Starting phenix.real_space_refine on Mon May 19 00:14:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cns_45758/05_2025/9cns_45758.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cns_45758/05_2025/9cns_45758.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cns_45758/05_2025/9cns_45758.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cns_45758/05_2025/9cns_45758.map" model { file = "/net/cci-nas-00/data/ceres_data/9cns_45758/05_2025/9cns_45758.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cns_45758/05_2025/9cns_45758.cif" } resolution = 3.25 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= 0.005 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 72 5.49 5 S 132 5.16 5 C 11058 2.51 5 N 3000 2.21 5 O 3564 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 17826 Number of models: 1 Model: "" Number of chains: 24 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: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 582 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 5, 'TRANS': 68} Chain: "C" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 582 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 5, 'TRANS': 68} 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} Chain: "D" 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: "E" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 582 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 5, 'TRANS': 68} Chain: "F" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 582 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 5, 'TRANS': 68} Chain: "D" 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} Chain: "G" 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: "H" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 582 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 5, 'TRANS': 68} Chain: "I" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 582 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 5, 'TRANS': 68} Chain: "G" 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} Chain: "J" 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: "K" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 582 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 5, 'TRANS': 68} Chain: "L" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 582 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 5, 'TRANS': 68} Chain: "J" 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} Chain: "M" 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: "N" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 582 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 5, 'TRANS': 68} Chain: "O" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 582 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 5, 'TRANS': 68} Chain: "M" 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} Chain: "P" 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: "Q" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 582 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 5, 'TRANS': 68} Chain: "R" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 582 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 5, 'TRANS': 68} Chain: "P" 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} 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 D 301 " occ=0.17 ... (34 atoms not shown) pdb=" P6 IHP D 301 " occ=0.17 residue: pdb=" C1 IHP D 302 " occ=0.17 ... (34 atoms not shown) pdb=" P6 IHP D 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 J 301 " occ=0.17 ... (34 atoms not shown) pdb=" P6 IHP J 301 " occ=0.17 residue: pdb=" C1 IHP J 302 " occ=0.17 ... (34 atoms not shown) pdb=" P6 IHP J 302 " occ=0.17 residue: pdb=" C1 IHP M 301 " occ=0.17 ... (34 atoms not shown) pdb=" P6 IHP M 301 " occ=0.17 residue: pdb=" C1 IHP M 302 " occ=0.17 ... (34 atoms not shown) pdb=" P6 IHP M 302 " occ=0.17 residue: pdb=" C1 IHP P 301 " occ=0.17 ... (34 atoms not shown) pdb=" P6 IHP P 301 " occ=0.17 residue: pdb=" C1 IHP P 302 " occ=0.17 ... (34 atoms not shown) pdb=" P6 IHP P 302 " occ=0.17 Time building chain proxies: 11.47, per 1000 atoms: 0.64 Number of scatterers: 17826 At special positions: 0 Unit cell: (183.534, 177.018, 82.536, 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 132 16.00 P 72 15.00 O 3564 8.00 N 3000 7.00 C 11058 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 198 " - pdb=" SG CYS A 218 " distance=2.03 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 218 " distance=2.03 Simple disulfide: pdb=" SG CYS C 198 " - pdb=" SG CYS C 218 " distance=2.02 Simple disulfide: pdb=" SG CYS D 198 " - pdb=" SG CYS D 218 " distance=2.03 Simple disulfide: pdb=" SG CYS E 198 " - pdb=" SG CYS E 218 " distance=2.03 Simple disulfide: pdb=" SG CYS F 198 " - pdb=" SG CYS F 218 " distance=2.02 Simple disulfide: pdb=" SG CYS G 198 " - pdb=" SG CYS G 218 " distance=2.03 Simple disulfide: pdb=" SG CYS H 198 " - pdb=" SG CYS H 218 " distance=2.03 Simple disulfide: pdb=" SG CYS I 198 " - pdb=" SG CYS I 218 " distance=2.02 Simple disulfide: pdb=" SG CYS J 198 " - pdb=" SG CYS J 218 " distance=2.03 Simple disulfide: pdb=" SG CYS K 198 " - pdb=" SG CYS K 218 " distance=2.03 Simple disulfide: pdb=" SG CYS L 198 " - pdb=" SG CYS L 218 " distance=2.02 Simple disulfide: pdb=" SG CYS M 198 " - pdb=" SG CYS M 218 " distance=2.03 Simple disulfide: pdb=" SG CYS N 198 " - pdb=" SG CYS N 218 " distance=2.03 Simple disulfide: pdb=" SG CYS O 198 " - pdb=" SG CYS O 218 " distance=2.02 Simple disulfide: pdb=" SG CYS P 198 " - pdb=" SG CYS P 218 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 198 " - pdb=" SG CYS Q 218 " distance=2.03 Simple disulfide: pdb=" SG CYS R 198 " - pdb=" SG CYS R 218 " distance=2.02 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 "HETATM17802 O16 IHP P 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8889 O16 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM14831 O16 IHP M 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5918 O16 IHP D 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11860 O16 IHP J 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2947 O16 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM17763 O13 IHP P 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8850 O13 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11821 O13 IHP J 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2908 O13 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM14792 O13 IHP M 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5879 O13 IHP D 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM17765 O15 IHP P 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8852 O15 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2910 O15 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11823 O15 IHP J 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM14794 O15 IHP M 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5881 O15 IHP D 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM17763 O13 IHP P 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8850 O13 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2908 O13 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11821 O13 IHP J 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5879 O13 IHP D 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM14792 O13 IHP M 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM17763 O13 IHP P 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8850 O13 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11821 O13 IHP J 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2908 O13 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM14792 O13 IHP M 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5879 O13 IHP D 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2906 O11 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11819 O11 IHP J 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5877 O11 IHP D 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM14790 O11 IHP M 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8848 O11 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM17761 O11 IHP P 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11822 O14 IHP J 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2909 O14 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM14793 O14 IHP M 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5880 O14 IHP D 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM17764 O14 IHP P 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8851 O14 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11858 O14 IHP J 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2945 O14 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8887 O14 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM17800 O14 IHP P 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11860 O16 IHP J 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2947 O16 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5916 O14 IHP D 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM14829 O14 IHP M 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5918 O16 IHP D 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM14831 O16 IHP M 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM17802 O16 IHP P 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8889 O16 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2947 O16 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11860 O16 IHP J 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM17802 O16 IHP P 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8889 O16 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM14831 O16 IHP M 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5918 O16 IHP D 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM17765 O15 IHP P 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8852 O15 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5881 O15 IHP D 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM14794 O15 IHP M 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11855 O11 IHP J 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2942 O11 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11823 O15 IHP J 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2910 O15 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5913 O11 IHP D 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM14826 O11 IHP M 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8884 O11 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM17797 O11 IHP P 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2945 O14 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11858 O14 IHP J 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8850 O13 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM17763 O13 IHP P 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8887 O14 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM17800 O14 IHP P 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5879 O13 IHP D 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM14792 O13 IHP M 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM14793 O14 IHP M 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM14829 O14 IHP M 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5916 O14 IHP D 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5880 O14 IHP D 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2909 O14 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11822 O14 IHP J 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM17764 O14 IHP P 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8851 O14 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11821 O13 IHP J 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2908 O13 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM17765 O15 IHP P 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8852 O15 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2910 O15 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11823 O15 IHP J 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5881 O15 IHP D 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM14794 O15 IHP M 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8885 O12 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM17798 O12 IHP P 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11820 O12 IHP J 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM14791 O12 IHP M 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11856 O12 IHP J 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2907 O12 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5878 O12 IHP D 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2943 O12 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8849 O12 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5914 O12 IHP D 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM17762 O12 IHP P 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM14827 O12 IHP M 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM17799 O13 IHP P 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8886 O13 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5915 O13 IHP D 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM14828 O13 IHP M 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2944 O13 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11857 O13 IHP J 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11860 O16 IHP J 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2947 O16 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM14831 O16 IHP M 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5918 O16 IHP D 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8849 O12 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM17762 O12 IHP P 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11820 O12 IHP J 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2907 O12 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM17802 O16 IHP P 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8889 O16 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM14791 O12 IHP M 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5878 O12 IHP D 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM17763 O13 IHP P 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8850 O13 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2911 O16 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11824 O16 IHP J 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8853 O16 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM17766 O16 IHP P 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5882 