Starting phenix.real_space_refine on Tue May 13 22:38:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cnv_45761/05_2025/9cnv_45761.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cnv_45761/05_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_45761/05_2025/9cnv_45761.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cnv_45761/05_2025/9cnv_45761.map" model { file = "/net/cci-nas-00/data/ceres_data/9cnv_45761/05_2025/9cnv_45761.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cnv_45761/05_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-5687/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: 4.37, per 1000 atoms: 0.38 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: 5.44 Conformation dependent library (CDL) restraints added in 1.5 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: 1.06 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: 2.93 Time building geometry restraints manager: 5.87 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: 0.380 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: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 27.180 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.200 ------------------------------------------------------------------------------- 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 : 1.312 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: 0.3044 time to fit residues: 133.8026 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 : 1.399 ------------------------------------------------------------------------------- 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 = 0.3663 r_free = 0.3663 target = 0.081210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.065602 restraints weight = 39079.555| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 5.30 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3299 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 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 = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| r_final: 0.3290 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.072 1.794 11683 Z= 3.622 Angle : 5.094 80.672 16032 Z= 1.731 Chirality : 0.291 3.793 1722 Planarity : 0.014 0.443 2040 Dihedral : 21.738 137.771 1992 Min Nonbonded Distance : 1.182 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % 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: 1.05 (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 0.07180 ( 552) hydrogen bonds : angle 5.04117 ( 1656) covalent geometry : bond 0.07184 (11670) covalent geometry : angle 5.09376 (16032) Misc. bond : bond 0.08456 ( 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 : 1.239 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: A 15 LEU cc_start: 0.8383 (tp) cc_final: 0.7941 (tt) REVERT: A 45 GLU cc_start: 0.9018 (tp30) cc_final: 0.8817 (tp30) REVERT: A 119 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7541 (ttp80) REVERT: A 152 ASP cc_start: 0.9286 (m-30) cc_final: 0.9063 (m-30) REVERT: C 15 LEU cc_start: 0.8121 (tp) cc_final: 0.7755 (tt) REVERT: C 25 LYS cc_start: 0.9160 (mtpt) cc_final: 0.8949 (mttm) REVERT: C 31 LYS cc_start: 0.9517 (mmtm) cc_final: 0.9045 (tmtt) REVERT: C 213 GLU cc_start: 0.9334 (mt-10) cc_final: 0.8835 (pt0) REVERT: E 15 LEU cc_start: 0.8119 (tp) cc_final: 0.7676 (tt) REVERT: E 32 PHE cc_start: 0.8962 (m-80) cc_final: 0.8725 (m-80) REVERT: F 2 VAL cc_start: 0.9405 (m) cc_final: 0.9191 (p) REVERT: G 15 LEU cc_start: 0.8383 (tp) cc_final: 0.7949 (tt) REVERT: G 119 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7561 (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: 0.9040 (tmtt) REVERT: I 122 ASN cc_start: 0.9366 (m110) cc_final: 0.9158 (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: 0.7746 (tt) REVERT: K 32 PHE cc_start: 0.8973 (m-80) cc_final: 0.8726 (m-80) REVERT: L 2 VAL cc_start: 0.9400 (m) cc_final: 0.9186 (p) outliers start: 20 outliers final: 8 residues processed: 261 average time/residue: 0.2994 time to fit residues: 102.6300 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 : 1.240 ------------------------------------------------------------------------------- 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: 8.9990 chunk 58 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 105 optimal weight: 0.6980 chunk 67 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 68 optimal weight: 0.0770 overall best weight: 1.3342 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 ASN E 135 GLN G 128 ASN G 135 GLN ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 135 GLN ** K 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 128 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.078339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.062240 restraints weight = 40570.255| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 5.52 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3249 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3249 r_free = 0.3249 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3246 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.5783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 1.346 11683 Z= 2.545 Angle : 4.200 85.740 16032 Z= 1.437 Chirality : 0.260 4.164 1722 Planarity : 0.009 0.236 2040 Dihedral : 21.935 144.518 1992 Min Nonbonded Distance : 1.437 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.92 % Allowed : 13.50 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.92 (0.23), residues: 1374 helix: 1.35 (0.18), residues: 840 sheet: -1.05 (0.57), residues: 54 loop : -0.41 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 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 0.056 0.002 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.05745 ( 552) hydrogen bonds : angle 4.57142 ( 1656) covalent geometry : bond 0.05057 (11670) covalent geometry : angle 4.19961 (16032) Misc. bond : bond 0.09059 ( 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 261 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 238 time to evaluate : 1.409 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: A 15 LEU cc_start: 0.8368 (tp) cc_final: 0.7984 (tp) REVERT: A 30 LYS