Starting phenix.real_space_refine on Sat Dec 28 04:52:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tbh_25799/12_2024/7tbh_25799.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tbh_25799/12_2024/7tbh_25799.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tbh_25799/12_2024/7tbh_25799.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tbh_25799/12_2024/7tbh_25799.map" model { file = "/net/cci-nas-00/data/ceres_data/7tbh_25799/12_2024/7tbh_25799.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tbh_25799/12_2024/7tbh_25799.cif" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 sd= 0.031 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 24 5.49 5 S 312 5.16 5 C 32424 2.51 5 N 9168 2.21 5 O 9840 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 51768 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "B" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "C" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "D" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "E" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "F" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "G" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "H" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "I" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "J" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "K" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "L" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "M" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "N" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "O" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "P" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "Q" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "R" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "S" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "T" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "U" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "V" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "W" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "X" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "a" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 157 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 2, 'TRANS': 16} Chain: "b" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 157 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 2, 'TRANS': 16} Chain: "c" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 157 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 2, 'TRANS': 16} Chain: "d" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 157 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 2, 'TRANS': 16} Chain: "e" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 157 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 2, 'TRANS': 16} Chain: "f" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 157 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 2, 'TRANS': 16} Chain: "g" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 157 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 2, 'TRANS': 16} Chain: "h" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 157 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 2, 'TRANS': 16} Chain: "i" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 157 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 2, 'TRANS': 16} Chain: "j" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 157 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 2, 'TRANS': 16} Chain: "k" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 157 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 2, 'TRANS': 16} Chain: "l" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 157 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 2, 'TRANS': 16} Chain: "m" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 157 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 2, 'TRANS': 16} Chain: "n" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 157 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 2, 'TRANS': 16} Chain: "o" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 157 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 2, 'TRANS': 16} Chain: "p" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 157 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 2, 'TRANS': 16} Chain: "q" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 157 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 2, 'TRANS': 16} Chain: "r" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 157 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 2, 'TRANS': 16} Chain: "s" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 157 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 2, 'TRANS': 16} Chain: "t" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 157 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 2, 'TRANS': 16} Chain: "u" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 157 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 2, 'TRANS': 16} Chain: "v" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 157 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 2, 'TRANS': 16} Chain: "w" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 157 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 2, 'TRANS': 16} Chain: "x" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 157 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 2, 'TRANS': 16} Time building chain proxies: 37.91, per 1000 atoms: 0.73 Number of scatterers: 51768 At special positions: 0 Unit cell: (173.02, 173.02, 173.02, 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 312 16.00 P 24 15.00 O 9840 8.00 N 9168 7.00 C 32424 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 27 " - pdb=" SG CYS J 169 " distance=2.04 Simple disulfide: pdb=" SG CYS A 31 " - pdb=" SG CYS J 237 " distance=2.04 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS J 27 " distance=2.02 Simple disulfide: pdb=" SG CYS A 237 " - pdb=" SG CYS J 31 " distance=2.01 Simple disulfide: pdb=" SG CYS B 27 " - pdb=" SG CYS I 169 " distance=2.04 Simple disulfide: pdb=" SG CYS B 31 " - pdb=" SG CYS I 237 " distance=2.04 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS I 27 " distance=2.02 Simple disulfide: pdb=" SG CYS B 237 " - pdb=" SG CYS I 31 " distance=2.02 Simple disulfide: pdb=" SG CYS C 27 " - pdb=" SG CYS L 169 " distance=2.04 Simple disulfide: pdb=" SG CYS C 31 " - pdb=" SG CYS L 237 " distance=2.04 Simple disulfide: pdb=" SG CYS C 169 " - pdb=" SG CYS L 27 " distance=2.02 Simple disulfide: pdb=" SG CYS C 