O16 IHP D 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11821 O13 IHP J 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM14795 O16 IHP M 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2908 O13 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM14792 O13 IHP M 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5879 O13 IHP D 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5916 O14 IHP D 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM14829 O14 IHP M 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8887 O14 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM17800 O14 IHP P 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2945 O14 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11858 O14 IHP J 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2906 O11 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11819 O11 IHP J 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2908 O13 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11821 O13 IHP J 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM14790 O11 IHP M 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5877 O11 IHP D 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM14792 O13 IHP M 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5879 O13 IHP D 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8848 O11 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM17761 O11 IHP P 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8850 O13 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM17763 O13 IHP P 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8850 O13 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM17763 O13 IHP P 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM14792 O13 IHP M 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5879 O13 IHP D 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2908 O13 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11821 O13 IHP J 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11822 O14 IHP J 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2909 O14 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5880 O14 IHP D 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM14793 O14 IHP M 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8851 O14 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM17764 O14 IHP P 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM14794 O15 IHP M 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5881 O15 IHP D 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11823 O15 IHP J 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2910 O15 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8852 O15 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM17765 O15 IHP P 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM17762 O12 IHP P 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11820 O12 IHP J 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8849 O12 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2907 O12 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5878 O12 IHP D 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM14791 O12 IHP M 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8886 O13 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM17799 O13 IHP P 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11857 O13 IHP J 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2944 O13 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5915 O13 IHP D 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM14828 O13 IHP M 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM14831 O16 IHP M 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5918 O16 IHP D 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8889 O16 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM17802 O16 IHP P 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2947 O16 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11860 O16 IHP J 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM14830 O15 IHP M 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5917 O15 IHP D 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2946 O15 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11859 O15 IHP J 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8888 O15 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM17801 O15 IHP P 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8889 O16 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM17802 O16 IHP P 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5918 O16 IHP D 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM14831 O16 IHP M 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8886 O13 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM17799 O13 IHP P 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11860 O16 IHP J 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2947 O16 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM14794 O15 IHP M 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5915 O13 IHP D 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11857 O13 IHP J 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5881 O15 IHP D 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM14828 O13 IHP M 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM17765 O15 IHP P 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2944 O13 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2907 O12 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8852 O15 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11820 O12 IHP J 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5878 O12 IHP D 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM14791 O12 IHP M 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM17762 O12 IHP P 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8849 O12 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11823 O15 IHP J 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2910 O15 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8884 O11 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM17797 O11 IHP P 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2947 O16 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11860 O16 IHP J 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM14831 O16 IHP M 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5918 O16 IHP D 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2942 O11 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11855 O11 IHP J 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8889 O16 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM17802 O16 IHP P 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11857 O13 IHP J 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM14826 O11 IHP M 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8850 O13 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM17763 O13 IHP P 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5913 O11 IHP D 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2944 O13 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11824 O16 IHP J 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2911 O16 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM14792 O13 IHP M 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5879 O13 IHP D 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM17799 O13 IHP P 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8886 O13 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM17766 O16 IHP P 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8853 O16 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5915 O13 IHP D 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5882 O16 IHP D 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM14795 O16 IHP M 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM14828 O13 IHP M 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11821 O13 IHP J 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2908 O13 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM14829 O14 IHP M 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5916 O14 IHP D 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5914 O12 IHP D 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM14827 O12 IHP M 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2943 O12 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11856 O12 IHP J 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5880 O14 IHP D 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM14793 O14 IHP M 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM17800 O14 IHP P 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8887 O14 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8885 O12 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM17798 O12 IHP P 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11821 O13 IHP J 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11822 O14 IHP J 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2909 O14 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2945 O14 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11858 O14 IHP J 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8851 O14 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2908 O13 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM17764 O14 IHP P 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM17763 O13 IHP P 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8850 O13 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM14793 O14 IHP M 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5880 O14 IHP D 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM14792 O13 IHP M 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5879 O13 IHP D 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8851 O14 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM17764 O14 IHP P 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2909 O14 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11822 O14 IHP J 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM17763 O13 IHP P 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8850 O13 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8849 O12 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM17762 O12 IHP P 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5879 O13 IHP D 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM14792 O13 IHP M 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM17800 O14 IHP P 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8887 O14 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5878 O12 IHP D 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM14791 O12 IHP M 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM14829 O14 IHP M 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2945 O14 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11858 O14 IHP J 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5916 O14 IHP D 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11821 O13 IHP J 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2908 O13 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11856 O12 IHP J 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2907 O12 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11820 O12 IHP J 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8885 O12 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2943 O12 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM17798 O12 IHP P 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5913 O11 IHP D 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM14826 O11 IHP M 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM14827 O12 IHP M 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2942 O11 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11855 O11 IHP J 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5914 O12 IHP D 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8884 O11 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM17797 O11 IHP P 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11855 O11 IHP J 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2942 O11 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM14826 O11 IHP M 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5913 O11 IHP D 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2947 O16 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8884 O11 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11860 O16 IHP J 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM17797 O11 IHP P 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5918 O16 IHP D 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM14831 O16 IHP M 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8848 O11 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM17761 O11 IHP P 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8889 O16 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM17802 O16 IHP P 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11857 O13 IHP J 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2942 O11 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2944 O13 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11855 O11 IHP J 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5877 O11 IHP D 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM14790 O11 IHP M 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8849 O12 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM17762 O12 IHP P 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5913 O11 IHP D 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM14826 O11 IHP M 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM14829 O14 IHP M 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2945 O14 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5916 O14 IHP D 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5915 O13 IHP D 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM14791 O12 IHP M 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5878 O12 IHP D 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11858 O14 IHP J 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM14828 O13 IHP M 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2906 O11 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11819 O11 IHP J 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM17799 O13 IHP P 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8886 O13 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8884 O11 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2907 O12 