Starting phenix.real_space_refine on Wed Sep 17 20:15:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cnv_45761/09_2025/9cnv_45761.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cnv_45761/09_2025/9cnv_45761.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cnv_45761/09_2025/9cnv_45761.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cnv_45761/09_2025/9cnv_45761.map" model { file = "/net/cci-nas-00/data/ceres_data/9cnv_45761/09_2025/9cnv_45761.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cnv_45761/09_2025/9cnv_45761.cif" } resolution = 3.16 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= 0.013 sd= 0.041 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: 5 Type Number sf(0) Gaussians P 72 5.49 5 S 72 5.16 5 C 7020 2.51 5 N 1908 2.21 5 O 2316 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-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11388 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1735 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 18, 'TRANS': 202} Chain: "B" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 91 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 3, 'TRANS': 8} Chain: "A" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 72 Unusual residues: {'IHP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: C, E, G, I, K, D, F, H, J, L Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" C1 IHP A 301 " occ=0.17 ... (34 atoms not shown) pdb=" P6 IHP A 301 " occ=0.17 residue: pdb=" C1 IHP A 302 " occ=0.17 ... (34 atoms not shown) pdb=" P6 IHP A 302 " occ=0.17 residue: pdb=" C1 IHP C 301 " occ=0.17 ... (34 atoms not shown) pdb=" P6 IHP C 301 " occ=0.17 residue: pdb=" C1 IHP C 302 " occ=0.17 ... (34 atoms not shown) pdb=" P6 IHP C 302 " occ=0.17 residue: pdb=" C1 IHP E 301 " occ=0.17 ... (34 atoms not shown) pdb=" P6 IHP E 301 " occ=0.17 residue: pdb=" C1 IHP E 302 " occ=0.17 ... (34 atoms not shown) pdb=" P6 IHP E 302 " occ=0.17 residue: pdb=" C1 IHP G 301 " occ=0.17 ... (34 atoms not shown) pdb=" P6 IHP G 301 " occ=0.17 residue: pdb=" C1 IHP G 302 " occ=0.17 ... (34 atoms not shown) pdb=" P6 IHP G 302 " occ=0.17 residue: pdb=" C1 IHP I 301 " occ=0.17 ... (34 atoms not shown) pdb=" P6 IHP I 301 " occ=0.17 residue: pdb=" C1 IHP I 302 " occ=0.17 ... (34 atoms not shown) pdb=" P6 IHP I 302 " occ=0.17 residue: pdb=" C1 IHP K 301 " occ=0.17 ... (34 atoms not shown) pdb=" P6 IHP K 301 " occ=0.17 residue: pdb=" C1 IHP K 302 " occ=0.17 ... (34 atoms not shown) pdb=" P6 IHP K 302 " occ=0.17 Time building chain proxies: 1.69, per 1000 atoms: 0.15 Number of scatterers: 11388 At special positions: 0 Unit cell: (120.684, 110.004, 80.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 P 72 15.00 O 2316 8.00 N 1908 7.00 C 7020 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 Atom "HETATM11323 O11 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9425 O11 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3731 O11 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5629 O11 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7527 O11 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1833 O11 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5634 O16 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11328 O16 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3736 O16 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9430 O16 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1838 O16 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7532 O16 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3733 O13 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9427 O13 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5631 O13 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11325 O13 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7529 O13 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1835 O13 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5631 O13 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11325 O13 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9427 O13 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3733 O13 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7529 O13 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1835 O13 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9427 O13 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3733 O13 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5629 O11 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1833 O11 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7527 O11 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11323 O11 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1835 O13 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7529 O13 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7568 O16 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9425 O11 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3731 O11 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1874 O16 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9466 O16 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3772 O16 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5631 O13 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11325 O13 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5670 O16 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11364 O16 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7568 O16 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1874 O16 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3772 O16 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9466 O16 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5670 O16 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11364 O16 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7529 O13 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1835 O13 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3733 O13 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9427 O13 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11325 O13 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5631 O13 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5632 O14 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11326 O14 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1836 O14 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7530 O14 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5633 O15 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11327 O15 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7531 O15 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1837 O15 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3734 O14 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9428 O14 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9429 O15 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3735 O15 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5630 O12 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11324 O12 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1834 O12 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9426 O12 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3732 O12 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7528 O12 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3769 O13 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9463 O13 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5667 O13 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11361 O13 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1871 O13 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7565 O13 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3732 O12 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9426 O12 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1834 O12 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7528 O12 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11324 O12 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5630 O12 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1874 O16 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7568 O16 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9466 O16 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3772 O16 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5670 O16 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11364 O16 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7568 O16 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1874 O16 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3772 O16 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9466 O16 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5670 O16 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11364 O16 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11323 O11 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5629 O11 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9425 O11 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3731 O11 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7527 O11 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1833 O11 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9466 O16 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3772 O16 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1874 O16 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7568 O16 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11364 O16 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5670 O16 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9427 O13 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3733 O13 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7568 O16 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5631 O13 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11325 O13 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5670 O16 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9466 O16 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1835 O13 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7529 O13 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3771 O15 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5669 O15 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1873 O15 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9465 O15 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3771 O15 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7567 O15 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1873 O15 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11363 O15 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5669 O15 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9429 O15 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7531 O15 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1837 O15 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1871 O13 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3735 O15 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7565 O13 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3769 O13 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9463 O13 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11327 O15 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5633 O15 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11361 O13 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5667 O13 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3734 O14 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9428 O14 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11326 O14 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5632 O14 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9427 O13 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3733 