Starting phenix.real_space_refine on Thu Sep 18 15:02:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cns_45758/09_2025/9cns_45758.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cns_45758/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9cns_45758/09_2025/9cns_45758.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cns_45758/09_2025/9cns_45758.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cns_45758/09_2025/9cns_45758.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cns_45758/09_2025/9cns_45758.map" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 4.19, per 1000 atoms: 0.24 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: 2.94 Conformation dependent library (CDL) restraints added in 969.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.56 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: 3.21 Time building geometry restraints manager: 3.51 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: 0.04 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: 6.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.190 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.060 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:1.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.650 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.018 0.003 ARG R 167 TYR 0.034 0.004 TYR D 50 PHE 0.020 0.004 PHE J 168 TRP 0.049 0.006 TRP R 184 HIS 0.004 0.001 HIS P 12 Details of bonding type rmsd covalent geometry : bond 0.01352 (18198) covalent geometry : angle 1.94998 (24870) SS BOND : bond 0.00852 ( 18) SS BOND : angle 1.36164 ( 36) hydrogen bonds : bond 0.24818 ( 919) hydrogen bonds : angle 8.28105 ( 2703) 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 : 0.481 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 outliers start: 12 outliers final: 6 residues processed: 554 average time/residue: 0.1567 time to fit residues: 124.1999 Evaluate side-chains 267 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 261 time to evaluate : 0.578 ------------------------------------------------------------------------------- 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 98 optimal weight: 10.0000 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 0.8980 chunk 212 optimal weight: 7.9990 chunk 77 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 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 121 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** L 208 ASN 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** O 208 ASN P 3 GLN P 62 HIS P 67 GLN P 121 GLN P 146 ASN P 187 GLN P 208 ASN Q 187 GLN R 187 GLN Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.066020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.050970 restraints weight = 95896.646| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 4.86 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3350 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 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 = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3347 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.037 1.248 18237 Z= 1.833 Angle : 3.523 76.934 24906 Z= 1.222 Chirality : 0.322 5.588 2754 Planarity : 0.008 0.146 3180 Dihedral : 29.676 176.887 2862 Min Nonbonded Distance : 1.456 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.42 % Allowed : 16.41 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.17), residues: 2178 helix: -0.41 (0.12), residues: 1494 sheet: -0.39 (0.80), residues: 54 loop : -1.71 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG D 18 TYR 0.025 0.002 TYR D 50 PHE 0.023 0.002 PHE I 161 TRP 0.018 0.002 TRP O 184 HIS 0.006 0.002 HIS M 84 Details of bonding type rmsd covalent geometry : bond 0.03655 (18198) covalent geometry : angle 3.52555 (24870) SS BOND : bond 0.00317 ( 18) SS BOND : angle 0.61691 ( 36) hydrogen bonds : bond 0.07040 ( 919) hydrogen bonds : angle 5.71972 ( 2703) Misc. bond : bond 0.05938 ( 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 363 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 297 time to evaluate : 0.711 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 31 LYS cc_start: 0.8818 (mmtt) cc_final: 0.8052 (tptp) REVERT: B 177 THR cc_start: 0.7310 (p) cc_final: 0.6677 (p) REVERT: B 182 LYS cc_start: 0.7897 (mmtt) cc_final: 0.7573 (mmtt) REVERT: D 31 LYS cc_start: 0.8828 (mmtt) cc_final: 0.8049 (tptp) REVERT: D 55 MET cc_start: 0.6932 (mtp) cc_final: 0.6718 (mtm) REVERT: E 177 THR cc_start: 0.7464 (p) cc_final: 0.7013 (p) REVERT: E 178 ASP cc_start: 0.5042 (t0) cc_final: 0.4777 (t70) REVERT: E 182 LYS cc_start: 0.7992 (mmtt) cc_final: 0.7468 (mmtt) REVERT: G 31 LYS cc_start: 0.8818 (mmtt) cc_final: 0.8609 (mmmt) REVERT: G 182 LYS cc_start: 0.8637 (mtpt) cc_final: 0.8367 (mttt) REVERT: H 178 ASP cc_start: 0.5110 (t0) cc_final: 0.4702 (t70) REVERT: I 184 TRP cc_start: 0.8617 (t60) cc_final: 0.8344 (t-100) REVERT: I 185 MET cc_start: 0.8866 (ptp) cc_final: 0.8599 (ptp) REVERT: I 214 MET cc_start: 0.9048 (mpp) cc_final: 0.8801 (mpp) REVERT: J 31 LYS cc_start: 0.8800 (mmtt) cc_final: 0.8031 (tptp) REVERT: K 177 THR cc_start: 0.7321 (p) cc_final: 0.6686 (p) REVERT: K 182 LYS cc_start: 0.7903 (mmtt) cc_final: 0.7578 (mmtt) REVERT: M 31 LYS cc_start: 0.8828 (mmtt) cc_final: 0.8048 (tptp) REVERT: N 177 THR cc_start: 0.7482 (p) cc_final: 0.7038 (p) REVERT: N 178 ASP cc_start: 0.5041 (t0) cc_final: 0.4781 (t70) REVERT: N 182 LYS cc_start: 0.7993 (mmtt) cc_final: 0.7470 (mmtt) REVERT: P 31 LYS cc_start: 0.8819 (mmtt) cc_final: 0.8607 (mmmt) REVERT: P 182 LYS cc_start: 0.8649 (mtpt) cc_final: 0.8350 (mttt) REVERT: Q 178 ASP cc_start: 0.5120 (t0) cc_final: 0.4785 (t70) REVERT: R 184 TRP cc_start: 0.8621 (t60) cc_final: 0.8412 (t-100) REVERT: R 185 MET cc_start: 0.8869 (ptp) cc_final: 0.8647 (ptp) REVERT: R 214 MET cc_start: 0.9051 (mpp) cc_final: 0.8803 (mpp) outliers start: 66 outliers final: 25 residues processed: 341 average time/residue: 0.1443 time to fit residues: 71.0824 Evaluate side-chains 232 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 207 time to evaluate : 0.641 ------------------------------------------------------------------------------- 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 59 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 43 LEU 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 Chi-restraints excluded: chain Q residue 181 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 84 optimal weight: 0.4980 chunk 6 optimal weight: 4.9990 chunk 165 optimal weight: 0.5980 chunk 160 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 chunk 126 optimal weight: 1.9990 chunk 156 optimal weight: 6.9990 chunk 170 optimal weight: 0.0270 chunk 211 optimal weight: 6.9990 chunk 104 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 overall best weight: 1.0242 ------------------------------------------------------------------------------- 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 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 J 121 GLN ** J 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 192 GLN M 84 HIS M 121 GLN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.064625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.049142 restraints weight = 96112.273| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 5.01 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3308 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3308 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.5669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.032 1.324 18237 Z= 1.599 Angle : 2.682 63.678 24906 Z= 0.939 Chirality : 0.261 4.987 2754 Planarity : 0.005 0.055 3180 Dihedral : 31.737 179.792 2862 Min Nonbonded Distance : 1.561 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.55 % Allowed : 17.08 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.17), residues: 2178 helix: 0.05 (0.13), residues: 1440 sheet: None (None), residues: 0 loop : -0.91 (0.24), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 18 TYR 0.022 0.002 TYR A 130 PHE 0.014 0.001 PHE C 161 TRP 0.012 0.001 TRP N 184 HIS 0.002 0.001 HIS G 62 Details of bonding type rmsd covalent geometry : bond 0.03178 (18198) covalent geometry : angle 2.68375 (24870) SS BOND : bond 0.00209 ( 18) SS BOND : angle 0.71194 ( 36) hydrogen bonds : bond 0.04892 ( 919) hydrogen bonds : angle 5.04256 ( 2703) Misc. bond : bond 0.05898 ( 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 283 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 253 time to evaluate : 0.588 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 158 LYS cc_start: 0.8767 (mmmt) cc_final: 0.8452 (mmmt) REVERT: B 177 THR cc_start: 0.7324 (p) cc_final: 0.6808 (p) REVERT: B 182 LYS cc_start: 0.7953 (mttt) cc_final: 0.7555 (mmtt) REVERT: C 182 LYS cc_start: 0.8849 (pptt) cc_final: 0.8025 (ptmt) REVERT: D 31 LYS cc_start: 0.8864 (mmtt) cc_final: 0.8035 (tptt) REVERT: D 117 MET cc_start: 0.7470 (ttm) cc_final: 0.7241 (mtp) REVERT: E 177 THR cc_start: 0.7565 (p) cc_final: 0.7070 (p) REVERT: E 178 ASP cc_start: 0.5858 (t0) cc_final: 0.5455 (t70) REVERT: E 182 LYS cc_start: 0.8036 (mmtt) cc_final: 0.7647 (mmtt) REVERT: F 182 LYS cc_start: 0.8974 (pptt) cc_final: 0.8209 (ptmt) REVERT: G 31 LYS cc_start: 0.8832 (mmtt) cc_final: 0.7995 (tptp) REVERT: G 158 LYS cc_start: 0.8800 (mmmt) cc_final: 0.8573 (mmmt) REVERT: G 182 LYS cc_start: 0.8599 (mtpt) cc_final: 0.8367 (mttt) REVERT: H 161 PHE cc_start: 0.6964 (OUTLIER) cc_final: 0.6714 (p90) REVERT: H 178 ASP cc_start: 0.5836 (t0) cc_final: 0.5621 (t70) REVERT: I 182 LYS cc_start: 0.8969 (pptt) cc_final: 0.8163 (ptmt) REVERT: I 184 TRP cc_start: 0.8609 (t60) cc_final: 0.8387 (t-100) REVERT: I 185 MET cc_start: 0.8771 (ptp) cc_final: 0.8559 (ptp) REVERT: I 214 MET cc_start: 0.9140 (mpp) cc_final: 0.8910 (mpp) REVERT: J 158 LYS cc_start: 0.8754 (mmmt) cc_final: 0.8439 (mmmt) REVERT: K 177 THR cc_start: 0.7307 (p) cc_final: 0.6787 (p) REVERT: K 182 LYS cc_start: 0.7961 (mttt) cc_final: 0.7562 (mmtt) REVERT: L 182 LYS cc_start: 0.8849 (pptt) cc_final: 0.8023 (ptmt) REVERT: M 31 LYS cc_start: 0.8877 (mmtt) cc_final: 0.8674 (mmmt) REVERT: M 117 MET cc_start: 0.7479 (ttm) cc_final: 0.7248 (mtp) REVERT: N 177 THR cc_start: 0.7513 (p) cc_final: 0.6959 (p) REVERT: N 178 ASP cc_start: 0.5855 (t0) cc_final: 0.5452 (t70) REVERT: N 182 LYS cc_start: 0.8035 (mmtt) cc_final: 0.7648 (mmtt) REVERT: O 182 LYS cc_start: 0.8969 (pptt) cc_final: 0.8189 (ptmt) REVERT: P 31 LYS cc_start: 0.8839 (mmtt) cc_final: 0.7998 (tptp) REVERT: P 182 LYS cc_start: 0.8590 (mtpt) cc_final: 0.8365 (mttt) REVERT: Q 161 PHE cc_start: 0.6943 (OUTLIER) cc_final: 0.6695 (p90) REVERT: Q 178 ASP cc_start: 0.5870 (t0) cc_final: 0.5580 (t70) REVERT: R 182 LYS cc_start: 0.8969 (pptt) cc_final: 0.8167 (ptmt) REVERT: R 184 TRP cc_start: 0.8621 (t60) cc_final: 0.8395 (t-100) REVERT: R 185 MET cc_start: 0.8791 (ptp) cc_final: 0.8580 (ptp) REVERT: R 214 MET cc_start: 0.9138 (mpp) cc_final: 0.8910 (mpp) outliers start: 30 outliers final: 21 residues processed: 278 average time/residue: 0.1513 time to fit residues: 60.7106 Evaluate side-chains 232 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 209 time to evaluate : 0.548 ------------------------------------------------------------------------------- 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 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 165 VAL Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain H residue 