Starting phenix.real_space_refine on Mon Jun 9 23:00:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cnv_45761/06_2025/9cnv_45761.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cnv_45761/06_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_45761/06_2025/9cnv_45761.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cnv_45761/06_2025/9cnv_45761.map" model { file = "/net/cci-nas-00/data/ceres_data/9cnv_45761/06_2025/9cnv_45761.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cnv_45761/06_2025/9cnv_45761.cif" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: D, F, H, J, L, C, E, G, I, K 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: 4.21, per 1000 atoms: 0.37 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: 5.32 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.04 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: 2.95 Time building geometry restraints manager: 5.81 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: 0.09 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' } 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: 0.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 27.000 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.900 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.041 0.005 TRP E 116 HIS 0.007 0.004 HIS E 62 PHE 0.019 0.004 PHE F 9 TYR 0.017 0.004 TYR K 118 ARG 0.012 0.004 ARG G 18 Details of bonding type rmsd hydrogen bonds : bond 0.26073 ( 552) hydrogen bonds : angle 7.75655 ( 1656) covalent geometry : bond 0.01407 (11670) covalent geometry : angle 1.88437 (16032) 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 : 1.279 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: 0.2972 time to fit residues: 130.9917 Evaluate side-chains 223 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 20.0000 chunk 104 optimal weight: 0.1980 chunk 58 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 chunk 55 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 chunk 125 optimal weight: 7.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- 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 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 162 GLN C 4 GLN C 94 GLN C 128 ASN E 94 GLN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 4 GLN G 94 GLN ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 GLN I 4 GLN I 94 GLN I 128 ASN K 94 GLN ** K 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.081177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.065570 restraints weight = 39094.220| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 5.29 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3302 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3302 r_free = 0.3302 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 72 | |-----------------------------------------------------------------------------| r_final: 0.3294 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.4604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.072 1.787 11683 Z= 3.622 Angle : 5.096 80.706 16032 Z= 1.732 Chirality : 0.292 3.782 1722 Planarity : 0.014 0.443 2040 Dihedral : 21.720 137.472 1992 Min Nonbonded Distance : 1.179 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.67 % Allowed : 13.08 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.22), residues: 1374 helix: 1.04 (0.17), residues: 846 sheet: -2.06 (0.45), residues: 54 loop : -0.82 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 184 HIS 0.003 0.001 HIS A 84 PHE 0.023 0.002 PHE J 4 TYR 0.034 0.003 TYR A 130 ARG 0.042 0.002 ARG K 18 Details of bonding type rmsd hydrogen bonds : bond 0.07185 ( 552) hydrogen bonds : angle 5.04271 ( 1656) covalent geometry : bond 0.07185 (11670) covalent geometry : angle 5.09560 (16032) Misc. bond : bond 0.08559 ( 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 269 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 249 time to evaluate : 1.338 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: A 15 LEU cc_start: 0.8383 (tp) cc_final: 0.7941 (tt) REVERT: A 45 GLU cc_start: 0.9020 (tp30) cc_final: 0.8819 (tp30) REVERT: A 119 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7509 (ttp80) REVERT: A 152 ASP cc_start: 0.9284 (m-30) cc_final: 0.9062 (m-30) REVERT: C 15 LEU cc_start: 0.8119 (tp) cc_final: 0.7753 (tt) REVERT: C 25 LYS cc_start: 0.9164 (mtpt) cc_final: 0.8951 (mttm) REVERT: C 31 LYS cc_start: 0.9517 (mmtm) cc_final: 0.9045 (tmtt) REVERT: C 213 GLU cc_start: 0.9333 (mt-10) cc_final: 0.8834 (pt0) REVERT: E 15 LEU cc_start: 0.8117 (tp) cc_final: 0.7675 (tt) REVERT: E 32 PHE cc_start: 0.8961 (m-80) cc_final: 0.8724 (m-80) REVERT: F 2 VAL cc_start: 0.9404 (m) cc_final: 0.9190 (p) REVERT: G 15 LEU cc_start: 0.8385 (tp) cc_final: 0.7948 (tt) REVERT: G 119 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7529 (ttp80) REVERT: G 152 ASP cc_start: 0.9282 (m-30) cc_final: 0.9057 (m-30) REVERT: I 15 LEU cc_start: 0.8135 (tp) cc_final: 0.7740 (tt) REVERT: I 31 LYS cc_start: 0.9513 (mmtm) cc_final: 0.9041 (tmtt) REVERT: I 122 ASN cc_start: 0.9367 (m110) cc_final: 0.9159 (t0) REVERT: J 2 VAL cc_start: 0.9523 (t) cc_final: 0.9318 (p) REVERT: K 15 LEU cc_start: 0.8175 (tp) cc_final: 0.7750 (tt) REVERT: K 32 PHE cc_start: 0.8971 (m-80) cc_final: 0.8725 (m-80) REVERT: L 2 VAL cc_start: 0.9400 (m) cc_final: 0.9185 (p) outliers start: 20 outliers final: 8 residues processed: 261 average time/residue: 0.3075 time to fit residues: 105.5042 Evaluate side-chains 217 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 207 time to evaluate : 1.217 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 109 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 37 optimal weight: 0.0980 chunk 40 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 67 optimal weight: 9.9990 chunk 83 optimal weight: 5.9990 chunk 78 optimal weight: 0.0970 chunk 68 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 122 ASN E 128 ASN E 135 GLN G 128 ASN ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 4 GLN I 135 GLN K 122 ASN K 128 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.079269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.062913 restraints weight = 