O13 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7530 O14 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1836 O14 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7529 O13 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1835 O13 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5631 O13 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11325 O13 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7564 O12 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1870 O12 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9462 O12 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3768 O12 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5666 O12 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11360 O12 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11359 O11 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5665 O11 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3767 O11 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9461 O11 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7563 O11 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1869 O11 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11326 O14 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5632 O14 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3734 O14 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9428 O14 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1836 O14 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7530 O14 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3771 O15 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9465 O15 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11363 O15 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5669 O15 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3767 O11 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7567 O15 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1873 O15 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9461 O11 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5665 O11 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11359 O11 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7563 O11 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1869 O11 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3767 O11 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9461 O11 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1869 O11 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7563 O11 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5665 O11 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11359 O11 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9466 O16 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3772 O16 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11364 O16 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5670 O16 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1874 O16 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7568 O16 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11361 O13 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5667 O13 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9463 O13 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3769 O13 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1871 O13 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7565 O13 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5666 O12 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1870 O12 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3768 O12 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7563 O11 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1869 O11 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3767 O11 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9461 O11 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5665 O11 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11359 O11 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9426 O12 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3732 O12 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11324 O12 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5630 O12 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1834 O12 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7528 O12 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11362 O14 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5668 O14 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1872 O14 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3770 O14 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7566 O14 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9464 O14 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11359 O11 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5665 O11 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1869 O11 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7563 O11 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3770 O14 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9461 O11 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3767 O11 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9464 O14 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1872 O14 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7566 O14 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5668 O14 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11362 O14 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1870 O12 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7564 O12 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11360 O12 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5666 O12 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3768 O12 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9462 O12 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11325 O13 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5631 O13 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7529 O13 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1835 O13 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3733 O13 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9427 O13 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1869 O11 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7563 O11 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5665 O11 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11359 O11 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9461 O11 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3767 O11 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1837 O15 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7531 O15 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11327 O15 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3735 O15 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5633 O15 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9429 O15 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5631 O13 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11325 O13 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7529 O13 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1835 O13 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9427 O13 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3733 O13 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5631 O13 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1869 O11 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7563 O11 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11325 O13 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9427 O13 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3733 O13 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11359 O11 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9461 O11 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5665 O11 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3767 O11 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7529 O13 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1835 O13 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11359 O11 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5665 O11 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9461 O11 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11361 O13 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3767 O11 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5667 O13 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7563 O11 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1869 O11 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3769 O13 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9463 O13 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1871 O13 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7565 O13 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3770 O14 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9464 O14 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11362 O14 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5668 O14 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1872 O14 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7566 O14 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1874 O16 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7568 O16 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7529 O13 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1835 O13 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9466 O16 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3772 O16 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3733 O13 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9427 O13 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11364 O16 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5670 O16 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5631 O13 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11325 O13 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7528 O12 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1834 O12 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9426 O12 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3732 O12 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11324 O12 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5630 O12 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11360 O12 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11359 O11 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5665 O11 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3733 O13 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9427 O13 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1869 O11 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7563 O11 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9461 O11 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3767 O11 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7564 O12 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9462 O12 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1835 O13 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7529 O13 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5631 O13 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11325 O13 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5665 O11 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11359 O11 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1869 O11 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7563 O11 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9461 O11 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3767 O11 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3736 O16 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9430 