161 PHE Chi-restraints excluded: chain I residue 149 ASN 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 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 165 VAL Chi-restraints excluded: chain P residue 86 ILE Chi-restraints excluded: chain Q residue 161 PHE Chi-restraints excluded: chain R residue 149 ASN Chi-restraints excluded: chain R residue 178 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 120 optimal weight: 5.9990 chunk 105 optimal weight: 8.9990 chunk 209 optimal weight: 20.0000 chunk 39 optimal weight: 0.7980 chunk 112 optimal weight: 6.9990 chunk 139 optimal weight: 10.0000 chunk 192 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 146 optimal weight: 1.9990 chunk 125 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 HIS A 146 ASN ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 GLN ** D 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 192 GLN G 84 HIS ** G 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 208 ASN J 84 HIS J 146 ASN ** J 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 192 GLN ** M 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 208 ASN O 192 GLN P 84 HIS ** P 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 208 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.062281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.046234 restraints weight = 94343.325| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 4.90 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3217 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3217 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.6760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.026 0.974 18237 Z= 1.281 Angle : 2.795 60.447 24906 Z= 0.974 Chirality : 0.214 3.518 2754 Planarity : 0.006 0.144 3180 Dihedral : 29.634 179.066 2862 Min Nonbonded Distance : 1.560 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.74 % Allowed : 15.11 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.18), residues: 2178 helix: 0.22 (0.13), residues: 1446 sheet: None (None), residues: 0 loop : -0.55 (0.25), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG P 18 TYR 0.023 0.002 TYR A 169 PHE 0.010 0.002 PHE O 161 TRP 0.016 0.002 TRP H 184 HIS 0.003 0.001 HIS A 62 Details of bonding type rmsd covalent geometry : bond 0.02557 (18198) covalent geometry : angle 2.79664 (24870) SS BOND : bond 0.00155 ( 18) SS BOND : angle 0.55037 ( 36) hydrogen bonds : bond 0.04267 ( 919) hydrogen bonds : angle 4.79219 ( 2703) Misc. bond : bond 0.03487 ( 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 298 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 245 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 LYS cc_start: 0.9119 (mmmt) cc_final: 0.8635 (tptp) REVERT: A 158 LYS cc_start: 0.8851 (mmmt) cc_final: 0.8557 (mmmt) REVERT: B 177 THR cc_start: 0.7311 (p) cc_final: 0.6698 (p) REVERT: B 182 LYS cc_start: 0.7985 (mttt) cc_final: 0.7493 (mmtt) REVERT: C 182 LYS cc_start: 0.8828 (pptt) cc_final: 0.7900 (ptmt) REVERT: D 31 LYS cc_start: 0.9020 (mmtt) cc_final: 0.8777 (mmtt) REVERT: D 117 MET cc_start: 0.7692 (ttm) cc_final: 0.7489 (mtp) REVERT: E 176 GLN cc_start: 0.9158 (OUTLIER) cc_final: 0.8938 (mt0) REVERT: E 177 THR cc_start: 0.7306 (p) cc_final: 0.6581 (p) REVERT: E 178 ASP cc_start: 0.6656 (t0) cc_final: 0.6277 (t70) REVERT: E 182 LYS cc_start: 0.8203 (mmtt) cc_final: 0.7953 (mmtt) REVERT: F 182 LYS cc_start: 0.8906 (pptt) cc_final: 0.8094 (ptmt) REVERT: F 214 MET cc_start: 0.9633 (mtm) cc_final: 0.9432 (mtp) REVERT: G 158 LYS cc_start: 0.8996 (mmmt) cc_final: 0.8706 (mmmt) REVERT: G 182 LYS cc_start: 0.8642 (mtpt) cc_final: 0.8421 (mttt) REVERT: H 161 PHE cc_start: 0.7102 (OUTLIER) cc_final: 0.6814 (p90) REVERT: H 178 ASP cc_start: 0.6540 (t0) cc_final: 0.6254 (t70) REVERT: I 182 LYS cc_start: 0.8757 (pptt) cc_final: 0.7883 (ptmt) REVERT: I 184 TRP cc_start: 0.8699 (t60) cc_final: 0.8480 (t-100) REVERT: I 202 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9217 (mm) REVERT: J 31 LYS cc_start: 0.9125 (mmmt) cc_final: 0.8633 (tptp) REVERT: J 158 LYS cc_start: 0.8862 (mmmt) cc_final: 0.8570 (mmmt) REVERT: K 177 THR cc_start: 0.7298 (p) cc_final: 0.6677 (p) REVERT: K 182 LYS cc_start: 0.7979 (mttt) cc_final: 0.7487 (mmtt) REVERT: L 182 LYS cc_start: 0.8829 (pptt) cc_final: 0.7896 (ptmt) REVERT: N 176 GLN cc_start: 0.9149 (OUTLIER) cc_final: 0.8935 (mt0) REVERT: N 177 THR cc_start: 0.7313 (p) cc_final: 0.6601 (p) REVERT: N 178 ASP cc_start: 0.6637 (t0) cc_final: 0.6260 (t70) REVERT: N 182 LYS cc_start: 0.8210 (mmtt) cc_final: 0.7957 (mmtt) REVERT: N 213 GLU cc_start: 0.9519 (mp0) cc_final: 0.9296 (mp0) REVERT: O 182 LYS cc_start: 0.8907 (pptt) cc_final: 0.8094 (ptmt) REVERT: P 158 LYS cc_start: 0.8975 (mmmt) cc_final: 0.8644 (mmmt) REVERT: P 182 LYS cc_start: 0.8649 (mtpt) cc_final: 0.8425 (mttt) REVERT: Q 161 PHE cc_start: 0.7092 (OUTLIER) cc_final: 0.6805 (p90) REVERT: Q 178 ASP cc_start: 0.6992 (t0) cc_final: 0.6779 (t70) REVERT: R 182 LYS cc_start: 0.8776 (pptt) cc_final: 0.7906 (ptmt) REVERT: R 184 TRP cc_start: 0.8689 (t60) cc_final: 0.8467 (t-100) REVERT: R 202 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9220 (mm) outliers start: 53 outliers final: 27 residues processed: 295 average time/residue: 0.1471 time to fit residues: 62.5411 Evaluate side-chains 240 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 207 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 191 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 18 ARG 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 E residue 181 VAL 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 202 LEU Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain J residue 191 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 