cc_start: 0.9419 (mmtp) cc_final: 0.9205 (mmtm) REVERT: A 97 ASP cc_start: 0.9247 (t0) cc_final: 0.8116 (p0) REVERT: A 119 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7650 (ttp-110) REVERT: A 130 TYR cc_start: 0.9043 (t80) cc_final: 0.8593 (t80) REVERT: A 143 ARG cc_start: 0.9187 (ttm110) cc_final: 0.8369 (ttp-110) REVERT: A 178 ASP cc_start: 0.8957 (t0) cc_final: 0.8646 (t0) REVERT: A 207 MET cc_start: 0.9317 (tmm) cc_final: 0.8751 (tmm) REVERT: A 208 ASN cc_start: 0.8888 (p0) cc_final: 0.8383 (p0) REVERT: C 28 GLU cc_start: 0.8336 (mm-30) cc_final: 0.8005 (mm-30) REVERT: C 29 ASP cc_start: 0.9465 (m-30) cc_final: 0.9104 (p0) REVERT: C 31 LYS cc_start: 0.9535 (mmtm) cc_final: 0.9106 (tmtt) REVERT: C 130 TYR cc_start: 0.9130 (t80) cc_final: 0.8818 (t80) REVERT: C 207 MET cc_start: 0.9408 (tmm) cc_final: 0.8943 (tmm) REVERT: C 208 ASN cc_start: 0.9016 (p0) cc_final: 0.8535 (p0) REVERT: C 212 GLU cc_start: 0.8945 (pm20) cc_final: 0.8366 (pm20) REVERT: E 15 LEU cc_start: 0.8268 (tp) cc_final: 0.8012 (tp) REVERT: E 25 LYS cc_start: 0.9088 (mtpt) cc_final: 0.8777 (ptpp) REVERT: E 30 LYS cc_start: 0.9334 (mmtp) cc_final: 0.9079 (mmtm) REVERT: E 45 GLU cc_start: 0.8984 (tp30) cc_final: 0.8470 (mm-30) REVERT: E 207 MET cc_start: 0.9264 (tmm) cc_final: 0.8721 (tmm) REVERT: E 208 ASN cc_start: 0.8984 (p0) cc_final: 0.8588 (p0) REVERT: F 2 VAL cc_start: 0.9404 (m) cc_final: 0.9140 (p) REVERT: G 15 LEU cc_start: 0.8380 (tp) cc_final: 0.8023 (tp) REVERT: G 28 GLU cc_start: 0.8243 (mm-30) cc_final: 0.8020 (mm-30) REVERT: G 29 ASP cc_start: 0.9456 (m-30) cc_final: 0.9014 (p0) REVERT: G 97 ASP cc_start: 0.9247 (t0) cc_final: 0.8122 (p0) REVERT: G 119 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7669 (ttp-110) REVERT: G 143 ARG cc_start: 0.9112 (ttm110) cc_final: 0.8322 (ttm110) REVERT: G 178 ASP cc_start: 0.8931 (t0) cc_final: 0.8639 (t0) REVERT: G 207 MET cc_start: 0.9324 (tmm) cc_final: 0.8766 (tmm) REVERT: G 208 ASN cc_start: 0.8892 (p0) cc_final: 0.8388 (p0) REVERT: I 28 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7986 (mm-30) REVERT: I 29 ASP cc_start: 0.9445 (m-30) cc_final: 0.9118 (p0) REVERT: I 31 LYS cc_start: 0.9538 (mmtm) cc_final: 0.9108 (tmtt) REVERT: I 130 TYR cc_start: 0.9132 (t80) cc_final: 0.8824 (t80) REVERT: I 207 MET cc_start: 0.9400 (tmm) cc_final: 0.8938 (tmm) REVERT: I 208 ASN cc_start: 0.9019 (p0) cc_final: 0.8541 (p0) REVERT: I 212 GLU cc_start: 0.8949 (pm20) cc_final: 0.8406 (pm20) REVERT: K 29 ASP cc_start: 0.9517 (m-30) cc_final: 0.9297 (m-30) REVERT: K 30 LYS cc_start: 0.9317 (mmtp) cc_final: 0.9060 (mmtm) REVERT: K 45 GLU cc_start: 0.8989 (tp30) cc_final: 0.8476 (mm-30) REVERT: K 207 MET cc_start: 0.9255 (tmm) cc_final: 0.8705 (tmm) REVERT: K 208 ASN cc_start: 0.8987 (p0) cc_final: 0.8599 (p0) REVERT: L 2 VAL cc_start: 0.9410 (m) cc_final: 0.9143 (p) outliers start: 23 outliers final: 5 residues processed: 256 average time/residue: 0.3576 time to fit residues: 116.3103 Evaluate side-chains 233 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 226 time to evaluate : 1.298 ------------------------------------------------------------------------------- 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 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: 9.9990 chunk 117 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 111 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 29 optimal weight: 9.9990 chunk 82 optimal weight: 0.9980 chunk 125 optimal weight: 20.0000 chunk 137 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 135 GLN E 122 ASN K 122 ASN K 135 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.075393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.059100 restraints weight = 38744.695| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 5.39 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3181 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3180 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.6502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.037 1.024 11683 Z= 1.888 Angle : 3.518 58.462 16032 Z= 1.211 Chirality : 0.272 4.943 1722 Planarity : 0.007 0.180 2040 Dihedral : 22.189 145.469 1992 Min Nonbonded Distance : 1.502 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.50 % Allowed : 12.67 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.14 (0.23), residues: 1374 helix: 1.34 (0.18), residues: 858 sheet: -0.86 (0.64), residues: 54 loop : 0.00 (0.31), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 80 HIS 0.002 0.001 HIS A 12 PHE 0.020 0.002 PHE J 4 TYR 0.026 0.003 TYR A 130 ARG 0.055 0.002 ARG K 18 Details of bonding type rmsd hydrogen bonds : bond 0.05007 ( 552) hydrogen bonds : angle 4.42955 ( 1656) covalent geometry : bond 0.03737 (11670) covalent geometry : angle 3.51784 (16032) Misc. bond : bond 0.08921 ( 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 267 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 249 time to evaluate : 1.278 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: 0.8297 (mm-30) cc_final: 0.8043 (mm-30) REVERT: A 29 ASP cc_start: 0.9450 (m-30) cc_final: 0.9166 (p0) REVERT: A 31 LYS cc_start: 0.9160 (pptt) cc_final: 0.8844 (tmtt) REVERT: A 45 GLU cc_start: 0.8938 (tp30) cc_final: 0.8657 (tp30) REVERT: A 71 GLU cc_start: 0.9183 (mm-30) cc_final: 0.8890 (mm-30) REVERT: A 107 THR cc_start: 0.9483 (OUTLIER) cc_final: 0.9246 (p) REVERT: A 119 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7531 (ttp80) REVERT: A 130 TYR cc_start: 0.9186 (t80) cc_final: 0.8883 (t80) REVERT: A 207 MET cc_start: 0.9248 (tmm) cc_final: 0.8736 (tmm) REVERT: A 214 MET cc_start: 0.9456 (mtm) cc_final: 0.9210 (mtm) REVERT: C 15 LEU cc_start: 0.8303 (tp) cc_final: 0.7927 (tp) REVERT: C 28 GLU cc_start: 0.8353 (mm-30) cc_final: 0.7992 (mm-30) REVERT: C 29 ASP cc_start: 0.9472 (m-30) cc_final: 0.9183 (p0) REVERT: C 31 LYS cc_start: 0.9560 (mmtm) cc_final: 0.9078 (tmtt) REVERT: C 35 GLU cc_start: 0.8994 (pm20) cc_final: 0.8789 (pm20) REVERT: C 45 GLU cc_start: 0.8955 (tp30) cc_final: 0.8545 (mm-30) REVERT: C 107 THR cc_start: 0.9520 (OUTLIER) cc_final: 0.9284 (p) REVERT: C 130 TYR cc_start: 0.9146 (t80) cc_final: 0.8926 (t80) REVERT: C 207 MET cc_start: 0.9319 (tmm) cc_final: 0.9047 (tmm) REVERT: C 208 ASN cc_start: 0.8919 (p0) cc_final: 0.8404 (p0) REVERT: E 28 GLU cc_start: 0.8372 (mm-30) cc_final: 0.8134 (mm-30) REVERT: E 29 ASP cc_start: 0.9512 (m-30) cc_final: 0.9238 (p0) REVERT: E 71 GLU cc_start: 0.9104 (mm-30) cc_final: 0.8814 (mm-30) REVERT: E 107 THR cc_start: 0.9478 (OUTLIER) cc_final: 0.9221 (p) REVERT: E 152 ASP cc_start: 0.9164 (m-30) cc_final: 0.8883 (p0) REVERT: E 207 MET cc_start: 0.9201 (tmm) cc_final: 0.8636 (tmm) REVERT: F 2 VAL cc_start: 0.9440 (m) cc_final: 0.9176 (p) REVERT: G 28 GLU cc_start: 0.8330 (mm-30) cc_final: 0.8021 (mm-30) REVERT: G 29 ASP cc_start: 0.9452 (m-30) cc_final: 0.9056 (p0) REVERT: G 45 GLU cc_start: 0.9018 (mm-30) cc_final: 0.8773 (tp30) REVERT: G 71 GLU cc_start: 0.9187 (mm-30) cc_final: 0.8897 (mm-30) REVERT: G 107 THR cc_start: 0.9492 (OUTLIER) cc_final: 0.9256 (p) REVERT: G 119 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7541 (ttp80) REVERT: G 130 TYR cc_start: 0.9156 (t80) cc_final: 0.8692 (t80) REVERT: G 207 MET cc_start: 0.9249 (tmm) cc_final: 0.8744 (tmm) REVERT: G 214 MET cc_start: 0.9452 (mtm) cc_final: 0.9203 (mtm) REVERT: I 25 LYS cc_start: 0.8983 (mtmm) cc_final: 0.8631 (mttm) REVERT: I 28 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8069 (mm-30) REVERT: I 29 ASP cc_start: 0.9486 (m-30) cc_final: 0.9171 (p0) REVERT: I 31 LYS cc_start: 0.9567 (mmtm) cc_final: 0.9079 (tmtt) REVERT: I 35 GLU cc_start: 0.8991 (pm20) cc_final: 0.8785 (pm20) REVERT: I 45 GLU cc_start: 0.8974 (tp30) cc_final: 0.8573 (mm-30) REVERT: I 107 THR cc_start: 0.9512 (OUTLIER) cc_final: 0.9269 (p) REVERT: I 130 TYR cc_start: 0.9150 (t80) cc_final: 0.8897 (t80) REVERT: I 207 MET cc_start: 0.9313 (tmm) cc_final: 0.9047 (tmm) REVERT: I 208 ASN cc_start: 0.8910 (p0) cc_final: 0.8362 (p0) REVERT: K 15 LEU cc_start: 0.8335 (tp) cc_final: 0.8022 (tp) REVERT: K 25 LYS cc_start: 0.8816 (mttm) cc_final: 0.8572 (mtmm) REVERT: K 45 GLU cc_start: 0.9005 (tp30) cc_final: 0.8629 (mm-30) REVERT: K 71 GLU cc_start: 0.9113 (mm-30) cc_final: 0.8823 (mm-30) REVERT: K 107 THR cc_start: 0.9461 (OUTLIER) cc_final: 0.9202 (p) REVERT: K 207 MET cc_start: 0.9205 (tmm) cc_final: 0.8582 (tmm) REVERT: L 2 VAL cc_start: 0.9439 (m) cc_final: 0.9171 (p) outliers start: 18 outliers final: 4 residues processed: 263 average time/residue: 0.3196 time to fit residues: 108.9176 Evaluate side-chains 238 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 226 time to evaluate : 1.298 ------------------------------------------------------------------------------- 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 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 107 THR Chi-restraints excluded: chain K residue 18 ARG Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 110 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 4 optimal weight: 4.9990 chunk 124 optimal weight: 20.0000 chunk 17 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 110 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 114 optimal weight: 0.0670 chunk 55 optimal weight: 20.0000 chunk 23 optimal weight: 20.0000 chunk 1 optimal weight: 2.9990 overall best weight: 2.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 149 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.073737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.057278 restraints weight = 39156.377| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 5.39 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3135 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.7074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.033 1.010 11683 Z= 1.661 Angle : 3.020 47.184 16032 Z= 1.048 Chirality : 0.265 5.614 1722 Planarity : 0.007 0.146 2040 Dihedral : 22.246 174.215 1992 Min Nonbonded Distance : 1.545 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.92 % Allowed : 11.50 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.23), residues: 1374 helix: 1.42 (0.18), residues: 858 sheet: -0.76 (0.66), residues: 54 loop : 0.17 (0.32), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 80 HIS 0.002 0.001 HIS A 12 PHE 0.007 0.001 PHE D 4 TYR 0.028 0.003 TYR I 50 ARG 0.029 0.001 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.04822 ( 552) hydrogen bonds : angle 4.39701 ( 1656) covalent geometry : bond 0.03293 (11670) covalent geometry : angle 3.01964 (16032) Misc. bond : bond 0.07846 ( 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 260 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 237 time to evaluate : 1.242 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: A 28 GLU cc_start: 0.8280 (mm-30) cc_final: 0.8046 (mm-30) REVERT: A 29 ASP cc_start: 0.9466 (m-30) cc_final: 0.9259 (p0) REVERT: A 31 LYS cc_start: 0.9167 (pptt) cc_final: 0.8826 (tmtt) REVERT: A 45 GLU cc_start: 0.8982 (tp30) cc_final: 0.8630 (tp30) REVERT: A 107 THR cc_start: 0.9534 (OUTLIER) cc_final: 0.9311 (p) REVERT: A 119 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.7669 (ttp80) REVERT: A 130 TYR cc_start: 0.9236 (t80) cc_final: 0.8962 (t80) REVERT: A 208 ASN cc_start: 0.9034 (p0) cc_final: 0.8748 (p0) REVERT: C 30 LYS cc_start: 0.9439 (mmtp) cc_final: 0.9033 (mmtm) REVERT: C 31 LYS cc_start: 0.9598 (mmtm) cc_final: 0.9062 (tmtt) REVERT: C 45 GLU cc_start: 0.8937 (tp30) cc_final: 0.8368 (tp30) REVERT: C 107 THR cc_start: 0.9534 (OUTLIER) cc_final: 0.9303 (p) REVERT: C 143 ARG cc_start: 0.9087 (ttp-110) cc_final: 0.8780 (ttm110) REVERT: C 214 MET cc_start: 0.9458 (mtm) cc_final: 0.9149 (mtm) REVERT: E 28 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8173 (mm-30) REVERT: E 29 ASP cc_start: 0.9492 (m-30) cc_final: 0.9273 (p0) REVERT: E 45 GLU cc_start: 0.8744 (tp30) cc_final: 0.8468 (mm-30) REVERT: E 71 GLU cc_start: 0.9164 (mm-30) cc_final: 0.8847 (mm-30) REVERT: E 107 THR cc_start: 0.9490 (OUTLIER) cc_final: 0.9259 (p) REVERT: E 152 ASP cc_start: 0.9189 (m-30) cc_final: 0.8877 (p0) REVERT: E 207 MET cc_start: 0.9283 (tmm) cc_final: 0.8996 (tpt) REVERT: E 208 ASN cc_start: 0.9014 (p0) cc_final: 0.8700 (p0) REVERT: F 2 VAL cc_start: 0.9464 (m) cc_final: 0.9204 (p) REVERT: G 28 