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM17797 O11 IHP P 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11820 O12 IHP J 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM17800 O14 IHP P 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8887 O14 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11859 O15 IHP J 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2946 O15 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5917 O15 IHP D 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM14830 O15 IHP M 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8888 O15 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM17801 O15 IHP P 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5877 O11 IHP D 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM14790 O11 IHP M 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11819 O11 IHP J 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2906 O11 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5917 O15 IHP D 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM14830 O15 IHP M 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2946 O15 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8888 O15 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11859 O15 IHP J 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM17801 O15 IHP P 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM17761 O11 IHP P 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8848 O11 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11824 O16 IHP J 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2911 O16 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11860 O16 IHP J 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2947 O16 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM17802 O16 IHP P 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8853 O16 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8889 O16 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM17766 O16 IHP P 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11855 O11 IHP J 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2942 O11 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5918 O16 IHP D 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM14831 O16 IHP M 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5878 O12 IHP D 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM14791 O12 IHP M 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5913 O11 IHP D 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2907 O12 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM14826 O11 IHP M 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5882 O16 IHP D 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM14795 O16 IHP M 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11820 O12 IHP J 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM17797 O11 IHP P 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8884 O11 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8849 O12 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11857 O13 IHP J 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2944 O13 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM17762 O12 IHP P 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5913 O11 IHP D 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM14826 O11 IHP M 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8884 O11 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8886 O13 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM14831 O16 IHP M 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5918 O16 IHP D 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM17799 O13 IHP P 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM17797 O11 IHP P 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2942 O11 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8889 O16 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM17802 O16 IHP P 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11855 O11 IHP J 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2947 O16 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11860 O16 IHP J 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5915 O13 IHP D 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM14828 O13 IHP M 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11821 O13 IHP J 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2908 O13 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM17763 O13 IHP P 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8850 O13 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM14792 O13 IHP M 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5913 O11 IHP D 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM14826 O11 IHP M 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5879 O13 IHP D 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2942 O11 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11855 O11 IHP J 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8884 O11 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM17797 O11 IHP P 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5913 O11 IHP D 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM14826 O11 IHP M 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8852 O15 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM17765 O15 IHP P 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2942 O11 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11823 O15 IHP J 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11855 O11 IHP J 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2910 O15 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5878 O12 IHP D 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM14791 O12 IHP M 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5881 O15 IHP D 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8884 O11 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM17797 O11 IHP P 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM14794 O15 IHP M 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2907 O12 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11820 O12 IHP J 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM14791 O12 IHP M 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5878 O12 IHP D 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2943 O12 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11856 O12 IHP J 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM17762 O12 IHP P 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8849 O12 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM17762 O12 IHP P 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM14827 O12 IHP M 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5914 O12 IHP D 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8849 O12 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11820 O12 IHP J 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2907 O12 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8885 O12 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM17798 O12 IHP P 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11858 O14 IHP J 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2945 O14 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11822 O14 IHP J 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2909 O14 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM17764 O14 IHP P 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM14829 O14 IHP M 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5916 O14 IHP D 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM17800 O14 IHP P 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8887 O14 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8851 O14 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM14793 O14 IHP M 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5880 O14 IHP D 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11859 O15 IHP J 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2946 O15 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5878 O12 IHP D 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM17801 O15 IHP P 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM14791 O12 IHP M 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8888 O15 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM14826 O11 IHP M 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5913 O11 IHP D 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2942 O11 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM14831 O16 IHP M 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM14830 O15 IHP M 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5917 O15 IHP D 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11855 O11 IHP J 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5918 O16 IHP D 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM17797 O11 IHP P 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8884 O11 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11822 O14 IHP J 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2909 O14 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM17799 O13 IHP P 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8886 O13 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM14790 O11 IHP M 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8889 O16 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM17802 O16 IHP P 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM17762 O12 IHP P 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5877 O11 IHP D 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11860 O16 IHP J 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2907 O12 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2947 O16 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8849 O12 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2906 O11 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11820 O12 IHP J 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11857 O13 IHP J 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11819 O11 IHP J 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2944 O13 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM17800 O14 IHP P 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8851 O14 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM17764 O14 IHP P 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8887 O14 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8848 O11 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5915 O13 IHP D 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM17761 O11 IHP P 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM14828 O13 IHP M 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM14829 O14 IHP M 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5916 O14 IHP D 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5877 O11 IHP D 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM14790 O11 IHP M 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11858 O14 IHP J 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2945 O14 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8848 O11 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM14793 O14 IHP M 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5880 O14 IHP D 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM17764 O14 IHP P 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM17761 O11 IHP P 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM14795 O16 IHP M 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5882 O16 IHP D 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8851 O14 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2906 O11 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11819 O11 IHP J 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5880 O14 IHP D 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM14793 O14 IHP M 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11822 O14 IHP J 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2911 O16 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8853 O16 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11824 O16 IHP J 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2909 O14 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM17766 O16 IHP P 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8889 O16 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM17802 O16 IHP P 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8889 O16 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM17802 O16 IHP P 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM14831 O16 IHP M 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5918 O16 IHP D 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8889 O16 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM17802 O16 IHP P 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5918 O16 IHP D 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM14831 O16 IHP M 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2947 O16 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11860 O16 IHP J 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2947 O16 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM17801 O15 IHP P 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8888 O15 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11860 O16 IHP J 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11860 O16 IHP J 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2947 O16 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5917 O15 IHP D 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM14830 O15 IHP M 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11859 O15 IHP J 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2946 O15 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM14831 O16 IHP M 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5918 O16 IHP D 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM14831 O16 IHP M 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11860 O16 IHP J 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5918 O16 IHP D 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2947 O16 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8889 O16 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM17802 O16 IHP P 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8851 O14 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM17764 O14 IHP P 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5880 O14 IHP D 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM14793 O14 IHP M 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2944 O13 IHP A 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11857 O13 IHP J 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM17799 O13 IHP P 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8886 O13 IHP G 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2909 O14 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5915 O13 IHP D 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM14828 O13 IHP M 302 .