N residue 181 VAL Chi-restraints excluded: chain N residue 210 THR 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 Q residue 210 THR Chi-restraints excluded: chain R residue 178 ASP Chi-restraints excluded: chain R residue 202 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 195 optimal weight: 0.0980 chunk 59 optimal weight: 7.9990 chunk 118 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 206 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 194 optimal weight: 8.9990 chunk 135 optimal weight: 4.9990 chunk 132 optimal weight: 8.9990 chunk 190 optimal weight: 0.0050 overall best weight: 3.4200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 HIS A 135 GLN ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 GLN ** D 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 ASN F 192 GLN G 84 HIS G 146 ASN ** G 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 84 HIS J 135 GLN ** J 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 GLN ** M 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 208 ASN O 192 GLN P 84 HIS P 146 ASN ** P 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.060354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.043696 restraints weight = 98358.760| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 5.05 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3130 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3129 r_free = 0.3129 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3129 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.7815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 0.375 18237 Z= 0.867 Angle : 2.304 46.093 24906 Z= 0.814 Chirality : 0.163 2.927 2754 Planarity : 0.005 0.061 3180 Dihedral : 28.255 179.372 2862 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.28 % Allowed : 15.68 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.18), residues: 2178 helix: 0.18 (0.13), residues: 1452 sheet: None (None), residues: 0 loop : -0.47 (0.25), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 18 TYR 0.020 0.002 TYR G 130 PHE 0.012 0.002 PHE O 161 TRP 0.019 0.002 TRP Q 184 HIS 0.003 0.001 HIS J 62 Details of bonding type rmsd covalent geometry : bond 0.01726 (18198) covalent geometry : angle 2.30550 (24870) SS BOND : bond 0.00202 ( 18) SS BOND : angle 0.48633 ( 36) hydrogen bonds : bond 0.04192 ( 919) hydrogen bonds : angle 4.81030 ( 2703) Misc. bond : bond 0.04590 ( 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 270 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 226 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LYS cc_start: 0.8991 (mmmt) cc_final: 0.8710 (mmmt) REVERT: C 182 LYS cc_start: 0.8755 (pptt) cc_final: 0.7921 (ptmt) REVERT: C 214 MET cc_start: 0.9442 (mtp) cc_final: 0.9141 (mpp) REVERT: D 117 MET cc_start: 0.7959 (ttm) cc_final: 0.7614 (mtp) REVERT: E 214 MET cc_start: 0.9290 (mtt) cc_final: 0.9060 (mtt) REVERT: F 182 LYS cc_start: 0.8931 (pptt) cc_final: 0.8177 (ptmt) REVERT: F 207 MET cc_start: 0.8661 (pmm) cc_final: 0.8416 (pmm) REVERT: F 214 MET cc_start: 0.9657 (mtm) cc_final: 0.9168 (mtp) REVERT: G 158 LYS cc_start: 0.9073 (mmmt) cc_final: 0.8781 (mmmt) REVERT: I 182 LYS cc_start: 0.8817 (pptt) cc_final: 0.7958 (ptmt) REVERT: J 158 LYS cc_start: 0.8980 (mmmt) cc_final: 0.8700 (mmmt) REVERT: L 182 LYS cc_start: 0.8741 (pptt) cc_final: 0.7898 (ptmt) REVERT: O 182 LYS cc_start: 0.8934 (pptt) cc_final: 0.8180 (ptmt) REVERT: O 203 LYS cc_start: 0.9500 (pttp) cc_final: 0.9289 (pttm) REVERT: P 158 LYS cc_start: 0.9025 (mmmt) cc_final: 0.8724 (mmmt) REVERT: R 182 LYS cc_start: 0.8821 (pptt) cc_final: 0.7961 (ptmt) outliers start: 44 outliers final: 24 residues processed: 267 average time/residue: 0.1517 time to fit residues: 58.2489 Evaluate side-chains 210 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 186 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 191 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 18 ARG 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 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 J residue 191 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 86 ILE Chi-restraints excluded: chain N residue 161 PHE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 179 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 108 optimal weight: 10.0000 chunk 161 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 82 optimal weight: 0.3980 chunk 46 optimal weight: 10.0000 chunk 186 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 HIS A 121 GLN A 135 GLN ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN ** D 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 GLN G 84 HIS ** G 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 84 HIS J 121 GLN J 135 GLN ** J 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 208 ASN M 135 GLN ** M 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 176 GLN P 84 HIS ** P 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.060922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.044181 restraints weight = 95369.306| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 4.98 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3144 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3144 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.8193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.327 18237 Z= 0.765 Angle : 2.130 57.018 24906 Z= 0.756 Chirality : 0.160 2.758 2754 Planarity : 0.005 0.053 3180 Dihedral : 28.049 178.985 2862 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.76 % Allowed : 16.10 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.18), residues: 2178 helix: 0.39 (0.13), residues: 1452 sheet: None (None), residues: 0 loop : -0.48 (0.25), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 18 TYR 0.024 0.002 TYR A 130 PHE 0.009 0.001 PHE F 161 TRP 0.017 0.001 TRP E 184 HIS 0.002 0.001 HIS G 84 Details of bonding type rmsd covalent geometry : bond 0.01515 (18198) covalent geometry : angle 2.13149 (24870) SS BOND : bond 0.00132 ( 18) SS BOND : angle 0.46299 ( 36) hydrogen bonds : bond 0.04131 ( 919) hydrogen bonds : angle 4.63132 ( 2703) Misc. bond : bond 0.04252 ( 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 258 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 224 time to evaluate : 0.696 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: A 158 LYS cc_start: 0.9033 (mmmt) cc_final: 0.8738 (mmmt) REVERT: A 214 MET cc_start: 0.8901 (mtt) cc_final: 0.8438 (mpp) REVERT: C 182 LYS cc_start: 0.8798 (pptt) cc_final: 0.7923 (ptmt) REVERT: D 117 MET cc_start: 0.7935 (ttm) cc_final: 0.7623 (mtp) REVERT: D 130 TYR cc_start: 0.6913 (t80) cc_final: 0.6639 (t80) REVERT: E 161 PHE cc_start: 0.7224 (OUTLIER) cc_final: 0.6266 (t80) REVERT: E 213 GLU cc_start: 0.9525 (mp0) cc_final: 0.9319 (mp0) REVERT: F 182 LYS cc_start: 0.8929 (pptt) cc_final: 0.8180 (ptmt) REVERT: F 214 MET cc_start: 0.9656 (mtm) cc_final: 0.9173 (mtp) REVERT: G 158 LYS cc_start: 0.9093 (mmmt) cc_final: 0.8819 (mmmt) REVERT: I 182 LYS cc_start: 0.8780 (pptt) cc_final: 0.7974 (ptmt) REVERT: I 214 MET cc_start: 0.9203 (mpp) cc_final: 0.8942 (mpp) REVERT: J 158 LYS cc_start: 0.9021 (mmmt) cc_final: 0.8724 (mmmt) REVERT: J 214 MET cc_start: 0.8908 (mtt) cc_final: 0.8444 (mpp) REVERT: L 182 LYS cc_start: 0.8803 (pptt) cc_final: 0.7929 (ptmt) REVERT: L 214 MET cc_start: 0.9395 (mtp) cc_final: 0.9146 (mpp) REVERT: N 161 PHE cc_start: 0.7166 (OUTLIER) cc_final: 0.6230 (t80) REVERT: O 182 LYS cc_start: 0.8938 (pptt) cc_final: 0.8213 (ptmt) REVERT: O 207 MET cc_start: 0.8742 (pmm) cc_final: 0.8494 (pmm) REVERT: P 158 LYS cc_start: 0.9054 (mmmt) cc_final: 0.8762 (mmmt) REVERT: R 182 LYS cc_start: 0.8782 (pptt) cc_final: 0.7906 (ptmt) REVERT: R 214 MET cc_start: 0.9208 (mpp) cc_final: 0.8949 (mpp) outliers start: 34 outliers final: 23 residues processed: 253 average time/residue: 0.1670 time to fit residues: 58.6144 Evaluate side-chains 228 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 203 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain B residue 161 PHE Chi-restraints excluded: chain C residue 178 ASP 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 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 J residue 191 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 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 34 optimal weight: 5.9990 chunk 172 optimal weight: 9.9990 chunk 78 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 157 optimal weight: 0.7980 chunk 215 optimal weight: 20.0000 chunk 134 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 191 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 HIS A 135 GLN A 208 ASN ** D 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 GLN G 84 HIS ** G 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 162 GLN J 84 HIS J 208 ASN M 121 GLN M 135 GLN M 208 ASN O 162 GLN P 84 HIS P 208 ASN R 162 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.059058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.042102 restraints weight = 93610.630| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 4.90 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3074 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3074 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.9161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.340 18237 Z= 0.701 Angle : 2.093 55.590 24906 Z= 0.755 Chirality : 0.136 2.206 2754 Planarity : 0.005 0.044 3180 Dihedral : 27.285 179.049 2862 Min Nonbonded Distance : 1.615 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.07 % Allowed : 15.68 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.18), residues: 2178 helix: 0.38 (0.13), residues: 1446 sheet: None (None), residues: 0 loop : -0.46 (0.25), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 96 TYR 0.026 0.002 TYR H 164 PHE 0.010 0.002 PHE M 40 TRP 0.022 0.002 TRP Q 184 HIS 0.003 0.001 HIS P 84 Details of bonding type rmsd covalent geometry : bond 0.01398 (18198) covalent geometry : angle 2.09417 (24870) SS BOND : bond 0.00178 ( 18) SS BOND : angle 0.48666 ( 36) hydrogen bonds : bond 0.04206 ( 919) hydrogen bonds : angle 4.75804 ( 2703) Misc. bond : bond 0.03804 ( 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 267 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 227 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.7565 (ptp90) REVERT: A 96 ARG cc_start: 0.6894 (ptt-90) cc_final: 0.6440 (ptt-90) REVERT: A 158 LYS cc_start: 0.9145 (mmmt) cc_final: 0.8805 (mmmt) REVERT: A 214 MET cc_start: 0.8972 (mtt) cc_final: 0.8494 (mpp) REVERT: B 213 GLU cc_start: 0.9531 (mp0) cc_final: 0.9162 (pm20) REVERT: C 182 LYS cc_start: 0.8741 (pptt) cc_final: 0.7933 (ptmt) REVERT: D 66 MET cc_start: 0.8919 (tpp) cc_final: 0.8674 (mmt) REVERT: D 117 MET cc_start: 0.8249 (ttm) cc_final: 0.7869 (mtp) REVERT: E 161 PHE cc_start: 0.7453 (OUTLIER) cc_final: 0.6767 (t80) REVERT: E 213 GLU cc_start: 0.9579 (mp0) cc_final: 0.9297 (mp0) REVERT: E 214 MET cc_start: 0.9065 (mtt) cc_final: 0.8860 (mtt) REVERT: F 182 LYS cc_start: 0.8831 (pptt) cc_final: 0.8112 (ptmt) REVERT: F 205 LEU cc_start: 0.8689 (tt) cc_final: 0.8399 (tt) REVERT: F 214 MET cc_start: 0.9684 (mtm) cc_final: 0.9179 (mtp) REVERT: G 96 ARG cc_start: 0.6682 (ptt-90) cc_final: 0.6451 (ptt-90) REVERT: G 158 LYS cc_start: 0.9205 (mmmt) cc_final: 0.8914 (mmmt) REVERT: I 182 LYS cc_start: 0.8808 (pptt) cc_final: 0.7999 (ptmt) REVERT: I 214 MET cc_start: 0.9247 (mpp) cc_final: 0.8961 (mpp) REVERT: J 96 ARG cc_start: 0.6887 (ptt-90) cc_final: 0.6434 (ptt-90) REVERT: J 158 LYS cc_start: 0.9135 (mmmt) cc_final: 0.8794 (mmmt) REVERT: J 214 MET cc_start: 0.8974 (mtt) cc_final: 0.8494 (mpp) REVERT: K 213 GLU cc_start: 0.9530 (mp0) cc_final: 0.9158 (pm20) REVERT: L 182 LYS cc_start: 0.8756 (pptt) cc_final: 0.7949 (ptmt) REVERT: L 214 MET cc_start: 0.9410 (mtp) cc_final: 0.9026 (mtt) REVERT: M 66 MET cc_start: 0.8926 (tpp) cc_final: 0.8682 (mmt) REVERT: N 161 PHE cc_start: 0.7455 (OUTLIER) cc_final: 0.6739 (t80) REVERT: O 182 LYS cc_start: 0.8832 (pptt) cc_final: 0.8113 (ptmt) REVERT: P 96 ARG cc_start: 0.6685 (ptt-90) cc_final: 0.6452 (ptt-90) REVERT: P 158 LYS cc_start: 0.9217 (mmmt) cc_final: 0.8901 (mmmt) REVERT: R 182 LYS cc_start: 0.8780 (pptt) cc_final: 0.7924 (ptmt) REVERT: R 214 MET cc_start: 0.9251 (mpp) cc_final: 0.8968 (mpp) outliers start: 40 outliers final: 28 residues processed: 264 average time/residue: 0.1756 time to fit residues: 63.5796 Evaluate side-chains 234 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 203 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 191 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 D residue 211 LEU Chi-restraints excluded: chain E residue 161 PHE 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 86 ILE Chi-restraints excluded: chain J residue 140 LYS Chi-restraints excluded: chain J residue 191 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 M residue 121 GLN Chi-restraints excluded: chain M residue 211 LEU 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 37 optimal weight: 3.9990 chunk 181 optimal weight: 0.7980 chunk 168 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 70 optimal weight: 6.9990 chunk 165 optimal weight: 0.3980 chunk 180 optimal weight: 0.9980 chunk 189 optimal weight: 9.9990 chunk 146 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 127 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 135 GLN D 208 ASN G 208 ASN ** J 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.060033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.043342 restraints weight = 92726.811| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 4.89 r_work (final): 0.3120 ------------------------------------------------------------------------------- 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 = 0.15 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 = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3119 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.9367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.371 18237 Z= 0.650 Angle : 1.961 38.926 24906 Z= 0.708 Chirality : 0.127 1.937 2754 Planarity : 0.005 0.082 3180 Dihedral : 27.062 179.818 2862 Min Nonbonded Distance : 1.577 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.66 % Allowed : 16.10 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.18), residues: 2178 helix: 0.54 (0.14), residues: 1452 sheet: None (None), residues: 0 loop : -0.47 (0.25), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG P 18 TYR 0.019 0.002 TYR H 164 PHE 0.012 0.001 PHE R 168 TRP 0.018 0.001 TRP Q 184 HIS 0.001 0.000 HIS P 84 Details of bonding type rmsd covalent geometry : bond 0.01285 (18198) covalent geometry : angle 1.96267 (24870) SS BOND : bond 0.00135 ( 18) SS BOND : angle 0.51839 ( 36) hydrogen bonds : bond 0.04059 ( 919) hydrogen bonds : angle 4.51519 ( 2703) Misc. bond : bond 0.03597 ( 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 266 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 234 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.6990 (ptt-90) cc_final: 0.6538 (ptt-90) REVERT: A 158 LYS cc_start: 0.9148 (mmmt) cc_final: 0.8803 (mmmt) REVERT: B 213 GLU cc_start: 0.9515 (mp0) cc_final: 0.9163 (pm20) REVERT: C 182 LYS cc_start: 0.8811 (pptt) cc_final: 0.8063 (ptmt) REVERT: C 214 MET cc_start: 0.9418 (mmm) cc_final: 0.8970 (mpp) REVERT: D 117 MET cc_start: 0.8349 (ttm) cc_final: 0.8048 (mtm) REVERT: E 161 PHE cc_start: 0.7462 (OUTLIER) cc_final: 0.6817 (t80) REVERT: E 213 GLU cc_start: 0.9584 (mp0) cc_final: 0.9367 (mp0) REVERT: F 182 LYS cc_start: 0.8847 (pptt) cc_final: 0.8198 (ptmt) REVERT: F 214 MET cc_start: 0.9643 (mtm) cc_final: 0.9119 (mtp) REVERT: G 96 ARG cc_start: 0.6910 (ptt-90) cc_final: 0.6670 (ptt-90) REVERT: G 158 LYS cc_start: 0.9205 (mmmt) cc_final: 0.8907 (mmmt) REVERT: I 182 LYS cc_start: 0.8837 (pptt) cc_final: 0.8076 (ptmt) REVERT: I 214 MET cc_start: 0.9229 (OUTLIER) cc_final: 0.8942 (mpp) REVERT: J 96 ARG cc_start: 0.6981 (ptt-90) cc_final: 0.6531 (ptt-90) REVERT: J 158 LYS cc_start: 0.9131 (mmmt) cc_final: 0.8782 (mmmt) REVERT: K 213 GLU cc_start: 0.9511 (mp0) cc_final: 0.9158 (pm20) REVERT: L 182 LYS cc_start: 0.8813 (pptt) cc_final: 0.8071 (ptmt) REVERT: N 161 PHE cc_start: 0.7410 (OUTLIER) cc_final: 0.6784 (t80) REVERT: O 182 LYS cc_start: 0.8809 (pptt) cc_final: 0.8156 (ptmt) REVERT: P 96 ARG cc_start: 0.6915 (ptt-90) cc_final: 0.6674 (ptt-90) REVERT: P 158 LYS cc_start: 0.9197 (mmmt) cc_final: 0.8890 (mmmt) REVERT: R 182 LYS cc_start: 0.8849 (pptt) cc_final: 0.8106 (ptmt) REVERT: R 214 MET cc_start: 0.9226 (OUTLIER) cc_final: 0.8941 (mpp) outliers start: 32 outliers final: 25 residues processed: 260 average time/residue: 0.1873 time to fit residues: 65.9894 Evaluate side-chains 227 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 198 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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 D residue 211 LEU Chi-restraints excluded: chain E residue 161 PHE 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 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 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 M residue 211 LEU Chi-restraints excluded: chain N residue 161 PHE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 190 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 170 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 138 optimal weight: 10.0000 chunk 2 optimal weight: 0.6980 chunk 215 optimal weight: 20.0000 chunk 15 optimal weight: 0.2980 chunk 24 optimal weight: 0.0970 chunk 93 optimal weight: 0.9990 chunk 55 optimal weight: 0.4980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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** ** J 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.060279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.043859 restraints weight = 92375.649| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 4.84 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3140 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 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 = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.9527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.309 18237 Z= 0.627 Angle : 1.930 41.117 24906 Z= 0.699 Chirality : 0.124 1.884 2754 Planarity : 0.006 0.124 3180 Dihedral : 26.672 178.228 2862 Min Nonbonded Distance : 1.646 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.86 % Allowed : 16.10 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.19), residues: 2178 helix: 0.53 (0.14), residues: 1452 sheet: None (None), residues: 0 loop : -0.46 (0.25), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG P 18 TYR 0.023 0.002 TYR H 164 PHE 0.010 0.001 PHE Q 161 TRP 0.019 0.002 TRP Q 184 HIS 0.001 0.000 HIS J 62 Details of bonding type rmsd covalent geometry : bond 0.01238 (18198) covalent geometry : angle 1.93086 (24870) SS BOND : bond 0.00113 ( 18) SS BOND : angle 0.54984 ( 36) hydrogen bonds : bond 0.03909 ( 919) hydrogen bonds : angle 4.56032 ( 2703) Misc. bond : bond 0.03580 ( 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 274 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 238 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7094 (ptt-90) cc_final: 0.6633 (ptt-90) REVERT: A 158 LYS cc_start: 0.9129 (mmmt) cc_final: 0.8800 (mmmt) REVERT: B 203 LYS cc_start: 0.9397 (mmmm) cc_final: 0.9178 (mmmm) REVERT: C 165 VAL cc_start: 0.8128 (OUTLIER) cc_final: 0.7829 (t) REVERT: C 182 LYS cc_start: 0.8778 (pptt) cc_final: 0.7954 (ptmt) REVERT: D 117 MET cc_start: 0.8299 (ttm) cc_final: 0.8069 (mtm) REVERT: E 161 PHE cc_start: 0.7505 (OUTLIER) cc_final: 0.6922 (t80) REVERT: E 203 LYS cc_start: 0.9297 (mmmm) cc_final: 0.9047 (mmmm) REVERT: F 182 LYS cc_start: 0.8945 (pptt) cc_final: 0.8295 (ptmt) REVERT: F 214 MET cc_start: 0.9560 (mtm) cc_final: 0.9163 (mtp) REVERT: G 96 ARG cc_start: 0.6852 (ptt-90) cc_final: 0.6635 (ptt-90) REVERT: G 143 ARG cc_start: 0.9312 (ttm-80) cc_final: 0.8958 (ttm-80) REVERT: G 158 LYS cc_start: 0.9216 (mmmt) cc_final: 0.8923 (mmmt) REVERT: I 182 LYS cc_start: 0.8806 (pptt) cc_final: 0.8015 (ptmt) REVERT: I 214 MET cc_start: 0.9205 (OUTLIER) cc_final: 0.8915 (mpp) REVERT: J 96 ARG cc_start: 0.7095 (ptt-90) cc_final: 0.6633 (ptt-90) REVERT: J 158 LYS cc_start: 0.9125 (mmmt) cc_final: 0.8795 (mmmt) REVERT: K 203 LYS cc_start: 0.9386 (mmmm) cc_final: 0.9169 (mmmm) REVERT: L 182 LYS cc_start: 0.8796 (pptt) cc_final: 0.7978 (ptmt) REVERT: L 214 MET cc_start: 0.9387 (mtp) cc_final: 0.9016 (mtt) REVERT: N 161 PHE cc_start: 0.7502 (OUTLIER) cc_final: 0.6938 (t80) REVERT: N 203 LYS cc_start: 0.9309 (mmmm) cc_final: 0.9048 (mmmm) REVERT: O 182 LYS cc_start: 0.8946 (pptt) cc_final: 0.8298 (ptmt) REVERT: P 96 ARG cc_start: 0.6836 (ptt-90) cc_final: 0.6618 (ptt-90) REVERT: P 143 ARG cc_start: 0.9305 (ttm-80) cc_final: 0.8951 (ttm-80) REVERT: P 158 LYS cc_start: 0.9192 (mmmt) cc_final: 0.8889 (mmmt) REVERT: R 182 LYS cc_start: 0.8869 (pptt) cc_final: 0.8089 (ptmt) REVERT: R 214 MET cc_start: 0.9211 (OUTLIER) cc_final: 0.8923 (mpp) outliers start: 36 outliers final: 25 residues processed: 263 average time/residue: 0.1815 time to fit residues: 65.8218 Evaluate side-chains 239 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 209 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain B residue 161 PHE Chi-restraints excluded: chain C residue 165 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 D residue 211 LEU Chi-restraints excluded: chain E residue 161 PHE 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 G residue 140 LYS Chi-restraints excluded: chain H residue 161 PHE 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 M residue 211 LEU Chi-restraints excluded: chain N residue 161 PHE 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 R residue 178 ASP Chi-restraints excluded: chain R residue 185 MET 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 0 optimal weight: 10.0000 chunk 187 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 chunk 205 optimal weight: 0.0050 chunk 161 optimal weight: 0.2980 chunk 55 optimal weight: 0.9980 chunk 118 optimal weight: 7.9990 chunk 194 optimal weight: 0.0970 chunk 115 optimal weight: 10.0000 chunk 173 optimal weight: 20.0000 overall best weight: 1.0794 ------------------------------------------------------------------------------- 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** B 176 GLN H 176 GLN I 208 ASN ** J 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 176 GLN M 208 ASN Q 176 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.060103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.043413 restraints weight = 93691.412| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 4.90 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3125 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.9816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.316 18237 Z= 