44143.452| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 5.79 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3273 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 72 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3271 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.5793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 1.340 11683 Z= 2.538 Angle : 4.155 87.833 16032 Z= 1.421 Chirality : 0.264 4.207 1722 Planarity : 0.013 0.404 2040 Dihedral : 21.963 139.254 1992 Min Nonbonded Distance : 1.488 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.92 % Allowed : 13.08 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.23), residues: 1374 helix: 1.32 (0.18), residues: 840 sheet: -1.00 (0.58), residues: 54 loop : -0.44 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 80 HIS 0.002 0.001 HIS A 62 PHE 0.010 0.001 PHE D 9 TYR 0.038 0.003 TYR I 130 ARG 0.054 0.002 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.05723 ( 552) hydrogen bonds : angle 4.56686 ( 1656) covalent geometry : bond 0.05045 (11670) covalent geometry : angle 4.15544 (16032) Misc. bond : bond 0.09077 ( 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 264 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 241 time to evaluate : 1.344 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: A 15 LEU cc_start: 0.8424 (tp) cc_final: 0.8011 (tp) REVERT: A 29 ASP cc_start: 0.9453 (m-30) cc_final: 0.9249 (m-30) REVERT: A 30 LYS cc_start: 0.9408 (mmtp) cc_final: 0.9202 (mmtm) REVERT: A 97 ASP cc_start: 0.9254 (t0) cc_final: 0.8129 (p0) REVERT: A 119 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7631 (ttp-110) REVERT: A 130 TYR cc_start: 0.9036 (t80) cc_final: 0.8600 (t80) REVERT: A 143 ARG cc_start: 0.9207 (ttm110) cc_final: 0.8517 (ttp-110) REVERT: A 178 ASP cc_start: 0.8981 (t0) cc_final: 0.8667 (t0) REVERT: A 207 MET cc_start: 0.9316 (tmm) cc_final: 0.8738 (tmm) REVERT: A 208 ASN cc_start: 0.8878 (p0) cc_final: 0.8360 (p0) REVERT: C 28 GLU cc_start: 0.8315 (mm-30) cc_final: 0.8078 (mm-30) REVERT: C 29 ASP cc_start: 0.9458 (m-30) cc_final: 0.9098 (p0) REVERT: C 31 LYS cc_start: 0.9533 (mmtm) cc_final: 0.9113 (tmtt) REVERT: C 45 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8694 (tp30) REVERT: C 130 TYR cc_start: 0.9106 (t80) cc_final: 0.8799 (t80) REVERT: C 207 MET cc_start: 0.9413 (tmm) cc_final: 0.8952 (tmm) REVERT: C 208 ASN cc_start: 0.9031 (p0) cc_final: 0.8571 (p0) REVERT: E 15 LEU cc_start: 0.8253 (tp) cc_final: 0.7995 (tp) REVERT: E 25 LYS cc_start: 0.9062 (mtpt) cc_final: 0.8741 (ptpp) REVERT: E 30 LYS cc_start: 0.9337 (mmtp) cc_final: 0.9089 (mmtm) REVERT: E 45 GLU cc_start: 0.9003 (tp30) cc_final: 0.8513 (mm-30) REVERT: E 207 MET cc_start: 0.9305 (tmm) cc_final: 0.8833 (tmm) REVERT: E 208 ASN cc_start: 0.8988 (p0) cc_final: 0.8584 (p0) REVERT: F 2 VAL cc_start: 0.9398 (m) cc_final: 0.9126 (p) REVERT: G 15 LEU cc_start: 0.8365 (tp) cc_final: 0.8023 (tp) REVERT: G 28 GLU cc_start: 0.8226 (mm-30) cc_final: 0.8006 (mm-30) REVERT: G 29 ASP cc_start: 0.9461 (m-30) cc_final: 0.9016 (p0) REVERT: G 45 GLU cc_start: 0.8986 (tp30) cc_final: 0.8466 (mm-30) REVERT: G 97 ASP cc_start: 0.9251 (t0) cc_final: 0.8127 (p0) REVERT: G 119 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7646 (ttp-110) REVERT: G 143 ARG cc_start: 0.9108 (ttm110) cc_final: 0.8329 (ttm110) REVERT: G 178 ASP cc_start: 0.8945 (t0) cc_final: 0.8639 (t0) REVERT: G 207 MET cc_start: 0.9332 (tmm) cc_final: 0.8769 (tmm) REVERT: G 208 ASN cc_start: 0.8897 (p0) cc_final: 0.8380 (p0) REVERT: I 19 THR cc_start: 0.8660 (m) cc_final: 0.8403 (p) REVERT: I 31 LYS cc_start: 0.9536 (mmtm) cc_final: 0.9118 (tmtt) REVERT: I 45 GLU cc_start: 0.8939 (mm-30) cc_final: 0.8729 (tp30) REVERT: I 130 TYR cc_start: 0.9104 (t80) cc_final: 0.8803 (t80) REVERT: I 207 MET cc_start: 0.9405 (tmm) cc_final: 0.8947 (tmm) REVERT: I 208 ASN cc_start: 0.9028 (p0) cc_final: 0.8547 (p0) REVERT: I 212 GLU cc_start: 0.8971 (pm20) cc_final: 0.8515 (pm20) REVERT: I 214 MET cc_start: 0.9444 (mtm) cc_final: 0.9244 (mtm) REVERT: J 4 PHE cc_start: 0.7613 (p90) cc_final: 0.7371 (p90) REVERT: K 29 ASP cc_start: 0.9520 (m-30) cc_final: 0.9305 (m-30) REVERT: K 30 LYS cc_start: 0.9321 (mmtp) cc_final: 0.9070 (mmtm) REVERT: K 45 GLU cc_start: 0.9013 (tp30) cc_final: 0.8526 (mm-30) REVERT: K 207 MET cc_start: 0.9303 (tmm) cc_final: 0.8826 (tmm) REVERT: K 208 ASN cc_start: 0.8982 (p0) cc_final: 0.8586 (p0) REVERT: L 2 VAL cc_start: 0.9405 (m) cc_final: 0.9131 (p) outliers start: 23 outliers final: 6 residues processed: 258 average time/residue: 0.3480 time to fit residues: 115.7055 Evaluate side-chains 231 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 223 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ARG Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain G residue 119 ARG Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 25 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 50 optimal weight: 4.9990 chunk 117 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 111 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 82 optimal weight: 0.8980 chunk 125 optimal weight: 20.0000 chunk 137 optimal weight: 10.0000 chunk 122 optimal weight: 9.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN C 135 GLN G 121 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.076753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.060704 restraints weight = 39177.461| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 5.43 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3216 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3216 r_free = 0.3216 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3215 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.6454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.038 0.996 11683 Z= 1.906 Angle : 3.530 60.630 16032 Z= 1.215 Chirality : 0.255 3.758 1722 Planarity : 0.009 0.277 2040 Dihedral : 22.075 145.339 1992 Min Nonbonded Distance : 1.526 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.17 % Allowed : 12.33 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.23), residues: 1374 helix: 1.28 (0.18), residues: 858 sheet: -0.79 (0.62), residues: 54 loop : -0.13 