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8073 (mm-30) REVERT: G 29 ASP cc_start: 0.9471 (m-30) cc_final: 0.9121 (p0) REVERT: G 45 GLU cc_start: 0.9029 (mm-30) cc_final: 0.8669 (tp30) REVERT: G 107 THR cc_start: 0.9527 (OUTLIER) cc_final: 0.9300 (p) REVERT: G 119 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.7683 (ttp80) REVERT: G 130 TYR cc_start: 0.9218 (t80) cc_final: 0.8883 (t80) REVERT: G 175 GLU cc_start: 0.8950 (tp30) cc_final: 0.8552 (tp30) REVERT: G 208 ASN cc_start: 0.9021 (p0) cc_final: 0.8729 (p0) REVERT: I 28 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8119 (mm-30) REVERT: I 29 ASP cc_start: 0.9517 (m-30) cc_final: 0.9199 (p0) REVERT: I 31 LYS cc_start: 0.9580 (mmtm) cc_final: 0.9063 (tmtt) REVERT: I 45 GLU cc_start: 0.8949 (tp30) cc_final: 0.8395 (tp30) REVERT: I 71 GLU cc_start: 0.9253 (mm-30) cc_final: 0.9051 (mm-30) REVERT: I 107 THR cc_start: 0.9530 (OUTLIER) cc_final: 0.9297 (p) REVERT: I 143 ARG cc_start: 0.9085 (ttp-110) cc_final: 0.8776 (ttm110) REVERT: I 214 MET cc_start: 0.9458 (mtm) cc_final: 0.9138 (mtm) REVERT: K 28 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7869 (mm-30) REVERT: K 29 ASP cc_start: 0.9555 (m-30) cc_final: 0.9158 (p0) REVERT: K 107 THR cc_start: 0.9484 (OUTLIER) cc_final: 0.9252 (p) REVERT: K 152 ASP cc_start: 0.9208 (m-30) cc_final: 0.8894 (p0) REVERT: K 207 MET cc_start: 0.9282 (tmm) cc_final: 0.8983 (tpt) REVERT: K 208 ASN cc_start: 0.9016 (p0) cc_final: 0.8702 (p0) REVERT: K 214 MET cc_start: 0.9444 (mtm) cc_final: 0.9180 (mtm) REVERT: L 2 VAL cc_start: 0.9464 (m) cc_final: 0.9206 (p) outliers start: 23 outliers final: 10 residues processed: 252 average time/residue: 0.3415 time to fit residues: 112.7713 Evaluate side-chains 220 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 202 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 119 ARG Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain E residue 213 GLU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 119 ARG Chi-restraints excluded: chain G residue 141 CYS Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 110 VAL 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: 4.9990 chunk 47 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 134 optimal weight: 2.9990 chunk 90 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 162 GLN G 12 HIS I 149 ASN I 162 GLN K 12 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.071561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.054430 restraints weight = 39632.293| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 5.45 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3069 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.7490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.031 1.042 11683 Z= 1.531 Angle : 2.912 48.872 16032 Z= 1.019 Chirality : 0.253 4.960 1722 Planarity : 0.009 0.297 2040 Dihedral : 22.736 169.539 1992 Min Nonbonded Distance : 1.627 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.33 % Allowed : 11.25 % Favored : 86.42 % 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: 1.47 (0.24), residues: 1374 helix: 1.49 (0.18), residues: 858 sheet: -0.62 (0.69), residues: 54 loop : 0.38 (0.32), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 184 HIS 0.003 0.001 HIS I 62 PHE 0.025 0.002 PHE J 4 TYR 0.033 0.004 TYR C 50 ARG 0.035 0.001 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.05021 ( 552) hydrogen bonds : angle 4.53157 ( 1656) covalent geometry : bond 0.03054 (11670) covalent geometry : angle 2.91151 (16032) Misc. bond : bond 0.06409 ( 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: 28 poor density : 214 time to evaluate : 1.261 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: A 45 GLU cc_start: 0.8900 (tp30) cc_final: 0.8521 (tp30) REVERT: A 97 ASP cc_start: 0.9228 (OUTLIER) cc_final: 0.8026 (p0) REVERT: A 107 THR cc_start: 0.9511 (OUTLIER) cc_final: 0.9235 (p) REVERT: A 119 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7636 (ttp80) REVERT: A 175 GLU cc_start: 0.8760 (tp30) cc_final: 0.8494 (tp30) REVERT: A 207 MET cc_start: 0.9523 (tpt) cc_final: 0.8898 (tmm) REVERT: C 28 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8133 (mm-30) REVERT: C 30 LYS cc_start: 0.9135 (mmtp) cc_final: 0.8701 (mmtm) REVERT: C 31 LYS cc_start: 0.9588 (mmtm) cc_final: 0.9131 (tmtt) REVERT: C 45 GLU cc_start: 0.8887 (tp30) cc_final: 0.8567 (tp30) REVERT: C 71 GLU cc_start: 0.9227 (mm-30) cc_final: 0.8896 (mm-30) REVERT: C 107 THR cc_start: 0.9542 (OUTLIER) cc_final: 0.9312 (p) REVERT: C 143 ARG cc_start: 0.9143 (ttp-110) cc_final: 0.8785 (ttm110) REVERT: E 18 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.7997 (ttm-80) REVERT: E 28 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8168 (mm-30) REVERT: E 45 GLU cc_start: 0.8715 (tp30) cc_final: 0.8379 (tp30) REVERT: E 71 GLU cc_start: 0.9142 (mm-30) cc_final: 0.8753 (mm-30) REVERT: E 107 THR cc_start: 0.9514 (OUTLIER) cc_final: 0.9286 (p) REVERT: F 2 VAL cc_start: 0.9493 (m) cc_final: 0.9255 (p) REVERT: G 25 LYS cc_start: 0.9331 (mtpt) cc_final: 0.9028 (mttm) REVERT: G 28 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8242 (mm-30) REVERT: G 29 ASP cc_start: 0.9469 (m-30) cc_final: 0.9156 (p0) REVERT: G 31 LYS cc_start: 0.9151 (pptt) cc_final: 0.8831 (tmtt) REVERT: G 45 GLU cc_start: 0.9026 (mm-30) cc_final: 0.8821 (tp30) REVERT: G 97 ASP cc_start: 0.9232 (OUTLIER) cc_final: 0.8034 (p0) REVERT: G 107 THR cc_start: 0.9512 (OUTLIER) cc_final: 0.9238 (p) REVERT: G 119 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.7657 (ttp80) REVERT: G 130 TYR cc_start: 0.9348 (t80) cc_final: 0.9114 (t80) REVERT: G 144 MET cc_start: 0.8549 (mmt) cc_final: 0.8341 (mmt) REVERT: G 175 GLU cc_start: 0.9034 (tp30) cc_final: 0.8653 (tp30) REVERT: G 207 MET cc_start: 0.9508 (tpt) cc_final: 0.8885 (tmm) REVERT: I 25 LYS cc_start: 0.9023 (mtmm) cc_final: 0.8603 (mttp) REVERT: I 28 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8037 (mm-30) REVERT: I 29 ASP cc_start: 0.9504 (m-30) cc_final: 0.9271 (p0) REVERT: I 31 LYS cc_start: 0.9597 (mmtm) cc_final: 0.9097 (tmtt) REVERT: I 45 GLU cc_start: 0.8886 (tp30) cc_final: 0.8578 (tp30) REVERT: I 71 GLU cc_start: 