 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: 6.96 (0.11), residues: 3245 helix: 4.50 (0.07), residues: 3095 sheet: None (None), residues: 0 loop : 3.83 (0.30), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.001 TYRAgA 24 PHE 0.024 0.001 PHEAnA 42 TRP 0.004 0.000 TRPEkE 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.16 (25535) covalent geometry : angle 0.51269 / 0.28 (34460) hydrogen bonds : bond 0.06682 / 4.53 ( 3020) hydrogen bonds : angle 3.49926 / 2.65 ( 9060) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 648 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: EEE 5 ASP cc_start: 0.7259 (t0) cc_final: 0.6706 (t0) REVERT: AaA 5 ASP cc_start: 0.7640 (t0) cc_final: 0.7093 (t0) REVERT: BaB 5 ASP cc_start: 0.7433 (t0) cc_final: 0.6974 (t0) REVERT: DaD 5 ASP cc_start: 0.7347 (t0) cc_final: 0.6975 (t0) REVERT: EaE 5 ASP cc_start: 0.7297 (t0) cc_final: 0.6817 (t0) REVERT: BbB 5 ASP cc_start: 0.7564 (t0) cc_final: 0.7168 (t0) REVERT: DbD 5 ASP cc_start: 0.7576 (t0) cc_final: 0.7208 (t0) REVERT: DbD 44 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8847 (ttmt) REVERT: EbE 5 ASP cc_start: 0.7333 (t0) cc_final: 0.6987 (t0) REVERT: DcD 5 ASP cc_start: 0.7858 (t0) cc_final: 0.7438 (t0) REVERT: BdB 28 MET cc_start: 0.9421 (ttm) cc_final: 0.9155 (ttp) REVERT: CdC 20 GLU cc_start: 0.9263 (mt-10) cc_final: 0.9039 (mt-10) REVERT: DdD 20 GLU cc_start: 0.9204 (mt-10) cc_final: 0.8963 (mt-10) REVERT: DeD 20 GLU cc_start: 0.9308 (mt-10) cc_final: 0.9065 (mt-10) REVERT: DeD 21 MET cc_start: 0.9297 (OUTLIER) cc_final: 0.9088 (mmm) REVERT: BfB 8 LYS cc_start: 0.8997 (mtpp) cc_final: 0.8740 (mmtt) REVERT: CfC 20 GLU cc_start: 0.9082 (mp0) cc_final: 0.8775 (mp0) REVERT: EfE 8 LYS cc_start: 0.9161 (mtpp) cc_final: 0.8909 (mmtt) REVERT: CgC 20 GLU cc_start: 0.9164 (pm20) cc_final: 0.8848 (pm20) REVERT: CgC 24 TYR cc_start: 0.9281 (m-10) cc_final: 0.8991 (m-10) REVERT: CiC 28 MET cc_start: 0.9213 (OUTLIER) cc_final: 0.8945 (ttm) REVERT: BkB 20 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8565 (mt-10) REVERT: CkC 20 GLU cc_start: 0.8979 (mt-10) cc_final: 0.8741 (mt-10) REVERT: AlA 20 GLU cc_start: 0.8974 (mt-10) cc_final: 0.8672 (mt-10) REVERT: AlA 44 LYS cc_start: 0.9439 (tttt) cc_final: 0.9228 (tmmm) REVERT: AlA 47 SER cc_start: 0.9123 (t) cc_final: 0.8703 (p) REVERT: BlB 47 SER cc_start: 0.9138 (t) cc_final: 0.8659 (p) REVERT: ClC 47 SER cc_start: 0.9011 (t) cc_final: 0.8589 (p) REVERT: DlD 22 ILE cc_start: 0.9270 (OUTLIER) cc_final: 0.9032 (mp) REVERT: DlD 47 SER cc_start: 0.9018 (t) cc_final: 0.8630 (p) REVERT: ElE 47 SER cc_start: 0.9189 (t) cc_final: 0.8780 (p) REVERT: ElE 48 LYS cc_start: 0.9269 (tppt) cc_final: 0.9046 (tppp) REVERT: AmA 20 GLU cc_start: 0.8920 (mt-10) cc_final: 0.8630 (mt-10) REVERT: BmB 47 SER cc_start: 0.8864 (t) cc_final: 0.8515 (p) REVERT: CmC 20 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8575 (mt-10) REVERT: DmD 22 ILE cc_start: 0.9299 (mt) cc_final: 0.9068 (mp) REVERT: EmE 20 GLU cc_start: 0.8949 (mt-10) cc_final: 0.8613 (mt-10) REVERT: AnA 44 LYS cc_start: 0.8812 (ttmm) cc_final: 0.8609 (tppt) REVERT: BnB 40 LYS cc_start: 0.8682 (tttt) cc_final: 0.8460 (tmtt) outliers start: 24 outliers final: 10 residues processed: 653 average time/residue: 0.5733 time to fit residues: 429.7520 Evaluate side-chains 627 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 613 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AAA residue 21 MET Chi-restraints excluded: chain AAA residue 48 LYS Chi-restraints excluded: chain AaA residue 21 MET Chi-restraints excluded: chain DbD residue 44 LYS Chi-restraints excluded: chain DeD residue 21 MET Chi-restraints excluded: chain DfD residue 37 ILE Chi-restraints excluded: chain AgA residue 37 ILE Chi-restraints excluded: chain BgB residue 32 ILE Chi-restraints excluded: chain BhB residue 28 MET Chi-restraints excluded: chain EhE residue 21 MET Chi-restraints excluded: chain CiC residue 28 MET Chi-restraints excluded: chain DjD residue 44 LYS Chi-restraints excluded: chain ClC residue 44 LYS Chi-restraints excluded: chain DlD residue 22 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 48 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 292 optimal weight: 8.9990 chunk 89 optimal weight: 6.9990 chunk 203 optimal weight: 0.9980 chunk 265 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 277 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 130 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 = 0.3543 r_free = 0.3543 target = 0.062396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.041540 restraints weight = 66933.542| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 2.59 r_work: 0.2769 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.5569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 25535 Z= 0.181 Angle : 0.544 8.978 34460 Z= 0.301 Chirality : 0.033 0.140 4140 Planarity : 0.003 0.022 4120 Dihedral : 2.661 13.241 3470 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.12 % Allowed : 31.16 % Favored : 67.73 % 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: 6.45 (0.11), residues: 3245 helix: 4.23 (0.07), residues: 3105 sheet: None (None), residues: 0 loop : 2.26 (0.18), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.001 TYRAgA 24 PHE 0.016 0.001 PHEBlB 45 TRP 0.006 0.001 TRPDhD 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.18 (25535) covalent geometry : angle 0.54446 / 0.30 (34460) hydrogen bonds : bond 0.07861 / 5.33 ( 3020) hydrogen bonds : angle 3.67905 / 2.78 ( 9060) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 624 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: EEE 5 ASP cc_start: 0.7574 (t0) cc_final: 0.7109 (t0) REVERT: AaA 5 ASP cc_start: 0.7818 (t0) cc_final: 0.7196 (t0) REVERT: BaB 5 ASP cc_start: 0.7648 (t0) cc_final: 0.7186 (t0) REVERT: DaD 5 ASP cc_start: 0.7533 (t0) cc_final: 0.7116 (t0) REVERT: EaE 5 ASP cc_start: 0.7743 (t0) cc_final: 0.7360 (t0) REVERT: BbB 5 ASP cc_start: 0.7771 (t0) cc_final: 0.7403 (t0) REVERT: DbD 5 ASP cc_start: 0.7664 (t0) cc_final: 0.7305 (t0) REVERT: DbD 44 LYS cc_start: 0.9152 (OUTLIER) cc_final: 0.8932 (ttmt) REVERT: EbE 5 ASP cc_start: 0.7592 (t0) cc_final: 0.7266 (t0) REVERT: DcD 5 ASP cc_start: 0.8021 (t0) cc_final: 0.7656 (t0) REVERT: AdA 20 GLU cc_start: 0.9002 (mt-10) cc_final: 