*. O " rejected from bonding due to valence issues. Atom "HETATM11822 O14 IHP J 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM17766 O16 IHP P 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 8853 O16 IHP G 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM11824 O16 IHP J 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 2911 O16 IHP A 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM14795 O16 IHP M 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 5882 O16 IHP D 301 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=21, symmetry=0 Number of additional bonds: simple=21, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.99 Conformation dependent library (CDL) restraints added in 2.1 seconds 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4128 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 6 sheets defined 69.4% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'A' and resid 16 through 28 Processing helix chain 'A' and resid 35 through 44 Processing helix chain 'A' and resid 48 through 59 removed outlier: 3.752A pdb=" N VAL A 59 " --> pdb=" O MET A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 84 removed outlier: 3.543A pdb=" N ASP A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 105 Processing helix chain 'A' and resid 109 through 119 Processing helix chain 'A' and resid 127 through 145 removed outlier: 3.926A pdb=" N ARG A 131 " --> pdb=" O GLY A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 160 through 175 removed outlier: 3.881A pdb=" N TYR A 164 " --> pdb=" O PRO A 160 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL A 165 " --> pdb=" O PHE A 161 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER A 171 " --> pdb=" O ARG A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 193 removed outlier: 4.597A pdb=" N LEU A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ILE A 191 " --> pdb=" O GLN A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 205 removed outlier: 3.651A pdb=" N VAL A 201 " --> pdb=" O ASP A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 218 Processing helix chain 'B' and resid 160 through 167 Processing helix chain 'B' and resid 168 through 175 removed outlier: 3.559A pdb=" N ALA B 174 " --> pdb=" O LYS B 170 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU B 175 " --> pdb=" O SER B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 188 Processing helix chain 'B' and resid 188 through 193 Processing helix chain 'B' and resid 195 through 206 removed outlier: 3.640A pdb=" N GLY B 206 " --> pdb=" O LEU B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 218 Processing helix chain 'C' and resid 164 through 176 removed outlier: 4.278A pdb=" N LYS C 170 " --> pdb=" O ASP C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 193 removed outlier: 4.290A pdb=" N TRP C 184 " --> pdb=" O ALA C 180 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N MET C 185 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N ILE C 191 " --> pdb=" O GLN C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 206 removed outlier: 4.394A pdb=" N VAL C 201 " --> pdb=" O ASP C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 218 Processing helix chain 'D' and resid 16 through 28 Processing helix chain 'D' and resid 35 through 44 Processing helix chain 'D' and resid 48 through 59 removed outlier: 3.752A pdb=" N VAL D 59 " --> pdb=" O MET D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 84 removed outlier: 3.543A pdb=" N ASP D 79 " --> pdb=" O ASP D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 105 Processing helix chain 'D' and resid 109 through 119 Processing helix chain 'D' and resid 127 through 145 removed outlier: 3.926A pdb=" N ARG D 131 " --> pdb=" O GLY D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 153 Processing helix chain 'D' and resid 160 through 175 removed outlier: 3.881A pdb=" N TYR D 164 " --> pdb=" O PRO D 160 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL D 165 " --> pdb=" O PHE D 161 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER D 171 " --> pdb=" O ARG D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 193 removed outlier: 4.597A pdb=" N LEU D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ILE D 191 " --> pdb=" O GLN D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 205 removed outlier: 3.651A pdb=" N VAL D 201 " --> pdb=" O ASP D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 218 Processing helix chain 'E' and resid 160 through 167 Processing helix chain 'E' and resid 168 through 175 removed outlier: 3.560A pdb=" N ALA E 174 " --> pdb=" O LYS E 170 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU E 175 " --> pdb=" O SER E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 188 Processing helix chain 'E' and resid 188 through 193 Processing helix chain 'E' and resid 195 through 206 removed outlier: 3.640A pdb=" N GLY E 206 " --> pdb=" O LEU E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 218 Processing helix chain 'F' and resid 164 through 176 removed outlier: 4.277A pdb=" N LYS F 170 " --> pdb=" O ASP F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 193 removed outlier: 4.290A pdb=" N TRP F 184 " --> pdb=" O ALA F 180 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N MET F 185 " --> pdb=" O VAL F 181 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU F 190 " --> pdb=" O THR F 186 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N ILE F 191 " --> pdb=" O GLN F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 206 removed outlier: 4.394A pdb=" N VAL F 201 " --> pdb=" O ASP F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 218 Processing helix chain 'G' and resid 16 through 28 Processing helix chain 'G' and resid 35 through 44 Processing helix chain 'G' and resid 48 through 59 removed outlier: 3.752A pdb=" N VAL G 59 " --> pdb=" O MET G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 84 removed outlier: 3.543A pdb=" N ASP G 79 " --> pdb=" O ASP G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 105 Processing helix chain 'G' and resid 109 through 119 Processing helix chain 'G' and resid 127 through 145 removed outlier: 3.927A pdb=" N ARG G 131 " --> pdb=" O GLY G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 153 Processing helix chain 'G' and resid 160 through 175 removed outlier: 3.881A pdb=" N TYR G 164 " --> pdb=" O PRO G 160 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL G 165 " --> pdb=" O PHE G 161 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER G 171 " --> pdb=" O ARG G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 193 removed outlier: 4.598A pdb=" N LEU G 190 " --> pdb=" O THR G 186 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ILE G 191 " --> pdb=" O GLN G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 205 removed outlier: 3.651A pdb=" N VAL G 201 " --> pdb=" O ASP G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 218 Processing helix chain 'H' and resid 160 through 167 Processing helix chain 'H' and resid 168 through 175 removed outlier: 3.560A pdb=" N ALA H 174 " --> pdb=" O LYS H 170 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU H 175 " --> pdb=" O SER H 171 " (cutoff:3.500A) Processing helix chain 'H' and resid 178 through 188 Processing helix chain 'H' and resid 188 through 193 Processing helix chain 'H' and resid 195 through 206 removed outlier: 3.639A pdb=" N GLY H 206 " --> pdb=" O LEU H 202 " (cutoff:3.500A) Processing helix chain 'H' and resid 210 through 218 Processing helix chain 'I' and resid 164 through 176 removed outlier: 4.278A pdb=" N LYS I 170 " --> pdb=" O ASP I 166 " (cutoff:3.500A) Processing helix chain 'I' and resid 178 through 193 removed outlier: 4.290A pdb=" N TRP I 184 " --> pdb=" O ALA I 180 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N MET I 185 " --> pdb=" O VAL I 181 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU I 190 " --> pdb=" O THR I 186 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N ILE I 191 " --> pdb=" O GLN I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 206 removed outlier: 4.394A pdb=" N VAL I 201 " --> pdb=" O ASP I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 210 through 218 Processing helix chain 'J' and resid 16 through 28 Processing helix chain 'J' and resid 35 through 44 Processing helix chain 'J' and resid 48 through 59 removed outlier: 3.752A pdb=" N VAL J 59 " --> pdb=" O MET J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 84 removed outlier: 3.543A pdb=" N ASP J 79 " --> pdb=" O ASP J 75 " (cutoff:3.500A) Processing helix chain 'J' and resid 99 through 105 Processing helix chain 'J' and resid 109 through 119 Processing helix chain 'J' and resid 127 through 145 removed outlier: 3.926A pdb=" N ARG J 131 " --> pdb=" O GLY J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 149 through 153 Processing helix chain 'J' and resid 160 through 175 removed outlier: 3.881A pdb=" N TYR J 164 " --> pdb=" O PRO J 160 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL J 165 " --> pdb=" O PHE J 161 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER J 171 " --> pdb=" O ARG J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 178 through 193 removed outlier: 4.597A pdb=" N LEU J 190 " --> pdb=" O THR J 186 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ILE J 191 " --> pdb=" O GLN J 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 195 through 205 removed outlier: 3.651A pdb=" N VAL J 201 " --> pdb=" O ASP J 197 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 218 Processing helix chain 'K' and resid 160 through 167 Processing helix chain 'K' and resid 168 through 175 removed outlier: 3.559A pdb=" N ALA K 174 " --> pdb=" O LYS K 170 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU K 175 " --> pdb=" O SER K 171 " (cutoff:3.500A) Processing helix chain 'K' and resid 178 through 188 Processing helix chain 'K' and resid 188 through 193 Processing helix chain 'K' and resid 195 through 206 removed outlier: 3.640A pdb=" N GLY K 206 " --> pdb=" O LEU K 202 " (cutoff:3.500A) Processing helix chain 'K' and resid 210 through 218 Processing helix chain 'L' and resid 164 through 176 removed outlier: 4.278A pdb=" N LYS L 170 " --> pdb=" O ASP L 166 " (cutoff:3.500A) Processing helix chain 'L' and resid 178 through 193 removed outlier: 4.290A pdb=" N TRP L 184 " --> pdb=" O ALA L 180 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N MET L 185 " --> pdb=" O VAL L 181 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU L 190 " --> pdb=" O THR L 186 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N ILE L 191 " --> pdb=" O GLN L 187 " (cutoff:3.500A) Processing helix chain 'L' and resid 195 through 206 removed outlier: 4.394A pdb=" N VAL L 201 " --> pdb=" O ASP L 197 " (cutoff:3.500A) Processing helix chain 'L' and resid 210 through 218 Processing helix chain 'M' and resid 16 through 28 Processing helix chain 'M' and resid 35 through 44 Processing helix chain 'M' and resid 48 through 59 removed outlier: 3.752A pdb=" N VAL M 59 " --> pdb=" O MET M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 84 removed outlier: 3.543A pdb=" N ASP M 79 " --> pdb=" O ASP M 75 " (cutoff:3.500A) Processing helix chain 'M' and resid 99 through 105 Processing helix chain 'M' and resid 109 through 119 Processing helix chain 'M' and resid 127 through 145 removed outlier: 3.926A pdb=" N ARG M 131 " --> pdb=" O GLY M 127 " (cutoff:3.500A) Processing helix chain 'M' and resid 149 through 153 Processing helix chain 'M' and resid 160 through 175 removed outlier: 3.881A pdb=" N TYR M 164 " --> pdb=" O PRO M 160 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL M 165 " --> pdb=" O PHE M 161 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER M 171 " --> pdb=" O ARG M 167 " (cutoff:3.500A) Processing helix chain 'M' and resid 178 through 193 removed outlier: 4.597A pdb=" N LEU M 190 " --> pdb=" O THR M 186 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ILE M 191 " --> pdb=" O GLN M 187 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 205 removed outlier: 3.651A pdb=" N VAL M 201 " --> pdb=" O ASP M 197 " (cutoff:3.500A) Processing helix chain 'M' and resid 210 through 218 Processing helix chain 'N' and resid 160 through 167 Processing helix chain 'N' and resid 168 through 175 removed outlier: 3.560A pdb=" N ALA N 174 " --> pdb=" O LYS N 170 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU N 175 " --> pdb=" O SER N 171 " (cutoff:3.500A) Processing helix chain 'N' and resid 178 through 188 Processing helix chain 'N' and resid 188 through 193 Processing helix chain 'N' and resid 195 through 206 removed outlier: 3.640A pdb=" N GLY N 206 " --> pdb=" O LEU N 202 " (cutoff:3.500A) Processing helix chain 'N' and resid 210 through 218 Processing helix chain 'O' and resid 164 through 176 removed outlier: 4.277A pdb=" N LYS O 170 " --> pdb=" O ASP O 166 " (cutoff:3.500A) Processing helix chain 'O' and resid 178 through 193 removed outlier: 4.290A pdb=" N TRP O 184 " --> pdb=" O ALA O 180 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N MET O 185 " --> pdb=" O VAL O 181 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU O 190 " --> pdb=" O THR O 186 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N ILE O 191 " --> pdb=" O GLN O 187 " (cutoff:3.500A) Processing helix chain 'O' and resid 195 through 206 removed outlier: 4.395A pdb=" N VAL O 201 " --> pdb=" O ASP O 197 " (cutoff:3.500A) Processing helix chain 'O' and resid 210 through 218 Processing helix chain 'P' and resid 16 through 28 Processing helix chain 'P' and resid 35 through 44 Processing helix chain 'P' and resid 48 through 59 removed outlier: 3.752A pdb=" N VAL P 59 " --> pdb=" O MET P 55 " (cutoff:3.500A) Processing helix chain 'P' and resid 62 through 84 removed outlier: 3.543A pdb=" N ASP P 79 " --> pdb=" O ASP P 75 " (cutoff:3.500A) Processing helix chain 'P' and resid 99 through 105 Processing helix chain 'P' and resid 109 through 119 Processing helix chain 'P' and resid 127 through 145 removed outlier: 3.926A pdb=" N ARG P 131 " --> pdb=" O GLY P 127 " (cutoff:3.500A) Processing helix chain 'P' and resid 149 through 153 Processing helix chain 'P' and resid 160 through 175 removed outlier: 3.881A pdb=" N TYR P 164 " --> pdb=" O PRO P 160 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER P 171 " --> pdb=" O ARG P 167 " (cutoff:3.500A) Processing helix chain 'P' and resid 178 through 193 removed outlier: 4.597A pdb=" N LEU P 190 " --> pdb=" O THR P 186 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ILE P 191 " --> pdb=" O GLN P 187 " (cutoff:3.500A) Processing helix chain 'P' and resid 195 through 205 removed outlier: 3.652A pdb=" N VAL P 201 " --> pdb=" O ASP P 197 " (cutoff:3.500A) Processing helix chain 'P' and resid 210 through 218 Processing helix chain 'Q' and resid 160 through 167 Processing helix chain 'Q' and resid 168 through 175 removed outlier: 3.560A pdb=" N ALA Q 174 " --> pdb=" O LYS Q 170 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU Q 175 " --> pdb=" O SER Q 171 " (cutoff:3.500A) Processing helix chain 'Q' and resid 178 through 188 Processing helix chain 'Q' and resid 188 through 193 Processing helix chain 'Q' and resid 195 through 206 removed outlier: 3.640A pdb=" N GLY Q 206 " --> pdb=" O LEU Q 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 210 through 218 Processing helix chain 'R' and resid 164 through 176 removed outlier: 4.277A pdb=" N LYS R 170 " --> pdb=" O ASP R 166 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 193 removed outlier: 4.290A pdb=" N TRP R 184 " --> pdb=" O ALA R 180 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N MET R 185 " --> pdb=" O VAL R 181 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU R 190 " --> pdb=" O THR R 186 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N ILE R 191 " --> pdb=" O GLN R 187 " (cutoff:3.500A) Processing helix chain 'R' and resid 195 through 206 removed outlier: 4.395A pdb=" N VAL R 201 " --> pdb=" O ASP R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 218 Processing sheet with id=1, first strand: chain 'A' and resid 2 through 3 Processing sheet with id=2, first strand: chain 'D' and resid 2 through 3 Processing sheet with id=3, first strand: chain 'G' and resid 2 through 3 Processing sheet with id=4, first strand: chain 'J' and resid 2 through 3 Processing sheet with id=5, first strand: chain 'M' and resid 2 through 3 Processing sheet with id=6, first strand: chain 'P' and resid 2 through 3 919 hydrogen bonds defined for protein. 2703 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: 5.37 Time building geometry restraints manager: 7.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3006 1.31 - 1.43: 4218 1.43 - 1.56: 10692 1.56 - 1.69: 72 1.69 - 1.82: 210 Bond restraints: 18198 Sorted by residual: bond pdb=" CA SER D 44 " pdb=" CB SER D 44 " ideal model delta sigma weight residual 1.530 1.465 0.065 1.39e-02 5.18e+03 2.19e+01 bond pdb=" CA SER A 44 " pdb=" CB SER A 44 " ideal model delta sigma weight residual 1.530 1.465 0.065 1.39e-02 5.18e+03 2.17e+01 bond pdb=" CA SER J 44 " pdb=" CB SER J 44 " ideal model delta sigma weight residual 1.530 1.465 0.065 1.39e-02 5.18e+03 2.17e+01 bond pdb=" CA SER G 44 " pdb=" CB SER G 44 " ideal model delta sigma weight residual 1.530 1.465 0.065 1.39e-02 5.18e+03 2.17e+01 bond pdb=" CA SER P 44 " pdb=" CB SER P 44 " ideal model delta sigma weight residual 1.530 1.465 0.065 1.39e-02 5.18e+03 2.17e+01 ... (remaining 18193 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 17667 2.05 - 4.10: 6254 4.10 - 6.15: 806 6.15 - 8.20: 131 8.20 - 10.25: 12 Bond angle restraints: 24870 Sorted by residual: angle pdb=" N PHE N 161 " pdb=" CA PHE N 161 " pdb=" C PHE N 161 " ideal model delta sigma weight residual 113.18 105.57 7.61 1.21e+00 6.83e-01 3.96e+01 angle pdb=" N PHE H 161 " pdb=" CA PHE H 161 " pdb=" C PHE H 161 " ideal model delta sigma weight residual 113.18 105.59 7.59 1.21e+00 6.83e-01 3.94e+01 angle pdb=" N PHE K 161 " pdb=" CA PHE K 161 " pdb=" C PHE K 161 " ideal model delta sigma weight residual 113.18 105.60 7.58 1.21e+00 6.83e-01 3.93e+01 angle pdb=" N PHE B 161 " pdb=" CA PHE B 161 " pdb=" C PHE B 161 " ideal model delta sigma weight residual 113.18 105.60 7.58 1.21e+00 6.83e-01 3.93e+01 angle pdb=" N PHE E 161 " pdb=" CA PHE E 161 " pdb=" C PHE E 161 " ideal model delta sigma weight residual 113.18 105.61 7.57 1.21e+00 6.83e-01 3.92e+01 ... (remaining 24865 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.18: 10585 25.18 - 50.36: 497 50.36 - 75.54: 240 75.54 - 100.72: 0 100.72 - 125.90: 144 Dihedral angle restraints: 11466 sinusoidal: 5076 harmonic: 6390 Sorted by residual: dihedral pdb=" CB CYS G 198 " pdb=" SG CYS G 198 " pdb=" SG CYS G 218 " pdb=" CB CYS G 218 " ideal model delta sinusoidal sigma weight residual -86.00 -151.51 65.51 1 1.00e+01 1.00e-02 5.62e+01 dihedral pdb=" CB CYS D 198 " pdb=" SG CYS D 198 " pdb=" SG CYS D 218 " pdb=" CB CYS D 218 " ideal model delta sinusoidal sigma weight residual -86.00 -151.51 65.51 1 1.00e+01 1.00e-02 5.62e+01 dihedral pdb=" CB CYS M 198 " pdb=" SG CYS M 198 " pdb=" SG CYS M 218 " pdb=" CB CYS M 218 " ideal model delta sinusoidal sigma weight residual -86.00 -151.50 65.50 1 1.00e+01 1.00e-02 5.62e+01 ... (remaining 11463 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 795 0.068 - 0.136: 1039 0.136 - 0.203: 673 0.203 - 0.271: 229 0.271 - 0.339: 18 Chirality restraints: 2754 Sorted by residual: chirality pdb=" C1 IHP M 301 " pdb=" C2 IHP M 301 " pdb=" C6 IHP M 301 " pdb=" O11 IHP M 301 " both_signs ideal model delta sigma weight residual False 2.32 2.65 -0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" C1 IHP P 301 " pdb=" C2 IHP P 301 " pdb=" C6 IHP P 301 " pdb=" O11 IHP P 301 " both_signs ideal model delta sigma weight residual False 2.32 2.65 -0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" C1 IHP J 301 " pdb=" C2 IHP J 301 " pdb=" C6 IHP J 301 " pdb=" O11 IHP J 301 " both_signs ideal model delta sigma weight residual False 2.32 2.65 -0.34 2.00e-01 2.50e+01 2.87e+00 ... (remaining 2751 not shown) Planarity restraints: 3180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 18 " 0.478 9.50e-02 1.11e+02 2.15e-01 2.82e+01 pdb=" NE ARG G 18 " -0.027 2.00e-02 2.50e+03 pdb=" CZ ARG G 18 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG G 18 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG G 18 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG M 18 " -0.478 9.50e-02 1.11e+02 2.14e-01 2.82e+01 pdb=" NE ARG M 18 " 0.027 2.00e-02 2.50e+03 pdb=" CZ ARG M 18 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG M 18 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG M 18 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 18 " 0.478 9.50e-02 1.11e+02 2.14e-01 2.82e+01 pdb=" NE ARG D 18 " -0.027 2.00e-02 2.50e+03 pdb=" CZ ARG D 18 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG D 18 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG D 18 " 0.017 2.00e-02 2.50e+03 ... (remaining 3177 not shown) Histogram of nonbonded interaction distances: 0.22 - 1.15: 656 1.15 - 2.09: 2004 2.09 - 3.03: 14759 3.03 - 3.96: 54683 3.96 - 4.90: 94264 Warning: very small nonbonded interaction distances. Nonbonded interactions: 166366 Sorted by model distance: nonbonded pdb=" O23 IHP D 302 " pdb=" O31 IHP J 302 " model vdw 0.218 3.040 nonbonded pdb=" O31 IHP A 302 " pdb=" O23 IHP M 302 " model vdw 0.219 3.040 nonbonded pdb=" O23 IHP J 302 " pdb=" O31 IHP P 302 " model vdw 0.221 3.040 nonbonded pdb=" O23 IHP A 302 " pdb=" O31 IHP G 302 " model vdw 0.221 3.040 nonbonded pdb=" O23 IHP G 302 " pdb=" O31 IHP M 302 " model vdw 0.232 3.040 ... (remaining 166361 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'M' selection = chain 'P' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' } 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=0.98 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: 4.740 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: 0.650 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 42.710 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5356 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 : 0.045 1.424 18237 Z= 4.369 Angle : 1.949 10.250 24906 Z= 1.416 Chirality : 0.128 0.339 2754 Planarity : 0.021 0.215 3180 Dihedral : 22.705 125.902 7284 Min Nonbonded Distance : 0.218 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.62 % Allowed : 4.71 % Favored : 94.67 % 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: -2.84 (0.15), residues: 2178 helix: -1.70 (0.11), residues: 1494 sheet: -1.42 (0.69), residues: 54 loop : -1.90 (0.22), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.006 TRP R 184 HIS 0.004 0.001 HIS P 12 PHE 0.020 0.004 PHE J 168 TYR 0.034 0.004 TYR D 50 ARG 0.018 0.003 ARG R 167 Details of bonding type rmsd hydrogen bonds : bond 0.24818 ( 919) hydrogen bonds : angle 8.28105 ( 2703) SS BOND : bond 0.00852 ( 18) SS BOND : angle 1.36164 ( 36) covalent geometry : bond 0.01352 (18198) covalent geometry : angle 1.94998 (24870) Misc. bond : bond 1.25793 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 548 time to evaluate : 2.020 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 12 outliers final: 6 residues processed: 554 average time/residue: 0.3459 time to fit residues: 271.8296 Evaluate side-chains 270 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 264 time to evaluate : 1.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 PHE Chi-restraints excluded: chain E residue 161 PHE Chi-restraints excluded: chain H residue 161 PHE Chi-restraints excluded: chain K residue 161 PHE Chi-restraints excluded: chain N residue 161 PHE Chi-restraints excluded: chain Q residue 161 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.8980 chunk 163 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 110 optimal weight: 0.6980 chunk 87 optimal weight: 5.9990 chunk 169 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 chunk 126 optimal weight: 7.9990 chunk 196 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN A 62 HIS A 67 GLN ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 ASN A 187 GLN A 208 ASN B 187 GLN C 187 GLN ** C 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN D 62 HIS D 67 GLN D 146 ASN D 187 GLN D 208 ASN E 187 GLN F 187 GLN ** F 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN G 62 HIS G 67 GLN G 146 ASN G 187 GLN G 208 ASN H 187 GLN I 187 GLN ** I 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN J 62 HIS J 67 GLN ** J 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 146 ASN J 187 GLN J 208 ASN K 187 GLN L 187 GLN ** L 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN M 62 HIS M 67 GLN M 146 ASN M 187 GLN M 208 ASN N 187 GLN O 187 GLN ** O 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 3 GLN P 62 HIS P 67 GLN P 146 ASN P 187 GLN P 208 ASN Q 187 GLN R 187 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.066335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.051247 restraints weight = 96952.380| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 4.90 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3361 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3358 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.037 1.249 18237 Z= 1.840 Angle : 3.500 76.352 24906 Z= 1.213 Chirality : 0.326 5.493 2754 Planarity : 0.008 0.130 3180 Dihedral : 29.668 175.502 2862 Min Nonbonded Distance : 1.594 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.16 % Allowed : 16.05 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.26 (0.17), residues: 2178 helix: -0.41 (0.12), residues: 1494 sheet: -0.38 (0.80), residues: 54 loop : -1.62 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP O 184 HIS 0.006 0.002 HIS D 84 PHE 0.023 0.002 PHE I 161 TYR 0.025 0.002 TYR D 50 ARG 0.022 0.001 ARG D 18 Details of bonding type rmsd hydrogen bonds : bond 0.07058 ( 919) hydrogen bonds : angle 5.69246 ( 2703) SS BOND : bond 0.00314 ( 18) SS BOND : angle 0.62509 ( 36) covalent geometry : bond 0.03674 (18198) covalent geometry : angle 3.50272 (24870) Misc. bond : bond 0.05282 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 305 time to evaluate : 2.058 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 31 LYS cc_start: 0.8720 (mmtt) cc_final: 0.7995 (tptp) REVERT: B 177 THR cc_start: 0.7281 (p) cc_final: 0.6748 (p) REVERT: B 182 LYS cc_start: 0.7886 (mmtt) cc_final: 0.7632 (mmtt) REVERT: D 31 LYS cc_start: 0.8817 (mmtt) cc_final: 0.8059 (tptp) REVERT: D 55 MET cc_start: 0.6951 (mtp) cc_final: 0.6748 (mtm) REVERT: E 177 THR cc_start: 0.7431 (p) cc_final: 0.6981 (p) REVERT: E 178 ASP cc_start: 0.5046 (t0) cc_final: 0.4775 (t70) REVERT: E 182 LYS cc_start: 0.7968 (mmtt) cc_final: 0.7440 (mmtt) REVERT: G 31 LYS cc_start: 0.8806 (mmtt) cc_final: 0.8597 (mmmt) REVERT: G 182 LYS cc_start: 0.8649 (mtpt) cc_final: 0.8352 (mttt) REVERT: H 178 ASP cc_start: 0.5094 (t0) cc_final: 0.4756 (t70) REVERT: I 184 TRP cc_start: 0.8623 (t60) cc_final: 0.8349 (t-100) REVERT: I 185 MET cc_start: 0.8870 (ptp) cc_final: 0.8606 (ptp) REVERT: I 214 MET cc_start: 0.8999 (mpp) cc_final: 0.8766 (mpp) REVERT: J 31 LYS cc_start: 0.8713 (mmtt) cc_final: 0.7986 (tptp) REVERT: K 177 THR cc_start: 0.7294 (p) cc_final: 0.6768 (p) REVERT: K 182 LYS cc_start: 0.7886 (mmtt) cc_final: 0.7633 (mmtt) REVERT: M 31 LYS cc_start: 0.8819 (mmtt) cc_final: 0.8057 (tptp) REVERT: N 177 THR cc_start: 0.7446 (p) cc_final: 0.6997 (p) REVERT: N 178 ASP cc_start: 0.5043 (t0) cc_final: 0.4774 (t70) REVERT: N 182 LYS cc_start: 0.7967 (mmtt) cc_final: 0.7440 (mmtt) REVERT: P 31 LYS cc_start: 0.8806 (mmtt) cc_final: 0.8595 (mmmt) REVERT: P 182 LYS cc_start: 0.8645 (mtpt) cc_final: 0.8350 (mttt) REVERT: Q 178 ASP cc_start: 0.5099 (t0) cc_final: 0.4766 (t70) REVERT: R 184 TRP cc_start: 0.8626 (t60) cc_final: 0.8418 (t-100) REVERT: R 185 MET cc_start: 0.8876 (ptp) cc_final: 0.8655 (ptp) REVERT: R 214 MET cc_start: 0.8998 (mpp) cc_final: 0.8762 (mpp) outliers start: 61 outliers final: 22 residues processed: 345 average time/residue: 0.3177 time to fit residues: 159.3417 Evaluate side-chains 243 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 221 time to evaluate : 1.