O16 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5634 O16 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11328 O16 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1838 O16 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7532 O16 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5669 O15 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11363 O15 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1873 O15 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7567 O15 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9465 O15 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3771 O15 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3732 O12 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9426 O12 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7528 O12 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1834 O12 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11324 O12 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5630 O12 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9466 O16 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3772 O16 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11364 O16 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5670 O16 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7568 O16 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1874 O16 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11362 O14 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5668 O14 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3770 O14 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9464 O14 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7566 O14 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1872 O14 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11324 O12 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5630 O12 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7565 O13 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1871 O13 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11361 O13 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5667 O13 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9463 O13 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3769 O13 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1834 O12 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9426 O12 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3732 O12 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7528 O12 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11363 O15 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5669 O15 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9465 O15 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3771 O15 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7567 O15 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1873 O15 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1870 O12 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7564 O12 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11360 O12 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5666 O12 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3768 O12 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9462 O12 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7564 O12 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1870 O12 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9462 O12 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3768 O12 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11360 O12 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5666 O12 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3771 O15 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9465 O15 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1873 O15 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7567 O15 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11363 O15 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5669 O15 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7529 O13 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1835 O13 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11325 O13 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5631 O13 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3733 O13 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9427 O13 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9428 O14 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3734 O14 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1836 O14 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7530 O14 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11326 O14 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5632 O14 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11360 O12 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5666 O12 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7564 O12 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1870 O12 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11327 O15 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5633 O15 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7531 O15 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1837 O15 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3768 O12 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9462 O12 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3735 O15 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9429 O15 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7564 O12 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1870 O12 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11360 O12 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5666 O12 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9462 O12 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3768 O12 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11362 O14 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5668 O14 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1872 O14 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7566 O14 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9464 O14 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3770 O14 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11360 O12 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5666 O12 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9462 O12 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3768 O12 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1870 O12 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7564 O12 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7528 O12 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1834 O12 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5630 O12 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9426 O12 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3732 O12 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11324 O12 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3734 O14 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9428 O14 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3732 O12 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9426 O12 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7530 O14 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1836 O14 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1834 O12 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7528 O12 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5632 O14 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11326 O14 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5630 O12 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11324 O12 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1872 O14 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7566 O14 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7528 O12 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1834 O12 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5630 O12 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11324 O12 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11362 O14 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5668 O14 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3732 O12 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9426 O12 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9464 O14 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3770 O14 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3770 O14 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9464 O14 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11362 O14 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5668 O14 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11361 O13 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5667 O13 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1872 O14 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7566 O14 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1871 O13 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7565 O13 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3769 O13 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3770 O14 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9463 O13 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9464 O14 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5668 O14 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11362 O14 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1872 O14 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7566 O14 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9465 O15 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3771 O15 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7567 O15 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1873 O15 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5669 O15 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11363 O15 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5630 O12 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11324 O12 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9426 O12 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3732 O12 IHP C 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7528 O12 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1834 O12 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11362 O14 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5668 O14 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7528 O12 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9466 O16 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3772 O16 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11324 O12 IHP K 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5630 O12 IHP E 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1834 O12 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11364 O16 IHP K 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5670 O16 IHP E 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7566 O14 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1872 O14 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9464 O14 IHP I 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3770 O14 IHP C 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 7568 O16 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 1874 O16 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9426 O12 IHP I 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3732 O12 IHP C 301 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=13, symmetry=0 Number of additional bonds: simple=13, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.72 Conformation dependent library (CDL) restraints added in 466.