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 80 HIS 0.001 0.000 HIS A 12 PHE 0.020 0.002 PHE L 4 TYR 0.028 0.003 TYR C 130 ARG 0.034 0.001 ARG K 18 Details of bonding type rmsd hydrogen bonds : bond 0.05087 ( 552) hydrogen bonds : angle 4.45223 ( 1656) covalent geometry : bond 0.03768 (11670) covalent geometry : angle 3.52961 (16032) Misc. bond : bond 0.09101 ( 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 268 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 242 time to evaluate : 1.330 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: 0.8172 (mm-30) cc_final: 0.7869 (mm-30) REVERT: A 29 ASP cc_start: 0.9454 (m-30) cc_final: 0.9072 (p0) REVERT: A 30 LYS cc_start: 0.9398 (mmtp) cc_final: 0.9007 (mmtp) REVERT: A 71 GLU cc_start: 0.9179 (mm-30) cc_final: 0.8897 (mm-30) REVERT: A 107 THR cc_start: 0.9502 (OUTLIER) cc_final: 0.9271 (p) REVERT: A 119 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7640 (ttp80) REVERT: A 130 TYR cc_start: 0.9147 (t80) cc_final: 0.8766 (t80) REVERT: A 207 MET cc_start: 0.9241 (tmm) cc_final: 0.8721 (tmm) REVERT: A 214 MET cc_start: 0.9463 (mtm) cc_final: 0.9192 (mtm) REVERT: C 28 GLU cc_start: 0.8345 (mm-30) cc_final: 0.7990 (mm-30) REVERT: C 29 ASP cc_start: 0.9452 (m-30) cc_final: 0.9148 (p0) REVERT: C 31 LYS cc_start: 0.9559 (mmtm) cc_final: 0.9069 (tmtt) REVERT: C 45 GLU cc_start: 0.8858 (mm-30) cc_final: 0.8584 (tp30) REVERT: C 107 THR cc_start: 0.9546 (OUTLIER) cc_final: 0.9330 (p) REVERT: C 207 MET cc_start: 0.9330 (tmm) cc_final: 0.8832 (tmm) REVERT: C 212 GLU cc_start: 0.8919 (pm20) cc_final: 0.8710 (pm20) REVERT: C 213 GLU cc_start: 0.9335 (OUTLIER) cc_final: 0.8960 (mp0) REVERT: E 28 GLU cc_start: 0.8309 (mm-30) cc_final: 0.8046 (mm-30) REVERT: E 29 ASP cc_start: 0.9518 (m-30) cc_final: 0.9227 (p0) REVERT: E 45 GLU cc_start: 0.9012 (tp30) cc_final: 0.8620 (mm-30) REVERT: E 71 GLU cc_start: 0.9102 (mm-30) cc_final: 0.8800 (mm-30) REVERT: E 107 THR cc_start: 0.9489 (OUTLIER) cc_final: 0.9239 (p) REVERT: E 152 ASP cc_start: 0.9135 (m-30) cc_final: 0.8856 (p0) REVERT: E 207 MET cc_start: 0.9256 (tmm) cc_final: 0.8741 (tmm) REVERT: E 213 GLU cc_start: 0.9395 (mt-10) cc_final: 0.9195 (pt0) REVERT: F 2 VAL cc_start: 0.9429 (m) cc_final: 0.9163 (p) REVERT: G 15 LEU cc_start: 0.8459 (tp) cc_final: 0.8241 (tp) REVERT: G 28 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7913 (mm-30) REVERT: G 29 ASP cc_start: 0.9463 (m-30) cc_final: 0.9076 (p0) REVERT: G 107 THR cc_start: 0.9491 (OUTLIER) cc_final: 0.9258 (p) REVERT: G 119 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7653 (ttp80) REVERT: G 130 TYR cc_start: 0.9124 (t80) cc_final: 0.8655 (t80) REVERT: G 207 MET cc_start: 0.9247 (tmm) cc_final: 0.8731 (tmm) REVERT: G 214 MET cc_start: 0.9458 (mtm) cc_final: 0.9172 (mtm) REVERT: I 25 LYS cc_start: 0.8719 (mtmm) cc_final: 0.8167 (mttm) REVERT: I 30 LYS cc_start: 0.9252 (mmtp) cc_final: 0.8940 (mmtm) REVERT: I 31 LYS cc_start: 0.9543 (mmtm) cc_final: 0.9078 (tmtt) REVERT: I 45 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8598 (tp30) REVERT: I 107 THR cc_start: 0.9524 (OUTLIER) cc_final: 0.9289 (p) REVERT: I 207 MET cc_start: 0.9330 (tmm) cc_final: 0.9061 (tmm) REVERT: I 208 ASN cc_start: 0.8950 (p0) cc_final: 0.8469 (p0) REVERT: K 25 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8507 (mtmm) REVERT: K 30 LYS cc_start: 0.9299 (mmtp) cc_final: 0.9094 (mmtm) REVERT: K 45 GLU cc_start: 0.9014 (tp30) cc_final: 0.8630 (mm-30) REVERT: K 71 GLU cc_start: 0.9097 (mm-30) cc_final: 0.8797 (mm-30) REVERT: K 107 THR cc_start: 0.9477 (OUTLIER) cc_final: 0.9225 (p) REVERT: K 207 MET cc_start: 0.9259 (tmm) cc_final: 0.8736 (tmm) REVERT: L 2 VAL cc_start: 0.9428 (m) cc_final: 0.9157 (p) outliers start: 26 outliers final: 5 residues processed: 259 average time/residue: 0.3410 time to fit residues: 113.1305 Evaluate side-chains 230 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 215 time to evaluate : 1.196 ------------------------------------------------------------------------------- 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 213 GLU 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 I residue 16 SER Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 25 LYS 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 4 optimal weight: 5.9990 chunk 124 optimal weight: 30.0000 chunk 17 optimal weight: 8.9990 chunk 12 optimal weight: 0.9980 chunk 110 optimal weight: 9.9990 chunk 87 optimal weight: 6.9990 chunk 116 optimal weight: 8.9990 chunk 114 optimal weight: 8.9990 chunk 55 optimal weight: 30.0000 chunk 23 optimal weight: 20.0000 chunk 1 optimal weight: 8.9990 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 HIS ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 12 HIS G 12 HIS G 135 GLN ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 12 HIS K 135 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.070259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.053415 restraints weight = 39399.079| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 5.36 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.7365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.033 1.046 11683 Z= 1.644 Angle : 3.049 47.994 16032 Z= 1.064 Chirality : 0.269 5.804 1722 Planarity : 0.008 0.167 2040 Dihedral : 22.010 171.641 1992 Min Nonbonded Distance : 1.634 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.83 % Allowed : 11.25 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.24), residues: 1374 helix: 1.49 (0.18), residues: 852 sheet: -0.89 (0.67), residues: 54 loop : 0.06 (0.32), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 23 HIS 0.004 0.001 HIS G 62 PHE 0.018 0.002 PHE D 4 TYR 0.030 0.003 TYR C 130 ARG 0.046 0.002 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.05162 ( 552) hydrogen bonds : angle 4.60689 ( 1656) covalent geometry : bond 0.03272 (11670) covalent geometry : angle 3.04946 (16032) Misc. bond : bond 0.07491 ( 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 238 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 216 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8314 (mm-30) cc_final: 0.8046 (mm-30) REVERT: A 29 ASP cc_start: 0.9428 (m-30) cc_final: 