0.8758 (mt-10) REVERT: BdB 28 MET cc_start: 0.9481 (ttm) cc_final: 0.9239 (ttp) REVERT: CdC 20 GLU cc_start: 0.9246 (mt-10) cc_final: 0.9022 (mt-10) REVERT: DdD 20 GLU cc_start: 0.9225 (mt-10) cc_final: 0.8909 (mt-10) REVERT: DeD 20 GLU cc_start: 0.9343 (mt-10) cc_final: 0.9075 (mt-10) REVERT: DeD 21 MET cc_start: 0.9317 (OUTLIER) cc_final: 0.9100 (mmm) REVERT: EeE 20 GLU cc_start: 0.9333 (mt-10) cc_final: 0.9093 (mt-10) REVERT: BfB 8 LYS cc_start: 0.8974 (mtpp) cc_final: 0.8664 (mmtt) REVERT: CfC 20 GLU cc_start: 0.9092 (mp0) cc_final: 0.8772 (mp0) REVERT: EfE 8 LYS cc_start: 0.9160 (mtpp) cc_final: 0.8941 (mmpt) REVERT: CgC 20 GLU cc_start: 0.9169 (pm20) cc_final: 0.8854 (pm20) REVERT: CgC 24 TYR cc_start: 0.9290 (m-10) cc_final: 0.9046 (m-10) REVERT: CkC 20 GLU cc_start: 0.9018 (mt-10) cc_final: 0.8797 (mt-10) REVERT: EkE 20 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8586 (mp0) REVERT: AlA 20 GLU cc_start: 0.9047 (mt-10) cc_final: 0.8752 (mt-10) REVERT: AlA 28 MET cc_start: 0.9326 (ttm) cc_final: 0.9124 (ttp) REVERT: AlA 47 SER cc_start: 0.9143 (t) cc_final: 0.8738 (p) REVERT: ClC 47 SER cc_start: 0.9017 (t) cc_final: 0.8622 (p) REVERT: DlD 22 ILE cc_start: 0.9351 (OUTLIER) cc_final: 0.9141 (mp) REVERT: DlD 47 SER cc_start: 0.9047 (t) cc_final: 0.8709 (p) REVERT: ElE 47 SER cc_start: 0.9183 (t) cc_final: 0.8755 (p) REVERT: ElE 48 LYS cc_start: 0.9288 (tppt) cc_final: 0.9061 (tppp) REVERT: AmA 20 GLU cc_start: 0.8957 (mt-10) cc_final: 0.8640 (mt-10) REVERT: BmB 47 SER cc_start: 0.8911 (t) cc_final: 0.8549 (p) REVERT: CmC 20 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8615 (mt-10) REVERT: DmD 22 ILE cc_start: 0.9370 (mt) cc_final: 0.9145 (mp) REVERT: EmE 20 GLU cc_start: 0.8953 (mt-10) cc_final: 0.8655 (mt-10) REVERT: AnA 44 LYS cc_start: 0.8820 (ttmm) cc_final: 0.8612 (tppt) outliers start: 28 outliers final: 10 residues processed: 633 average time/residue: 0.5940 time to fit residues: 429.5327 Evaluate side-chains 618 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 605 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AAA residue 21 MET Chi-restraints excluded: chain BBB residue 21 MET Chi-restraints excluded: chain AaA residue 21 MET Chi-restraints excluded: chain DbD residue 44 LYS Chi-restraints excluded: chain DeD residue 21 MET Chi-restraints excluded: chain BgB residue 17 SER Chi-restraints excluded: chain BgB residue 32 ILE Chi-restraints excluded: chain DgD residue 17 SER Chi-restraints excluded: chain BhB residue 28 MET Chi-restraints excluded: chain EhE residue 21 MET Chi-restraints excluded: chain DjD residue 44 LYS Chi-restraints excluded: chain ClC residue 44 LYS Chi-restraints excluded: chain DlD residue 22 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 253 optimal weight: 0.9980 chunk 232 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 137 optimal weight: 7.9990 chunk 230 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 159 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.3521 r_free = 0.3521 target = 0.061287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.040481 restraints weight = 