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2568 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 6 sheets defined 63.1% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 16 through 30 Processing helix chain 'A' and resid 35 through 44 removed outlier: 3.601A pdb=" N GLN A 41 " --> pdb=" O VAL A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 59 removed outlier: 3.619A pdb=" N VAL A 59 " --> pdb=" O MET A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 84 removed outlier: 3.549A pdb=" N MET A 66 " --> pdb=" O HIS A 62 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 105 removed outlier: 3.733A pdb=" N ALA A 104 " --> pdb=" O GLY A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 118 Processing helix chain 'A' and resid 125 through 146 removed outlier: 3.504A pdb=" N TYR A 130 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 175 removed outlier: 4.010A pdb=" N TYR A 164 " --> pdb=" O PRO A 160 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA A 174 " --> pdb=" O LYS A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 186 Processing helix chain 'A' and resid 188 through 193 Processing helix chain 'A' and resid 197 through 204 Processing helix chain 'A' and resid 210 through 218 removed outlier: 3.524A pdb=" N CYS A 218 " --> pdb=" O MET A 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 30 Processing helix chain 'C' and resid 35 through 44 removed outlier: 3.601A pdb=" N GLN C 41 " --> pdb=" O VAL C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 59 removed outlier: 3.619A pdb=" N VAL C 59 " --> pdb=" O MET C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 84 removed outlier: 3.550A pdb=" N MET C 66 " --> pdb=" O HIS C 62 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP C 75 " --> pdb=" O GLU C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 105 removed outlier: 3.734A pdb=" N ALA C 104 " --> pdb=" O GLY C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 118 Processing helix chain 'C' and resid 125 through 146 removed outlier: 3.504A pdb=" N TYR C 130 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 175 removed outlier: 4.010A pdb=" N TYR C 164 " --> pdb=" O PRO C 160 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA C 174 " --> pdb=" O LYS C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 186 Processing helix chain 'C' and resid 188 through 193 Processing helix chain 'C' and resid 197 through 204 Processing helix chain 'C' and resid 210 through 218 removed outlier: 3.524A pdb=" N CYS C 218 " --> pdb=" O MET C 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 30 Processing helix chain 'E' and resid 35 through 44 removed outlier: 3.601A pdb=" N GLN E 41 " --> pdb=" O VAL E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 59 removed outlier: 3.619A pdb=" N VAL E 59 " --> pdb=" O MET E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 84 removed outlier: 3.549A pdb=" N MET E 66 " --> pdb=" O HIS E 62 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 105 removed outlier: 3.733A pdb=" N ALA E 104 " --> pdb=" O GLY E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 118 Processing helix chain 'E' and resid 125 through 146 removed outlier: 3.503A pdb=" N TYR E 130 " --> pdb=" O VAL E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 175 removed outlier: 4.010A pdb=" N TYR E 164 " --> pdb=" O PRO E 160 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA E 174 " --> pdb=" O LYS E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 186 Processing helix chain 'E' and resid 188 through 193 Processing helix chain 'E' and resid 197 through 204 Processing helix chain 'E' and resid 210 through 218 removed outlier: 3.524A pdb=" N CYS E 218 " --> pdb=" O MET E 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 30 Processing helix chain 'G' and resid 35 through 44 removed outlier: 3.601A pdb=" N GLN G 41 " --> pdb=" O VAL G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 59 removed outlier: 3.619A pdb=" N VAL G 59 " --> pdb=" O MET G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 84 removed outlier: 3.549A pdb=" N MET G 66 " --> pdb=" O HIS G 62 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP G 75 " --> pdb=" O GLU G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 105 removed outlier: 3.733A pdb=" N ALA G 104 " --> pdb=" O GLY G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 118 Processing helix chain 'G' and resid 125 through 146 removed outlier: 3.504A pdb=" N TYR G 130 " --> pdb=" O VAL G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 175 removed outlier: 4.010A pdb=" N TYR G 164 " --> pdb=" O PRO G 160 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA G 174 " --> pdb=" O LYS G 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 186 Processing helix chain 'G' and resid 188 through 193 Processing helix chain 'G' and resid 197 through 204 Processing helix chain 'G' and resid 210 through 218 removed outlier: 3.524A pdb=" N CYS G 218 " --> pdb=" O MET G 214 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 30 Processing helix chain 'I' and resid 35 through 44 removed outlier: 3.601A pdb=" N GLN I 41 " --> pdb=" O VAL I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 59 removed outlier: 3.619A pdb=" N VAL I 59 " --> pdb=" O MET I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 84 removed outlier: 3.549A pdb=" N MET I 66 " --> pdb=" O HIS I 62 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP I 75 " --> pdb=" O GLU I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 105 removed outlier: 3.732A pdb=" N ALA I 104 " --> pdb=" O GLY I 100 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 118 Processing helix chain 'I' and resid 125 through 146 removed outlier: 3.504A pdb=" N TYR I 130 " --> pdb=" O VAL I 126 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 175 removed outlier: 4.010A pdb=" N TYR I 164 " --> pdb=" O PRO I 160 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA I 174 " --> pdb=" O LYS I 170 " (cutoff:3.500A) Processing helix chain 'I' and resid 178 through 186 Processing helix chain 'I' and resid 188 through 193 Processing helix chain 'I' and resid 197 through 204 Processing helix chain 'I' and resid 210 through 218 removed outlier: 3.524A pdb=" N CYS I 218 " --> pdb=" O MET I 214 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 30 Processing helix chain 'K' and resid 35 through 44 removed outlier: 3.601A pdb=" N GLN K 41 " --> pdb=" O VAL K 37 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 59 removed outlier: 3.619A pdb=" N VAL K 59 " --> pdb=" O MET K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 84 removed outlier: 3.549A pdb=" N MET K 66 " --> pdb=" O HIS K 62 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP K 75 " --> pdb=" O GLU K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 99 through 105 removed outlier: 3.733A pdb=" N ALA K 104 " --> pdb=" O GLY K 100 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 118 Processing helix chain 'K' and resid 125 through 146 removed outlier: 3.504A pdb=" N TYR K 130 " --> pdb=" O VAL K 126 " (cutoff:3.500A) Processing helix chain 'K' and resid 160 through 175 removed outlier: 4.010A pdb=" N TYR K 164 " --> pdb=" O PRO K 160 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA K 174 " --> pdb=" O LYS K 170 " (cutoff:3.500A) Processing helix chain 'K' and resid 178 through 186 Processing helix chain 'K' and resid 188 through 193 Processing helix chain 'K' and resid 197 through 204 Processing helix chain 'K' and resid 210 through 218 removed outlier: 3.524A pdb=" N CYS K 218 " --> pdb=" O MET K 214 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 2 through 4 Processing sheet with id=2, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=3, first strand: chain 'E' and resid 2 through 4 Processing sheet with id=4, first strand: chain 'G' and resid 2 through 4 Processing sheet with id=5, first strand: chain 'I' and resid 2 through 4 Processing sheet with id=6, first strand: chain 'K' and resid 2 through 4 552 hydrogen bonds defined for protein. 1656 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: 1.70 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1896 1.32 - 1.44: 2766 1.44 - 1.57: 6822 1.57 - 1.69: 72 1.69 - 1.82: 114 Bond restraints: 11670 Sorted by residual: bond pdb=" CA SER K 108 " pdb=" CB SER K 108 " ideal model delta sigma weight residual 1.535 1.480 0.055 1.32e-02 5.74e+03 1.75e+01 bond pdb=" CA SER A 108 " pdb=" CB SER A 108 " ideal model delta sigma weight residual 1.535 1.480 0.055 1.32e-02 5.74e+03 1.71e+01 bond pdb=" CA SER G 108 " pdb=" CB SER G 108 " ideal model delta sigma weight residual 1.535 1.480 0.055 1.32e-02 5.74e+03 1.71e+01 bond pdb=" CA SER I 108 " pdb=" CB SER I 108 " ideal model delta sigma weight residual 1.535 1.480 0.054 1.32e-02 5.74e+03 1.69e+01 bond pdb=" CA SER C 108 " pdb=" CB SER C 108 " ideal model delta sigma weight residual 1.535 1.480 0.054 1.32e-02 5.74e+03 1.69e+01 ... (remaining 11665 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 11040 1.93 - 3.87: 4331 3.87 - 5.80: 577 5.80 - 7.74: 66 7.74 - 9.67: 18 Bond angle restraints: 16032 Sorted by residual: angle pdb=" C ALA I 92 " pdb=" CA ALA I 92 " pdb=" CB ALA I 92 " ideal model delta sigma weight residual 116.63 111.11 5.52 1.16e+00 7.43e-01 2.27e+01 angle pdb=" C ALA K 92 " pdb=" CA ALA K 92 " pdb=" CB ALA K 92 " ideal model delta sigma weight residual 116.54 111.09 5.45 1.15e+00 7.56e-01 2.25e+01 angle pdb=" C ALA E 92 " pdb=" CA ALA E 92 " pdb=" CB ALA E 92 " ideal model delta sigma weight residual 116.54 111.09 5.45 1.15e+00 7.56e-01 2.25e+01 angle pdb=" C ALA C 92 " pdb=" CA ALA C 92 " pdb=" CB ALA C 92 " ideal model delta sigma weight residual 116.54 111.11 5.43 1.15e+00 7.56e-01 2.23e+01 angle pdb=" C ALA G 92 " pdb=" CA ALA G 92 " pdb=" CB ALA G 92 " ideal model delta sigma weight residual 116.54 111.11 5.43 1.15e+00 7.56e-01 2.23e+01 ... (remaining 16027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.90: 6768 26.90 - 53.81: 342 53.81 - 80.71: 150 80.71 - 107.61: 48 107.61 - 134.52: 24 Dihedral angle restraints: 7332 sinusoidal: 3336 harmonic: 3996 Sorted by residual: dihedral pdb=" O11 IHP K 302 " pdb=" C1 IHP K 302 " pdb=" C6 IHP K 302 " pdb=" O16 IHP K 302 " ideal model delta sinusoidal sigma weight residual 307.52 173.00 134.52 1 3.00e+01 1.11e-03 1.81e+01 dihedral pdb=" O11 IHP G 302 " pdb=" C1 IHP G 302 " pdb=" C6 IHP G 302 " pdb=" O16 IHP G 302 " ideal model delta sinusoidal sigma weight residual 307.52 173.02 134.50 1 3.00e+01 1.11e-03 1.81e+01 dihedral pdb=" O11 IHP A 302 " pdb=" C1 IHP A 302 " pdb=" C6 IHP A 302 " pdb=" O16 IHP A 302 " ideal model delta sinusoidal sigma weight residual 307.52 173.02 134.50 1 3.00e+01 1.11e-03 1.81e+01 ... (remaining 7329 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 440 0.065 - 0.131: 729 0.131 - 0.196: 393 0.196 - 0.262: 142 0.262 - 0.327: 18 Chirality restraints: 1722 Sorted by residual: chirality pdb=" C1 IHP E 301 " pdb=" C2 IHP E 301 " pdb=" C6 IHP E 301 " pdb=" O11 IHP E 301 " both_signs ideal model delta sigma weight residual False 2.32 2.64 -0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" C1 IHP I 301 " pdb=" C2 IHP I 301 " pdb=" C6 IHP I 301 " pdb=" O11 IHP I 301 " both_signs ideal model delta sigma weight residual False 2.32 2.64 -0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" C1 IHP C 301 " pdb=" C2 IHP C 301 " pdb=" C6 IHP C 301 " pdb=" O11 IHP C 301 " both_signs ideal model delta sigma weight residual False 2.32 2.64 -0.33 2.00e-01 2.50e+01 2.67e+00 ... (remaining 1719 not shown) Planarity restraints: 2040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG I 70 " -0.557 9.50e-02 1.11e+02 2.50e-01 3.85e+01 pdb=" NE ARG I 70 " 0.037 2.00e-02 2.50e+03 pdb=" CZ ARG I 70 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG I 70 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG I 70 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 70 " -0.557 9.50e-02 1.11e+02 2.50e-01 3.85e+01 pdb=" NE ARG G 70 " 0.037 2.00e-02 2.50e+03 pdb=" CZ ARG G 70 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG G 70 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG G 70 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 70 " 0.557 9.50e-02 1.11e+02 2.50e-01 3.85e+01 pdb=" NE ARG A 70 " -0.037 2.00e-02 2.50e+03 pdb=" CZ ARG A 70 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 70 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG A 70 " 0.015 2.00e-02 2.50e+03 ... (remaining 2037 not shown) Histogram of nonbonded interaction distances: 0.19 - 1.13: 484 1.13 - 2.07: 1837 2.07 - 3.02: 10834 3.02 - 3.96: 37666 3.96 - 4.90: 63219 Warning: very small nonbonded interaction distances. Nonbonded interactions: 114040 Sorted by model distance: nonbonded pdb=" O43 IHP C 301 " pdb=" O31 IHP K 301 " model vdw 0.189 3.040 nonbonded pdb=" O31 IHP E 301 " pdb=" O43 IHP I 301 " model vdw 0.190 3.040 nonbonded pdb=" O31 IHP G 301 " pdb=" O43 IHP K 301 " model vdw 0.191 3.040 nonbonded pdb=" O31 IHP A 301 " pdb=" O43 IHP E 301 " model vdw 0.192 3.040 nonbonded pdb=" O31 IHP C 301 " pdb=" O43 IHP G 301 " model vdw 0.194 3.040 ... (remaining 114035 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' } 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=0.17 max=1.00 mean=0.97 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: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.030 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6582 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 : 0.038 1.285 11683 Z= 3.706 Angle : 1.884 9.674 16032 Z= 1.376 Chirality : 0.125 0.327 1722 Planarity : 0.026 0.250 2040 Dihedral : 20.729 134.516 4764 Min Nonbonded Distance : 0.189 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.59 (0.20), residues: 1374 helix: -0.32 (0.17), residues: 756 sheet: -2.95 (0.42), residues: 54 loop : -1.81 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.004 ARG G 18 TYR 0.017 0.004 TYR K 118 PHE 0.019 0.004 PHE F 9 TRP 0.041 0.005 TRP E 116 HIS 0.007 0.004 HIS E 62 Details of bonding type rmsd covalent geometry : bond 0.01407 (11670) covalent geometry : angle 1.88437 (16032) hydrogen bonds : bond 0.26073 ( 552) hydrogen bonds : angle 7.75655 ( 1656) Misc. bond : bond 1.07355 ( 13) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 334 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 334 average time/residue: 0.1370 time to fit residues: 60.9857 Evaluate side-chains 205 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 30.0000 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 55 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN A 94 GLN ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 162 GLN C 4 GLN C 94 GLN C 128 ASN E 94 GLN E 122 ASN G 4 GLN G 94 GLN ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 GLN I 4 GLN I 94 GLN I 128 ASN K 94 GLN K 122 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.079213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.063728 restraints weight = 39523.830| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 5.26 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3262 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3254 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.4662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.071 1.771 11683 Z= 3.574 Angle : 5.132 84.275 16032 Z= 1.740 Chirality : 0.304 3.875 1722 Planarity : 0.014 0.451 2040 Dihedral : 21.999 133.350 1992 Min Nonbonded Distance : 1.226 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.08 % Allowed : 12.33 % Favored : 85.58 % 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 aren not related in a simple way. whole: 0.32 (0.22), residues: 1374 helix: 1.00 (0.17), residues: 846 sheet: -2.18 (0.44), residues: 54 loop : -0.83 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.038 0.002 ARG C 18 TYR 0.033 0.003 TYR I 130 PHE 0.023 0.002 PHE J 4 TRP 0.014 0.002 TRP E 184 HIS 0.003 0.001 HIS A 84 Details of bonding type rmsd covalent geometry : bond 0.07135 (11670) covalent geometry : angle 5.13201 (16032) hydrogen bonds : bond 0.07250 ( 552) hydrogen bonds : angle 5.10062 ( 1656) Misc. bond : bond 0.07826 ( 13) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 232 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LEU cc_start: 0.8395 (tp) cc_final: 0.8151 (tp) REVERT: A 45 GLU cc_start: 0.9042 (tp30) cc_final: 0.8819 (tp30) REVERT: A 119 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7504 (ttp80) REVERT: C 15 LEU cc_start: 0.8192 (tp) cc_final: 0.7819 (tt) REVERT: C 25 LYS cc_start: 0.9164 (mtpt) cc_final: 0.8958 (mttm) REVERT: C 31 LYS cc_start: 0.9531 (mmtm) cc_final: 0.9057 (tmtt) REVERT: C 45 GLU cc_start: 0.9135 (tp30) cc_final: 0.8883 (tp30) REVERT: C 122 ASN cc_start: 0.9354 (m110) cc_final: 0.9139 (t0) REVERT: C 213 GLU cc_start: 0.9342 (mt-10) cc_final: 0.8865 (pt0) REVERT: E 15 LEU cc_start: 0.8242 (tp) cc_final: 0.7793 (tt) REVERT: E 214 MET cc_start: 0.9471 (mtm) cc_final: 0.9140 (mtm) REVERT: G 15 LEU cc_start: 0.8386 (tp) cc_final: 0.8155 (tp) REVERT: G 45 GLU cc_start: 0.9049 (tp30) cc_final: 0.8836 (tp30) REVERT: G 119 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7531 (ttp80) REVERT: I 15 LEU cc_start: 0.8154 (tp) cc_final: 0.7767 (tt) REVERT: I 31 LYS cc_start: 0.9526 (mmtm) cc_final: 0.9054 (tmtt) REVERT: I 45 GLU cc_start: 0.9136 (tp30) cc_final: 0.8881 (tp30) REVERT: I 122 ASN cc_start: 0.9385 (m110) cc_final: 0.9177 (t0) REVERT: J 2 VAL cc_start: 0.9533 (t) cc_final: 0.9327 (p) REVERT: K 15 LEU cc_start: 0.8296 (tp) cc_final: 0.7859 (tt) outliers start: 25 outliers final: 10 residues processed: 251 average time/residue: 0.1400 time to fit residues: 45.8610 Evaluate side-chains 205 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 193 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 119 ARG Chi-restraints excluded: chain E residue 61 ASP Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain G residue 61 ASP Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 119 ARG Chi-restraints excluded: chain K residue 61 ASP Chi-restraints excluded: chain K residue 110 VAL Chi-restraints excluded: chain K residue 149 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 29 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 115 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 121 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 113 optimal weight: 9.9990 chunk 109 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN B 11 GLN E 128 ASN E 135 GLN ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 GLN K 128 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.075664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.059690 restraints weight = 39228.254| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 5.32 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3191 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.5817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.050 1.368 11683 Z= 2.510 Angle : 4.247 86.793 16032 Z= 1.453 Chirality : 0.265 4.087 1722 Planarity : 0.013 0.397 2040 Dihedral : 22.224 139.315 1992 Min Nonbonded Distance : 1.464 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.00 % Allowed : 13.25 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.23), residues: 1374 helix: 1.31 (0.18), residues: 852 sheet: -1.27 (0.57), residues: 54 loop : -0.18 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.043 0.002 ARG A 18 TYR 0.037 0.003 TYR I 130 PHE 0.008 0.001 PHE J 4 TRP 0.009 0.001 TRP G 80 HIS 0.002 0.001 HIS E 12 Details of bonding type rmsd covalent geometry : bond 0.04989 (11670) covalent geometry : angle 4.24749 (16032) hydrogen bonds : bond 0.05831 ( 552) hydrogen bonds : angle 4.64494 ( 1656) Misc. bond : bond 0.09066 ( 13) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 219 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LEU cc_start: 0.8511 (tp) cc_final: 0.8105 (tp) REVERT: A 28 GLU cc_start: 0.8337 (mm-30) cc_final: 0.8102 (mm-30) REVERT: A 29 ASP cc_start: 0.9439 (m-30) cc_final: 0.9016 (p0) REVERT: A 30 LYS cc_start: 0.9432 (mmtp) cc_final: 0.8941 (mmtp) REVERT: A 119 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7931 (ttp-110) REVERT: A 130 TYR cc_start: 0.9111 (t80) cc_final: 0.8715 (t80) REVERT: A 207 MET cc_start: 0.9217 (tmm) cc_final: 0.8596 (tmm) REVERT: B 2 VAL cc_start: 0.9502 (m) cc_final: 0.9299 (p) REVERT: C 28 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8170 (mm-30) REVERT: C 29 ASP cc_start: 0.9458 (m-30) cc_final: 0.9136 (p0) REVERT: C 31 LYS cc_start: 0.9536 (mmtm) cc_final: 0.9073 (tmtt) REVERT: C 45 GLU cc_start: 0.9110 (tp30) cc_final: 0.8875 (mm-30) REVERT: C 122 ASN cc_start: 0.9420 (m110) cc_final: 0.9208 (t0) REVERT: C 130 TYR cc_start: 0.9174 (t80) cc_final: 0.8906 (t80) REVERT: C 207 MET cc_start: 0.9316 (tmm) cc_final: 0.8967 (tmm) REVERT: C 208 ASN cc_start: 0.9149 (p0) cc_final: 0.8860 (p0) REVERT: E 25 LYS cc_start: 0.9110 (mtpt) cc_final: 0.8785 (ptpp) REVERT: E 30 LYS cc_start: 0.9362 (mmtp) cc_final: 0.9131 (mmtm) REVERT: G 15 LEU cc_start: 0.8464 (tp) cc_final: 0.8250 (tp) REVERT: G 28 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8140 (mm-30) REVERT: G 29 ASP cc_start: 0.9441 (m-30) cc_final: 0.9019 (p0) REVERT: G 30 LYS cc_start: 0.9442 (mmtp) cc_final: 0.8921 (mmtp) REVERT: G 119 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7942 (ttp-110) REVERT: G 130 TYR cc_start: 0.9147 (t80) cc_final: 0.8750 (t80) REVERT: G 207 MET cc_start: 0.9226 (tmm) cc_final: 0.8608 (tmm) REVERT: H 2 VAL cc_start: 0.9500 (m) cc_final: 0.9293 (p) REVERT: I 28 GLU cc_start: 0.8398 (mm-30) cc_final: 0.8133 (mm-30) REVERT: I 29 ASP cc_start: 0.9452 (m-30) cc_final: 0.9146 (p0) REVERT: I 31 LYS cc_start: 0.9538 (mmtm) cc_final: 0.9068 (tmtt) REVERT: I 45 GLU cc_start: 0.9117 (tp30) cc_final: 0.8880 (mm-30) REVERT: I 130 TYR cc_start: 0.9169 (t80) cc_final: 0.8908 (t80) REVERT: I 207 MET cc_start: 0.9304 (tmm) cc_final: 0.8955 (tmm) REVERT: I 208 ASN cc_start: 0.9129 (p0) cc_final: 0.8852 (p0) REVERT: K 25 LYS cc_start: 0.9251 (mtpt) cc_final: 0.8893 (mttp) REVERT: K 28 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8291 (mm-30) REVERT: K 29 ASP cc_start: 0.9551 (m-30) cc_final: 0.9180 (p0) REVERT: K 71 GLU cc_start: 0.9053 (mm-30) cc_final: 0.8802 (mm-30) outliers start: 24 outliers final: 5 residues processed: 239 average time/residue: 0.1680 time to fit residues: 50.9628 Evaluate side-chains 210 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 203 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ARG Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain G residue 119 ARG Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain K residue 18 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 1 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 118 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 120 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 33 optimal weight: 20.0000 chunk 82 optimal weight: 0.6980 chunk 53 optimal weight: 9.9990 chunk 14 optimal weight: 0.5980 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 135 GLN G 135 GLN I 135 GLN K 135 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.074604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.058137 restraints weight = 41705.470| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 