0.9096 (p0) REVERT: A 30 LYS cc_start: 0.9294 (mmtp) cc_final: 0.8885 (mmtp) REVERT: A 45 GLU cc_start: 0.8927 (tp30) cc_final: 0.8581 (tp30) REVERT: A 107 THR cc_start: 0.9528 (OUTLIER) cc_final: 0.9255 (p) REVERT: A 175 GLU cc_start: 0.9045 (tp30) cc_final: 0.8679 (tp30) REVERT: A 208 ASN cc_start: 0.9073 (p0) cc_final: 0.8749 (p0) REVERT: C 31 LYS cc_start: 0.9611 (mmtm) cc_final: 0.9089 (tmtt) REVERT: C 107 THR cc_start: 0.9550 (OUTLIER) cc_final: 0.9283 (p) REVERT: E 25 LYS cc_start: 0.9232 (ptpp) cc_final: 0.8986 (ptpp) REVERT: E 28 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8145 (mm-30) REVERT: E 45 GLU cc_start: 0.8864 (tp30) cc_final: 0.8349 (tp30) REVERT: E 58 CYS cc_start: 0.9066 (m) cc_final: 0.8826 (t) REVERT: E 71 GLU cc_start: 0.9122 (mm-30) cc_final: 0.8797 (mm-30) REVERT: E 107 THR cc_start: 0.9500 (OUTLIER) cc_final: 0.9227 (p) REVERT: E 207 MET cc_start: 0.9300 (tmm) cc_final: 0.9018 (tpt) REVERT: E 208 ASN cc_start: 0.9003 (p0) cc_final: 0.8683 (p0) REVERT: E 213 GLU cc_start: 0.9377 (mt-10) cc_final: 0.9125 (pt0) REVERT: F 2 VAL cc_start: 0.9511 (m) cc_final: 0.9274 (p) REVERT: G 25 LYS cc_start: 0.9317 (mtpt) cc_final: 0.9008 (mtmm) REVERT: G 107 THR cc_start: 0.9528 (OUTLIER) cc_final: 0.9255 (p) REVERT: G 130 TYR cc_start: 0.9368 (t80) cc_final: 0.9102 (t80) REVERT: G 208 ASN cc_start: 0.9048 (p0) cc_final: 0.8749 (p0) REVERT: I 31 LYS cc_start: 0.9609 (mmtm) cc_final: 0.9015 (tmtt) REVERT: I 107 THR cc_start: 0.9530 (OUTLIER) cc_final: 0.9261 (p) REVERT: I 214 MET cc_start: 0.9406 (mtt) cc_final: 0.9180 (mtt) REVERT: K 25 LYS cc_start: 0.8819 (mttm) cc_final: 0.8568 (ptpp) REVERT: K 28 GLU cc_start: 0.8419 (mm-30) cc_final: 0.8176 (mm-30) REVERT: K 29 ASP cc_start: 0.9512 (m-30) cc_final: 0.9170 (p0) REVERT: K 30 LYS cc_start: 0.9139 (mmtp) cc_final: 0.8713 (mmtm) REVERT: K 58 CYS cc_start: 0.9023 (m) cc_final: 0.8805 (t) REVERT: K 107 THR cc_start: 0.9492 (OUTLIER) cc_final: 0.9219 (p) REVERT: K 207 MET cc_start: 0.9301 (tmm) cc_final: 0.9013 (tpt) REVERT: K 208 ASN cc_start: 0.9052 (p0) cc_final: 0.8697 (p0) REVERT: L 2 VAL cc_start: 0.9508 (m) cc_final: 0.9274 (p) outliers start: 22 outliers final: 7 residues processed: 232 average time/residue: 0.3300 time to fit residues: 99.4093 Evaluate side-chains 205 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 192 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain C residue 107 THR 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 107 THR Chi-restraints excluded: chain G residue 141 CYS Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 213 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 6 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 132 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 45 optimal weight: 9.9990 chunk 134 optimal weight: 8.9990 chunk 90 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 HIS C 149 ASN E 62 HIS I 149 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.070396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.053839 restraints weight = 39206.905| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 5.34 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3051 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3051 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.7774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.030 1.034 11683 Z= 1.513 Angle : 2.889 48.648 16032 Z= 1.012 Chirality : 0.244 4.760 1722 Planarity : 0.009 0.207 2040 Dihedral : 22.304 164.976 1992 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.17 % Allowed : 11.00 % Favored : 86.83 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.24), residues: 1374 helix: 1.43 (0.18), residues: 852 sheet: -0.67 (0.69), residues: 54 loop : 0.13 (0.32), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 23 HIS 0.002 0.001 HIS C 12 PHE 0.022 0.002 PHE L 4 TYR 0.033 0.003 TYR A 130 ARG 0.030 0.001 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.04821 ( 552) hydrogen bonds : angle 4.43394 ( 1656) covalent geometry : bond 0.03014 (11670) covalent geometry : angle 2.88939 (16032) Misc. bond : bond 0.06180 ( 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 242 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 216 time to evaluate : 1.323 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: A 28 GLU cc_start: 0.8452 (mm-30) cc_final: 0.8214 (mm-30) REVERT: A 29 ASP cc_start: 0.9382 (m-30) cc_final: 0.9151 (p0) REVERT: A 30 LYS cc_start: 0.9210 (mmtp) cc_final: 0.8862 (mmtp) REVERT: A 32 PHE cc_start: 0.9435 (m-80) cc_final: 0.9115 (m-80) REVERT: A 97 ASP cc_start: 0.9228 (OUTLIER) cc_final: 0.8067 (p0) REVERT: A 107 THR cc_start: 0.9510 (OUTLIER) cc_final: 0.9254 (p) REVERT: A 119 ARG cc_start: 0.8470 (ttp80) cc_final: 0.8180 (ttp-110) REVERT: A 175 GLU cc_start: 0.9109 (tp30) cc_final: 0.8758 (tp30) REVERT: A 207 MET cc_start: 0.9544 (tpt) cc_final: 0.8972 (tmm) REVERT: C 15 LEU cc_start: 0.8803 (tp) cc_final: 0.8557 (tp) REVERT: C 25 LYS cc_start: 0.8983 (ptpp) cc_final: 0.8749 (ptpp) REVERT: C 28 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8155 (mm-30) REVERT: C 29 ASP cc_start: 0.9461 (m-30) cc_final: 0.9240 (p0) REVERT: C 31 LYS cc_start: 0.9594 (mmtm) cc_final: 0.9165 (tmtt) REVERT: C 45 GLU cc_start: 0.8858 (tp30) cc_final: 0.8433 (mm-30) REVERT: C 107 THR cc_start: 0.9542 (OUTLIER) cc_final: 0.9317 (p) REVERT: E 25 LYS cc_start: 0.9324 (ptpp) cc_final: 0.8933 (ptpp) REVERT: E 28 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8497 (mm-30) REVERT: E 31 LYS cc_start: 0.9574 (mmmt) cc_final: 0.9133 (tmtt) REVERT: E 107 THR cc_start: 0.9505 (OUTLIER) cc_final: 0.9275 (p) REVERT: F 2 VAL cc_start: 0.9508 (m) cc_final: 0.9291 (p) REVERT: G 29 ASP cc_start: 0.9296 (m-30) cc_final: 0.9019 (p0) REVERT: G 31 LYS cc_start: 0.9201 (pptt) cc_final: 0.8901 (tmtt) REVERT: G 45 GLU cc_start: 0.8815 (tp30) cc_final: 0.8208 (tp30) REVERT: G 97 ASP cc_start: 0.9234 (OUTLIER) cc_final: 0.8072 (p0) REVERT: G 107 THR cc_start: 0.9531 (OUTLIER) cc_final: 0.9290 (p) REVERT: G 119 ARG cc_start: 0.8450 (ttp80) cc_final: 0.8162 (ttp-110) REVERT: G 130 TYR cc_start: 0.9301 (t80) cc_final: 0.9044 (t80) REVERT: G 175 GLU cc_start: 