0.9309 (mm-30) cc_final: 0.9010 (mm-30) REVERT: I 107 THR cc_start: 0.9539 (OUTLIER) cc_final: 0.9314 (p) REVERT: I 143 ARG cc_start: 0.9148 (ttp-110) cc_final: 0.8788 (ttm110) REVERT: K 25 LYS cc_start: 0.8835 (mttm) cc_final: 0.8588 (mttm) REVERT: K 29 ASP cc_start: 0.9561 (m-30) cc_final: 0.9307 (p0) REVERT: K 61 ASP cc_start: 0.8988 (m-30) cc_final: 0.8525 (p0) REVERT: K 107 THR cc_start: 0.9502 (OUTLIER) cc_final: 0.9266 (p) REVERT: L 2 VAL cc_start: 0.9496 (m) cc_final: 0.9257 (p) outliers start: 28 outliers final: 10 residues processed: 236 average time/residue: 0.3453 time to fit residues: 103.8372 Evaluate side-chains 211 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 190 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 119 ARG Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 119 ARG Chi-restraints excluded: chain G residue 213 GLU Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 163 SER Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 166 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 126 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 9 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 105 optimal weight: 0.8980 chunk 69 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 12 optimal weight: 0.0050 overall best weight: 3.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 HIS A 162 GLN C 12 HIS E 12 HIS E 193 ASN G 162 GLN K 193 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.071036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.053920 restraints weight = 44226.095| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 5.75 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3050 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.7871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.029 0.988 11683 Z= 1.453 Angle : 2.785 49.114 16032 Z= 0.983 Chirality : 0.230 4.168 1722 Planarity : 0.010 0.279 2040 Dihedral : 22.103 174.148 1992 Min Nonbonded Distance : 1.689 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.67 % Allowed : 11.83 % Favored : 85.50 % 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: 1.37 (0.18), residues: 858 sheet: -0.51 (0.69), residues: 54 loop : 0.37 (0.32), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 80 HIS 0.002 0.001 HIS C 62 PHE 0.020 0.002 PHE A 32 TYR 0.031 0.003 TYR A 130 ARG 0.022 0.001 ARG G 18 Details of bonding type rmsd hydrogen bonds : bond 0.04903 ( 552) hydrogen bonds : angle 4.55089 ( 1656) covalent geometry : bond 0.02893 (11670) covalent geometry : angle 2.78460 (16032) Misc. bond : bond 0.05975 ( 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 246 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 214 time to evaluate : 1.334 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: A 71 GLU cc_start: 0.9247 (mm-30) cc_final: 0.8953 (mm-30) REVERT: A 107 THR cc_start: 0.9506 (OUTLIER) cc_final: 0.9250 (p) REVERT: A 119 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7657 (ttp80) REVERT: A 207 MET cc_start: 0.9451 (tpt) cc_final: 0.9148 (tpt) REVERT: A 208 ASN cc_start: 0.9165 (p0) cc_final: 0.8771 (p0) REVERT: C 25 LYS cc_start: 0.8866 (ptpp) cc_final: 0.8372 (ptpp) REVERT: C 31 LYS cc_start: 0.9569 (mmtm) cc_final: 0.9072 (tmtt) REVERT: C 45 GLU cc_start: 0.8855 (tp30) cc_final: 0.8451 (tp30) REVERT: C 71 GLU cc_start: 0.9203 (mm-30) cc_final: 0.8958 (mm-30) REVERT: C 107 THR cc_start: 0.9564 (OUTLIER) cc_final: 0.9351 (p) REVERT: C 143 ARG cc_start: 0.9124 (ttp-110) cc_final: 0.8726 (ttm110) REVERT: E 31 LYS cc_start: 0.9484 (mmmt) cc_final: 0.9134 (tmtt) REVERT: E 45 GLU cc_start: 0.8699 (tp30) cc_final: 0.7525 (tp30) REVERT: E 71 GLU cc_start: 0.9202 (mm-30) cc_final: 0.8901 (mm-30) REVERT: E 107 THR cc_start: 0.9517 (OUTLIER) cc_final: 0.9294 (p) REVERT: F 2 VAL cc_start: 0.9489 (OUTLIER) cc_final: 0.9264 (p) REVERT: G 25 LYS cc_start: 0.9366 (mtpt) cc_final: 0.8992 (mttm) REVERT: G 31 LYS cc_start: 0.9157 (pptt) cc_final: 0.8824 (tmtt) REVERT: G 45 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8733 (tp30) REVERT: G 71 GLU cc_start: 0.9162 (mm-30) cc_final: 0.8897 (mm-30) REVERT: G 107 THR cc_start: 0.9519 (OUTLIER) cc_final: 0.9265 (p) REVERT: G 175 GLU cc_start: 0.9102 (tp30) cc_final: 0.8761 (tp30) REVERT: G 207 MET cc_start: 0.9446 (tpt) cc_final: 0.9147 (tpt) REVERT: G 208 ASN cc_start: 0.9170 (p0) cc_final: 0.8768 (p0) REVERT: I 28 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8069 (mm-30) REVERT: I 29 ASP cc_start: 0.9495 (m-30) cc_final: 0.9253 (p0) REVERT: I 31 LYS cc_start: 0.9588 (mmtm) cc_final: 0.9088 (tmtt) REVERT: I 45 GLU cc_start: 0.8866 (tp30) cc_final: 0.8471 (tp30) REVERT: I 71 GLU cc_start: 0.9312 (mm-30) cc_final: 0.9081 (mm-30) REVERT: I 107 THR cc_start: 0.9555 (OUTLIER) cc_final: 0.9337 (p) REVERT: I 143 ARG cc_start: 0.9138 (ttp-110) cc_final: 0.8739 (ttm110) REVERT: K 31 LYS cc_start: 0.9512 (mmmt) cc_final: 0.9075 (tmtt) REVERT: K 107 THR cc_start: 0.9513 (OUTLIER) cc_final: 0.9279 (p) REVERT: K 208 ASN cc_start: 0.8871 (p0) cc_final: 0.8585 (p0) REVERT: L 2 VAL cc_start: 0.9489 (OUTLIER) cc_final: 0.9264 (p) outliers start: 32 outliers final: 14 residues processed: 233 average time/residue: 0.3331 time to fit residues: 99.7123 Evaluate side-chains 220 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 197 time to evaluate : 1.241 ------------------------------------------------------------------------------- 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 141 CYS Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 166 ASP Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 119 ARG Chi-restraints excluded: chain G residue 145 TYR Chi-restraints excluded: chain 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 145 TYR Chi-restraints excluded: chain K residue 213 GLU Chi-restraints excluded: chain L residue 2 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 0.2980 chunk 133 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 10 optimal weight: 20.0000 chunk 92 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 96 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN E 62 HIS E 193 ASN G 121 GLN ** G 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 