237 " - pdb=" SG CYS L 31 " distance=2.02 Simple disulfide: pdb=" SG CYS D 27 " - pdb=" SG CYS K 169 " distance=2.04 Simple disulfide: pdb=" SG CYS D 31 " - pdb=" SG CYS K 237 " distance=2.04 Simple disulfide: pdb=" SG CYS D 169 " - pdb=" SG CYS K 27 " distance=2.02 Simple disulfide: pdb=" SG CYS D 237 " - pdb=" SG CYS K 31 " distance=2.03 Simple disulfide: pdb=" SG CYS E 27 " - pdb=" SG CYS N 169 " distance=2.04 Simple disulfide: pdb=" SG CYS E 31 " - pdb=" SG CYS N 237 " distance=2.03 Simple disulfide: pdb=" SG CYS E 169 " - pdb=" SG CYS N 27 " distance=2.03 Simple disulfide: pdb=" SG CYS E 237 " - pdb=" SG CYS N 31 " distance=2.03 Simple disulfide: pdb=" SG CYS F 27 " - pdb=" SG CYS M 169 " distance=2.03 Simple disulfide: pdb=" SG CYS F 31 " - pdb=" SG CYS M 237 " distance=2.03 Simple disulfide: pdb=" SG CYS F 169 " - pdb=" SG CYS M 27 " distance=2.02 Simple disulfide: pdb=" SG CYS F 237 " - pdb=" SG CYS M 31 " distance=2.02 Simple disulfide: pdb=" SG CYS G 27 " - pdb=" SG CYS P 169 " distance=2.04 Simple disulfide: pdb=" SG CYS G 31 " - pdb=" SG CYS P 237 " distance=2.04 Simple disulfide: pdb=" SG CYS G 169 " - pdb=" SG CYS P 27 " distance=2.02 Simple disulfide: pdb=" SG CYS G 237 " - pdb=" SG CYS P 31 " distance=2.03 Simple disulfide: pdb=" SG CYS H 27 " - pdb=" SG CYS O 169 " distance=2.03 Simple disulfide: pdb=" SG CYS H 31 " - pdb=" SG CYS O 237 " distance=2.04 Simple disulfide: pdb=" SG CYS H 169 " - pdb=" SG CYS O 27 " distance=2.02 Simple disulfide: pdb=" SG CYS H 237 " - pdb=" SG CYS O 31 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 27 " - pdb=" SG CYS X 169 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 31 " - pdb=" SG CYS X 237 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 169 " - pdb=" SG CYS X 27 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 237 " - pdb=" SG CYS X 31 " distance=2.02 Simple disulfide: pdb=" SG CYS R 27 " - pdb=" SG CYS W 169 " distance=2.04 Simple disulfide: pdb=" SG CYS R 31 " - pdb=" SG CYS W 237 " distance=2.04 Simple disulfide: pdb=" SG CYS R 169 " - pdb=" SG CYS W 27 " distance=2.02 Simple disulfide: pdb=" SG CYS R 237 " - pdb=" SG CYS W 31 " distance=2.03 Simple disulfide: pdb=" SG CYS S 27 " - pdb=" SG CYS V 169 " distance=2.04 Simple disulfide: pdb=" SG CYS S 31 " - pdb=" SG CYS V 237 " distance=2.04 Simple disulfide: pdb=" SG CYS S 169 " - pdb=" SG CYS V 27 " distance=2.02 Simple disulfide: pdb=" SG CYS S 237 " - pdb=" SG CYS V 31 " distance=2.02 Simple disulfide: pdb=" SG CYS T 27 " - pdb=" SG CYS U 169 " distance=2.03 Simple disulfide: pdb=" SG CYS T 31 " - pdb=" SG CYS U 237 " distance=2.04 Simple disulfide: pdb=" SG CYS T 169 " - pdb=" SG CYS U 27 " distance=2.02 Simple disulfide: pdb=" SG CYS T 237 " - pdb=" SG CYS U 31 " distance=2.03 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 Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.27 Conformation dependent library (CDL) restraints added in 8.3 seconds 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12240 Finding SS restraints... Secondary structure from input PDB file: 240 helices and 0 sheets defined 79.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.01 Creating SS restraints... Processing helix chain 'A' and resid 9 through 25 removed outlier: 3.536A pdb=" N LEU A 20 " --> pdb=" O LEU A 16 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL A 21 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLN A 22 " --> pdb=" O HIS A 18 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE A 25 " --> pdb=" O VAL A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 55 removed outlier: 3.512A pdb=" N GLU A 39 " --> pdb=" O ASP A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 77 removed outlier: 4.100A pdb=" N GLU A 76 " --> pdb=" O LYS A 72 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU A 77 " --> pdb=" O ILE A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 117 removed outlier: 3.640A pdb=" N ASP A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 152 Processing helix chain 'A' and resid 171 through 199 Processing helix chain 'A' and resid 201 through 212 removed outlier: 3.560A pdb=" N CYS A 205 " --> pdb=" O ASP A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 234 Processing helix chain 'A' and resid 238 through 249 removed outlier: 4.037A pdb=" N GLU A 242 " --> pdb=" O ALA A 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 25 removed outlier: 3.536A pdb=" N LEU B 20 " --> pdb=" O LEU B 16 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL B 21 " --> pdb=" O VAL B 17 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLN B 22 " --> pdb=" O HIS B 18 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE B 25 " --> pdb=" O VAL B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 55 removed outlier: 3.512A pdb=" N GLU B 39 " --> pdb=" O ASP B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 77 removed outlier: 4.100A pdb=" N GLU B 76 " --> pdb=" O LYS B 72 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU B 77 " --> pdb=" O ILE B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 117 removed outlier: 3.641A pdb=" N ASP B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 152 Processing helix chain 'B' and resid 171 through 199 Processing helix chain 'B' and resid 201 through 212 removed outlier: 3.560A pdb=" N CYS B 205 " --> pdb=" O ASP B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 234 Processing helix chain 'B' and resid 238 through 249 removed outlier: 4.037A pdb=" N GLU B 242 " --> pdb=" O ALA B 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 25 removed outlier: 3.536A pdb=" N LEU C 20 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL C 21 " --> pdb=" O VAL C 17 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN C 22 " --> pdb=" O HIS C 18 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE C 25 " --> pdb=" O VAL C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 55 removed outlier: 3.513A pdb=" N GLU C 39 " --> pdb=" O ASP C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 77 removed outlier: 4.100A pdb=" N GLU C 76 " --> pdb=" O LYS C 72 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU C 77 " --> pdb=" O ILE C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 117 removed outlier: 3.640A pdb=" N ASP C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 152 Processing helix chain 'C' and resid 171 through 199 Processing helix chain 'C' and resid 201 through 212 removed outlier: 3.560A pdb=" N CYS C 205 " --> pdb=" O ASP C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 234 Processing helix