0.9096 (tp30) cc_final: 0.8840 (tp30) REVERT: G 207 MET cc_start: 0.9548 (tpt) cc_final: 0.8981 (tmm) REVERT: G 213 GLU cc_start: 0.9391 (mt-10) cc_final: 0.9160 (pt0) REVERT: I 30 LYS cc_start: 0.9025 (mmtm) cc_final: 0.8747 (mmtm) REVERT: I 31 LYS cc_start: 0.9604 (mmtm) cc_final: 0.8909 (tmtt) REVERT: I 45 GLU cc_start: 0.8864 (tp30) cc_final: 0.8431 (mm-30) REVERT: I 71 GLU cc_start: 0.9329 (mm-30) cc_final: 0.9014 (mm-30) REVERT: I 107 THR cc_start: 0.9545 (OUTLIER) cc_final: 0.9313 (p) REVERT: I 214 MET cc_start: 0.9366 (mtt) cc_final: 0.9117 (mtt) REVERT: K 29 ASP cc_start: 0.9488 (m-30) cc_final: 0.9073 (p0) REVERT: K 107 THR cc_start: 0.9523 (OUTLIER) cc_final: 0.9297 (p) REVERT: L 2 VAL cc_start: 0.9507 (m) cc_final: 0.9293 (p) outliers start: 26 outliers final: 13 residues processed: 232 average time/residue: 0.3220 time to fit residues: 96.9615 Evaluate side-chains 212 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 191 time to evaluate : 1.296 ------------------------------------------------------------------------------- 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 145 TYR Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 213 GLU 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 59 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 141 CYS Chi-restraints excluded: chain G residue 145 TYR Chi-restraints excluded: chain I residue 18 ARG Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 145 TYR Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 213 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 126 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 70 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 9 optimal weight: 20.0000 chunk 15 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN C 162 GLN ** D 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 GLN G 162 GLN I 162 GLN ** J 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 162 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.070268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.053251 restraints weight = 42971.700| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 5.67 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3059 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.8075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.028 0.992 11683 Z= 1.427 Angle : 2.697 47.817 16032 Z= 0.950 Chirality : 0.226 4.234 1722 Planarity : 0.008 0.197 2040 Dihedral : 22.366 175.382 1992 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.08 % Allowed : 11.83 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.24), residues: 1374 helix: 1.55 (0.18), residues: 852 sheet: -0.61 (0.68), residues: 54 loop : 0.24 (0.32), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 23 HIS 0.003 0.001 HIS C 62 PHE 0.021 0.002 PHE D 4 TYR 0.029 0.003 TYR A 130 ARG 0.043 0.001 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.04826 ( 552) hydrogen bonds : angle 4.48554 ( 1656) covalent geometry : bond 0.02842 (11670) covalent geometry : angle 2.69653 (16032) Misc. bond : bond 0.05727 ( 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 254 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 217 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8386 (mm-30) REVERT: A 45 GLU cc_start: 0.8879 (tp30) cc_final: 0.8594 (tp30) REVERT: A 71 GLU cc_start: 0.9258 (mm-30) cc_final: 0.8923 (mm-30) REVERT: A 97 ASP cc_start: 0.9266 (OUTLIER) cc_final: 0.8145 (p0) REVERT: A 107 THR cc_start: 0.9524 (OUTLIER) cc_final: 0.9274 (p) REVERT: A 143 ARG cc_start: 0.8954 (ttp80) cc_final: 0.8673 (ttp-110) REVERT: A 162 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.8318 (pp30) REVERT: A 175 GLU cc_start: 0.9106 (tp30) cc_final: 0.8862 (tp30) REVERT: A 207 MET cc_start: 0.9453 (tpt) cc_final: 0.9150 (tpt) REVERT: A 208 ASN cc_start: 0.9189 (p0) cc_final: 0.8800 (p0) REVERT: C 30 LYS cc_start: 0.9154 (mmtm) cc_final: 0.8767 (mmmm) REVERT: C 31 LYS cc_start: 0.9530 (mmtm) cc_final: 0.9166 (tmtt) REVERT: C 45 GLU cc_start: 0.8827 (tp30) cc_final: 0.8552 (tp30) REVERT: C 107 THR cc_start: 0.9557 (OUTLIER) cc_final: 0.9349 (p) REVERT: C 143 ARG cc_start: 0.9029 (ttm110) cc_final: 0.8817 (ttm110) REVERT: C 207 MET cc_start: 0.9317 (tmm) cc_final: 0.8955 (tmm) REVERT: C 208 ASN cc_start: 0.9166 (p0) cc_final: 0.8901 (p0) REVERT: D 4 PHE cc_start: 0.8039 (p90) cc_final: 0.7765 (p90) REVERT: E 29 ASP cc_start: 0.8523 (p0) cc_final: 0.8226 (p0) REVERT: E 31 LYS cc_start: 0.9515 (mmmt) cc_final: 0.9117 (tmtt) REVERT: E 107 THR cc_start: 0.9534 (OUTLIER) cc_final: 0.9304 (p) REVERT: E 208 ASN cc_start: 0.8903 (p0) cc_final: 0.8680 (p0) REVERT: E 214 MET cc_start: 0.9347 (mtm) cc_final: 0.9076 (mpp) REVERT: F 2 VAL cc_start: 0.9520 (m) cc_final: 0.9314 (p) REVERT: F 4 PHE cc_start: 0.7954 (p90) cc_final: 0.7677 (p90) REVERT: G 25 LYS cc_start: 0.9318 (mtpt) cc_final: 0.9054 (mttm) REVERT: G 28 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8489 (mm-30) REVERT: G 45 GLU cc_start: 0.8808 (tp30) cc_final: 0.8246 (tp30) REVERT: G 97 ASP cc_start: 0.9258 (OUTLIER) cc_final: 0.8130 (p0) REVERT: G 107 THR cc_start: 0.9528 (OUTLIER) cc_final: 0.9298 (p) REVERT: G 162 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8307 (pp30) REVERT: G 175 GLU cc_start: 0.9084 (tp30) cc_final: 0.8751 (tp30) REVERT: G 207 MET cc_start: 0.9468 (tpt) cc_final: 0.9141 (tpt) REVERT: G 208 ASN cc_start: 0.9159 (p0) cc_final: 0.8703 (p0) REVERT: I 31 LYS cc_start: 0.9634 (mmtm) cc_final: 0.8900 (tmtt) REVERT: I 45 GLU cc_start: 0.8834 (tp30) cc_final: 0.8554 (tp30) REVERT: I 50 TYR cc_start: 0.8649 (t80) cc_final: 0.8306 (t80) REVERT: I 107 THR cc_start: 0.9558 (OUTLIER) cc_final: 0.9345 (p) REVERT: I 143 ARG cc_start: 0.9026 (ttm110) cc_final: 0.8815 (ttm110) REVERT: I 207 MET cc_start: 0.9537 (tpt) cc_final: 0.9237 (tmm) REVERT: I 208 ASN cc_start: 0.9270 (p0) cc_final: 0.8898 (p0) REVERT: J 4 PHE cc_start: 0.7992 (p90) cc_final: 0.7709 (p90) REVERT: K 29 ASP cc_start: 0.9478 (m-30) cc_final: 0.9227 (p0) REVERT: K 31 LYS cc_start: 0.9442 (mmtm) cc_final: 0.8914 (tmtt) REVERT: K 71 GLU cc_start: 0.9194 (mm-30) cc_final: 0.8894 (mm-30) REVERT: K 107 THR cc_start: 0.9538 (OUTLIER) cc_final: 