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain B residue 161 PHE Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain E residue 161 PHE Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain H residue 161 PHE Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain K residue 161 PHE Chi-restraints excluded: chain L residue 165 VAL Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain N residue 161 PHE Chi-restraints excluded: chain O residue 165 VAL Chi-restraints excluded: chain P residue 59 VAL Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain Q residue 161 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 159 optimal weight: 0.8980 chunk 82 optimal weight: 8.9990 chunk 110 optimal weight: 0.9990 chunk 72 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 chunk 112 optimal weight: 3.9990 chunk 170 optimal weight: 0.8980 chunk 154 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 134 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 HIS ** D 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 121 GLN ** J 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 84 HIS ** M 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 208 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 = 0.3749 r_free = 0.3749 target = 0.063741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.048240 restraints weight = 94683.233| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 4.92 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3284 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3283 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.5707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.032 1.303 18237 Z= 1.595 Angle : 2.736 80.812 24906 Z= 0.956 Chirality : 0.257 4.858 2754 Planarity : 0.006 0.081 3180 Dihedral : 32.063 179.608 2862 Min Nonbonded Distance : 1.605 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.29 % Allowed : 17.24 % Favored : 81.47 % 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: -0.52 (0.17), residues: 2178 helix: 0.01 (0.13), residues: 1440 sheet: None (None), residues: 0 loop : -0.83 (0.24), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 184 HIS 0.003 0.001 HIS P 62 PHE 0.013 0.002 PHE O 161 TYR 0.020 0.003 TYR J 50 ARG 0.009 0.001 ARG G 18 Details of bonding type rmsd hydrogen bonds : bond 0.04869 ( 919) hydrogen bonds : angle 5.04666 ( 2703) SS BOND : bond 0.00188 ( 18) SS BOND : angle 0.71085 ( 36) covalent geometry : bond 0.03175 (18198) covalent geometry : angle 2.73742 (24870) Misc. bond : bond 0.05954 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 259 time to evaluate : 1.905 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LYS cc_start: 0.8775 (mmmt) cc_final: 0.8467 (mmmt) REVERT: B 177 THR cc_start: 0.7226 (p) cc_final: 0.6715 (p) REVERT: B 182 LYS cc_start: 0.8001 (mmtt) cc_final: 0.7610 (mmtt) REVERT: C 182 LYS cc_start: 0.8867 (pptt) cc_final: 0.8007 (ptmt) REVERT: D 31 LYS cc_start: 0.8928 (mmtt) cc_final: 0.8005 (tptt) REVERT: D 117 MET cc_start: 0.7524 (ttm) cc_final: 0.7276 (mtp) REVERT: E 177 THR cc_start: 0.7341 (p) cc_final: 0.6830 (p) REVERT: E 178 ASP cc_start: 0.6243 (t0) cc_final: 0.5830 (t70) REVERT: E 182 LYS cc_start: 0.8094 (mmtt) cc_final: 0.7738 (mmtt) REVERT: E 213 GLU cc_start: 0.9482 (mp0) cc_final: 0.9276 (mp0) REVERT: F 182 LYS cc_start: 0.9002 (pptt) cc_final: 0.8223 (ptmt) REVERT: G 31 LYS cc_start: 0.8920 (mmtt) cc_final: 0.8039 (tptp) REVERT: G 158 LYS cc_start: 0.8829 (mmmt) cc_final: 0.8588 (mmmt) REVERT: G 182 LYS cc_start: 0.8635 (mtpt) cc_final: 0.8405 (mttt) REVERT: H 161 PHE cc_start: 0.6996 (OUTLIER) cc_final: 0.6743 (p90) REVERT: I 182 LYS cc_start: 0.8933 (pptt) cc_final: 0.8140 (ptmt) REVERT: I 184 TRP cc_start: 0.8637 (t60) cc_final: 0.8407 (t-100) REVERT: I 185 MET cc_start: 0.8796 (ptp) cc_final: 0.8586 (ptp) REVERT: I 214 MET cc_start: 0.9083 (mpp) cc_final: 0.8780 (mpp) REVERT: J 158 LYS cc_start: 0.8776 (mmmt) cc_final: 0.8472 (mmmt) REVERT: K 177 THR cc_start: 0.7226 (p) cc_final: 0.6711 (p) REVERT: K 182 LYS cc_start: 0.8009 (mmtt) cc_final: 0.7615 (mmtt) REVERT: L 182 LYS cc_start: 0.8866 (pptt) cc_final: 0.8068 (ptmt) REVERT: M 31 LYS cc_start: 0.8934 (mmtt) cc_final: 0.8012 (tptt) REVERT: M 117 MET cc_start: 0.7545 (ttm) cc_final: 0.7296 (mtp) REVERT: N 177 THR cc_start: 0.7347 (p) cc_final: 0.6842 (p) REVERT: N 178 ASP cc_start: 0.6233 (t0) cc_final: 0.5819 (t70) REVERT: N 182 LYS cc_start: 0.8092 (mmtt) cc_final: 0.7737 (mmtt) REVERT: O 182 LYS cc_start: 0.9009 (pptt) cc_final: 0.8228 (ptmt) REVERT: P 31 LYS cc_start: 0.8922 (mmtt) cc_final: 0.8035 (tptp) REVERT: P 158 LYS cc_start: 0.8829 (mmmt) cc_final: 0.8597 (mmmt) REVERT: P 182 LYS cc_start: 0.8636 (mtpt) cc_final: 0.8405 (mttt) REVERT: Q 161 PHE cc_start: 0.6970 (OUTLIER) cc_final: 0.6723 (p90) REVERT: R 182 LYS cc_start: 0.8929 (pptt) cc_final: 0.8137 (ptmt) REVERT: R 184 TRP cc_start: 0.8650 (t60) cc_final: 0.8416 (t-100) REVERT: R 185 MET cc_start: 0.8803 (ptp) cc_final: 0.8594 (ptp) REVERT: R 214 MET cc_start: 0.9077 (mpp) cc_final: 0.8774 (mpp) outliers start: 25 outliers final: 17 residues processed: 282 average time/residue: 0.3280 time to fit residues: 132.8495 Evaluate side-chains 238 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 219 time to evaluate : 1.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain B residue 161 PHE Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain E residue 161 PHE Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain H residue 161 PHE Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain K residue 161 PHE Chi-restraints excluded: chain M residue 86 ILE Chi-restraints excluded: chain N residue 161 PHE Chi-restraints excluded: chain N residue 181 VAL Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain O residue 165 VAL Chi-restraints excluded: chain P residue 18 ARG Chi-restraints excluded: chain P residue 86 ILE Chi-restraints excluded: chain Q residue 161 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 57 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 8 optimal weight: 0.0670 chunk 3 optimal weight: 0.8980 chunk 204 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 179 optimal weight: 7.9990 chunk 203 optimal weight: 5.9990 chunk 51 optimal weight: 0.0870 chunk 67 optimal weight: 6.9990 overall best weight: 0.7898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN A 146 ASN ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 GLN C 192 GLN ** D 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 GLN G 121 GLN G 146 ASN ** G 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 162 GLN I 192 GLN J 135 GLN J 146 ASN ** J 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 192 GLN L 192 GLN ** M 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 192 GLN P 121 GLN P 146 ASN ** P 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 162 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.063354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.047748 restraints weight = 95092.313| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 4.91 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3266 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3266 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.6422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.026 1.229 18237 Z= 1.333 Angle : 2.774 57.778 24906 Z= 0.968 Chirality : 0.218 3.541 2754 Planarity : 0.005 0.071 3180 Dihedral : 29.900 179.130 2862 Min Nonbonded Distance : 1.570 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.97 % Allowed : 16.05 % Favored : 81.99 % 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: -0.12 (0.18), residues: 2178 helix: 0.26 (0.13), residues: 1434 sheet: None (None), residues: 0 loop : -0.52 (0.24), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 184 HIS 0.002 0.001 HIS J 84 PHE 0.014 0.001 PHE F 168 TYR 0.024 0.002 TYR D 145 ARG 0.016 0.001 ARG F 173 Details of bonding type rmsd hydrogen bonds : bond 0.04218 ( 919) hydrogen bonds : angle 4.73253 ( 2703) SS BOND : bond 0.00089 ( 18) SS BOND : angle 0.60417 ( 36) covalent geometry : bond 0.02642 (18198) covalent geometry : angle 2.77628 (24870) Misc. bond : bond 0.03676 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 259 time to evaluate : 1.924 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 revert: symmetry clash revert: symmetry clash REVERT: A 84 HIS cc_start: 0.8806 (OUTLIER) cc_final: 0.8289 (m-70) REVERT: A 158 LYS cc_start: 0.8840 (mmmt) cc_final: 0.8539 (mmmt) REVERT: B 177 THR cc_start: 0.7534 (p) cc_final: 0.7317 (p) REVERT: C 182 LYS cc_start: 0.8786 (pptt) cc_final: 0.7893 (ptmt) REVERT: D 31 LYS cc_start: 0.8953 (mmtt) cc_final: 0.7963 (tptt) REVERT: E 176 GLN cc_start: 0.9135 (OUTLIER) cc_final: 0.8909 (mt0) REVERT: E 177 THR cc_start: 0.7286 (p) cc_final: 0.6557 (p) REVERT: E 178 ASP cc_start: 0.6580 (t0) cc_final: 0.6195 (t70) REVERT: E 182 LYS cc_start: 0.8138 (mmtt) cc_final: 0.7871 (mmtt) REVERT: F 182 LYS cc_start: 0.8911 (pptt) cc_final: 0.8155 (ptmt) REVERT: G 31 LYS cc_start: 0.8904 (mmtt) cc_final: 0.8629 (mmmt) REVERT: G 158 LYS cc_start: 0.8933 (mmmt) cc_final: 0.8639 (mmmt) REVERT: H 161 PHE cc_start: 0.7076 (OUTLIER) cc_final: 0.6797 (p90) REVERT: I 182 LYS cc_start: 0.8770 (pptt) cc_final: 0.7976 (ptmt) REVERT: I 184 TRP cc_start: 0.8687 (t60) cc_final: 0.8480 (t-100) REVERT: J 84 HIS cc_start: 0.8800 (OUTLIER) cc_final: 0.8284 (m-70) REVERT: J 117 MET cc_start: 0.7826 (ttm) cc_final: 0.7624 (mtp) REVERT: J 158 LYS cc_start: 0.8845 (mmmt) cc_final: 0.8550 (mmmt) REVERT: K 177 THR cc_start: 0.7536 (p) cc_final: 0.7316 (p) REVERT: L 182 LYS cc_start: 0.8788 (pptt) cc_final: 0.7895 (ptmt) REVERT: M 31 LYS cc_start: 0.8955 (mmtt) cc_final: 0.7967 (tptt) REVERT: N 176 GLN cc_start: 0.9121 (OUTLIER) cc_final: 0.8904 (mt0) REVERT: N 177 THR cc_start: 0.7305 (p) cc_final: 0.6593 (p) REVERT: N 178 ASP cc_start: 0.6581 (t0) cc_final: 0.6196 (t70) REVERT: N 182 LYS cc_start: 0.8162 (mmtt) cc_final: 0.7905 (mmtt) REVERT: O 165 VAL cc_start: 0.7715 (OUTLIER) cc_final: 0.7513 (t) REVERT: O 182 LYS cc_start: 0.8911 (pptt) cc_final: 0.8156 (ptmt) REVERT: P 31 LYS cc_start: 0.8907 (mmtt) cc_final: 0.8626 (mmmt) REVERT: P 158 LYS cc_start: 0.8884 (mmmt) cc_final: 0.8612 (mmmt) REVERT: Q 161 PHE cc_start: 0.7050 (OUTLIER) cc_final: 0.6781 (p90) REVERT: R 182 LYS cc_start: 0.8770 (pptt) cc_final: 0.7975 (ptmt) REVERT: R 184 TRP cc_start: 0.8672 (t60) cc_final: 0.8463 (t-100) outliers start: 38 outliers final: 19 residues processed: 293 average time/residue: 0.3254 time to fit residues: 138.5227 Evaluate side-chains 244 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 218 time to evaluate : 2.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 HIS Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain B residue 161 PHE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain E residue 161 PHE Chi-restraints excluded: chain E residue 176 GLN Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain H residue 161 PHE Chi-restraints excluded: chain I residue 178 ASP Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 84 HIS Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain K residue 161 PHE Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain L residue 178 ASP Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 86 ILE Chi-restraints excluded: chain N residue 161 PHE Chi-restraints excluded: chain N residue 176 GLN Chi-restraints excluded: chain O residue 165 VAL Chi-restraints excluded: chain P residue 18 ARG Chi-restraints excluded: chain P residue 86 ILE Chi-restraints excluded: chain Q residue 161 PHE Chi-restraints excluded: chain R residue 178 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 155 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 100 optimal weight: 20.0000 chunk 187 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 chunk 75 optimal weight: 0.0060 chunk 62 optimal weight: 0.9980 chunk 210 optimal weight: 8.9990 chunk 42 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 overall best weight: 3.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 GLN ** D 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 GLN F 192 GLN G 84 HIS G 135 GLN ** G 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 121 GLN ** M 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 208 ASN O 162 GLN O 192 GLN P 84 HIS P 135 GLN ** P 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.061142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.044776 restraints weight = 94476.701| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 4.93 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3169 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3169 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.7422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 0.381 18237 Z= 0.877 Angle : 2.287 47.708 24906 Z= 0.809 Chirality : 0.167 3.027 2754 Planarity : 0.005 0.088 3180 Dihedral : 28.078 179.379 2862 Min Nonbonded Distance : 1.644 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.17 % Allowed : 16.46 % Favored : 81.37 % 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: -0.04 (0.18), residues: 2178 helix: 0.26 (0.13), residues: 1452 sheet: None (None), residues: 0 loop : -0.38 (0.25), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP Q 184 HIS 0.003 0.001 HIS J 62 PHE 0.011 0.002 PHE I 161 TYR 0.022 0.002 TYR G 130 ARG 0.010 0.001 ARG P 18 Details of bonding type rmsd hydrogen bonds : bond 0.04140 ( 919) hydrogen bonds : angle 4.73541 ( 2703) SS BOND : bond 0.00148 ( 18) SS BOND : angle 0.58446 ( 36) covalent geometry : bond 0.01741 (18198) covalent geometry : angle 2.28863 (24870) Misc. bond : bond 0.04428 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 238 time to evaluate : 1.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 84 HIS cc_start: 0.8798 (OUTLIER) cc_final: 0.8197 (m-70) REVERT: A 158 LYS cc_start: 0.8963 (mmmt) cc_final: 0.8653 (mmmt) REVERT: C 182 LYS cc_start: 0.8772 (pptt) cc_final: 0.7950 (ptmt) REVERT: D 31 LYS cc_start: 0.9035 (mmtt) cc_final: 0.7942 (tptt) REVERT: D 182 LYS cc_start: 0.8531 (ptpt) cc_final: 0.8128 (ptpp) REVERT: F 182 LYS cc_start: 0.8924 (pptt) cc_final: 0.8152 (ptmt) REVERT: F 207 MET cc_start: 0.8643 (pmm) cc_final: 0.8358 (pmm) REVERT: G 158 LYS cc_start: 0.9010 (mmmt) cc_final: 0.8724 (mmmt) REVERT: H 161 PHE cc_start: 0.7197 (OUTLIER) cc_final: 0.6770 (p90) REVERT: I 182 LYS cc_start: 0.8798 (pptt) cc_final: 0.7965 (ptmt) REVERT: J 84 HIS cc_start: 0.8780 (OUTLIER) cc_final: 0.8190 (m-70) REVERT: J 117 MET cc_start: 0.8043 (ttm) cc_final: 0.7747 (mtp) REVERT: J 158 LYS cc_start: 0.8960 (mmmt) cc_final: 0.8652 (mmmt) REVERT: L 182 LYS cc_start: 0.8763 (pptt) cc_final: 0.7941 (ptmt) REVERT: M 31 LYS cc_start: 0.9050 (mmtt) cc_final: 0.7937 (tptt) REVERT: M 182 LYS cc_start: 0.8534 (ptpt) cc_final: 0.8131 (ptpp) REVERT: O 182 LYS cc_start: 0.8928 (pptt) cc_final: 0.8157 (ptmt) REVERT: O 207 MET cc_start: 0.8680 (pmm) cc_final: 0.8418 (pmm) REVERT: O 214 MET cc_start: 0.9575 (mtp) cc_final: 0.9358 (mtt) REVERT: P 158 LYS cc_start: 0.9060 (mmmt) cc_final: 0.8749 (mmmt) REVERT: Q 161 PHE cc_start: 0.7134 (OUTLIER) cc_final: 0.6713 (p90) REVERT: R 182 LYS cc_start: 0.8795 (pptt) cc_final: 0.7902 (ptmt) outliers start: 42 outliers final: 25 residues processed: 275 average time/residue: 0.3582 time to fit residues: 139.3128 Evaluate side-chains 223 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 194 time to evaluate : 2.