chain 'C' and resid 238 through 249 removed outlier: 4.037A pdb=" N GLU C 242 " --> pdb=" O ALA C 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 25 removed outlier: 3.535A pdb=" N LEU D 20 " --> pdb=" O LEU D 16 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL D 21 " --> pdb=" O VAL D 17 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLN D 22 " --> pdb=" O HIS D 18 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE D 25 " --> pdb=" O VAL D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 55 removed outlier: 3.512A pdb=" N GLU D 39 " --> pdb=" O ASP D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 77 removed outlier: 4.099A pdb=" N GLU D 76 " --> pdb=" O LYS D 72 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU D 77 " --> pdb=" O ILE D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 117 removed outlier: 3.641A pdb=" N ASP D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 152 Processing helix chain 'D' and resid 171 through 199 Processing helix chain 'D' and resid 201 through 212 removed outlier: 3.560A pdb=" N CYS D 205 " --> pdb=" O ASP D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 234 Processing helix chain 'D' and resid 238 through 249 removed outlier: 4.036A pdb=" N GLU D 242 " --> pdb=" O ALA D 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 25 removed outlier: 3.536A pdb=" N LEU E 20 " --> pdb=" O LEU E 16 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL E 21 " --> pdb=" O VAL E 17 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLN E 22 " --> pdb=" O HIS E 18 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE E 25 " --> pdb=" O VAL E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 55 removed outlier: 3.512A pdb=" N GLU E 39 " --> pdb=" O ASP E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 77 removed outlier: 4.099A pdb=" N GLU E 76 " --> pdb=" O LYS E 72 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU E 77 " --> pdb=" O ILE E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 117 removed outlier: 3.640A pdb=" N ASP E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 152 Processing helix chain 'E' and resid 171 through 199 Processing helix chain 'E' and resid 201 through 212 removed outlier: 3.560A pdb=" N CYS E 205 " --> pdb=" O ASP E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 234 Processing helix chain 'E' and resid 238 through 249 removed outlier: 4.037A pdb=" N GLU E 242 " --> pdb=" O ALA E 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 25 removed outlier: 3.536A pdb=" N LEU F 20 " --> pdb=" O LEU F 16 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL F 21 " --> pdb=" O VAL F 17 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLN F 22 " --> pdb=" O HIS F 18 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE F 25 " --> pdb=" O VAL F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 55 removed outlier: 3.512A pdb=" N GLU F 39 " --> pdb=" O ASP F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 77 removed outlier: 4.099A pdb=" N GLU F 76 " --> pdb=" O LYS F 72 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU F 77 " --> pdb=" O ILE F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 117 removed outlier: 3.641A pdb=" N ASP F 117 " --> pdb=" O SER F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 152 Processing helix chain 'F' and resid 171 through 199 Processing helix chain 'F' and resid 201 through 212 removed outlier: 3.560A pdb=" N CYS F 205 " --> pdb=" O ASP F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 234 Processing helix chain 'F' and resid 238 through 249 removed outlier: 4.037A pdb=" N GLU F 242 " --> pdb=" O ALA F 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 25 removed outlier: 3.536A pdb=" N LEU G 20 " --> pdb=" O LEU G 16 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL G 21 " --> pdb=" O VAL G 17 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN G 22 " --> pdb=" O HIS G 18 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE G 25 " --> pdb=" O VAL G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 55 removed outlier: 3.512A pdb=" N GLU G 39 " --> pdb=" O ASP G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 77 removed outlier: 4.100A pdb=" N GLU G 76 " --> pdb=" O LYS G 72 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU G 77 " --> pdb=" O ILE G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 117 removed outlier: 3.640A pdb=" N ASP G 117 " --> pdb=" O SER G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 152 Processing helix chain 'G' and resid 171 through 199 Processing helix chain 'G' and resid 201 through 212 removed outlier: 3.560A pdb=" N CYS G 205 " --> pdb=" O ASP G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 234 Processing helix chain 'G' and resid 238 through 249 removed outlier: 4.037A pdb=" N GLU G 242 " --> pdb=" O ALA G 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 25 removed outlier: 3.535A pdb=" N LEU H 20 " --> pdb=" O LEU H 16 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL H 21 " --> pdb=" O VAL H 17 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLN H 22 " --> pdb=" O HIS H 18 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE H 25 " --> pdb=" O VAL H 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 55 removed outlier: 3.512A pdb=" N GLU H 39 " --> pdb=" O ASP H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 77 removed outlier: 4.100A pdb=" N GLU H 76 " --> pdb=" O LYS H 72 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU H 77 " --> pdb=" O ILE H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 117 removed outlier: 3.641A pdb=" N ASP H 117 " --> pdb=" O SER H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 123 through 152 Processing helix chain 'H' and resid 171 through 199 Processing helix chain 'H' and resid 201 through 212 removed outlier: 3.560A pdb=" N CYS H 205 " --> pdb=" O ASP H 201 " (cutoff:3.500A) Processing helix chain 'H' and resid 212 through 234 Processing helix chain 'H' and resid 238 through 249 removed outlier: 4.037A pdb=" N GLU H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 25 removed outlier: 3.535A pdb=" N LEU I 20 " --> pdb=" O LEU I 16 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL I 21 " --> pdb=" O VAL I 17 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN I 22 " --> pdb=" O HIS I 18 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE I 25 " --> pdb=" O VAL I 21 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 55 removed outlier: 3.512A pdb=" N GLU I 39 " --> pdb=" O ASP I 35 