0.9311 (p) REVERT: K 208 ASN cc_start: 0.8887 (p0) cc_final: 0.8658 (p0) REVERT: L 4 PHE cc_start: 0.7925 (p90) cc_final: 0.7648 (p90) outliers start: 37 outliers final: 17 residues processed: 235 average time/residue: 0.3211 time to fit residues: 98.5052 Evaluate side-chains 232 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 205 time to evaluate : 1.091 ------------------------------------------------------------------------------- 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 145 TYR Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain C residue 163 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 141 CYS Chi-restraints excluded: chain E residue 145 TYR Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 162 GLN Chi-restraints excluded: chain G residue 163 SER Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 145 TYR Chi-restraints excluded: chain I residue 163 SER 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 163 SER Chi-restraints excluded: chain K residue 213 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 5.9990 chunk 133 optimal weight: 9.9990 chunk 81 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 107 optimal weight: 8.9990 chunk 96 optimal weight: 9.9990 chunk 5 optimal weight: 0.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.068898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.052326 restraints weight = 40409.144| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 5.42 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.8356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.028 0.958 11683 Z= 1.403 Angle : 2.614 48.529 16032 Z= 0.935 Chirality : 0.209 4.006 1722 Planarity : 0.013 0.443 2040 Dihedral : 22.462 158.777 1992 Min Nonbonded Distance : 1.641 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.17 % Allowed : 12.17 % Favored : 85.67 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.24), residues: 1374 helix: 1.50 (0.18), residues: 852 sheet: -0.71 (0.66), residues: 54 loop : 0.20 (0.32), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 23 HIS 0.003 0.001 HIS C 62 PHE 0.013 0.002 PHE K 40 TYR 0.035 0.003 TYR C 50 ARG 0.027 0.001 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.04929 ( 552) hydrogen bonds : angle 4.54900 ( 1656) covalent geometry : bond 0.02797 (11670) covalent geometry : angle 2.61440 (16032) Misc. bond : bond 0.05393 ( 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 235 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 209 time to evaluate : 1.343 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: A 30 LYS cc_start: 0.9103 (mmtp) cc_final: 0.8895 (mmtm) REVERT: A 45 GLU cc_start: 0.8816 (tp30) cc_final: 0.8495 (tp30) REVERT: A 97 ASP cc_start: 0.9253 (OUTLIER) cc_final: 0.8136 (p0) REVERT: A 107 THR cc_start: 0.9524 (OUTLIER) cc_final: 0.9281 (p) REVERT: A 143 ARG cc_start: 0.8994 (ttp80) cc_final: 0.8762 (ttm110) REVERT: A 175 GLU cc_start: 0.9108 (tp30) cc_final: 0.8790 (tp30) REVERT: A 207 MET cc_start: 0.9457 (tpt) cc_final: 0.9130 (tpt) REVERT: A 208 ASN cc_start: 0.9227 (p0) cc_final: 0.8789 (p0) REVERT: A 214 MET cc_start: 0.9336 (mtt) cc_final: 0.9062 (mpp) REVERT: C 25 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8935 (ptpp) REVERT: C 30 LYS cc_start: 0.9124 (mmtm) cc_final: 0.8638 (mmmm) REVERT: C 31 LYS cc_start: 0.9536 (mmtm) cc_final: 0.9177 (tmtt) REVERT: C 45 GLU cc_start: 0.8805 (tp30) cc_final: 0.8474 (tp30) REVERT: C 107 THR cc_start: 0.9566 (OUTLIER) cc_final: 0.9347 (p) REVERT: C 207 MET cc_start: 0.9293 (tmm) cc_final: 0.8896 (tmm) REVERT: C 208 ASN cc_start: 0.9206 (p0) cc_final: 0.8884 (p0) REVERT: E 31 LYS cc_start: 0.9580 (mmmt) cc_final: 0.9081 (tmtt) REVERT: E 45 GLU cc_start: 0.8756 (tp30) cc_final: 0.8170 (tp30) REVERT: E 107 THR cc_start: 0.9530 (OUTLIER) cc_final: 0.9298 (p) REVERT: E 193 ASN cc_start: 0.8803 (OUTLIER) cc_final: 0.8422 (t0) REVERT: F 2 VAL cc_start: 0.9541 (OUTLIER) cc_final: 0.9340 (p) REVERT: G 30 LYS cc_start: 0.9040 (mmtp) cc_final: 0.8839 (mmtm) REVERT: G 45 GLU cc_start: 0.8774 (tp30) cc_final: 0.8214 (tp30) REVERT: G 71 GLU cc_start: 0.9234 (mm-30) cc_final: 0.8920 (mm-30) REVERT: G 97 ASP cc_start: 0.9255 (OUTLIER) cc_final: 0.8135 (p0) REVERT: G 107 THR cc_start: 0.9522 (OUTLIER) cc_final: 0.9300 (p) REVERT: G 143 ARG cc_start: 0.8930 (ttp80) cc_final: 0.8614 (ttp-110) REVERT: G 144 MET cc_start: 0.8402 (mmp) cc_final: 0.8161 (mmt) REVERT: G 175 GLU cc_start: 0.9083 (tp30) cc_final: 0.8764 (tp30) REVERT: G 207 MET cc_start: 0.9494 (tpt) cc_final: 0.9171 (tpt) REVERT: G 208 ASN cc_start: 0.9192 (p0) cc_final: 0.8739 (p0) REVERT: G 213 GLU cc_start: 0.9583 (OUTLIER) cc_final: 0.8655 (mp0) REVERT: I 31 LYS cc_start: 0.9641 (mmtm) cc_final: 0.8865 (tmtt) REVERT: I 45 GLU cc_start: 0.8802 (tp30) cc_final: 0.8472 (tp30) REVERT: I 107 THR cc_start: 0.9566 (OUTLIER) cc_final: 0.9344 (p) REVERT: K 15 LEU cc_start: 0.8563 (tp) cc_final: 0.8261 (tp) REVERT: K 25 LYS cc_start: 0.9040 (ptpp) cc_final: 0.8685 (ptpp) REVERT: K 28 GLU cc_start: 0.8434 (mm-30) cc_final: 0.8161 (mm-30) REVERT: K 31 LYS cc_start: 0.9391 (mmtm) cc_final: 0.9009 (tmtt) REVERT: K 71 GLU cc_start: 0.9180 (mm-30) cc_final: 0.8859 (mm-30) REVERT: K 107 THR cc_start: 0.9537 (OUTLIER) cc_final: 0.9306 (p) outliers start: 26 outliers final: 11 residues processed: 226 average time/residue: 0.3339 time to fit residues: 98.1873 Evaluate side-chains 201 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 178 time to evaluate : 1.170 ------------------------------------------------------------------------------- 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 145 TYR Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain C residue 25 LYS 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 30 LYS 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 F residue 2 VAL Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 163 SER Chi-restraints excluded: chain G residue 213 GLU Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 145 TYR Chi-restraints excluded: chain K residue 59 VAL Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 213 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 87 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 5 optimal weight: 0.1980 chunk 112 optimal weight: 3.9990 chunk 77 optimal weight: 20.0000 chunk 107 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 83 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 130 optimal weight: 0.