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 HIS Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain B residue 161 PHE Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain E residue 161 PHE Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain H residue 161 PHE Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain I residue 178 ASP Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 84 HIS Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain K residue 161 PHE Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain L residue 178 ASP Chi-restraints excluded: chain L residue 210 THR Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 86 ILE Chi-restraints excluded: chain N residue 161 PHE Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain P residue 86 ILE Chi-restraints excluded: chain P residue 103 ILE Chi-restraints excluded: chain Q residue 161 PHE Chi-restraints excluded: chain Q residue 210 THR Chi-restraints excluded: chain R residue 178 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 28 optimal weight: 1.9990 chunk 211 optimal weight: 8.9990 chunk 76 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 163 optimal weight: 5.9990 chunk 71 optimal weight: 20.0000 chunk 200 optimal weight: 0.0980 chunk 34 optimal weight: 5.9990 chunk 168 optimal weight: 0.9990 chunk 145 optimal weight: 8.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 84 HIS ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 GLN ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 GLN E 208 ASN G 84 HIS ** G 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 208 ASN J 84 HIS ** J 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 GLN ** M 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 176 GLN P 84 HIS ** P 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 208 ASN R 149 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.060056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.043299 restraints weight = 94888.305| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 4.98 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3119 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3119 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.8356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.354 18237 Z= 0.741 Angle : 2.157 78.267 24906 Z= 0.768 Chirality : 0.146 2.371 2754 Planarity : 0.005 0.143 3180 Dihedral : 27.276 179.539 2862 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.48 % Allowed : 16.10 % Favored : 81.42 % 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: 0.08 (0.18), residues: 2178 helix: 0.38 (0.13), residues: 1452 sheet: None (None), residues: 0 loop : -0.39 (0.25), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP Q 184 HIS 0.002 0.001 HIS G 84 PHE 0.010 0.002 PHE D 40 TYR 0.020 0.002 TYR D 169 ARG 0.026 0.001 ARG P 18 Details of bonding type rmsd hydrogen bonds : bond 0.04164 ( 919) hydrogen bonds : angle 4.65343 ( 2703) SS BOND : bond 0.00078 ( 18) SS BOND : angle 0.47333 ( 36) covalent geometry : bond 0.01474 (18198) covalent geometry : angle 2.15812 (24870) Misc. bond : bond 0.04105 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 235 time to evaluate : 2.246 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: A 158 LYS cc_start: 0.9095 (mmmt) cc_final: 0.8727 (mmmt) REVERT: C 182 LYS cc_start: 0.8804 (pptt) cc_final: 0.7937 (ptmt) REVERT: C 205 LEU cc_start: 0.8825 (tt) cc_final: 0.8429 (tt) REVERT: C 214 MET cc_start: 0.8932 (mtt) cc_final: 0.8636 (mtt) REVERT: D 158 LYS cc_start: 0.8952 (mmmt) cc_final: 0.8725 (mmmt) REVERT: D 182 LYS cc_start: 0.8726 (ptpt) cc_final: 0.8283 (ptpp) REVERT: E 161 PHE cc_start: 0.7210 (OUTLIER) cc_final: 0.6272 (t80) REVERT: F 182 LYS cc_start: 0.8777 (pptt) cc_final: 0.8020 (ptmt) REVERT: G 158 LYS cc_start: 0.9106 (mmmt) cc_final: 0.8836 (mmmt) REVERT: I 182 LYS cc_start: 0.8767 (pptt) cc_final: 0.7826 (ptmt) REVERT: J 117 MET cc_start: 0.8005 (ttm) cc_final: 0.7653 (mtp) REVERT: J 158 LYS cc_start: 0.9088 (mmmt) cc_final: 0.8721 (mmmt) REVERT: L 182 LYS cc_start: 0.8806 (pptt) cc_final: 0.7939 (ptmt) REVERT: L 214 MET cc_start: 0.9527 (OUTLIER) cc_final: 0.9094 (mmm) REVERT: M 158 LYS cc_start: 0.8930 (mmmt) cc_final: 0.8667 (mmmt) REVERT: M 182 LYS cc_start: 0.8728 (ptpt) cc_final: 0.8284 (ptpp) REVERT: N 161 PHE cc_start: 0.7207 (OUTLIER) cc_final: 0.6280 (t80) REVERT: O 182 LYS cc_start: 0.8785 (pptt) cc_final: 0.8026 (ptmt) REVERT: O 214 MET cc_start: 0.9526 (mtp) cc_final: 0.9288 (mtt) REVERT: P 158 LYS cc_start: 0.9072 (mmmt) cc_final: 0.8802 (mmmt) REVERT: R 182 LYS cc_start: 0.8748 (pptt) cc_final: 0.7967 (ptmt) outliers start: 48 outliers final: 24 residues processed: 276 average time/residue: 0.4019 time to fit residues: 154.6103 Evaluate side-chains 226 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 199 time to evaluate : 1.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain B residue 161 PHE Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain E residue 161 PHE Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain G residue 18 ARG Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain H residue 161 PHE Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain I residue 178 ASP Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain K residue 161 PHE Chi-restraints excluded: chain L residue 178 ASP Chi-restraints excluded: chain L residue 214 MET Chi-restraints excluded: chain M residue 86 ILE Chi-restraints excluded: chain N residue 161 PHE Chi-restraints excluded: chain N residue 181 VAL Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain O residue 210 THR Chi-restraints excluded: chain P residue 86 ILE Chi-restraints excluded: chain Q residue 161 PHE Chi-restraints excluded: chain Q residue 210 THR Chi-restraints excluded: chain R residue 178 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 169 optimal weight: 0.9990 chunk 205 optimal weight: 6.9990 chunk 112 optimal weight: 4.9990 chunk 126 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 188 optimal weight: 0.6980 chunk 80 optimal weight: 6.9990 chunk 186 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 ASN ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 208 ASN ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 208 ASN ** J 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 208 ASN ** M 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 208 ASN P 84 HIS ** P 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 208 ASN Q 187 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.060432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.043657 restraints weight = 93564.161| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 4.95 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3130 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3130 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.8818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.347 18237 Z= 0.657 Angle : 1.952 40.002 24906 Z= 0.701 Chirality : 0.128 1.924 2754 Planarity : 0.006 0.117 3180 Dihedral : 26.710 178.558 2862 Min Nonbonded Distance : 1.618 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.60 % Allowed : 17.08 % Favored : 81.31 % 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: 0.26 (0.18), residues: 2178 helix: 0.56 (0.14), residues: 1440 sheet: None (None), residues: 0 loop : -0.40 (0.25), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP Q 184 HIS 0.002 0.001 HIS G 84 PHE 0.008 0.001 PHE E 161 TYR 0.021 0.002 TYR Q 164 ARG 0.020 0.001 ARG D 18 Details of bonding type rmsd hydrogen bonds : bond 0.03930 ( 919) hydrogen bonds : angle 4.50168 ( 2703) SS BOND : bond 0.00107 ( 18) SS BOND : angle 0.50360 ( 36) covalent geometry : bond 0.01300 (18198) covalent geometry : angle 1.95334 (24870) Misc. bond : bond 0.03767 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 228 time to evaluate : 2.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 HIS cc_start: 0.8936 (OUTLIER) cc_final: 0.8544 (t-90) REVERT: A 96 ARG cc_start: 0.6928 (ptt-90) cc_final: 0.6715 (ptt-90) REVERT: A 158 LYS cc_start: 0.9087 (mmmt) cc_final: 0.8734 (mmmt) REVERT: C 182 LYS cc_start: 0.8782 (pptt) cc_final: 0.8072 (ptmt) REVERT: C 214 MET cc_start: 0.8943 (mtt) cc_final: 0.8649 (mtt) REVERT: D 158 LYS cc_start: 0.8961 (mmmt) cc_final: 0.8694 (mmmt) REVERT: D 182 LYS cc_start: 0.8688 (ptpt) cc_final: 0.8226 (ptpp) REVERT: E 161 PHE cc_start: 0.7231 (OUTLIER) cc_final: 0.6485 (t80) REVERT: F 182 LYS cc_start: 0.8825 (pptt) cc_final: 0.8159 (ptmt) REVERT: F 205 LEU cc_start: 0.8717 (tt) cc_final: 0.8397 (tt) REVERT: G 158 LYS cc_start: 0.9160 (mmmt) cc_final: 0.8862 (mmmt) REVERT: I 182 LYS cc_start: 0.8849 (pptt) cc_final: 0.8078 (ptmt) REVERT: J 117 MET cc_start: 0.7994 (ttm) cc_final: 0.7703 (mtp) REVERT: J 158 LYS cc_start: 0.9074 (mmmt) cc_final: 0.8719 (mmmt) REVERT: L 182 LYS cc_start: 0.8787 (pptt) cc_final: 0.8071 (ptmt) REVERT: L 214 MET cc_start: 0.9513 (mmm) cc_final: 0.8962 (mmm) REVERT: M 158 LYS cc_start: 0.8950 (mmmt) cc_final: 0.8676 (mmmt) REVERT: M 182 LYS cc_start: 0.8685 (ptpt) cc_final: 0.8223 (ptpp) REVERT: N 161 PHE cc_start: 0.7234 (OUTLIER) cc_final: 0.6452 (t80) REVERT: O 182 LYS cc_start: 0.8838 (pptt) cc_final: 0.8170 (ptmt) REVERT: O 205 LEU cc_start: 0.8751 (tt) cc_final: 0.8476 (tt) REVERT: O 214 MET cc_start: 0.9527 (mtp) cc_final: 0.9302 (mtt) REVERT: P 158 LYS cc_start: 0.9117 (mmmt) cc_final: 0.8867 (mmmt) REVERT: R 182 LYS cc_start: 0.8768 (pptt) cc_final: 0.7971 (ptmt) outliers start: 31 outliers final: 22 residues processed: 254 average time/residue: 0.3778 time to fit residues: 135.7924 Evaluate side-chains 231 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 206 time to evaluate : 1.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 HIS Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain B residue 161 PHE Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain E residue 161 PHE Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain H residue 161 PHE Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain I residue 178 ASP Chi-restraints excluded: chain I residue 214 MET Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain K residue 161 PHE Chi-restraints excluded: chain L residue 178 ASP Chi-restraints excluded: chain M residue 86 ILE Chi-restraints excluded: chain N residue 161 PHE Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain O residue 210 THR Chi-restraints excluded: chain P residue 86 ILE Chi-restraints excluded: chain Q residue 161 PHE Chi-restraints excluded: chain Q residue 210 THR Chi-restraints excluded: chain R residue 178 ASP Chi-restraints excluded: chain R residue 214 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 77 optimal weight: 3.9990 chunk 133 optimal weight: 0.0070 chunk 188 optimal weight: 2.9990 chunk 106 optimal weight: 20.0000 chunk 151 optimal weight: 6.9990 chunk 97 optimal weight: 0.8980 chunk 177 optimal weight: 3.9990 chunk 179 optimal weight: 9.9990 chunk 49 optimal weight: 0.6980 chunk 199 optimal weight: 3.9990 chunk 165 optimal weight: 0.9980 overall best weight: 1.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 135 GLN J 84 HIS ** J 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 135 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.060532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.043871 restraints weight = 94971.530| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 4.98 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3137 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3137 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.9088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.316 18237 Z= 0.634 Angle : 1.910 40.807 24906 Z= 0.687 Chirality : 0.124 1.946 2754 Planarity : 0.005 0.105 3180 Dihedral : 26.795 179.402 2862 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.71 % Allowed : 16.98 % Favored : 81.31 % 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: 0.29 (0.18), residues: 2178 helix: 0.58 (0.14), residues: 1440 sheet: None (None), residues: 0 loop : -0.38 (0.25), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP Q 184 HIS 0.001 0.001 HIS D 62 PHE 0.009 0.001 PHE Q 161 TYR 0.022 0.002 TYR H 164 ARG 0.014 0.001 ARG D 18 Details of bonding type rmsd hydrogen bonds : bond 0.03840 ( 919) hydrogen bonds : angle 4.47256 ( 2703) SS BOND : bond 0.00102 ( 18) SS BOND : angle 0.52576 ( 36) covalent geometry : bond 0.01254 (18198) covalent geometry : angle 1.91107 (24870) Misc. bond : bond 0.03653 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 227 time to evaluate : 1.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 HIS cc_start: 0.8913 (OUTLIER) cc_final: 0.8505 (t-90) REVERT: A 96 ARG cc_start: 0.6968 (ptt-90) cc_final: 0.6750 (ptt-90) REVERT: A 158 LYS cc_start: 0.9092 (mmmt) cc_final: 0.8752 (mmmt) REVERT: C 182 LYS cc_start: 0.8807 (pptt) cc_final: 0.8029 (ptmt) REVERT: C 214 MET cc_start: 0.8869 (mtt) cc_final: 0.8593 (mtt) REVERT: D 158 LYS cc_start: 0.8979 (mmmt) cc_final: 0.8701 (mmmt) REVERT: D 182 LYS cc_start: 0.8832 (ptpt) cc_final: 0.8428 (pttm) REVERT: E 161 PHE cc_start: 0.7522 (OUTLIER) cc_final: 0.6969 (t80) REVERT: F 182 LYS cc_start: 0.8891 (pptt) cc_final: 0.8196 (ptmt) REVERT: G 158 LYS cc_start: 0.9206 (mmmt) cc_final: 0.8908 (mmmt) REVERT: I 182 LYS cc_start: 0.8896 (pptt) cc_final: 0.8136 (ptmt) REVERT: J 117 MET cc_start: 0.7967 (ttm) cc_final: 0.7723 (mtp) REVERT: J 158 LYS cc_start: 0.9100 (mmmt) cc_final: 0.8762 (mmmt) REVERT: L 182 LYS cc_start: 0.8813 (pptt) cc_final: 0.8034 (ptmt) REVERT: L 205 LEU cc_start: 0.8950 (tt) cc_final: 0.8607 (pp) REVERT: L 214 MET cc_start: 0.9472 (mmm) cc_final: 0.9081 (mmm) REVERT: M 158 LYS cc_start: 0.8967 (mmmt) cc_final: 0.8685 (mmmt) REVERT: M 182 LYS cc_start: 0.8844 (ptpt) cc_final: 0.8456 (pttm) REVERT: N 161 PHE cc_start: 0.7514 (OUTLIER) cc_final: 0.6969 (t80) REVERT: O 182 LYS cc_start: 0.8937 (pptt) cc_final: 0.8246 (ptmt) REVERT: P 158 LYS cc_start: 0.9142 (mmmt) cc_final: 0.8902 (mmmt) REVERT: R 182 LYS cc_start: 0.8874 (pptt) cc_final: 0.8155 (ptmt) REVERT: R 185 MET cc_start: 0.8543 (ptp) cc_final: 0.8339 (ptp) outliers start: 33 outliers final: 24 residues processed: 256 average time/residue: 0.3723 time to fit residues: 134.1529 Evaluate side-chains 233 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 206 time to evaluate : 2.