193 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.070343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.053019 restraints weight = 42569.508| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 5.59 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3069 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 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 = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3068 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.8136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.028 0.964 11683 Z= 1.408 Angle : 2.658 47.804 16032 Z= 0.943 Chirality : 0.211 3.919 1722 Planarity : 0.007 0.133 2040 Dihedral : 22.062 164.048 1992 Min Nonbonded Distance : 1.681 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.92 % Allowed : 11.75 % Favored : 85.33 % 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: 1.54 (0.24), residues: 1374 helix: 1.47 (0.18), residues: 852 sheet: -0.54 (0.68), residues: 54 loop : 0.57 (0.33), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 23 HIS 0.003 0.001 HIS A 62 PHE 0.025 0.002 PHE J 4 TYR 0.034 0.003 TYR G 130 ARG 0.042 0.002 ARG C 18 Details of bonding type rmsd hydrogen bonds : bond 0.04771 ( 552) hydrogen bonds : angle 4.64174 ( 1656) covalent geometry : bond 0.02807 (11670) covalent geometry : angle 2.65833 (16032) Misc. bond : bond 0.05361 ( 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 249 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 214 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.9455 (m-30) cc_final: 0.9172 (p0) REVERT: A 45 GLU cc_start: 0.8874 (tp30) cc_final: 0.8600 (tp30) REVERT: A 97 ASP cc_start: 0.9238 (OUTLIER) cc_final: 0.8102 (p0) REVERT: A 107 THR cc_start: 0.9511 (OUTLIER) cc_final: 0.9268 (p) REVERT: A 175 GLU cc_start: 0.8914 (tp30) cc_final: 0.8640 (tp30) REVERT: A 207 MET cc_start: 0.9499 (tpt) cc_final: 0.9193 (tpt) REVERT: A 208 ASN cc_start: 0.9231 (p0) cc_final: 0.8812 (p0) REVERT: C 25 LYS cc_start: 0.8786 (ptpp) cc_final: 0.8549 (ptpp) REVERT: C 30 LYS cc_start: 0.8876 (mmtm) cc_final: 0.8626 (mmtm) REVERT: C 31 LYS cc_start: 0.9627 (mmtm) cc_final: 0.8987 (tmtt) REVERT: C 45 GLU cc_start: 0.8808 (tp30) cc_final: 0.8363 (tp30) REVERT: C 58 CYS cc_start: 0.9241 (OUTLIER) cc_final: 0.8961 (t) REVERT: C 71 GLU cc_start: 0.9272 (mm-30) cc_final: 0.9061 (mm-30) REVERT: C 107 THR cc_start: 0.9550 (OUTLIER) cc_final: 0.9329 (p) REVERT: E 31 LYS cc_start: 0.9486 (mmmt) cc_final: 0.9054 (tmtt) REVERT: E 45 GLU cc_start: 0.8645 (tp30) cc_final: 0.8398 (tp30) REVERT: E 71 GLU cc_start: 0.9194 (mm-30) cc_final: 0.8877 (mm-30) REVERT: E 107 THR cc_start: 0.9540 (OUTLIER) cc_final: 0.9330 (p) REVERT: F 2 VAL cc_start: 0.9507 (OUTLIER) cc_final: 0.9295 (p) REVERT: G 18 ARG cc_start: 0.8856 (mtp-110) cc_final: 0.8633 (ttm110) REVERT: G 25 LYS cc_start: 0.9347 (mtpt) cc_final: 0.9048 (mttm) REVERT: G 29 ASP cc_start: 0.9369 (m-30) cc_final: 0.9029 (p0) REVERT: G 31 LYS cc_start: 0.9160 (pptt) cc_final: 0.8866 (tmtt) REVERT: G 45 GLU cc_start: 0.8911 (mm-30) cc_final: 0.8620 (tp30) REVERT: G 97 ASP cc_start: 0.9247 (OUTLIER) cc_final: 0.8111 (p0) REVERT: G 107 THR cc_start: 0.9509 (OUTLIER) cc_final: 0.9265 (p) REVERT: G 175 GLU cc_start: 0.9073 (tp30) cc_final: 0.8735 (tp30) REVERT: G 207 MET cc_start: 0.9498 (tpt) cc_final: 0.9200 (tpt) REVERT: G 208 ASN cc_start: 0.9243 (p0) cc_final: 0.8821 (p0) REVERT: I 28 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8069 (mm-30) REVERT: I 29 ASP cc_start: 0.9502 (m-30) cc_final: 0.9268 (p0) REVERT: I 31 LYS cc_start: 0.9600 (mmtm) cc_final: 0.9090 (tmtt) REVERT: I 45 GLU cc_start: 0.8848 (tp30) cc_final: 0.8425 (tp30) REVERT: I 71 GLU cc_start: 0.9277 (mm-30) cc_final: 0.9011 (mm-30) REVERT: I 107 THR cc_start: 0.9553 (OUTLIER) cc_final: 0.9336 (p) REVERT: K 29 ASP cc_start: 0.9565 (m-30) cc_final: 0.9085 (p0) REVERT: K 31 LYS cc_start: 0.9478 (mmmt) cc_final: 0.9112 (tmtt) REVERT: K 71 GLU cc_start: 0.9200 (mm-30) cc_final: 0.8872 (mm-30) REVERT: K 107 THR cc_start: 0.9522 (OUTLIER) cc_final: 0.9288 (p) REVERT: L 2 VAL cc_start: 0.9511 (OUTLIER) cc_final: 0.9301 (p) outliers start: 35 outliers final: 14 residues processed: 233 average time/residue: 0.3252 time to fit residues: 98.7015 Evaluate side-chains 215 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 190 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 119 ARG Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain C residue 58 CYS 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 E residue 145 TYR Chi-restraints excluded: chain E residue 166 ASP 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 119 ARG Chi-restraints excluded: chain G residue 145 TYR Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain I residue 145 TYR Chi-restraints excluded: chain K residue 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 Chi-restraints excluded: chain L residue 2 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 87 optimal weight: 9.9990 chunk 84 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 112 optimal weight: 9.9990 chunk 77 optimal weight: 20.0000 chunk 107 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 122 optimal weight: 6.9990 chunk 130 optimal weight: 6.