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 77 removed outlier: 4.100A pdb=" N GLU I 76 " --> pdb=" O LYS I 72 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU I 77 " --> pdb=" O ILE I 73 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 117 removed outlier: 3.641A pdb=" N ASP I 117 " --> pdb=" O SER I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 123 through 152 Processing helix chain 'I' and resid 171 through 199 Processing helix chain 'I' and resid 201 through 212 removed outlier: 3.560A pdb=" N CYS I 205 " --> pdb=" O ASP I 201 " (cutoff:3.500A) Processing helix chain 'I' and resid 212 through 234 Processing helix chain 'I' and resid 238 through 249 removed outlier: 4.037A pdb=" N GLU I 242 " --> pdb=" O ALA I 238 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 25 removed outlier: 3.535A pdb=" N LEU J 20 " --> pdb=" O LEU J 16 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL J 21 " --> pdb=" O VAL J 17 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN J 22 " --> pdb=" O HIS J 18 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE J 25 " --> pdb=" O VAL J 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 35 through 55 removed outlier: 3.512A pdb=" N GLU J 39 " --> pdb=" O ASP J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 77 removed outlier: 4.100A pdb=" N GLU J 76 " --> pdb=" O LYS J 72 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU J 77 " --> pdb=" O ILE J 73 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 117 removed outlier: 3.641A pdb=" N ASP J 117 " --> pdb=" O SER J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 123 through 152 Processing helix chain 'J' and resid 171 through 199 Processing helix chain 'J' and resid 201 through 212 removed outlier: 3.560A pdb=" N CYS J 205 " --> pdb=" O ASP J 201 " (cutoff:3.500A) Processing helix chain 'J' and resid 212 through 234 Processing helix chain 'J' and resid 238 through 249 removed outlier: 4.037A pdb=" N GLU J 242 " --> pdb=" O ALA J 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 25 removed outlier: 3.536A pdb=" N LEU K 20 " --> pdb=" O LEU K 16 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL K 21 " --> pdb=" O VAL K 17 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN K 22 " --> pdb=" O HIS K 18 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE K 25 " --> pdb=" O VAL K 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 35 through 55 removed outlier: 3.512A pdb=" N GLU K 39 " --> pdb=" O ASP K 35 " (cutoff:3.500A) Processing helix chain 'K' and resid 59 through 77 removed outlier: 4.099A pdb=" N GLU K 76 " --> pdb=" O LYS K 72 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU K 77 " --> pdb=" O ILE K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 117 removed outlier: 3.641A pdb=" N ASP K 117 " --> pdb=" O SER K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 152 Processing helix chain 'K' and resid 171 through 199 Processing helix chain 'K' and resid 201 through 212 removed outlier: 3.559A pdb=" N CYS K 205 " --> pdb=" O ASP K 201 " (cutoff:3.500A) Processing helix chain 'K' and resid 212 through 234 Processing helix chain 'K' and resid 238 through 249 removed outlier: 4.037A pdb=" N GLU K 242 " --> pdb=" O ALA K 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 25 removed outlier: 3.536A pdb=" N LEU L 20 " --> pdb=" O LEU L 16 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL L 21 " --> pdb=" O VAL L 17 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN L 22 " --> pdb=" O HIS L 18 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE L 25 " --> pdb=" O VAL L 21 " (cutoff:3.500A) Processing helix chain 'L' and resid 35 through 55 removed outlier: 3.512A pdb=" N GLU L 39 " --> pdb=" O ASP L 35 " (cutoff:3.500A) Processing helix chain 'L' and resid 59 through 77 removed outlier: 4.099A pdb=" N GLU L 76 " --> pdb=" O LYS L 72 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU L 77 " --> pdb=" O ILE L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 117 removed outlier: 3.641A pdb=" N ASP L 117 " --> pdb=" O SER L 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 152 Processing helix chain 'L' and resid 171 through 199 Processing helix chain 'L' and resid 201 through 212 removed outlier: 3.560A pdb=" N CYS L 205 " --> pdb=" O ASP L 201 " (cutoff:3.500A) Processing helix chain 'L' and resid 212 through 234 Processing helix chain 'L' and resid 238 through 249 removed outlier: 4.037A pdb=" N GLU L 242 " --> pdb=" O ALA L 238 " (cutoff:3.500A) Processing helix chain 'M' and resid 10 through 25 removed outlier: 3.535A pdb=" N LEU M 20 " --> pdb=" O LEU M 16 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL M 21 " --> pdb=" O VAL M 17 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN M 22 " --> pdb=" O HIS M 18 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE M 25 " --> pdb=" O VAL M 21 " (cutoff:3.500A) Processing helix chain 'M' and resid 35 through 55 removed outlier: 3.512A pdb=" N GLU M 39 " --> pdb=" O ASP M 35 " (cutoff:3.500A) Processing helix chain 'M' and resid 59 through 77 removed outlier: 4.099A pdb=" N GLU M 76 " --> pdb=" O LYS M 72 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU M 77 " --> pdb=" O ILE M 73 " (cutoff:3.500A) Processing helix chain 'M' and resid 88 through 117 removed outlier: 3.640A pdb=" N ASP M 117 " --> pdb=" O SER M 113 " (cutoff:3.500A) Processing helix chain 'M' and resid 123 through 152 Processing helix chain 'M' and resid 171 through 199 Processing helix chain 'M' and resid 201 through 212 removed outlier: 3.560A pdb=" N CYS M 205 " --> pdb=" O ASP M 201 " (cutoff:3.500A) Processing helix chain 'M' and resid 212 through 234 Processing helix chain 'M' and resid 238 through 249 removed outlier: 4.037A pdb=" N GLU M 242 " --> pdb=" O ALA M 238 " (cutoff:3.500A) Processing helix chain 'N' and resid 10 through 25 removed outlier: 3.536A pdb=" N LEU N 20 " --> pdb=" O LEU N 16 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL N 21 " --> pdb=" O VAL N 17 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN N 22 " --> pdb=" O HIS N 18 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE N 25 " --> pdb=" O VAL N 21 " (cutoff:3.500A) Processing helix chain 'N' and resid 35 through 55 removed outlier: 3.512A pdb=" N GLU N 39 " --> pdb=" O ASP N 35 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 77 removed outlier: 4.100A pdb=" N GLU N 76 " --> pdb=" O LYS N 72 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU N 77 " --> pdb=" O ILE N 73 " (cutoff:3.500A) Processing helix chain 'N' and resid 88 through 