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 HIS Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain B residue 161 PHE Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain E residue 161 PHE Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain H residue 161 PHE Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain I residue 178 ASP Chi-restraints excluded: chain I residue 214 MET Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain K residue 161 PHE Chi-restraints excluded: chain L residue 178 ASP Chi-restraints excluded: chain L residue 210 THR Chi-restraints excluded: chain M residue 86 ILE Chi-restraints excluded: chain N residue 161 PHE Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain O residue 210 THR Chi-restraints excluded: chain P residue 86 ILE Chi-restraints excluded: chain Q residue 161 PHE Chi-restraints excluded: chain Q residue 210 THR Chi-restraints excluded: chain R residue 178 ASP Chi-restraints excluded: chain R residue 214 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 68 optimal weight: 10.0000 chunk 186 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 214 optimal weight: 10.0000 chunk 166 optimal weight: 5.9990 chunk 174 optimal weight: 10.0000 chunk 211 optimal weight: 9.9990 chunk 2 optimal weight: 0.6980 chunk 185 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 98 optimal weight: 0.0040 overall best weight: 2.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 HIS B 208 ASN ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 HIS ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 149 ASN J 84 HIS ** J 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 135 GLN K 208 ASN ** M 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.058652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.041757 restraints weight = 96035.565| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 4.97 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3069 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.041 | | 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: 0.8246 moved from start: 0.9946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.323 18237 Z= 0.633 Angle : 1.917 41.470 24906 Z= 0.700 Chirality : 0.122 2.001 2754 Planarity : 0.005 0.056 3180 Dihedral : 26.804 178.754 2862 Min Nonbonded Distance : 1.653 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.97 % Allowed : 16.67 % Favored : 81.37 % 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: 0.16 (0.18), residues: 2178 helix: 0.50 (0.14), residues: 1434 sheet: None (None), residues: 0 loop : -0.48 (0.25), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP Q 184 HIS 0.003 0.001 HIS M 62 PHE 0.010 0.001 PHE R 168 TYR 0.023 0.002 TYR Q 164 ARG 0.014 0.001 ARG G 18 Details of bonding type rmsd hydrogen bonds : bond 0.04053 ( 919) hydrogen bonds : angle 4.66580 ( 2703) SS BOND : bond 0.00131 ( 18) SS BOND : angle 0.48830 ( 36) covalent geometry : bond 0.01263 (18198) covalent geometry : angle 1.91815 (24870) Misc. bond : bond 0.03654 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 234 time to evaluate : 1.937 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: A 96 ARG cc_start: 0.7105 (ptt-90) cc_final: 0.6752 (ptt-90) REVERT: A 158 LYS cc_start: 0.9237 (mmmt) cc_final: 0.8855 (mmmt) REVERT: A 214 MET cc_start: 0.9099 (mtt) cc_final: 0.8644 (mpp) REVERT: B 203 LYS cc_start: 0.9386 (mmmm) cc_final: 0.9107 (mmmm) REVERT: B 213 GLU cc_start: 0.9519 (mp0) cc_final: 0.9092 (pm20) REVERT: B 214 MET cc_start: 0.9152 (mtt) cc_final: 0.8724 (mtt) REVERT: C 182 LYS cc_start: 0.8869 (pptt) cc_final: 0.8132 (ptmt) REVERT: C 205 LEU cc_start: 0.8860 (tt) cc_final: 0.8555 (pp) REVERT: D 182 LYS cc_start: 0.8977 (ptpt) cc_final: 0.8528 (pttm) REVERT: E 161 PHE cc_start: 0.7698 (OUTLIER) cc_final: 0.7165 (t80) REVERT: E 203 LYS cc_start: 0.9277 (mmmm) cc_final: 0.8982 (mmmm) REVERT: F 182 LYS cc_start: 0.8790 (pptt) cc_final: 0.8121 (ptmt) REVERT: G 18 ARG cc_start: 0.7613 (ptp90) cc_final: 0.7257 (ptp90) REVERT: G 143 ARG cc_start: 0.9312 (ttm-80) cc_final: 0.8997 (ttm-80) REVERT: G 158 LYS cc_start: 0.9280 (mmmt) cc_final: 0.9023 (mmmt) REVERT: I 182 LYS cc_start: 0.8994 (pptt) cc_final: 0.8200 (ptmt) REVERT: J 117 MET cc_start: 0.8119 (ttm) cc_final: 0.7760 (mtp) REVERT: J 158 LYS cc_start: 0.9235 (mmmt) cc_final: 0.8854 (mmmt) REVERT: K 203 LYS cc_start: 0.9389 (mmmm) cc_final: 0.9112 (mmmm) REVERT: K 213 GLU cc_start: 0.9514 (mp0) cc_final: 0.9089 (pm20) REVERT: K 214 MET cc_start: 0.9154 (mtt) cc_final: 0.8725 (mtt) REVERT: L 182 LYS cc_start: 0.8855 (pptt) cc_final: 0.8059 (ptmt) REVERT: L 205 LEU cc_start: 0.8924 (tt) cc_final: 0.8600 (pp) REVERT: L 214 MET cc_start: 0.9468 (mmm) cc_final: 0.9086 (mmm) REVERT: M 31 LYS cc_start: 0.9266 (mmtt) cc_final: 0.9051 (mmmt) REVERT: M 158 LYS cc_start: 0.9153 (mmmt) cc_final: 0.8952 (mmmt) REVERT: M 182 LYS cc_start: 0.8977 (ptpt) cc_final: 0.8529 (pttm) REVERT: N 161 PHE cc_start: 0.7690 (OUTLIER) cc_final: 0.7180 (t80) REVERT: N 203 LYS cc_start: 0.9304 (mmmm) cc_final: 0.9002 (mmmm) REVERT: O 182 LYS cc_start: 0.8846 (pptt) cc_final: 0.8179 (ptmt) REVERT: O 205 LEU cc_start: 0.8764 (tt) cc_final: 0.8553 (pp) REVERT: P 18 ARG cc_start: 0.7817 (mtm-85) cc_final: 0.7560 (ptp90) REVERT: P 143 ARG cc_start: 0.9315 (ttm-80) cc_final: 0.9002 (ttm-80) REVERT: P 158 LYS cc_start: 0.9311 (mmmt) cc_final: 0.9037 (mmmt) REVERT: R 182 LYS cc_start: 0.8964 (pptt) cc_final: 0.8165 (ptmt) outliers start: 38 outliers final: 29 residues processed: 267 average time/residue: 0.3986 time to fit residues: 146.0670 Evaluate side-chains 242 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 211 time to evaluate : 2.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 140 LYS Chi-restraints excluded: chain B residue 161 PHE Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain E residue 161 PHE Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 140 LYS Chi-restraints excluded: chain H residue 161 PHE Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain I residue 178 ASP Chi-restraints excluded: chain I residue 214 MET Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain J residue 140 LYS Chi-restraints excluded: chain K residue 161 PHE Chi-restraints excluded: chain L residue 178 ASP Chi-restraints excluded: chain L residue 210 THR Chi-restraints excluded: chain M residue 86 ILE Chi-restraints excluded: chain N residue 161 PHE Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain O residue 210 THR Chi-restraints excluded: chain P residue 86 ILE Chi-restraints excluded: chain P residue 140 LYS Chi-restraints excluded: chain Q residue 161 PHE Chi-restraints excluded: chain Q residue 210 THR Chi-restraints excluded: chain R residue 178 ASP Chi-restraints excluded: chain R residue 214 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 155 optimal weight: 2.9990 chunk 150 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 184 optimal weight: 0.9990 chunk 133 optimal weight: 0.9980 chunk 198 optimal weight: 3.9990 chunk 194 optimal weight: 7.9990 chunk 209 optimal weight: 0.0970 chunk 54 optimal weight: 6.9990 chunk 169 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 176 GLN ** J 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 176 GLN ** M 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 176 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.059905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.043207 restraints weight = 93242.616| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 4.95 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 1.0069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.291 18237 Z= 0.600 Angle : 1.897 42.643 24906 Z= 0.685 Chirality : 0.120 1.854 2754 Planarity : 0.005 0.093 3180 Dihedral : 26.808 179.822 2862 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.35 % Allowed : 17.39 % Favored : 81.26 % 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 (0.19), residues: 2178 helix: 0.68 (0.14), residues: 1440 sheet: None (None), residues: 0 loop : -0.43 (0.25), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 184 HIS 0.001 0.000 HIS P 84 PHE 0.011 0.001 PHE Q 161 TYR 0.016 0.002 TYR A 130 ARG 0.016 0.001 ARG A 18 Details of bonding type rmsd hydrogen bonds : bond 0.03746 ( 919) hydrogen bonds : angle 4.45280 ( 2703) SS BOND : bond 0.00113 ( 18) SS BOND : angle 0.54426 ( 36) covalent geometry : bond 0.01183 (18198) covalent geometry : angle 1.89835 (24870) Misc. bond : bond 0.03625 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 242 time to evaluate : 1.955 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: A 96 ARG cc_start: 0.7155 (ptt-90) cc_final: 0.6796 (ptt-90) REVERT: A 99 ARG cc_start: 0.8522 (mmm160) cc_final: 0.8214 (mmm160) REVERT: A 158 LYS cc_start: 0.9205 (mmmt) cc_final: 0.8829 (mmmt) REVERT: B 203 LYS cc_start: 0.9353 (mmmm) cc_final: 0.9130 (mmmm) REVERT: B 213 GLU cc_start: 0.9520 (mp0) cc_final: 0.9248 (pm20) REVERT: C 182 LYS cc_start: 0.8844 (pptt) cc_final: 0.8043 (ptmt) REVERT: C 205 LEU cc_start: 0.8910 (tt) cc_final: 0.8707 (pp) REVERT: C 214 MET cc_start: 0.8877 (mtt) cc_final: 0.8663 (mtt) REVERT: D 182 LYS cc_start: 0.8939 (ptpt) cc_final: 0.8398 (ptpp) REVERT: E 161 PHE cc_start: 0.7609 (OUTLIER) cc_final: 0.7109 (t80) REVERT: E 203 LYS cc_start: 0.9341 (mmmm) cc_final: 0.9110 (mmmm) REVERT: E 214 MET cc_start: 0.9049 (mtt) cc_final: 0.8736 (mtt) REVERT: F 182 LYS cc_start: 0.8932 (pptt) cc_final: 0.8333 (ptmt) REVERT: G 96 ARG cc_start: 0.6744 (ptt-90) cc_final: 0.6499 (ptt-90) REVERT: G 99 ARG cc_start: 0.8698 (mmm-85) cc_final: 0.8438 (mmm160) REVERT: G 143 ARG cc_start: 0.9266 (ttm-80) cc_final: 0.8934 (ttm-80) REVERT: G 158 LYS cc_start: 0.9276 (mmmt) cc_final: 0.9014 (mmmt) REVERT: H 164 TYR cc_start: 0.7640 (t80) cc_final: 0.7314 (t80) REVERT: I 182 LYS cc_start: 0.8951 (pptt) cc_final: 0.8284 (ptmt) REVERT: J 96 ARG cc_start: 0.7095 (ptt-90) cc_final: 0.6828 (ptt-90) REVERT: J 99 ARG cc_start: 0.8500 (mmm160) cc_final: 0.8211 (mmm160) REVERT: J 117 MET cc_start: 0.8072 (ttm) cc_final: 0.7848 (mtp) REVERT: J 158 LYS cc_start: 0.9204 (mmmt) cc_final: 0.8827 (mmmt) REVERT: K 203 LYS cc_start: 0.9349 (mmmm) cc_final: 0.9128 (mmmm) REVERT: K 213 GLU cc_start: 0.9513 (mp0) cc_final: 0.9241 (pm20) REVERT: L 182 LYS cc_start: 0.8843 (pptt) cc_final: 0.8047 (ptmt) REVERT: L 205 LEU cc_start: 0.8919 (tt) cc_final: 0.8662 (pp) REVERT: L 214 MET cc_start: 0.9453 (mmm) cc_final: 0.9071 (mmm) REVERT: M 158 LYS cc_start: 0.9133 (mmmt) cc_final: 0.8924 (mmmt) REVERT: M 182 LYS cc_start: 0.8956 (ptpt) cc_final: 0.8391 (ptpp) REVERT: N 161 PHE cc_start: 0.7594 (OUTLIER) cc_final: 0.7101 (t80) REVERT: N 203 LYS cc_start: 0.9338 (mmmm) cc_final: 0.9084 (mmmm) REVERT: O 182 LYS cc_start: 0.8897 (pptt) cc_final: 0.8279 (ptmt) REVERT: P 96 ARG cc_start: 0.6731 (ptt-90) cc_final: 0.6482 (ptt-90) REVERT: P 99 ARG cc_start: 0.8682 (mmm-85) cc_final: 0.8423 (mmm160) REVERT: P 143 ARG cc_start: 0.9271 (ttm-80) cc_final: 0.8940 (ttm-80) REVERT: P 158 LYS cc_start: 0.9265 (mmmt) cc_final: 0.9000 (mmmt) REVERT: Q 164 TYR cc_start: 0.7651 (t80) cc_final: 0.7318 (t80) REVERT: R 182 LYS cc_start: 0.8902 (pptt) cc_final: 0.8152 (ptmt) outliers start: 26 outliers final: 24 residues processed: 265 average time/residue: 0.4234 time to fit residues: 151.7621 Evaluate side-chains 247 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 221 time to evaluate : 1.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain B residue 161 PHE Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain E residue 161 PHE Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain H residue 161 PHE Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain I residue 178 ASP Chi-restraints excluded: chain I residue 214 MET Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain K residue 161 PHE Chi-restraints excluded: chain L residue 178 ASP Chi-restraints excluded: chain L residue 210 THR Chi-restraints excluded: chain M residue 86 ILE Chi-restraints excluded: chain N residue 161 PHE Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain O residue 210 THR Chi-restraints excluded: chain P residue 86 ILE Chi-restraints excluded: chain Q residue 161 PHE Chi-restraints excluded: chain Q residue 210 THR Chi-restraints excluded: chain R residue 178 ASP Chi-restraints excluded: chain R residue 214 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 59 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 168 optimal weight: 6.9990 chunk 173 optimal weight: 30.0000 chunk 143 optimal weight: 3.9990 chunk 9 optimal weight: 20.0000 chunk 124 optimal weight: 7.9990 chunk 84 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 chunk 127 optimal weight: 6.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 187 GLN ** J 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.059032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.042081 restraints weight = 95185.188| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 4.98 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3078 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3078 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 1.0425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.297 18237 Z= 0.593 Angle : 1.926 43.354 24906 Z= 0.699 Chirality : 0.122 1.874 2754 Planarity : 0.006 0.086 3180 Dihedral : 26.708 179.536 2862 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.45 % Allowed : 17.34 % Favored : 81.21 % 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: 0.29 (0.18), residues: 2178 helix: 0.63 (0.14), residues: 1434 sheet: None (None), residues: 0 loop : -0.48 (0.25), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP Q 184 HIS 0.002 0.001 HIS D 12 PHE 0.009 0.001 PHE N 161 TYR 0.018 0.002 TYR H 164 ARG 0.012 0.001 ARG P 18 Details of bonding type rmsd hydrogen bonds : bond 0.03899 ( 919) hydrogen bonds : angle 4.58397 ( 2703) SS BOND : bond 0.00111 ( 18) SS BOND : angle 0.56516 ( 36) covalent geometry : bond 0.01176 (18198) covalent geometry : angle 1.92776 (24870) Misc. bond : bond 0.03640 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8470.05 seconds wall clock time: 147 minutes 43.57 seconds (8863.57 seconds total)