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN A 193 ASN ** E 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 GLN G 193 ASN ** K 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 62 HIS ** K 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.070691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.054350 restraints weight = 40106.069| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 5.36 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3102 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3103 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.8451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.028 0.960 11683 Z= 1.376 Angle : 2.562 48.658 16032 Z= 0.917 Chirality : 0.197 3.235 1722 Planarity : 0.010 0.225 2040 Dihedral : 21.356 150.763 1992 Min Nonbonded Distance : 1.688 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.42 % Allowed : 13.83 % Favored : 83.75 % 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: 1.43 (0.24), residues: 1374 helix: 1.42 (0.18), residues: 852 sheet: -0.63 (0.66), residues: 54 loop : 0.46 (0.33), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 23 HIS 0.003 0.001 HIS I 62 PHE 0.021 0.002 PHE A 32 TYR 0.030 0.003 TYR A 130 ARG 0.014 0.001 ARG A 18 Details of bonding type rmsd hydrogen bonds : bond 0.05010 ( 552) hydrogen bonds : angle 4.66794 ( 1656) covalent geometry : bond 0.02750 (11670) covalent geometry : angle 2.56242 (16032) Misc. bond : bond 0.04849 ( 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 235 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 206 time to evaluate : 1.277 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: A 45 GLU cc_start: 0.8788 (tp30) cc_final: 0.8527 (tp30) REVERT: A 71 GLU cc_start: 0.9163 (mm-30) cc_final: 0.8857 (mm-30) REVERT: A 97 ASP cc_start: 0.9218 (OUTLIER) cc_final: 0.8075 (p0) REVERT: A 107 THR cc_start: 0.9514 (OUTLIER) cc_final: 0.9276 (p) REVERT: A 119 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.8276 (ttp-110) REVERT: A 175 GLU cc_start: 0.8933 (tp30) cc_final: 0.8652 (tp30) REVERT: A 207 MET cc_start: 0.9396 (tpt) cc_final: 0.9036 (tpt) REVERT: A 208 ASN cc_start: 0.9167 (p0) cc_final: 0.8721 (p0) REVERT: C 31 LYS cc_start: 0.9645 (mmtm) cc_final: 0.8966 (tmtt) REVERT: C 45 GLU cc_start: 0.8771 (tp30) cc_final: 0.8312 (tp30) REVERT: C 71 GLU cc_start: 0.9224 (mm-30) cc_final: 0.8969 (mm-30) REVERT: C 107 THR cc_start: 0.9534 (OUTLIER) cc_final: 0.9321 (p) REVERT: C 203 LYS cc_start: 0.9246 (pttt) cc_final: 0.9046 (tptp) REVERT: C 207 MET cc_start: 0.9629 (tpp) cc_final: 0.9176 (tmm) REVERT: E 31 LYS cc_start: 0.9560 (mmmt) cc_final: 0.9022 (tmtt) REVERT: E 71 GLU cc_start: 0.9182 (mm-30) cc_final: 0.8852 (mm-30) REVERT: E 107 THR cc_start: 0.9538 (OUTLIER) cc_final: 0.9334 (p) REVERT: E 208 ASN cc_start: 0.9036 (p0) cc_final: 0.8747 (p0) REVERT: F 2 VAL cc_start: 0.9517 (OUTLIER) cc_final: 0.9314 (p) REVERT: G 18 ARG cc_start: 0.8885 (mtp-110) cc_final: 0.8525 (mtm180) REVERT: G 31 LYS cc_start: 0.9192 (pptt) cc_final: 0.8899 (tmtt) REVERT: G 45 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8650 (tp30) REVERT: G 71 GLU cc_start: 0.9112 (mm-30) cc_final: 0.8819 (mm-30) REVERT: G 97 ASP cc_start: 0.9241 (OUTLIER) cc_final: 0.8119 (p0) REVERT: G 107 THR cc_start: 0.9520 (OUTLIER) cc_final: 0.9281 (p) REVERT: G 175 GLU cc_start: 0.9088 (tp30) cc_final: 0.8761 (tp30) REVERT: G 207 MET cc_start: 0.9448 (tpt) cc_final: 0.9074 (tpt) REVERT: G 208 ASN cc_start: 0.9188 (p0) cc_final: 0.8751 (p0) REVERT: I 28 GLU cc_start: 0.8400 (mm-30) cc_final: 0.8036 (mm-30) REVERT: I 29 ASP cc_start: 0.9505 (m-30) cc_final: 0.9273 (p0) REVERT: I 31 LYS cc_start: 0.9594 (mmtm) cc_final: 0.9058 (tmtt) REVERT: I 45 GLU cc_start: 0.8818 (tp30) cc_final: 0.8370 (tp30) REVERT: I 71 GLU cc_start: 0.9267 (mm-30) cc_final: 0.8980 (mm-30) REVERT: I 107 THR cc_start: 0.9553 (OUTLIER) cc_final: 0.9331 (p) REVERT: I 207 MET cc_start: 0.9628 (tpp) cc_final: 0.9159 (tmm) REVERT: K 31 LYS cc_start: 0.9564 (mmmt) cc_final: 0.9084 (tmtt) REVERT: K 71 GLU cc_start: 0.9202 (mm-30) cc_final: 0.8863 (mm-30) REVERT: K 107 THR cc_start: 0.9542 (OUTLIER) cc_final: 0.9313 (p) REVERT: K 208 ASN cc_start: 0.9077 (p0) cc_final: 0.8862 (p0) REVERT: K 214 MET cc_start: 0.9441 (mtm) cc_final: 0.9089 (mpp) REVERT: L 2 VAL cc_start: 0.9516 (OUTLIER) cc_final: 0.9315 (p) outliers start: 29 outliers final: 11 residues processed: 224 average time/residue: 0.3510 time to fit residues: 100.8004 Evaluate side-chains 208 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 186 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 119 ARG Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain E residue 18 ARG Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 145 TYR Chi-restraints excluded: chain E residue 166 ASP 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 145 TYR 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 K residue 107 THR Chi-restraints excluded: chain K residue 145 TYR Chi-restraints excluded: chain K residue 213 GLU Chi-restraints excluded: chain L residue 2 VAL 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: 8.9990 chunk 58 optimal weight: 0.7980 chunk 88 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 119 optimal weight: 9.9990 chunk 79 optimal weight: 20.0000 chunk 89 optimal weight: 10.0000 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN A 193 ASN ** E 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 GLN ** G 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 12 HIS ** K 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.070237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.053529 restraints weight = 40795.829| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 5.71 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3057 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 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 = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3057 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.8690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.027 0.940 11683 Z= 1.362 Angle : 2.488 47.998 16032 Z= 0.903 Chirality : 0.199 3.422 1722 Planarity : 0.011 0.348 2040 Dihedral : 21.814 172.568 1992 Min Nonbonded Distance : 1.627 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.17 % Allowed : 13.83 % Favored : 84.00 % Cbeta Deviations : 0.08 % 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: 1.44 (0.24), residues: 1374 helix: 1.43 (0.18), residues: 852 sheet: -0.65 (0.66), residues: 54 loop : 0.48 (0.33), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 23 HIS 0.003 0.001 HIS A 62 PHE 0.024 0.002 PHE J 4 TYR 0.031 0.003 TYR G 130 ARG 0.056 0.002 ARG K 18 Details of bonding type rmsd hydrogen bonds : bond 0.05044 ( 552) hydrogen bonds : angle 4.74142 ( 1656) covalent geometry : bond 0.02724 (11670) covalent geometry : angle 2.48779 (16032) Misc. bond : bond 0.04818 ( 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 235 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 209 time to evaluate : 1.375 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 25 LYS cc_start: 0.9183 (mmtm) cc_final: 0.8958 (mmtm) REVERT: A 29 ASP cc_start: 0.9440 (m-30) cc_final: 0.9176 (p0) REVERT: A 45 GLU cc_start: 0.8793 (tp30) cc_final: 0.8539 (tp30) REVERT: A 71 GLU cc_start: 0.9249 (mm-30) cc_final: 0.8926 (mm-30) REVERT: A 97 ASP cc_start: 0.9192 (OUTLIER) cc_final: 0.8052 (p0) REVERT: A 107 THR cc_start: 0.9488 (OUTLIER) cc_final: 0.9250 (p) REVERT: A 119 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.8160 (ttp-110) REVERT: A 175 GLU cc_start: 0.8918 (tp30) cc_final: 0.8643 (tp30) REVERT: A 193 ASN cc_start: 0.8748 (OUTLIER) cc_final: 0.8547 (t0) REVERT: A 207 MET cc_start: 0.9465 (tpt) cc_final: 0.9090 (tpt) REVERT: A 208 ASN cc_start: 0.9250 (p0) cc_final: 0.8728 (p0) REVERT: C 31 LYS cc_start: 0.9653 (mmtm) cc_final: 0.8951 (tmtt) REVERT: C 45 GLU cc_start: 0.8789 (tp30) cc_final: 0.8296 (tp30) REVERT: C 71 GLU cc_start: 0.9334 (mm-30) cc_final: 0.9082 (mm-30) REVERT: C 107 THR cc_start: 0.9526 (OUTLIER) cc_final: 0.9300 (p) REVERT: C 143 ARG cc_start: 0.8969 (ttp-110) cc_final: 0.8741 (ttm110) REVERT: C 200 LEU cc_start: 0.9683 (tp) cc_final: 0.9197 (mt) REVERT: C 203 LYS cc_start: 0.9313 (pttt) cc_final: 0.9073 (tptp) REVERT: C 207 MET cc_start: 0.9659 (tpp) cc_final: 0.8927 (tmm) REVERT: C 208 ASN cc_start: 0.9394 (p0) cc_final: 0.8201 (p0) REVERT: E 31 LYS cc_start: 0.9562 (mmmt) cc_final: 0.8996 (tmtt) REVERT: E 71 GLU cc_start: 0.9220 (mm-30) cc_final: 0.8881 (mm-30) REVERT: E 107 THR cc_start: 0.9523 (OUTLIER) cc_final: 0.9286 (p) REVERT: E 175 GLU cc_start: 0.8915 (tp30) cc_final: 0.8537 (tm-30) REVERT: E 177 THR cc_start: 0.7590 (p) cc_final: 0.7138 (p) REVERT: E 208 ASN cc_start: 0.9073 (p0) cc_final: 0.8789 (p0) REVERT: F 2 VAL cc_start: 0.9496 (OUTLIER) cc_final: 0.9283 (p) REVERT: G 21 ASN cc_start: 0.9391 (m-40) cc_final: 0.9059 (m-40) REVERT: G 25 LYS cc_start: 0.9392 (mtpt) cc_final: 0.9092 (mttp) REVERT: G 29 ASP cc_start: 0.9339 (m-30) cc_final: 0.9036 (p0) REVERT: G 31 LYS cc_start: 0.9219 (pptt) cc_final: 0.8995 (tmtt) REVERT: G 45 GLU cc_start: 0.8911 (mm-30) cc_final: 0.8645 (tp30) REVERT: G 71 GLU cc_start: 0.9184 (mm-30) cc_final: 0.8871 (mm-30) REVERT: G 97 ASP cc_start: 0.9188 (OUTLIER) cc_final: 0.8041 (p0) REVERT: G 107 THR cc_start: 0.9487 (OUTLIER) cc_final: 0.9249 (p) REVERT: G 119 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.8152 (ttp-110) REVERT: G 175 GLU cc_start: 0.9088 (tp30) cc_final: 0.8770 (tp30) REVERT: G 207 MET cc_start: 0.9506 (tpt) cc_final: 0.9125 (tpt) REVERT: G 208 ASN cc_start: 0.9255 (p0) cc_final: 0.8757 (p0) REVERT: I 28 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8117 (mm-30) REVERT: I 29 ASP cc_start: 0.9532 (m-30) cc_final: 0.9303 (p0) REVERT: I 31 LYS cc_start: 0.9597 (mmtm) cc_final: 0.9044 (tmtt) REVERT: I 45 GLU cc_start: 0.8834 (tp30) cc_final: 0.8379 (tp30) REVERT: I 71 GLU cc_start: 0.9366 (mm-30) cc_final: 0.9091 (mm-30) REVERT: I 107 THR cc_start: 0.9539 (OUTLIER) cc_final: 0.9310 (p) REVERT: I 143 ARG cc_start: 0.8972 (ttp-110) cc_final: 0.8751 (ttm110) REVERT: I 200 LEU cc_start: 0.9548 (tp) cc_final: 0.9286 (mt) REVERT: I 207 MET cc_start: 0.9646 (tpp) cc_final: 0.9097 (tmm) REVERT: K 31 LYS cc_start: 0.9577 (mmmt) cc_final: 0.9052 (tmtt) REVERT: K 71 GLU cc_start: 0.9238 (mm-30) cc_final: 0.8901 (mm-30) REVERT: K 107 THR cc_start: 0.9553 (OUTLIER) cc_final: 0.9299 (p) REVERT: K 214 MET cc_start: 0.9435 (mtm) cc_final: 0.9011 (mpp) REVERT: L 2 VAL cc_start: 0.9495 (OUTLIER) cc_final: 0.9289 (p) outliers start: 26 outliers final: 12 residues processed: 223 average time/residue: 0.3198 time to fit residues: 92.8910 Evaluate side-chains 221 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 196 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 119 ARG Chi-restraints excluded: chain A residue 145 TYR Chi-restraints excluded: chain A residue 162 GLN Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 145 TYR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 145 TYR Chi-restraints excluded: chain E residue 166 ASP 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 119 ARG Chi-restraints excluded: chain G residue 145 TYR 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 K residue 107 THR Chi-restraints excluded: chain K residue 145 TYR Chi-restraints excluded: chain K residue 213 GLU Chi-restraints excluded: chain L residue 2 VAL 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: 3.9990 chunk 100 optimal weight: 0.3980 chunk 62 optimal weight: 6.9990 chunk 91 optimal weight: 0.2980 chunk 81 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 chunk 69 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN A 193 ASN E 21 ASN ** E 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 193 ASN ** K 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.070463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.053572 restraints weight = 39487.996| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 5.25 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3071 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.8828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.027 0.938 11683 Z= 1.342 Angle : 2.428 48.739 16032 Z= 0.884 Chirality : 0.194 3.268 1722 Planarity : 0.007 0.163 2040 Dihedral : 21.896 170.229 1992 Min Nonbonded Distance : 1.655 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.00 % Allowed : 14.42 % Favored : 83.58 % Cbeta Deviations : 0.08 % 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: 1.46 (0.24), residues: 1374 helix: 1.45 (0.18), residues: 852 sheet: -0.74 (0.64), residues: 54 loop : 0.49 (0.33), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 23 HIS 0.003 0.001 HIS A 62 PHE 0.013 0.002 PHE D 4 TYR 0.027 0.003 TYR I 130 ARG 0.024 0.001 ARG K 18 Details of bonding type rmsd hydrogen bonds : bond 0.04900 ( 552) hydrogen bonds : angle 4.83949 ( 1656) covalent geometry : bond 0.02683 (11670) covalent geometry : angle 2.42801 (16032) Misc. bond : bond 0.04589 ( 13) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4879.72 seconds wall clock time: 85 minutes 41.28 seconds (5141.28 seconds total)