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN E 162 GLN ** E 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.070209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.053480 restraints weight = 40044.412| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 5.42 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3091 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3090 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.8501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.028 0.949 11683 Z= 1.381 Angle : 2.597 49.725 16032 Z= 0.933 Chirality : 0.198 3.819 1722 Planarity : 0.010 0.327 2040 Dihedral : 22.627 173.620 1992 Min Nonbonded Distance : 1.686 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.00 % Allowed : 14.33 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.24), residues: 1374 helix: 1.51 (0.18), residues: 852 sheet: -0.80 (0.64), residues: 54 loop : 0.12 (0.32), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 23 HIS 0.002 0.001 HIS I 62 PHE 0.023 0.002 PHE F 4 TYR 0.031 0.003 TYR G 130 ARG 0.035 0.002 ARG C 18 Details of bonding type rmsd hydrogen bonds : bond 0.05182 ( 552) hydrogen bonds : angle 4.54916 ( 1656) covalent geometry : bond 0.02752 (11670) covalent geometry : angle 2.59747 (16032) Misc. bond : bond 0.05160 ( 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 217 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8734 (tp30) cc_final: 0.8431 (tp30) REVERT: A 97 ASP cc_start: 0.9237 (OUTLIER) cc_final: 0.8120 (p0) REVERT: A 107 THR cc_start: 0.9522 (OUTLIER) cc_final: 0.9287 (p) REVERT: A 143 ARG cc_start: 0.8979 (ttp80) cc_final: 0.8746 (ttp-110) REVERT: A 203 LYS cc_start: 0.9264 (pttt) cc_final: 0.9051 (tptp) REVERT: A 207 MET cc_start: 0.9432 (tpt) cc_final: 0.9072 (tpt) REVERT: A 208 ASN cc_start: 0.9207 (p0) cc_final: 0.8729 (p0) REVERT: A 214 MET cc_start: 0.9270 (mtt) cc_final: 0.8878 (mtt) REVERT: C 25 LYS cc_start: 0.9152 (ptpp) cc_final: 0.8649 (ptpp) REVERT: C 28 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8237 (mm-30) REVERT: C 29 ASP cc_start: 0.9461 (m-30) cc_final: 0.9210 (p0) REVERT: C 31 LYS cc_start: 0.9514 (mmtm) cc_final: 0.9179 (tmtt) REVERT: C 45 GLU cc_start: 0.8730 (tp30) cc_final: 0.8381 (tp30) REVERT: C 107 THR cc_start: 0.9542 (OUTLIER) cc_final: 0.9326 (p) REVERT: C 207 MET cc_start: 0.9310 (tmm) cc_final: 0.9001 (tmm) REVERT: C 208 ASN cc_start: 0.9206 (p0) cc_final: 0.8914 (p0) REVERT: D 4 PHE cc_start: 0.8094 (p90) cc_final: 0.7778 (p90) REVERT: D 7 GLN cc_start: 0.8685 (tp40) cc_final: 0.8444 (tp40) REVERT: E 31 LYS cc_start: 0.9589 (mmmt) cc_final: 0.9073 (tmtt) REVERT: E 45 GLU cc_start: 0.8699 (tp30) cc_final: 0.8146 (tp30) REVERT: E 107 THR cc_start: 0.9535 (OUTLIER) cc_final: 0.9327 (p) REVERT: E 175 GLU cc_start: 0.9008 (tp30) cc_final: 0.8738 (tp30) REVERT: E 193 ASN cc_start: 0.8993 (OUTLIER) cc_final: 0.8501 (t0) REVERT: E 213 GLU cc_start: 0.9554 (mt-10) cc_final: 0.8991 (mt-10) REVERT: E 214 MET cc_start: 0.9369 (mtm) cc_final: 0.9109 (mpp) REVERT: F 4 PHE cc_start: 0.7995 (p90) cc_final: 0.7694 (p90) REVERT: G 97 ASP cc_start: 0.9242 (OUTLIER) cc_final: 0.8127 (p0) REVERT: G 107 THR cc_start: 0.9534 (OUTLIER) cc_final: 0.9302 (p) REVERT: G 143 ARG cc_start: 0.8921 (ttp80) cc_final: 0.8573 (ttp-110) REVERT: G 144 MET cc_start: 0.8393 (mmp) cc_final: 0.8156 (mmt) REVERT: G 207 MET cc_start: 0.9463 (tpt) cc_final: 0.9113 (tpt) REVERT: G 208 ASN cc_start: 0.9195 (p0) cc_final: 0.8788 (p0) REVERT: G 214 MET cc_start: 0.9099 (mtt) cc_final: 0.8857 (mpp) REVERT: I 30 LYS cc_start: 0.9184 (mmtt) cc_final: 0.8706 (mmmm) REVERT: I 31 LYS cc_start: 0.9626 (mmtm) cc_final: 0.8835 (tmtt) REVERT: I 45 GLU cc_start: 0.8763 (tp30) cc_final: 0.8434 (tp30) REVERT: I 107 THR cc_start: 0.9560 (OUTLIER) cc_final: 0.9345 (p) REVERT: J 4 PHE cc_start: 0.8049 (p90) cc_final: 0.7717 (p90) REVERT: J 7 GLN cc_start: 0.8656 (tp40) cc_final: 0.8403 (tp40) REVERT: K 25 LYS cc_start: 0.8929 (ptpp) cc_final: 0.8610 (ptpp) REVERT: K 30 LYS cc_start: 0.9246 (mmtp) cc_final: 0.8998 (mmtt) REVERT: K 31 LYS cc_start: 0.9457 (mmtm) cc_final: 0.8885 (tmtt) REVERT: K 71 GLU cc_start: 0.9177 (mm-30) cc_final: 0.8839 (mm-30) REVERT: K 107 THR cc_start: 0.9567 (OUTLIER) cc_final: 0.9348 (p) REVERT: L 4 PHE cc_start: 0.8007 (p90) cc_final: 0.7662 (p90) outliers start: 24 outliers final: 9 residues processed: 209 average time/residue: 0.3507 time to fit residues: 94.5138 Evaluate side-chains 195 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 177 time to evaluate : 1.375 ------------------------------------------------------------------------------- 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 145 TYR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 145 TYR 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 162 GLN 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 I residue 107 THR Chi-restraints excluded: chain I residue 145 TYR 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 213 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 29 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 68 optimal weight: 9.9990 chunk 100 optimal weight: 0.1980 chunk 39 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 79 optimal weight: 20.0000 chunk 89 optimal weight: 8.9990 overall best weight: 4.