5.58 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3153 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3152 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.6504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.037 0.967 11683 Z= 1.896 Angle : 3.472 69.017 16032 Z= 1.201 Chirality : 0.268 4.922 1722 Planarity : 0.007 0.195 2040 Dihedral : 21.667 145.317 1992 Min Nonbonded Distance : 1.583 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.83 % Allowed : 13.25 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.23), residues: 1374 helix: 1.26 (0.18), residues: 858 sheet: -0.82 (0.64), residues: 54 loop : 0.15 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.067 0.002 ARG C 18 TYR 0.029 0.003 TYR G 130 PHE 0.019 0.002 PHE J 4 TRP 0.009 0.001 TRP G 80 HIS 0.002 0.000 HIS A 12 Details of bonding type rmsd covalent geometry : bond 0.03717 (11670) covalent geometry : angle 3.47249 (16032) hydrogen bonds : bond 0.04898 ( 552) hydrogen bonds : angle 4.41957 ( 1656) Misc. bond : bond 0.08793 ( 13) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 228 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LEU cc_start: 0.8541 (tp) cc_final: 0.8297 (tp) REVERT: A 28 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7986 (mm-30) REVERT: A 29 ASP cc_start: 0.9443 (m-30) cc_final: 0.9054 (p0) REVERT: A 30 LYS cc_start: 0.9369 (mmtp) cc_final: 0.8995 (mmtp) REVERT: A 107 THR cc_start: 0.9480 (OUTLIER) cc_final: 0.9240 (p) REVERT: A 119 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7494 (ttp80) REVERT: A 130 TYR cc_start: 0.9195 (t80) cc_final: 0.8892 (t80) REVERT: A 207 MET cc_start: 0.9126 (tmm) cc_final: 0.8492 (tmm) REVERT: B 2 VAL cc_start: 0.9518 (OUTLIER) cc_final: 0.9313 (p) REVERT: C 28 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8088 (mm-30) REVERT: C 29 ASP cc_start: 0.9460 (m-30) cc_final: 0.9178 (p0) REVERT: C 31 LYS cc_start: 0.9549 (mmtm) cc_final: 0.9046 (tmtt) REVERT: C 45 GLU cc_start: 0.9091 (tp30) cc_final: 0.8839 (tp30) REVERT: C 107 THR cc_start: 0.9521 (OUTLIER) cc_final: 0.9286 (p) REVERT: C 122 ASN cc_start: 0.9463 (m110) cc_final: 0.9229 (t0) REVERT: C 207 MET cc_start: 0.9288 (tmm) cc_final: 0.8658 (tmm) REVERT: E 28 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8201 (mm-30) REVERT: E 29 ASP cc_start: 0.9516 (m-30) cc_final: 0.9247 (p0) REVERT: E 50 TYR cc_start: 0.8479 (t80) cc_final: 0.8241 (t80) REVERT: E 107 THR cc_start: 0.9487 (OUTLIER) cc_final: 0.9255 (p) REVERT: E 214 MET cc_start: 0.9420 (mtm) cc_final: 0.9095 (mtm) REVERT: G 15 LEU cc_start: 0.8573 (tp) cc_final: 0.8352 (tp) REVERT: G 28 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7991 (mm-30) REVERT: G 29 ASP cc_start: 0.9431 (m-30) cc_final: 0.9040 (p0) REVERT: G 30 LYS cc_start: 0.9390 (mmtp) cc_final: 0.8964 (mmtp) REVERT: G 107 THR cc_start: 0.9486 (OUTLIER) cc_final: 0.9247 (p) REVERT: G 119 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7521 (ttp80) REVERT: G 130 TYR cc_start: 0.9215 (t80) cc_final: 0.8847 (t80) REVERT: G 207 MET cc_start: 0.9143 (tmm) cc_final: 0.8510 (tmm) REVERT: H 2 VAL cc_start: 0.9512 (OUTLIER) cc_final: 0.9307 (p) REVERT: I 25 LYS cc_start: 0.8973 (mtmm) cc_final: 0.8615 (mttm) REVERT: I 28 GLU cc_start: 0.8409 (mm-30) cc_final: 0.8103 (mm-30) REVERT: I 29 ASP cc_start: 0.9463 (m-30) cc_final: 0.9162 (p0) REVERT: I 31 LYS cc_start: 0.9545 (mmtm) cc_final: 0.9050 (tmtt) REVERT: I 45 GLU cc_start: 0.9091 (tp30) cc_final: 0.8838 (tp30) REVERT: I 107 THR cc_start: 0.9509 (OUTLIER) cc_final: 0.9265 (p) REVERT: I 207 MET cc_start: 0.9259 (tmm) cc_final: 0.8633 (tmm) REVERT: K 15 LEU cc_start: 0.8437 (tp) cc_final: 0.8146 (tp) REVERT: K 28 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8219 (mm-30) REVERT: K 29 ASP cc_start: 0.9546 (m-30) cc_final: 0.9198 (p0) REVERT: K 50 TYR cc_start: 0.8481 (t80) cc_final: 0.8240 (t80) REVERT: K 71 GLU cc_start: 0.9131 (mm-30) cc_final: 0.8805 (mm-30) REVERT: K 107 THR cc_start: 0.9477 (OUTLIER) cc_final: 0.9241 (p) REVERT: K 175 GLU cc_start: 0.8418 (tp30) cc_final: 0.8187 (tp30) outliers start: 22 outliers final: 6 residues processed: 241 average time/residue: 0.1491 time to fit residues: 46.4364 Evaluate side-chains 224 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 208 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 119 ARG Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 119 ARG Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 110 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 115 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 84 optimal weight: 0.0570 chunk 109 optimal weight: 20.0000 chunk 53 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 68 optimal weight: 10.0000 chunk 132 optimal weight: 4.9990 overall best weight: 3.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.074345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.058351 restraints weight = 37803.358| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 5.55 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3093 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3092 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.7151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.033 1.025 11683 Z= 1.669 Angle : 2.978 49.643 16032 Z= 1.037 Chirality : 0.267 5.733 1722 Planarity : 0.006 0.074 2040 Dihedral : 22.027 167.116 1992 Min Nonbonded Distance : 1.406 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.33 % Allowed : 11.33 % Favored : 86.33 % 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 aren not related in a simple way. whole: 1.41 (0.24), residues: 1374 helix: 1.45 (0.18), residues: 858 sheet: -0.81 (0.66), residues: 54 loop : 0.36 (0.32), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.001 ARG E 18 TYR 0.030 0.003 TYR I 130 PHE 0.012 0.001 PHE G 32 TRP 0.009 0.001 TRP C 23 HIS 0.002 0.001 HIS G 62 Details of bonding type rmsd covalent geometry : bond 0.03317 (11670) covalent geometry : angle 2.97793 (16032) hydrogen bonds : bond 0.04834 ( 552) hydrogen bonds : angle 4.42068 ( 1656) Misc. bond : bond 0.07504 ( 13) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 213 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LEU cc_start: 0.8711 (tp) cc_final: 0.8497 (tp) REVERT: A 19 THR cc_start: 0.8462 (OUTLIER) cc_final: 0.8228 (p) REVERT: A 28 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8123 (mm-30) REVERT: A 29 ASP cc_start: 0.9428 (m-30) cc_final: 0.9087 (p0) REVERT: A 30 LYS cc_start: 0.9260 (mmtp) cc_final: 0.8894 (mmtp) REVERT: A 107 THR cc_start: 0.9496 (OUTLIER) cc_final: 0.9216 (p) REVERT: A 119 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7444 (ttp80) REVERT: A 130 TYR cc_start: 0.9281 (t80) cc_final: 0.9041 (t80) REVERT: A 207 MET cc_start: 0.9130 (tmm) cc_final: 0.8525 (tmm) REVERT: C 15 LEU cc_start: 0.8464 (tp) cc_final: 0.8148 (tp) REVERT: C 19 THR cc_start: 0.8043 (m) cc_final: 0.7785 (p) REVERT: C 28 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8209 (mm-30) REVERT: C 29 ASP cc_start: 0.9470 (m-30) cc_final: 0.9243 (p0) REVERT: C 31 LYS cc_start: 0.9582 (mmtm) cc_final: 0.9044 (tmtt) REVERT: C 45 GLU cc_start: 0.9051 (tp30) cc_final: 0.8726 (tp30) REVERT: C 71 GLU cc_start: 0.9320 (mm-30) cc_final: 0.9094 (mm-30) REVERT: C 107 THR cc_start: 0.9513 (OUTLIER) cc_final: 0.9242 (p) REVERT: C 122 ASN cc_start: 0.9487 (m110) cc_final: 0.9256 (t0) REVERT: C 143 ARG cc_start: 0.9087 (ttp-110) cc_final: 0.8811 (ttm110) REVERT: C 207 MET cc_start: 0.9317 (tmm) cc_final: 0.8706 (tmm) REVERT: E 28 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8167 (mm-30) REVERT: E 29 ASP cc_start: 0.9499 (m-30) cc_final: 0.9298 (p0) REVERT: E 107 THR cc_start: 0.9492 (OUTLIER) cc_final: 0.9260 (p) REVERT: G 28 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8194 (mm-30) REVERT: G 29 ASP cc_start: 0.9437 (m-30) cc_final: 0.9129 (p0) REVERT: G 30 LYS cc_start: 0.9284 (mmtp) cc_final: 0.8919 (mmtp) REVERT: G 32 PHE cc_start: 0.9276 (m-80) cc_final: 0.9023 (m-80) REVERT: G 107 THR cc_start: 0.9495 (OUTLIER) cc_final: 0.9217 (p) REVERT: G 119 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7470 (ttp80) REVERT: G 130 TYR cc_start: 0.9295 (t80) cc_final: 0.9063 (t80) REVERT: G 207 MET cc_start: 0.9141 (tmm) cc_final: 0.8537 (tmm) REVERT: I 28 GLU cc_start: 0.8414 (mm-30) cc_final: 0.8052 (mm-30) REVERT: I 29 ASP cc_start: 0.9510 (m-30) cc_final: 0.9210 (p0) REVERT: I 31 LYS cc_start: 0.9569 (mmtm) cc_final: 0.9044 (tmtt) REVERT: I 45 GLU cc_start: 0.9042 (tp30) cc_final: 0.8722 (tp30) REVERT: I 71 GLU cc_start: 0.9330 (mm-30) cc_final: 0.9103 (mm-30) REVERT: I 107 THR cc_start: 0.9511 (OUTLIER) cc_final: 0.9239 (p) REVERT: I 143 ARG cc_start: 0.9093 (ttp-110) cc_final: 0.8821 (ttm110) REVERT: I 207 MET cc_start: 0.9287 (tmm) cc_final: 0.8666 (tmm) REVERT: K 28 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8182 (mm-30) REVERT: K 29 ASP cc_start: 0.9559 (m-30) cc_final: 0.9194 (p0) REVERT: K 71 GLU cc_start: 0.9167 (mm-30) cc_final: 0.8831 (mm-30) REVERT: K 107 THR cc_start: 0.9491 (OUTLIER) cc_final: 0.9266 (p) REVERT: K 208 ASN cc_start: 0.8935 (p0) cc_final: 0.8707 (p0) REVERT: K 212 GLU cc_start: 0.8775 (pm20) cc_final: 0.8550 (pm20) outliers start: 28 outliers final: 10 residues processed: 234 average time/residue: 0.1626 time to fit residues: 48.8928 Evaluate side-chains 212 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 193 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 119 ARG Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 119 ARG Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 107 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 66 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 108 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 56 optimal weight: 20.0000 chunk 82 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 112 optimal weight: 0.0970 chunk 52 optimal weight: 0.4980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 GLN ** I 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.073380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.056662 restraints weight = 41258.998| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 5.50 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3115 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3114 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.7475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.031 0.996 11683 Z= 1.580 Angle : 2.835 50.926 16032 Z= 0.989 Chirality : 0.254 5.689 1722 Planarity : 0.006 0.145 2040 Dihedral : 21.407 167.557 1992 Min Nonbonded Distance : 1.457 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.92 % Allowed : 11.08 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.24), residues: 1374 helix: 1.40 (0.18), residues: 852 sheet: -0.64 (0.63), residues: 54 loop : 0.49 (0.32), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.002 ARG K 18 TYR 0.029 0.003 TYR I 130 PHE 0.023 0.002 PHE J 4 TRP 0.008 0.001 TRP E 23 HIS 0.001 0.000 HIS A 62 Details of bonding type rmsd covalent geometry : bond 0.03127 (11670) covalent geometry : angle 2.83549 (16032) hydrogen bonds : bond 0.04605 ( 552) hydrogen bonds : angle 4.30333 ( 1656) Misc. bond : bond 0.06466 ( 13) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 214 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8333 (mm-30) REVERT: A 29 ASP cc_start: 0.9401 (m-30) cc_final: 0.9140 (p0) REVERT: A 30 LYS cc_start: 0.9268 (mmtp) cc_final: 0.8912 (mmtp) REVERT: A 97 ASP cc_start: 0.9218 (OUTLIER) cc_final: 0.8019 (p0) REVERT: A 107 THR cc_start: 0.9540 (OUTLIER) cc_final: 0.9303 (p) REVERT: A 119 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7660 (ttp80) REVERT: A 130 TYR cc_start: 