117 removed outlier: 3.641A pdb=" N ASP N 117 " --> pdb=" O SER N 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 123 through 152 Processing helix chain 'N' and resid 171 through 199 Processing helix chain 'N' and resid 201 through 212 removed outlier: 3.559A pdb=" N CYS N 205 " --> pdb=" O ASP N 201 " (cutoff:3.500A) Processing helix chain 'N' and resid 212 through 234 Processing helix chain 'N' and resid 238 through 249 removed outlier: 4.037A pdb=" N GLU N 242 " --> pdb=" O ALA N 238 " (cutoff:3.500A) Processing helix chain 'O' and resid 10 through 25 removed outlier: 3.535A pdb=" N LEU O 20 " --> pdb=" O LEU O 16 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL O 21 " --> pdb=" O VAL O 17 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN O 22 " --> pdb=" O HIS O 18 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE O 25 " --> pdb=" O VAL O 21 " (cutoff:3.500A) Processing helix chain 'O' and resid 35 through 55 removed outlier: 3.512A pdb=" N GLU O 39 " --> pdb=" O ASP O 35 " (cutoff:3.500A) Processing helix chain 'O' and resid 59 through 77 removed outlier: 4.100A pdb=" N GLU O 76 " --> pdb=" O LYS O 72 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU O 77 " --> pdb=" O ILE O 73 " (cutoff:3.500A) Processing helix chain 'O' and resid 88 through 117 removed outlier: 3.641A pdb=" N ASP O 117 " --> pdb=" O SER O 113 " (cutoff:3.500A) Processing helix chain 'O' and resid 123 through 152 Processing helix chain 'O' and resid 171 through 199 Processing helix chain 'O' and resid 201 through 212 removed outlier: 3.560A pdb=" N CYS O 205 " --> pdb=" O ASP O 201 " (cutoff:3.500A) Processing helix chain 'O' and resid 212 through 234 Processing helix chain 'O' and resid 238 through 249 removed outlier: 4.037A pdb=" N GLU O 242 " --> pdb=" O ALA O 238 " (cutoff:3.500A) Processing helix chain 'P' and resid 10 through 25 removed outlier: 3.536A pdb=" N LEU P 20 " --> pdb=" O LEU P 16 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL P 21 " --> pdb=" O VAL P 17 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLN P 22 " --> pdb=" O HIS P 18 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE P 25 " --> pdb=" O VAL P 21 " (cutoff:3.500A) Processing helix chain 'P' and resid 35 through 55 removed outlier: 3.512A pdb=" N GLU P 39 " --> pdb=" O ASP P 35 " (cutoff:3.500A) Processing helix chain 'P' and resid 59 through 77 removed outlier: 4.100A pdb=" N GLU P 76 " --> pdb=" O LYS P 72 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU P 77 " --> pdb=" O ILE P 73 " (cutoff:3.500A) Processing helix chain 'P' and resid 88 through 117 removed outlier: 3.641A pdb=" N ASP P 117 " --> pdb=" O SER P 113 " (cutoff:3.500A) Processing helix chain 'P' and resid 123 through 152 Processing helix chain 'P' and resid 171 through 199 Processing helix chain 'P' and resid 201 through 212 removed outlier: 3.560A pdb=" N CYS P 205 " --> pdb=" O ASP P 201 " (cutoff:3.500A) Processing helix chain 'P' and resid 212 through 234 Processing helix chain 'P' and resid 238 through 249 removed outlier: 4.037A pdb=" N GLU P 242 " --> pdb=" O ALA P 238 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 25 removed outlier: 3.535A pdb=" N LEU Q 20 " --> pdb=" O LEU Q 16 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL Q 21 " --> pdb=" O VAL Q 17 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLN Q 22 " --> pdb=" O HIS Q 18 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE Q 25 " --> pdb=" O VAL Q 21 " (cutoff:3.500A) Processing helix chain 'Q' and resid 35 through 55 removed outlier: 3.512A pdb=" N GLU Q 39 " --> pdb=" O ASP Q 35 " (cutoff:3.500A) Processing helix chain 'Q' and resid 59 through 77 removed outlier: 4.100A pdb=" N GLU Q 76 " --> pdb=" O LYS Q 72 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU Q 77 " --> pdb=" O ILE Q 73 " (cutoff:3.500A) Processing helix chain 'Q' and resid 88 through 117 removed outlier: 3.641A pdb=" N ASP Q 117 " --> pdb=" O SER Q 113 " (cutoff:3.500A) Processing helix chain 'Q' and resid 123 through 152 Processing helix chain 'Q' and resid 171 through 199 Processing helix chain 'Q' and resid 201 through 212 removed outlier: 3.560A pdb=" N CYS Q 205 " --> pdb=" O ASP Q 201 " (cutoff:3.500A) Processing helix chain 'Q' and resid 212 through 234 Processing helix chain 'Q' and resid 238 through 249 removed outlier: 4.037A pdb=" N GLU Q 242 " --> pdb=" O ALA Q 238 " (cutoff:3.500A) Processing helix chain 'R' and resid 10 through 25 removed outlier: 3.536A pdb=" N LEU R 20 " --> pdb=" O LEU R 16 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL R 21 " --> pdb=" O VAL R 17 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN R 22 " --> pdb=" O HIS R 18 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE R 25 " --> pdb=" O VAL R 21 " (cutoff:3.500A) Processing helix chain 'R' and resid 35 through 55 removed outlier: 3.512A pdb=" N GLU R 39 " --> pdb=" O ASP R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 77 removed outlier: 4.099A pdb=" N GLU R 76 " --> pdb=" O LYS R 72 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU R 77 " --> pdb=" O ILE R 73 " (cutoff:3.500A) Processing helix chain 'R' and resid 88 through 117 removed outlier: 3.640A pdb=" N ASP R 117 " --> pdb=" O SER R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 123 through 152 Processing helix chain 'R' and resid 171 through 199 Processing helix chain 'R' and resid 201 through 212 removed outlier: 3.560A pdb=" N CYS R 205 " --> pdb=" O ASP R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 212 through 234 Processing helix chain 'R' and resid 238 through 249 removed outlier: 4.037A pdb=" N GLU R 242 " --> pdb=" O ALA R 238 " (cutoff:3.500A) Processing helix chain 'S' and resid 10 through 25 removed outlier: 3.536A pdb=" N LEU S 20 " --> pdb=" O LEU S 16 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL S 21 " --> pdb=" O VAL S 17 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN S 22 " --> pdb=" O HIS S 18 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE S 25 " --> pdb=" O VAL S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 35 through 55 removed outlier: 3.512A pdb=" N GLU S 39 " --> pdb=" O ASP S 35 " (cutoff:3.500A) Processing helix chain 'S' and resid 59 through 77 removed outlier: 4.100A pdb=" N GLU S 76 " --> pdb=" O LYS S 72 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU S 77 " --> pdb=" O ILE S 73 " (cutoff:3.500A) Processing helix chain 'S' and resid 88 through 117 removed outlier: 3.640A pdb=" N ASP S 117 " --> pdb=" O SER S 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 