0.617 Angle : 1.920 40.625 24906 Z= 0.698 Chirality : 0.124 1.961 2754 Planarity : 0.006 0.128 3180 Dihedral : 26.618 176.580 2862 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.60 % Allowed : 16.41 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.19), residues: 2178 helix: 0.66 (0.14), residues: 1434 sheet: None (None), residues: 0 loop : -0.53 (0.25), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG P 18 TYR 0.022 0.002 TYR H 164 PHE 0.010 0.001 PHE Q 161 TRP 0.023 0.002 TRP P 184 HIS 0.001 0.000 HIS J 62 Details of bonding type rmsd covalent geometry : bond 0.01221 (18198) covalent geometry : angle 1.92165 (24870) SS BOND : bond 0.00142 ( 18) SS BOND : angle 0.50651 ( 36) hydrogen bonds : bond 0.03791 ( 919) hydrogen bonds : angle 4.54373 ( 2703) Misc. bond : bond 0.03570 ( 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 260 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 229 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ARG cc_start: 0.7123 (ptt-90) cc_final: 0.6762 (ptt-90) REVERT: A 158 LYS cc_start: 0.9173 (mmmt) cc_final: 0.8860 (mmmt) REVERT: B 203 LYS cc_start: 0.9382 (mmmm) cc_final: 0.9128 (mmmm) REVERT: C 182 LYS cc_start: 0.8807 (pptt) cc_final: 0.8002 (ptmt) REVERT: C 214 MET cc_start: 0.9312 (mmm) cc_final: 0.9057 (mmm) REVERT: D 117 MET cc_start: 0.8392 (ttm) cc_final: 0.8179 (mtm) REVERT: E 161 PHE cc_start: 0.7597 (OUTLIER) cc_final: 0.7055 (t80) REVERT: E 203 LYS cc_start: 0.9332 (mmmm) cc_final: 0.9094 (mmmm) REVERT: F 182 LYS cc_start: 0.8959 (pptt) cc_final: 0.8307 (ptmt) REVERT: F 214 MET cc_start: 0.9534 (mtm) cc_final: 0.9136 (mtt) REVERT: G 96 ARG cc_start: 0.6873 (ptt-90) cc_final: 0.6651 (ptt-90) REVERT: G 143 ARG cc_start: 0.9292 (ttm-80) cc_final: 0.9027 (ttm-80) REVERT: G 158 LYS cc_start: 0.9273 (mmmt) cc_final: 0.8993 (mmmt) REVERT: G 185 MET cc_start: 0.9157 (mtt) cc_final: 0.8672 (mpp) REVERT: I 182 LYS cc_start: 0.8847 (pptt) cc_final: 0.8132 (ptmt) REVERT: I 214 MET cc_start: 0.9204 (OUTLIER) cc_final: 0.8876 (mpp) REVERT: J 96 ARG cc_start: 0.7138 (ptt-90) cc_final: 0.6776 (ptt-90) REVERT: J 158 LYS cc_start: 0.9198 (mmmt) cc_final: 0.8883 (mmmt) REVERT: K 203 LYS cc_start: 0.9373 (mmmm) cc_final: 0.9123 (mmmm) REVERT: L 182 LYS cc_start: 0.8878 (pptt) cc_final: 0.8114 (ptmt) REVERT: L 214 MET cc_start: 0.9380 (mtp) cc_final: 0.9027 (mtt) REVERT: N 161 PHE cc_start: 0.7553 (OUTLIER) cc_final: 0.7076 (t80) REVERT: N 203 LYS cc_start: 0.9330 (mmmm) cc_final: 0.9085 (mmmm) REVERT: O 182 LYS cc_start: 0.8960 (pptt) cc_final: 0.8310 (ptmt) REVERT: P 96 ARG cc_start: 0.6869 (ptt-90) cc_final: 0.6646 (ptt-90) REVERT: P 143 ARG cc_start: 0.9290 (ttm-80) cc_final: 0.9027 (ttm-80) REVERT: P 158 LYS cc_start: 0.9248 (mmmt) cc_final: 0.8957 (mmmt) REVERT: P 185 MET cc_start: 0.9113 (mtt) cc_final: 0.8673 (mpp) REVERT: Q 192 GLN cc_start: 0.9418 (mm-40) cc_final: 0.9071 (mm-40) REVERT: R 182 LYS cc_start: 0.8850 (pptt) cc_final: 0.8135 (ptmt) REVERT: R 214 MET cc_start: 0.9205 (OUTLIER) cc_final: 0.8881 (mpp) outliers start: 31 outliers final: 25 residues processed: 252 average time/residue: 0.1819 time to fit residues: 62.6133 Evaluate side-chains 237 residues out of total 1932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 208 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG 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 D residue 211 LEU Chi-restraints excluded: chain E residue 161 PHE 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 G residue 140 LYS Chi-restraints excluded: chain H residue 161 PHE 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 M residue 211 LEU Chi-restraints excluded: chain N residue 161 PHE Chi-restraints excluded: chain O residue 210 THR Chi-restraints excluded: chain P residue 86 ILE Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 140 LYS Chi-restraints excluded: chain Q residue 161 PHE 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 165 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 126 optimal weight: 7.9990 chunk 12 optimal weight: 0.0970 chunk 41 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 104 optimal weight: 0.5980 chunk 213 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 212 optimal weight: 6.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- 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** ** D 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.059379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.042460 restraints weight = 97774.553| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 5.01 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3091 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3091 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 1.0180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.330 18237 Z= 0.612 Angle : 1.918 42.267 24906 Z= 0.703 Chirality : 0.125 1.995 2754 Planarity : 0.006 0.113 3180 Dihedral : 26.598 178.531 2862 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.81 % Allowed : 16.98 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.19), residues: 2178 helix: 0.64 (0.14), residues: 1434 sheet: None (None), residues: 0 loop : -0.49 (0.25), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG P 18 TYR 0.020 0.002 TYR H 164 PHE 0.010 0.001 PHE E 161 TRP 0.021 0.002 TRP Q 184 HIS 0.002 0.001 HIS A 62 Details of bonding type rmsd covalent geometry : bond 0.01216 (18198) covalent geometry : angle 1.91957 (24870) SS BOND : bond 0.00099 ( 18) SS BOND : angle 0.41965 ( 36) hydrogen bonds : bond 0.03990 ( 919) hydrogen bonds : angle 4.62391 ( 2703) Misc. bond : bond 0.03577 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4191.30 seconds wall clock time: 72 minutes 31.18 seconds (4351.18 seconds total)