66895.727| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 2.57 r_work: 0.2738 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.5420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 25535 Z= 0.189 Angle : 0.558 9.612 34460 Z= 0.312 Chirality : 0.034 0.150 4140 Planarity : 0.003 0.021 4120 Dihedral : 2.719 13.760 3470 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.72 % Allowed : 32.19 % Favored : 67.09 % 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: 6.23 (0.11), residues: 3245 helix: 4.10 (0.07), residues: 3105 sheet: None (None), residues: 0 loop : 1.78 (0.17), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.023 0.001 TYRAgA 24 PHE 0.025 0.001 PHEAnA 42 TRP 0.006 0.001 TRPAbA 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.19 (25535) covalent geometry : angle 0.55843 / 0.31 (34460) hydrogen bonds : bond 0.08193 / 5.55 ( 3020) hydrogen bonds : angle 3.74694 / 2.83 ( 9060) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6490 Ramachandran restraints generated. 3245 Oldfield, 0 Emsley, 3245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 624 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: EEE 5 ASP cc_start: 0.7794 (t0) cc_final: 0.7429 (t0) REVERT: AaA 5 ASP cc_start: 0.7937 (t0) cc_final: 0.7283 (t0) REVERT: BaB 5 ASP cc_start: 0.7808 (t0) cc_final: 0.7413 (t0) REVERT: DaD 5 ASP cc_start: 0.7708 (t0) cc_final: 0.7235 (t0) REVERT: EaE 5 ASP cc_start: 0.7871 (t0) cc_final: 0.7472 (t0) REVERT: BbB 5 ASP cc_start: 0.7943 (t0) cc_final: 0.7604 (t0) REVERT: DbD 5 ASP cc_start: 0.7881 (t0) cc_final: 0.7573 (t0) REVERT: DbD 44 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8925 (ttmt) REVERT: DcD 5 ASP cc_start: 0.7976 (t0) cc_final: 0.7657 (t0) REVERT: AdA 20 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8739 (mt-10) REVERT: BdB 28 MET cc_start: 0.9487 (ttm) cc_final: 0.9233 (ttp) REVERT: CdC 20 GLU cc_start: 0.9253 (mt-10) cc_final: 0.9024 (mt-10) REVERT: DdD 20 GLU cc_start: 0.9220 (mt-10) cc_final: 0.8920 (mt-10) REVERT: DeD 20 GLU cc_start: 0.9356 (mt-10) cc_final: 0.9083 (mt-10) REVERT: EeE 20 GLU cc_start: 0.9338 (mt-10) cc_final: 0.9103 (mt-10) REVERT: BfB 8 LYS cc_start: 0.8883 (mtpp) cc_final: 0.8659 (mmtm) REVERT: CfC 20 GLU cc_start: 0.9076 (mp0) cc_final: 0.8749 (mp0) REVERT: EfE 8 LYS cc_start: 0.9157 (mtpp) cc_final: 0.8928 (mmpt) REVERT: BgB 20 GLU cc_start: 0.9156 (pm20) cc_final: 0.8786 (pm20) REVERT: BgB 24 TYR cc_start: 0.9125 (m-80) cc_final: 0.8482 (m-80) REVERT: CgC 20 GLU cc_start: 0.9162 (pm20) cc_final: 0.8860 (pm20) REVERT: CgC 24 TYR cc_start: 0.9338 (m-10) cc_final: 0.9036 (m-10) REVERT: BkB 5 ASP cc_start: 0.8264 (t0) cc_final: 0.8060 (t0) REVERT: BkB 20 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8613 (mt-10) REVERT: CkC 20 GLU cc_start: 0.9026 (mt-10) cc_final: 0.8793 (mt-10) REVERT: AlA 20 GLU cc_start: 0.9059 (mt-10) cc_final: 0.8726 (mt-10) REVERT: AlA 28 MET cc_start: 0.9332 (ttm) cc_final: 0.9130 (ttp) REVERT: AlA 44 LYS cc_start: 0.9485 (tttt) cc_final: 0.9243 (tmmm) REVERT: AlA 47 SER cc_start: 0.9124 (t) cc_final: 0.8691 (p) REVERT: ClC 47 SER cc_start: 0.9034 (t) cc_final: 0.8631 (p) REVERT: DlD 22 ILE cc_start: 0.9377 (OUTLIER) cc_final: 0.9176 (mp) REVERT: ElE 47 SER cc_start: 0.9188 (t) cc_final: 0.8787 (p) REVERT: ElE 48 LYS cc_start: 0.9321 (tppt) cc_final: 0.9084 (tppp) REVERT: AmA 20 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8610 (mt-10) REVERT: BmB 47 SER cc_start: 0.8916 (t) cc_final: 0.8566 (p) REVERT: CmC 20 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8635 (mt-10) REVERT: DmD 20 GLU cc_start: 0.9157 (mt-10) cc_final: 0.8914 (mt-10) REVERT: DmD 22 ILE cc_start: 0.9381 (mt) cc_final: 0.9162 (mp) REVERT: EmE 20 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8673 (mt-10) REVERT: AnA 44 LYS cc_start: 0.8815 (ttmm) cc_final: 0.8585 (tppt) outliers start: 18 outliers final: 11 residues processed: 629 average time/residue: 0.6005 time to fit residues: 431.5276 Evaluate side-chains 619 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 606 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AAA residue 21 MET Chi-restraints excluded: chain BBB residue 21 MET Chi-restraints excluded: chain AaA residue 21 MET Chi-restraints excluded: chain DbD residue 44 LYS Chi-restraints excluded: chain BgB residue 32 ILE Chi-restraints excluded: chain DgD residue 17 SER Chi-restraints excluded: chain DgD residue 28 MET Chi-restraints excluded: chain BhB residue 28 MET Chi-restraints excluded: chain EhE residue 21 MET Chi-restraints excluded: chain DjD residue 44 LYS Chi-restraints excluded: chain ClC residue 44 LYS Chi-restraints excluded: chain DlD residue 22 ILE Chi-restraints excluded: chain CmC residue 41 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 262 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 268 optimal weight: 4.9990 chunk 215 optimal weight: 0.9990 chunk 115 optimal weight: 0.8980 chunk 227 optimal weight: 0.9980 chunk 219 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 245 optimal weight: 0.8980 chunk 156 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3626 r_free = 0.3626 target = 0.066401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.045828 restraints weight = 66625.607| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.58 r_work: 0.2861 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.6011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 25535 Z= 0.163 Angle : 0.545 9.647 34460 Z= 0.300 Chirality : 0.034 0.146 4140 Planarity : 0.002 0.022 4120 Dihedral : 2.687 13.100 3470 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.03 % Favored : 99.97 % Rotamer: Outliers : 0.76 % Allowed : 32.23 % Favored : 67.01 % 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: 6.60 (0.11), residues: 3245 helix: 4.31 (0.07), residues: 3105 sheet: None (None), residues: 0 loop : 2.62 (0.18), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.021 0.001 TYRAgA 24 PHE 0.024 0.001 PHECnC 42 TRP 0.005 0.000 TRPEnE 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.16 (25535) covalent geometry : angle 0.54475 / 0.30 (34460) hydrogen bonds : bond 0.06930 / 4.69 ( 3020) hydrogen bonds : angle 3.59958 / 2.72 ( 9060) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 9406.04 seconds wall clock time: 160 minutes 1.46 seconds (9601.46 seconds total)