123 through 152 Processing helix chain 'S' and resid 171 through 199 Processing helix chain 'S' and resid 201 through 212 removed outlier: 3.560A pdb=" N CYS S 205 " --> pdb=" O ASP S 201 " (cutoff:3.500A) Processing helix chain 'S' and resid 212 through 234 Processing helix chain 'S' and resid 238 through 249 removed outlier: 4.037A pdb=" N GLU S 242 " --> pdb=" O ALA S 238 " (cutoff:3.500A) Processing helix chain 'T' and resid 10 through 25 removed outlier: 3.536A pdb=" N LEU T 20 " --> pdb=" O LEU T 16 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL T 21 " --> pdb=" O VAL T 17 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN T 22 " --> pdb=" O HIS T 18 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE T 25 " --> pdb=" O VAL T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 35 through 55 removed outlier: 3.512A pdb=" N GLU T 39 " --> pdb=" O ASP T 35 " (cutoff:3.500A) Processing helix chain 'T' and resid 59 through 77 removed outlier: 4.100A pdb=" N GLU T 76 " --> pdb=" O LYS T 72 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU T 77 " --> pdb=" O ILE T 73 " (cutoff:3.500A) Processing helix chain 'T' and resid 88 through 117 removed outlier: 3.640A pdb=" N ASP T 117 " --> pdb=" O SER T 113 " (cutoff:3.500A) Processing helix chain 'T' and resid 123 through 152 Processing helix chain 'T' and resid 171 through 199 Processing helix chain 'T' and resid 201 through 212 removed outlier: 3.560A pdb=" N CYS T 205 " --> pdb=" O ASP T 201 " (cutoff:3.500A) Processing helix chain 'T' and resid 212 through 234 Processing helix chain 'T' and resid 238 through 249 removed outlier: 4.037A pdb=" N GLU T 242 " --> pdb=" O ALA T 238 " (cutoff:3.500A) Processing helix chain 'U' and resid 10 through 25 removed outlier: 3.536A pdb=" N LEU U 20 " --> pdb=" O LEU U 16 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL U 21 " --> pdb=" O VAL U 17 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLN U 22 " --> pdb=" O HIS U 18 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE U 25 " --> pdb=" O VAL U 21 " (cutoff:3.500A) Processing helix chain 'U' and resid 35 through 55 removed outlier: 3.512A pdb=" N GLU U 39 " --> pdb=" O ASP U 35 " (cutoff:3.500A) Processing helix chain 'U' and resid 59 through 77 removed outlier: 4.101A pdb=" N GLU U 76 " --> pdb=" O LYS U 72 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU U 77 " --> pdb=" O ILE U 73 " (cutoff:3.500A) Processing helix chain 'U' and resid 88 through 117 removed outlier: 3.640A pdb=" N ASP U 117 " --> pdb=" O SER U 113 " (cutoff:3.500A) Processing helix chain 'U' and resid 123 through 152 Processing helix chain 'U' and resid 171 through 199 Processing helix chain 'U' and resid 201 through 212 removed outlier: 3.559A pdb=" N CYS U 205 " --> pdb=" O ASP U 201 " (cutoff:3.500A) Processing helix chain 'U' and resid 212 through 234 Processing helix chain 'U' and resid 238 through 249 removed outlier: 4.037A pdb=" N GLU U 242 " --> pdb=" O ALA U 238 " (cutoff:3.500A) Processing helix chain 'V' and resid 10 through 25 removed outlier: 3.535A pdb=" N LEU V 20 " --> pdb=" O LEU V 16 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL V 21 " --> pdb=" O VAL V 17 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN V 22 " --> pdb=" O HIS V 18 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE V 25 " --> pdb=" O VAL V 21 " (cutoff:3.500A) Processing helix chain 'V' and resid 35 through 55 removed outlier: 3.512A pdb=" N GLU V 39 " --> pdb=" O ASP V 35 " (cutoff:3.500A) Processing helix chain 'V' and resid 59 through 77 removed outlier: 4.100A pdb=" N GLU V 76 " --> pdb=" O LYS V 72 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU V 77 " --> pdb=" O ILE V 73 " (cutoff:3.500A) Processing helix chain 'V' and resid 88 through 117 removed outlier: 3.641A pdb=" N ASP V 117 " --> pdb=" O SER V 113 " (cutoff:3.500A) Processing helix chain 'V' and resid 123 through 152 Processing helix chain 'V' and resid 171 through 199 Processing helix chain 'V' and resid 201 through 212 removed outlier: 3.559A pdb=" N CYS V 205 " --> pdb=" O ASP V 201 " (cutoff:3.500A) Processing helix chain 'V' and resid 212 through 234 Processing helix chain 'V' and resid 238 through 249 removed outlier: 4.037A pdb=" N GLU V 242 " --> pdb=" O ALA V 238 " (cutoff:3.500A) Processing helix chain 'W' and resid 10 through 25 removed outlier: 3.536A pdb=" N LEU W 20 " --> pdb=" O LEU W 16 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL W 21 " --> pdb=" O VAL W 17 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN W 22 " --> pdb=" O HIS W 18 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE W 25 " --> pdb=" O VAL W 21 " (cutoff:3.500A) Processing helix chain 'W' and resid 35 through 55 removed outlier: 3.512A pdb=" N GLU W 39 " --> pdb=" O ASP W 35 " (cutoff:3.500A) Processing helix chain 'W' and resid 59 through 77 removed outlier: 4.100A pdb=" N GLU W 76 " --> pdb=" O LYS W 72 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU W 77 " --> pdb=" O ILE W 73 " (cutoff:3.500A) Processing helix chain 'W' and resid 88 through 117 removed outlier: 3.641A pdb=" N ASP W 117 " --> pdb=" O SER W 113 " (cutoff:3.500A) Processing helix chain 'W' and resid 123 through 152 Processing helix chain 'W' and resid 171 through 199 Processing helix chain 'W' and resid 201 through 212 removed outlier: 3.559A pdb=" N CYS W 205 " --> pdb=" O ASP W 201 " (cutoff:3.500A) Processing helix chain 'W' and resid 212 through 234 Processing helix chain 'W' and resid 238 through 249 removed outlier: 4.037A pdb=" N GLU W 242 " --> pdb=" O ALA W 238 " (cutoff:3.500A) Processing helix chain 'X' and resid 10 through 25 removed outlier: 3.535A pdb=" N LEU X 20 " --> pdb=" O LEU X 16 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL X 21 " --> pdb=" O VAL X 17 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN X 22 " --> pdb=" O HIS X 18 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE X 25 " --> pdb=" O VAL X 21 " (cutoff:3.500A) Processing helix chain 'X' and resid 35 through 55 removed outlier: 3.512A pdb=" N GLU X 39 " --> pdb=" O ASP X 35 " (cutoff:3.500A) Processing helix chain 'X' and resid 59 through 77 removed outlier: 4.100A pdb=" N GLU X 76 " --> pdb=" O LYS X 72 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU X 77 " --> pdb=" O ILE X 73 " (cutoff:3.500A) Processing helix chain 'X' and resid 88 through 117 removed outlier: 3.641A pdb=" N ASP X 117 " --> pdb=" O SER X 113 " (cutoff:3.500A) Processing helix chain 'X' and resid 123 through 152 Processing helix chain 'X' and resid 171 through 