0.9281 (t80) cc_final: 0.9051 (t80) REVERT: C 28 GLU cc_start: 0.8389 (mm-30) cc_final: 0.7962 (mm-30) REVERT: C 29 ASP cc_start: 0.9454 (m-30) cc_final: 0.9250 (p0) REVERT: C 31 LYS cc_start: 0.9581 (mmtm) cc_final: 0.9087 (tmtt) REVERT: C 45 GLU cc_start: 0.9081 (tp30) cc_final: 0.8657 (tp30) REVERT: C 71 GLU cc_start: 0.9350 (mm-30) cc_final: 0.9078 (mm-30) REVERT: C 107 THR cc_start: 0.9543 (OUTLIER) cc_final: 0.9330 (p) REVERT: E 28 GLU cc_start: 0.8367 (mm-30) cc_final: 0.7534 (mm-30) REVERT: E 45 GLU cc_start: 0.8911 (tp30) cc_final: 0.8063 (tp30) REVERT: E 61 ASP cc_start: 0.8922 (m-30) cc_final: 0.8612 (p0) REVERT: E 71 GLU cc_start: 0.9185 (mm-30) cc_final: 0.8856 (mm-30) REVERT: E 107 THR cc_start: 0.9582 (OUTLIER) cc_final: 0.9367 (p) REVERT: E 207 MET cc_start: 0.9042 (tmm) cc_final: 0.8599 (tmm) REVERT: E 213 GLU cc_start: 0.9430 (mt-10) cc_final: 0.9203 (pt0) REVERT: G 28 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8280 (mm-30) REVERT: G 29 ASP cc_start: 0.9406 (m-30) cc_final: 0.9136 (p0) REVERT: G 30 LYS cc_start: 0.9312 (mmtp) cc_final: 0.8897 (mmtp) REVERT: G 97 ASP cc_start: 0.9234 (OUTLIER) cc_final: 0.8041 (p0) REVERT: G 107 THR cc_start: 0.9537 (OUTLIER) cc_final: 0.9300 (p) REVERT: G 119 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7665 (ttp80) REVERT: G 130 TYR cc_start: 0.9291 (t80) cc_final: 0.9071 (t80) REVERT: I 25 LYS cc_start: 0.9004 (mtmm) cc_final: 0.8589 (mttp) REVERT: I 28 GLU cc_start: 0.8372 (mm-30) cc_final: 0.8021 (mm-30) REVERT: I 29 ASP cc_start: 0.9493 (m-30) cc_final: 0.9210 (p0) REVERT: I 31 LYS cc_start: 0.9590 (mmtm) cc_final: 0.9067 (tmtt) REVERT: I 45 GLU cc_start: 0.9072 (tp30) cc_final: 0.8348 (tp30) REVERT: I 71 GLU cc_start: 0.9351 (mm-30) cc_final: 0.9083 (mm-30) REVERT: I 107 THR cc_start: 0.9541 (OUTLIER) cc_final: 0.9330 (p) REVERT: K 25 LYS cc_start: 0.8977 (ptpp) cc_final: 0.8591 (ptpp) REVERT: K 28 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8066 (mm-30) REVERT: K 29 ASP cc_start: 0.9577 (m-30) cc_final: 0.9232 (p0) REVERT: K 45 GLU cc_start: 0.8922 (tp30) cc_final: 0.8062 (tp30) REVERT: K 71 GLU cc_start: 0.9178 (mm-30) cc_final: 0.8842 (mm-30) REVERT: K 107 THR cc_start: 0.9563 (OUTLIER) cc_final: 0.9353 (p) outliers start: 23 outliers final: 8 residues processed: 234 average time/residue: 0.1508 time to fit residues: 45.6859 Evaluate side-chains 202 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 184 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 119 ARG Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 25 LYS Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 119 ARG Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 107 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 chunk 133 optimal weight: 0.8980 chunk 128 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 137 optimal weight: 0.5980 chunk 129 optimal weight: 8.9990 chunk 32 optimal weight: 20.0000 chunk 103 optimal weight: 5.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 HIS C 12 HIS ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 HIS ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 ASN ** I 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 12 HIS ** K 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 193 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.072543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.055712 restraints weight = 39343.097| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 5.33 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3145 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.7840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.029 1.014 11683 Z= 1.464 Angle : 2.785 48.024 16032 Z= 0.978 Chirality : 0.253 5.492 1722 Planarity : 0.008 0.276 2040 Dihedral : 21.748 174.827 1992 Min Nonbonded Distance : 1.701 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.17 % Allowed : 12.42 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 aren not related in a simple way. whole: 1.62 (0.24), residues: 1374 helix: 1.57 (0.18), residues: 852 sheet: -0.56 (0.65), residues: 54 loop : 0.55 (0.33), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.035 0.002 ARG A 18 TYR 0.032 0.003 TYR I 50 PHE 0.012 0.001 PHE K 32 TRP 0.009 0.001 TRP I 23 HIS 0.003 0.001 HIS C 62 Details of bonding type rmsd covalent geometry : bond 0.02915 (11670) covalent geometry : angle 2.78467 (16032) hydrogen bonds : bond 0.04425 ( 552) hydrogen bonds : angle 4.40437 ( 1656) Misc. bond : bond 0.05863 ( 13) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 205 time to evaluate : 0.479 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: A 28 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8443 (mm-30) REVERT: A 30 LYS cc_start: 0.9286 (mmtp) cc_final: 0.8920 (mmtp) REVERT: A 97 ASP cc_start: 0.9232 (OUTLIER) cc_final: 0.8054 (p0) REVERT: A 107 THR cc_start: 0.9543 (OUTLIER) cc_final: 0.9312 (p) REVERT: A 119 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7574 (ttp80) REVERT: A 207 MET cc_start: 0.8809 (tmm) cc_final: 0.8459 (tmm) REVERT: C 28 GLU cc_start: 0.8324 (mm-30) cc_final: 0.7912 (mm-30) REVERT: C 29 ASP cc_start: 0.9480 (m-30) cc_final: 0.9229 (p0) REVERT: C 31 LYS cc_start: 0.9603 (mmtm) cc_final: 0.9120 (tmtt) REVERT: C 45 GLU cc_start: 0.9026 (tp30) cc_final: 0.8477 (tp30) REVERT: C 71 GLU cc_start: 0.9269 (mm-30) cc_final: 0.8950 (mm-30) REVERT: C 107 THR cc_start: 0.9539 (OUTLIER) cc_final: 0.9328 (p) REVERT: D 4 PHE cc_start: 0.8010 (p90) cc_final: 0.7638 (p90) REVERT: D 7 GLN cc_start: 0.8979 (tt0) cc_final: 0.8702 (tp40) REVERT: E 45 GLU cc_start: 0.8840 (tp30) cc_final: 0.8326 (mm-30) REVERT: E 71 GLU cc_start: 0.9188 (mm-30) cc_final: 0.8879 (mm-30) REVERT: E 107 THR cc_start: 0.9591 (OUTLIER) cc_final: 0.9371 (p) REVERT: E 193 ASN cc_start: 0.8729 (OUTLIER) cc_final: 0.8489 (t0) REVERT: E 208 ASN cc_start: 0.9037 (p0) cc_final: 0.8618 (p0) REVERT: G 97 ASP cc_start: 0.9228 (OUTLIER) cc_final: 0.8042 (p0) REVERT: G 107 THR cc_start: 0.9545 (OUTLIER) cc_final: 0.9313 (p) REVERT: G 119 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7593 (ttp80) REVERT: G 207 MET cc_start: 0.8801 (tmm) cc_final: 0.8459 (tmm) REVERT: I 25 LYS cc_start: 0.9014 (mtmm) cc_final: 0.8575 (mttp) REVERT: I 28 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8045 (mm-30) REVERT: I 29 ASP cc_start: 0.9472 (m-30) cc_final: 0.9210 (p0) REVERT: I 31 LYS cc_start: 0.9584 (mmtm) cc_final: 0.9084 (tmtt) REVERT: I 45 GLU cc_start: 0.9028 (tp30) cc_final: 0.8493 (tp30) REVERT: I 71 GLU cc_start: 0.9283 (mm-30) cc_final: 0.8967 (mm-30) REVERT: I 107 THR cc_start: 0.9553 (OUTLIER) cc_final: 0.9339 (p) REVERT: K 25 LYS cc_start: 0.9165 (OUTLIER) cc_final: 0.8798 (ptpp) REVERT: K 28 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8155 (mm-30) REVERT: K 29 ASP cc_start: 0.9551 (m-30) cc_final: 0.9278 (p0) REVERT: K 45 GLU cc_start: 0.8861 (tp30) cc_final: 0.8317 (tp30) REVERT: K 71 GLU cc_start: 0.9205 (mm-30) cc_final: 0.8901 (mm-30) REVERT: K 107 THR cc_start: 0.9588 (OUTLIER) cc_final: 0.9370 (p) REVERT: K 193 ASN cc_start: 0.8730 (OUTLIER) cc_final: 0.8493 (t0) outliers start: 26 outliers final: 9 residues processed: 225 average time/residue: 0.1594 time to fit residues: 46.3064 Evaluate side-chains 212 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 190 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 119 ARG Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 145 TYR Chi-restraints excluded: chain E residue 193 ASN Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 119 ARG Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 145 TYR Chi-restraints excluded: chain K residue 25 LYS Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 145 TYR Chi-restraints excluded: chain K residue 193 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 63 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 116 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 131 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 12 HIS G 162 GLN ** I 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.070418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.053589 restraints weight = 39257.625| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 5.41 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3045 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3045 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.8124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.028 1.001 11683 Z= 1.420 Angle : 2.651 48.528 16032 Z= 0.938 Chirality : 0.237 5.149 1722 Planarity : 0.010 0.269 2040 Dihedral : 22.166 168.943 1992 Min Nonbonded Distance : 1.647 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.17 % Allowed : 13.58 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 aren not related in a simple way. whole: 1.48 (0.24), residues: 1374 helix: 1.50 (0.18), residues: 858 sheet: -0.62 (0.66), residues: 54 loop : 0.36 (0.33), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.001 ARG K 18 TYR 0.031 0.003 TYR G 130 PHE 0.026 0.002 PHE J 4 TRP 0.009 0.001 TRP E 23 HIS 0.003 0.001 HIS C 62 Details of bonding type rmsd covalent geometry : bond 0.02833 (11670) covalent geometry : angle 2.65093 (16032) hydrogen bonds : bond 0.04595 ( 552) hydrogen bonds : angle 4.45801 ( 1656) Misc. bond : bond 0.05670 ( 13) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 195 time to evaluate : 0.487 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: A 30 LYS cc_start: 0.9091 (mmtp) cc_final: 0.8875 (mmtm) REVERT: A 97 ASP cc_start: 0.9220 (OUTLIER) cc_final: 0.8067 (p0) REVERT: A 107 THR cc_start: 0.9533 (OUTLIER) cc_final: 0.9269 (p) REVERT: A 119 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7580 (ttp80) REVERT: C 28 GLU cc_start: 0.8382 (mm-30) cc_final: 0.7967 (mm-30) REVERT: C 29 ASP cc_start: 0.9517 (m-30) cc_final: 0.9307 (p0) REVERT: C 31 LYS cc_start: 0.9611 (mmtm) cc_final: 0.9100 (tmtt) REVERT: C 45 GLU cc_start: 0.9020 (tp30) cc_final: 0.8443 (tp30) REVERT: C 71 GLU cc_start: 0.9316 (mm-30) cc_final: 0.9046 (mm-30) REVERT: C 107 THR cc_start: 0.9559 (OUTLIER) cc_final: 0.9349 (p) REVERT: C 208 ASN cc_start: 0.9204 (p0) cc_final: 0.8947 (p0) REVERT: D 4 PHE cc_start: 0.8022 (p90) cc_final: 0.7649 (p90) REVERT: D 7 GLN cc_start: 0.8992 (tt0) cc_final: 0.8771 (tp40) REVERT: E 32 PHE cc_start: 0.9241 (m-80) cc_final: 0.8779 (m-80) REVERT: E 45 GLU cc_start: 0.8847 (tp30) cc_final: 0.7864 (tp30) REVERT: E 71 GLU cc_start: 0.9197 (mm-30) cc_final: 0.8869 (mm-30) REVERT: E 107 THR cc_start: 0.9588 (OUTLIER) cc_final: 0.9377 (p) REVERT: E 175 GLU cc_start: 0.8862 (tp30) cc_final: 0.8560 (tp30) REVERT: E 200 LEU cc_start: 0.9356 (mt) cc_final: 0.8849 (mt) REVERT: E 208 ASN cc_start: 0.8989 (p0) cc_final: 0.8658 (p0) REVERT: G 45 GLU cc_start: 0.8817 (tp30) cc_final: 0.8497 (tp30) REVERT: G 71 GLU cc_start: 0.9349 (mm-30) cc_final: 0.9137 (mm-30) REVERT: G 97 ASP cc_start: 0.9224 (OUTLIER) cc_final: 0.8069 (p0) REVERT: G 107 THR cc_start: 0.9546 (OUTLIER) cc_final: 0.9285 (p) REVERT: G 119 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.7589 (ttp80) REVERT: I 28 GLU cc_start: 0.8419 (mm-30) cc_final: 0.8090 (mm-30) REVERT: I 29 ASP cc_start: 0.9507 (m-30) cc_final: 0.9260 (p0) REVERT: I 31 LYS cc_start: 0.9593 (mmtm) cc_final: 0.9092 (tmtt) REVERT: I 45 GLU cc_start: 0.9045 (tp30) cc_final: 0.8469 (tp30) REVERT: I 71 GLU cc_start: 0.9342 (mm-30) cc_final: 0.9059 (mm-30) REVERT: I 107 THR cc_start: 0.9554 (OUTLIER) cc_final: 0.9340 (p) REVERT: K 28 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8108 (mm-30) REVERT: K 29 ASP cc_start: 0.9551 (m-30) cc_final: 0.9291 (p0) REVERT: K 45 GLU cc_start: 0.8827 (tp30) cc_final: 0.7853 (tp30) REVERT: K 66 MET cc_start: 0.9006 (mmt) cc_final: 0.8785 (mmt) REVERT: K 71 GLU cc_start: 0.9214 (mm-30) cc_final: 0.8892 (mm-30) REVERT: K 107 THR cc_start: 0.9585 (OUTLIER) cc_final: 0.9375 (p) outliers start: 26 outliers final: 9 residues processed: 211 average time/residue: 0.1589 time to fit residues: 43.0341 Evaluate side-chains 189 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 170 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 119 ARG Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain E residue 16 SER Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 145 TYR Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 119 ARG Chi-restraints excluded: chain G residue 145 TYR Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 145 TYR Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 145 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 40 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 58 optimal weight: 7.9990 chunk 131 optimal weight: 10.0000 chunk 105 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 32 optimal weight: 0.0060 chunk 3 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 60 optimal weight: 8.9990 chunk 21 optimal weight: 7.