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 162 GLN E 162 GLN I 12 HIS I 162 GLN K 162 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.068547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.051992 restraints weight = 40896.022| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 5.33 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3030 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.8779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.027 0.944 11683 Z= 1.368 Angle : 2.546 49.143 16032 Z= 0.925 Chirality : 0.188 3.966 1722 Planarity : 0.010 0.327 2040 Dihedral : 23.184 167.428 1992 Min Nonbonded Distance : 1.718 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.92 % Allowed : 14.67 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.24), residues: 1374 helix: 1.56 (0.18), residues: 852 sheet: -0.87 (0.64), residues: 54 loop : 0.11 (0.33), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 23 HIS 0.004 0.001 HIS C 62 PHE 0.024 0.002 PHE L 4 TYR 0.031 0.003 TYR G 130 ARG 0.025 0.001 ARG C 18 Details of bonding type rmsd hydrogen bonds : bond 0.05010 ( 552) hydrogen bonds : angle 4.66616 ( 1656) covalent geometry : bond 0.02734 (11670) covalent geometry : angle 2.54612 (16032) Misc. bond : bond 0.04862 ( 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 217 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 194 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.8726 (tp30) cc_final: 0.8481 (tp30) REVERT: A 97 ASP cc_start: 0.9261 (OUTLIER) cc_final: 0.8177 (p0) REVERT: A 107 THR cc_start: 0.9545 (OUTLIER) cc_final: 0.9279 (p) REVERT: A 203 LYS cc_start: 0.9282 (pttt) cc_final: 0.9038 (tptp) REVERT: A 207 MET cc_start: 0.9434 (tpt) cc_final: 0.9036 (tpt) REVERT: A 208 ASN cc_start: 0.9229 (p0) cc_final: 0.8729 (p0) REVERT: A 214 MET cc_start: 0.9261 (mtt) cc_final: 0.8854 (mtt) REVERT: C 25 LYS cc_start: 0.9162 (ptpp) cc_final: 0.8914 (ptpp) REVERT: C 30 LYS cc_start: 0.9202 (mmtm) cc_final: 0.8790 (mmmm) REVERT: C 31 LYS cc_start: 0.9486 (mmtm) cc_final: 0.9216 (tmtt) REVERT: C 45 GLU cc_start: 0.8816 (tp30) cc_final: 0.8472 (tp30) REVERT: C 71 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8891 (mm-30) REVERT: C 107 THR cc_start: 0.9554 (OUTLIER) cc_final: 0.9344 (p) REVERT: C 143 ARG cc_start: 0.9088 (ttp-110) cc_final: 0.8865 (ttm110) REVERT: C 200 LEU cc_start: 0.9643 (tp) cc_final: 0.9175 (mt) REVERT: C 203 LYS cc_start: 0.9268 (pttt) cc_final: 0.9027 (tptp) REVERT: C 208 ASN cc_start: 0.9222 (p0) cc_final: 0.8855 (p0) REVERT: D 4 PHE cc_start: 0.8092 (p90) cc_final: 0.7693 (p90) REVERT: D 7 GLN cc_start: 0.8658 (tp40) cc_final: 0.8406 (tp40) REVERT: E 31 LYS cc_start: 0.9594 (mmmt) cc_final: 0.8999 (tmtt) REVERT: E 45 GLU cc_start: 0.8729 (tp30) cc_final: 0.8283 (tp30) REVERT: E 71 GLU cc_start: 0.9195 (mm-30) cc_final: 0.8700 (mm-30) REVERT: E 107 THR cc_start: 0.9522 (OUTLIER) cc_final: 0.9300 (p) REVERT: E 193 ASN cc_start: 0.9055 (OUTLIER) cc_final: 0.8621 (t0) REVERT: E 214 MET cc_start: 0.9379 (mtm) cc_final: 0.9049 (mpp) REVERT: F 4 PHE cc_start: 0.8019 (p90) cc_final: 0.7727 (p90) REVERT: G 97 ASP cc_start: 0.9254 (OUTLIER) cc_final: 0.8164 (p0) REVERT: G 107 THR cc_start: 0.9544 (OUTLIER) cc_final: 0.9268 (p) REVERT: G 143 ARG cc_start: 0.8951 (ttp80) cc_final: 0.8660 (ttm110) REVERT: G 144 MET cc_start: 0.8386 (mmp) cc_final: 0.8142 (mmt) REVERT: G 207 MET cc_start: 0.9441 (tpt) cc_final: 0.9088 (tpt) REVERT: G 208 ASN cc_start: 0.9198 (p0) cc_final: 0.8730 (p0) REVERT: G 214 MET cc_start: 0.9108 (mtt) cc_final: 0.8853 (mpp) REVERT: I 30 LYS cc_start: 0.9129 (mmtt) cc_final: 0.8631 (mmmm) REVERT: I 31 LYS cc_start: 0.9631 (mmtm) cc_final: 0.8867 (tmtt) REVERT: I 107 THR cc_start: 0.9572 (OUTLIER) cc_final: 0.9354 (p) REVERT: I 200 LEU cc_start: 0.9444 (mm) cc_final: 0.8870 (mt) REVERT: I 207 MET cc_start: 0.9503 (tpt) cc_final: 0.9292 (tmm) REVERT: I 208 ASN cc_start: 0.9218 (p0) cc_final: 0.8935 (p0) REVERT: J 4 PHE cc_start: 0.8022 (p90) cc_final: 0.7608 (p90) REVERT: J 7 GLN cc_start: 0.8627 (tp40) cc_final: 0.8357 (tp40) REVERT: K 25 LYS cc_start: 0.8947 (ptpp) cc_final: 0.8675 (ptpt) REVERT: K 29 ASP cc_start: 0.9309 (p0) cc_final: 0.8983 (p0) REVERT: K 30 LYS cc_start: 0.9231 (mmtp) cc_final: 0.8972 (mmtt) REVERT: K 31 LYS cc_start: 0.9467 (mmtm) cc_final: 0.8816 (tmtt) REVERT: K 45 GLU cc_start: 0.8783 (tp30) cc_final: 0.8330 (tp30) REVERT: K 71 GLU cc_start: 0.9179 (mm-30) cc_final: 0.8844 (mm-30) REVERT: K 107 THR cc_start: 0.9554 (OUTLIER) cc_final: 0.9313 (p) REVERT: K 175 GLU cc_start: 0.9033 (tp30) cc_final: 0.8796 (tp30) REVERT: L 4 PHE cc_start: 0.8017 (p90) cc_final: 0.7712 (p90) outliers start: 23 outliers final: 8 residues processed: 210 average time/residue: 0.3320 time to fit residues: 90.5407 Evaluate side-chains 197 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 180 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 107 THR 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 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 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 Chi-restraints excluded: chain K residue 213 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 7 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 100 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 130 optimal weight: 20.0000 chunk 69 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN C 162 GLN G 162 GLN I 162 GLN K 162 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.069270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.052877 restraints weight = 39817.455| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 5.30 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3052 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3051 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.8937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.027 0.936 11683 Z= 1.358 Angle : 2.443 48.596 16032 Z= 0.885 Chirality : 0.186 3.916 1722 Planarity : 0.015 0.448 2040 Dihedral : 22.589 158.969 1992 Min Nonbonded Distance : 1.661 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.83 % Allowed : 15.17 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.24), residues: 1374 helix: 1.51 (0.18), residues: 858 sheet: -0.95 (0.64), residues: 54 loop : 0.25 (0.33), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 23 HIS 0.003 0.001 HIS G 62 PHE 0.022 0.002 PHE L 4 TYR 0.031 0.003 TYR I 50 ARG 0.083 0.002 ARG K 18 Details of bonding type rmsd hydrogen bonds : bond 0.04839 ( 552) hydrogen bonds : angle 4.68914 ( 1656) covalent geometry : bond 0.02716 (11670) covalent geometry : angle 2.44334 (16032) Misc. bond : bond 0.04732 ( 13) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4840.84 seconds wall clock time: 84 minutes 11.15 seconds (5051.15 seconds total)