199 Processing helix chain 'X' and resid 201 through 212 removed outlier: 3.560A pdb=" N CYS X 205 " --> pdb=" O ASP X 201 " (cutoff:3.500A) Processing helix chain 'X' and resid 212 through 234 Processing helix chain 'X' and resid 238 through 249 removed outlier: 4.037A pdb=" N GLU X 242 " --> pdb=" O ALA X 238 " (cutoff:3.500A) Processing helix chain 'a' and resid 4 through 18 removed outlier: 4.281A pdb=" N ARG a 8 " --> pdb=" O ARG a 4 " (cutoff:3.500A) Processing helix chain 'b' and resid 4 through 18 removed outlier: 4.281A pdb=" N ARG b 8 " --> pdb=" O ARG b 4 " (cutoff:3.500A) Processing helix chain 'c' and resid 4 through 18 removed outlier: 4.281A pdb=" N ARG c 8 " --> pdb=" O ARG c 4 " (cutoff:3.500A) Processing helix chain 'd' and resid 4 through 18 removed outlier: 4.281A pdb=" N ARG d 8 " --> pdb=" O ARG d 4 " (cutoff:3.500A) Processing helix chain 'e' and resid 4 through 18 removed outlier: 4.281A pdb=" N ARG e 8 " --> pdb=" O ARG e 4 " (cutoff:3.500A) Processing helix chain 'f' and resid 4 through 18 removed outlier: 4.281A pdb=" N ARG f 8 " --> pdb=" O ARG f 4 " (cutoff:3.500A) Processing helix chain 'g' and resid 4 through 18 removed outlier: 4.281A pdb=" N ARG g 8 " --> pdb=" O ARG g 4 " (cutoff:3.500A) Processing helix chain 'h' and resid 4 through 18 removed outlier: 4.281A pdb=" N ARG h 8 " --> pdb=" O ARG h 4 " (cutoff:3.500A) Processing helix chain 'i' and resid 4 through 18 removed outlier: 4.281A pdb=" N ARG i 8 " --> pdb=" O ARG i 4 " (cutoff:3.500A) Processing helix chain 'j' and resid 4 through 18 removed outlier: 4.281A pdb=" N ARG j 8 " --> pdb=" O ARG j 4 " (cutoff:3.500A) Processing helix chain 'k' and resid 4 through 18 removed outlier: 4.281A pdb=" N ARG k 8 " --> pdb=" O ARG k 4 " (cutoff:3.500A) Processing helix chain 'l' and resid 4 through 18 removed outlier: 4.281A pdb=" N ARG l 8 " --> pdb=" O ARG l 4 " (cutoff:3.500A) Processing helix chain 'm' and resid 4 through 18 removed outlier: 4.281A pdb=" N ARG m 8 " --> pdb=" O ARG m 4 " (cutoff:3.500A) Processing helix chain 'n' and resid 4 through 18 removed outlier: 4.281A pdb=" N ARG n 8 " --> pdb=" O ARG n 4 " (cutoff:3.500A) Processing helix chain 'o' and resid 4 through 18 removed outlier: 4.281A pdb=" N ARG o 8 " --> pdb=" O ARG o 4 " (cutoff:3.500A) Processing helix chain 'p' and resid 4 through 18 removed outlier: 4.281A pdb=" N ARG p 8 " --> pdb=" O ARG p 4 " (cutoff:3.500A) Processing helix chain 'q' and resid 4 through 18 removed outlier: 4.281A pdb=" N ARG q 8 " --> pdb=" O ARG q 4 " (cutoff:3.500A) Processing helix chain 'r' and resid 4 through 18 removed outlier: 4.281A pdb=" N ARG r 8 " --> pdb=" O ARG r 4 " (cutoff:3.500A) Processing helix chain 's' and resid 4 through 18 removed outlier: 4.281A pdb=" N ARG s 8 " --> pdb=" O ARG s 4 " (cutoff:3.500A) Processing helix chain 't' and resid 4 through 18 removed outlier: 4.281A pdb=" N ARG t 8 " --> pdb=" O ARG t 4 " (cutoff:3.500A) Processing helix chain 'u' and resid 4 through 18 removed outlier: 4.281A pdb=" N ARG u 8 " --> pdb=" O ARG u 4 " (cutoff:3.500A) Processing helix chain 'v' and resid 4 through 18 removed outlier: 4.281A pdb=" N ARG v 8 " --> pdb=" O ARG v 4 " (cutoff:3.500A) Processing helix chain 'w' and resid 4 through 18 removed outlier: 4.281A pdb=" N ARG w 8 " --> pdb=" O ARG w 4 " (cutoff:3.500A) Processing helix chain 'x' and resid 4 through 18 removed outlier: 4.281A pdb=" N ARG x 8 " --> pdb=" O ARG x 4 " (cutoff:3.500A) 3745 hydrogen bonds defined for protein. 11211 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: 12.96 Time building geometry restraints manager: 10.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 17424 1.35 - 1.46: 11516 1.46 - 1.58: 23284 1.58 - 1.69: 96 1.69 - 1.81: 480 Bond restraints: 52800 Sorted by residual: bond pdb=" CA LEU W 77 " pdb=" CB LEU W 77 " ideal model delta sigma weight residual 1.524 1.505 0.019 1.41e-02 5.03e+03 1.75e+00 bond pdb=" CA LEU V 77 " pdb=" CB LEU V 77 " ideal model delta sigma weight residual 1.524 1.505 0.019 1.41e-02 5.03e+03 1.75e+00 bond pdb=" CA LEU A 77 " pdb=" CB LEU A 77 " ideal model delta sigma weight residual 1.524 1.505 0.019 1.41e-02 5.03e+03 1.75e+00 bond pdb=" CA LEU C 77 " pdb=" CB LEU C 77 " ideal model delta sigma weight residual 1.524 1.505 0.018 1.41e-02 5.03e+03 1.70e+00 bond pdb=" CA LEU S 77 " pdb=" CB LEU S 77 " ideal model delta sigma weight residual 1.524 1.505 0.018 1.41e-02 5.03e+03 1.70e+00 ... (remaining 52795 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 69452 1.24 - 2.48: 1346 2.48 - 3.73: 146 3.73 - 4.97: 48 4.97 - 6.21: 72 Bond angle restraints: 71064 Sorted by residual: angle pdb=" CA LEU A 33 " pdb=" C LEU A 33 " pdb=" O LEU A 33 " ideal model delta sigma weight residual 117.94 121.55 -3.61 5.80e-01 2.97e+00 3.87e+01 angle pdb=" CA LEU Q 33 " pdb=" C LEU Q 33 " pdb=" O LEU Q 33 " ideal model delta sigma weight residual 117.94 121.52 -3.58 5.80e-01 2.97e+00 3.82e+01 angle pdb=" CA LEU R 33 " pdb=" C LEU R 33 " pdb=" O LEU R 33 " ideal model delta sigma weight residual 117.94 121.52 -3.58 5.80e-01 2.97e+00 3.82e+01 angle pdb=" CA LEU B 33 " pdb=" C LEU B 33 " pdb=" O LEU B 33 " ideal model delta sigma weight residual 117.94 121.51 -3.57 5.80e-01 2.97e+00 3.80e+01 angle pdb=" CA LEU N 33 " pdb=" C LEU N 33 " pdb=" O LEU N 33 " ideal model delta sigma weight residual 117.94 121.51 -3.57 5.80e-01 2.97e+00 3.80e+01 ... (remaining 71059 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.52: 31400 14.52 - 29.03: 1068 29.03 - 43.55: 292 43.55 - 58.06: 24 58.06 - 72.58: 24 Dihedral angle restraints: 32808 sinusoidal: 13920 harmonic: 18888 Sorted by residual: dihedral pdb=" CA AARG X 138 " pdb=" CB AARG X 138 " pdb=" CG AARG X 138 " pdb=" CD AARG X 138 " ideal model delta sinusoidal sigma weight residual -180.00 -122.95 -57.05 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" CA AARG I 138 " pdb=" CB AARG I 138 " pdb=" CG AARG I 138 " pdb=" CD AARG I 138 " ideal model delta sinusoidal sigma weight residual -180.00 -122.98 -57.02 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" CA AARG K 138 " pdb=" CB AARG K 138 " pdb=" CG AARG K 138 " pdb=" CD AARG K 138 " ideal model delta sinusoidal sigma weight residual -180.00 -122.98 -57.02 3 1.50e+01 4.44e-03 9.42e+00 ... (remaining 32805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 5567 0.028 - 0.056: 1537 0.056 - 0.085: 288 0.085 - 0.113: 68 0.113 - 0.141: 28 Chirality restraints: 7488 Sorted by residual: chirality pdb=" CG LEU A 77 " pdb=" CB LEU A 77 " pdb=" CD1 LEU A 77 " pdb=" CD2 LEU A 77 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 