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN C 149 ASN ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 GLN I 149 ASN ** K 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.076582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.060112 restraints weight = 39402.157| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 5.70 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.8326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.028 0.946 11683 Z= 1.387 Angle : 2.559 47.734 16032 Z= 0.918 Chirality : 0.210 4.745 1722 Planarity : 0.009 0.273 2040 Dihedral : 21.883 171.476 1992 Min Nonbonded Distance : 1.719 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.58 % Allowed : 14.58 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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 aren not related in a simple way. whole: 1.37 (0.24), residues: 1374 helix: 1.39 (0.18), residues: 852 sheet: -0.59 (0.63), residues: 54 loop : 0.39 (0.32), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.051 0.002 ARG K 18 TYR 0.031 0.003 TYR I 50 PHE 0.018 0.002 PHE A 32 TRP 0.012 0.001 TRP E 23 HIS 0.003 0.000 HIS A 62 Details of bonding type rmsd covalent geometry : bond 0.02763 (11670) covalent geometry : angle 2.55941 (16032) hydrogen bonds : bond 0.04690 ( 552) hydrogen bonds : angle 4.69302 ( 1656) Misc. bond : bond 0.05380 ( 13) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 192 time to evaluate : 0.288 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: A 45 GLU cc_start: 0.8797 (tp30) cc_final: 0.8499 (tp30) REVERT: A 107 THR cc_start: 0.9526 (OUTLIER) cc_final: 0.9323 (p) REVERT: A 119 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7522 (ttp80) REVERT: C 28 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8046 (mm-30) REVERT: C 29 ASP cc_start: 0.9495 (m-30) cc_final: 0.9277 (p0) REVERT: C 31 LYS cc_start: 0.9610 (mmtm) cc_final: 0.9074 (tmtt) REVERT: C 45 GLU cc_start: 0.9041 (tp30) cc_final: 0.8498 (mm-30) REVERT: C 71 GLU cc_start: 0.9412 (mm-30) cc_final: 0.9078 (mm-30) REVERT: C 107 THR cc_start: 0.9535 (OUTLIER) cc_final: 0.9331 (p) REVERT: D 4 PHE cc_start: 0.7956 (p90) cc_final: 0.7502 (p90) REVERT: E 28 GLU cc_start: 0.8777 (mm-30) cc_final: 0.7802 (mm-30) REVERT: E 31 LYS cc_start: 0.9380 (mmtm) cc_final: 0.8963 (tmtt) REVERT: E 45 GLU cc_start: 0.8795 (tp30) cc_final: 0.7774 (tp30) REVERT: E 61 ASP cc_start: 0.8934 (m-30) cc_final: 0.8413 (p0) REVERT: E 71 GLU cc_start: 0.9279 (mm-30) cc_final: 0.8990 (mm-30) REVERT: E 107 THR cc_start: 0.9581 (OUTLIER) cc_final: 0.9380 (p) REVERT: E 208 ASN cc_start: 0.9063 (p0) cc_final: 0.8820 (p0) REVERT: G 28 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8479 (mm-30) REVERT: G 29 ASP cc_start: 0.9454 (m-30) cc_final: 0.9175 (p0) REVERT: G 45 GLU cc_start: 0.8781 (tp30) cc_final: 0.8481 (tp30) REVERT: G 119 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7528 (ttp80) REVERT: G 175 GLU cc_start: 0.9044 (tp30) cc_final: 0.8819 (tp30) REVERT: I 28 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8102 (mm-30) REVERT: I 29 ASP cc_start: 0.9538 (m-30) cc_final: 0.9274 (p0) REVERT: I 31 LYS cc_start: 0.9596 (mmtm) cc_final: 0.9051 (tmtt) REVERT: I 45 GLU cc_start: 0.9031 (tp30) cc_final: 0.8398 (tp30) REVERT: I 55 MET cc_start: 0.9286 (mtp) cc_final: 0.9080 (ttm) REVERT: I 71 GLU cc_start: 0.9392 (mm-30) cc_final: 0.9069 (mm-30) REVERT: I 208 ASN cc_start: 0.9323 (p0) cc_final: 0.9047 (p0) REVERT: K 28 GLU cc_start: 0.8422 (mm-30) cc_final: 0.8089 (mm-30) REVERT: K 29 ASP cc_start: 0.9581 (m-30) cc_final: 0.9267 (p0) REVERT: K 45 GLU cc_start: 0.8817 (tp30) cc_final: 0.7790 (tp30) REVERT: K 71 GLU cc_start: 0.9291 (mm-30) cc_final: 0.9005 (mm-30) REVERT: K 107 THR cc_start: 0.9574 (OUTLIER) cc_final: 0.9371 (p) REVERT: K 175 GLU cc_start: 0.9011 (tp30) cc_final: 0.8735 (tp30) outliers start: 19 outliers final: 7 residues processed: 204 average time/residue: 0.1509 time to fit residues: 39.5218 Evaluate side-chains 195 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 182 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 119 ARG Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 145 TYR Chi-restraints excluded: chain G residue 119 ARG Chi-restraints excluded: chain G residue 145 TYR Chi-restraints excluded: chain I residue 145 TYR Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 145 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 3 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 24 optimal weight: 0.1980 chunk 105 optimal weight: 0.9980 chunk 116 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 40 optimal weight: 7.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 GLN ** K 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.074206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.057606 restraints weight = 39573.934| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 5.42 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.8614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.027 0.928 11683 Z= 1.352 Angle : 2.451 46.537 16032 Z= 0.890 Chirality : 0.198 4.165 1722 Planarity : 0.010 0.231 2040 Dihedral : 20.895 156.282 1992 Min Nonbonded Distance : 1.599 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.42 % Allowed : 15.42 % Favored : 83.17 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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 aren not related in a simple way. whole: 1.35 (0.24), residues: 1374 helix: 1.42 (0.18), residues: 852 sheet: -0.47 (0.63), residues: 54 loop : 0.26 (0.32), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.002 ARG C 18 TYR 0.030 0.003 TYR G 130 PHE 0.022 0.002 PHE J 4 TRP 0.015 0.001 TRP E 23 HIS 0.004 0.001 HIS A 62 Details of bonding type rmsd covalent geometry : bond 0.02697 (11670) covalent geometry : angle 2.45085 (16032) hydrogen bonds : bond 0.04701 ( 552) hydrogen bonds : angle 4.72813 ( 1656) Misc. bond : bond 0.04789 ( 13) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 194 time to evaluate : 0.397 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: A 45 GLU cc_start: 0.8719 (tp30) cc_final: 0.8387 (tp30) REVERT: A 97 ASP cc_start: 0.9210 (OUTLIER) cc_final: 0.8053 (p0) REVERT: A 107 THR cc_start: 0.9565 (OUTLIER) cc_final: 0.9341 (p) REVERT: A 119 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7506 (ttp80) REVERT: C 31 LYS cc_start: 0.9617 (mmtm) cc_final: 0.9084 (tmtt) REVERT: C 45 GLU cc_start: 0.9001 (tp30) cc_final: 0.8519 (mm-30) REVERT: C 71 GLU cc_start: 0.9277 (mm-30) cc_final: 0.8955 (mm-30) REVERT: E 31 LYS cc_start: 0.9386 (mmtm) cc_final: 0.8975 (tmtt) REVERT: E 45 GLU cc_start: 0.8795 (tp30) cc_final: 0.8017 (tp30) REVERT: E 71 GLU cc_start: 0.9200 (mm-30) cc_final: 0.8968 (mm-30) REVERT: E 177 THR cc_start: 0.7671 (p) cc_final: 0.7454 (p) REVERT: E 208 ASN cc_start: 0.8938 (p0) cc_final: 0.8701 (p0) REVERT: G 15 LEU cc_start: 0.9003 (tp) cc_final: 0.8761 (tt) REVERT: G 28 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8491 (mm-30) REVERT: G 29 ASP cc_start: 0.9435 (m-30) cc_final: 0.9151 (p0) REVERT: G 45 GLU cc_start: 0.8681 (tp30) cc_final: 0.8382 (tp30) REVERT: G 50 TYR cc_start: 0.8541 (t80) cc_final: 0.7803 (t80) REVERT: G 97 ASP cc_start: 0.9224 (OUTLIER) cc_final: 0.8065 (p0) REVERT: G 119 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7639 (ttp80) REVERT: G 175 GLU cc_start: 0.8981 (tp30) cc_final: 0.8781 (tp30) REVERT: G 200 LEU cc_start: 0.9584 (tp) cc_final: 0.9085 (mt) REVERT: I 28 GLU cc_start: 0.8412 (mm-30) cc_final: 0.8081 (mm-30) REVERT: I 29 ASP cc_start: 0.9496 (m-30) cc_final: 0.9240 (p0) REVERT: I 31 LYS cc_start: 0.9583 (mmtm) cc_final: 0.9046 (tmtt) REVERT: I 45 GLU cc_start: 0.8990 (tp30) cc_final: 0.8416 (tp30) REVERT: I 71 GLU cc_start: 0.9258 (mm-30) cc_final: 0.8943 (mm-30) REVERT: I 203 LYS cc_start: 0.9260 (pttt) cc_final: 0.9035 (tptp) REVERT: K 28 GLU cc_start: 0.8322 (mm-30) cc_final: 0.7523 (mm-30) REVERT: K 29 ASP cc_start: 0.9516 (m-30) cc_final: 0.9210 (p0) REVERT: K 45 GLU cc_start: 0.8888 (tp30) cc_final: 0.8395 (tp30) REVERT: K 71 GLU cc_start: 0.9185 (mm-30) cc_final: 0.8905 (mm-30) REVERT: K 175 GLU cc_start: 0.8993 (tp30) cc_final: 0.8701 (tp30) REVERT: K 185 MET cc_start: 0.9546 (mtm) cc_final: 0.9322 (mtp) outliers start: 17 outliers final: 6 residues processed: 205 average time/residue: 0.1563 time to fit residues: 41.2525 Evaluate side-chains 194 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 183 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 119 ARG Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 119 ARG Chi-restraints excluded: chain G residue 145 TYR Chi-restraints excluded: chain I residue 145 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 11 optimal weight: 0.9990 chunk 54 optimal weight: 0.0270 chunk 57 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 127 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 83 optimal weight: 10.0000 overall best weight: 2.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 HIS A 162 GLN C 193 ASN ** D 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 GLN I 193 ASN K 62 HIS ** K 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.073428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.056775 restraints weight = 39500.805| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 5.50 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.8825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.026 0.897 11683 Z= 1.326 Angle : 2.374 47.091 16032 Z= 0.868 Chirality : 0.189 3.851 1722 Planarity : 0.012 0.350 2040 Dihedral : 21.220 153.461 1992 Min Nonbonded Distance : 1.608 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.33 % Allowed : 16.42 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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 aren not related in a simple way. whole: 1.46 (0.24), residues: 1374 helix: 1.44 (0.18), residues: 852 sheet: -0.34 (0.64), residues: 54 loop : 0.43 (0.33), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.071 0.002 ARG C 18 TYR 0.030 0.003 TYR G 130 PHE 0.020 0.002 PHE A 32 TRP 0.028 0.001 TRP C 23 HIS 0.003 0.001 HIS K 62 Details of bonding type rmsd covalent geometry : bond 0.02647 (11670) covalent geometry : angle 2.37363 (16032) hydrogen bonds : bond 0.04906 ( 552) hydrogen bonds : angle 4.81740 ( 1656) Misc. bond : bond 0.04528 ( 13) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2223.18 seconds wall clock time: 39 minutes 4.41 seconds (2344.41 seconds total)