4.98e-01 chirality pdb=" CG LEU V 77 " pdb=" CB LEU V 77 " pdb=" CD1 LEU V 77 " pdb=" CD2 LEU V 77 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 4.94e-01 chirality pdb=" CG LEU W 77 " pdb=" CB LEU W 77 " pdb=" CD1 LEU W 77 " pdb=" CD2 LEU W 77 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 4.94e-01 ... (remaining 7485 not shown) Planarity restraints: 9264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SEP x 6 " -0.006 2.00e-02 2.50e+03 1.24e-02 1.53e+00 pdb=" C SEP x 6 " 0.021 2.00e-02 2.50e+03 pdb=" O SEP x 6 " -0.008 2.00e-02 2.50e+03 pdb=" N TYR x 7 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SEP d 6 " -0.006 2.00e-02 2.50e+03 1.24e-02 1.53e+00 pdb=" C SEP d 6 " 0.021 2.00e-02 2.50e+03 pdb=" O SEP d 6 " -0.008 2.00e-02 2.50e+03 pdb=" N TYR d 7 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SEP e 6 " 0.006 2.00e-02 2.50e+03 1.24e-02 1.53e+00 pdb=" C SEP e 6 " -0.021 2.00e-02 2.50e+03 pdb=" O SEP e 6 " 0.008 2.00e-02 2.50e+03 pdb=" N TYR e 7 " 0.007 2.00e-02 2.50e+03 ... (remaining 9261 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 888 2.69 - 3.24: 50844 3.24 - 3.80: 85570 3.80 - 4.35: 104284 4.35 - 4.90: 173216 Nonbonded interactions: 414802 Sorted by model distance: nonbonded pdb=" O ALA B 67 " pdb=" CD2 TYR B 71 " model vdw 2.141 3.340 nonbonded pdb=" O ALA V 67 " pdb=" CD2 TYR V 71 " model vdw 2.142 3.340 nonbonded pdb=" O ALA M 67 " pdb=" CD2 TYR M 71 " model vdw 2.143 3.340 nonbonded pdb=" O ALA H 67 " pdb=" CD2 TYR H 71 " model vdw 2.143 3.340 nonbonded pdb=" O ALA A 67 " pdb=" CD2 TYR A 71 " model vdw 2.143 3.340 ... (remaining 414797 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'B' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'C' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'D' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'E' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'F' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'G' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'H' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'I' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'J' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'K' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'L' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'M' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'N' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'O' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'P' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'Q' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'R' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'S' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'T' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'U' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'V' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'W' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'X' and (resid 9 through 137 or resid 139 through 251)) } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' } 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=0.50 max=1.00 mean=1.00 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: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 1.530 Check model and map are aligned: 0.290 Set scattering table: 0.360 Process input model: 98.660 Find NCS groups from input model: 1.790 Set up NCS constraints: 0.370 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: 0.010 Load rotamer database and sin/cos tables:12.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 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 : 0.001 0.019 52800 Z= 0.091 Angle : 0.427 6.212 71064 Z= 0.291 Chirality : 0.029 0.141 7488 Planarity : 0.002 0.021 9264 Dihedral : 8.124 72.580 20424 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.78 % Allowed : 7.84 % Favored : 91.37 % Rotamer: Outliers : 0.43 % Allowed : 3.88 % Favored : 95.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.10), residues: 6144 helix: 1.67 (0.07), residues: 4704 sheet: None (None), residues: 0 loop : -3.53 (0.14), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP H 168 HIS 0.002 0.000 HIS T 193 PHE 0.002 0.000 PHE F 126 TYR 0.008 0.001 TYR F 71 ARG 0.002 0.000 ARG A 36 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1448 residues out of total 5568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 1424 time to evaluate : 4.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 PRO cc_start: 0.8183 (Cg_endo) cc_final: 0.7964 (Cg_exo) REVERT: A 201 ASP cc_start: 0.7212 (t0) cc_final: 0.6957 (t0) REVERT: B 26 PRO cc_start: 0.8157 (Cg_endo) cc_final: 0.7956 (Cg_exo) REVERT: B 201 ASP cc_start: 0.7219 (t0) cc_final: 0.6963 (t0) REVERT: C 26 PRO cc_start: 0.8180 (Cg_endo) cc_final: 0.7962 (Cg_exo) REVERT: C 201 ASP cc_start: 0.7222 (t0) cc_final: 0.6970 (t0) REVERT: D 26 PRO cc_start: 0.8182 (Cg_endo) cc_final: 0.7964 (Cg_exo) REVERT: D 201 ASP cc_start: 0.7223 (t0) cc_final: 0.6976 (t0) REVERT: E 26 PRO cc_start: 0.8176 (Cg_endo) cc_final: 0.7956 (Cg_exo) REVERT: E 201 ASP cc_start: 0.7209 (t0) cc_final: 0.6950 (t0) REVERT: F 26 PRO cc_start: 0.8175 (Cg_endo) cc_final: 0.7968 (Cg_exo) REVERT: F 201 ASP cc_start: 0.7222 (t0) cc_final: 0.6973 (t0) REVERT: G 26 PRO cc_start: 0.8218 (Cg_endo) cc_final: 0.8007 (Cg_exo) REVERT: G 201 ASP cc_start: 0.7225 (t0) cc_final: 0.6977 (t0) REVERT: H 26 PRO cc_start: 0.8188 (Cg_endo) cc_final: 0.7972 (Cg_exo) REVERT: H 201 ASP cc_start: 0.7220 (t0) cc_final: 0.6973 (t0) REVERT: I 26 PRO cc_start: 0.8191 (Cg_endo) cc_final: 0.7983 (Cg_exo) REVERT: I 201 ASP cc_start: 0.7248 (t0) cc_final: 0.6999 (t0) REVERT: J 26 PRO cc_start: 0.8187 (Cg_endo) cc_final: 0.7984 (Cg_exo) REVERT: J 201 ASP cc_start: 0.7249 (t0) cc_final: 0.7002 (t0) REVERT: K 26 PRO cc_start: 0.8192 (Cg_endo) cc_final: 0.7981 (Cg_exo) REVERT: K 201 ASP cc_start: 0.7257 (t0) cc_final: 0.7009 (t0) REVERT: L 26 PRO cc_start: 0.8187 (Cg_endo) cc_final: 0.7982 (Cg_exo) REVERT: L 201 ASP cc_start: 0.7245 (t0) cc_final: 0.7000 (t0) REVERT: M 26 PRO cc_start: 0.8187 (Cg_endo) cc_final: 0.7984 (Cg_exo) REVERT: M 201 ASP cc_start: 0.7249 (t0) cc_final: 0.7005 (t0) REVERT: N 26 PRO cc_start: 0.8184 (Cg_endo) cc_final: 0.7977 (Cg_exo) REVERT: N 201 ASP cc_start: 0.7258 (t0) cc_final: 0.7012 (t0) REVERT: O 26 PRO cc_start: 0.8187 (Cg_endo) cc_final: 0.7976 (Cg_exo) REVERT: O 201 ASP cc_start: 0.7239 (t0) cc_final: 0.6990 (t0) REVERT: P 26 PRO cc_start: 0.8189 (Cg_endo) cc_final: 0.7984 (Cg_exo) REVERT: P 201 ASP cc_start: 0.7248 (t0) cc_final: 0.7000 (t0) REVERT: Q 26 PRO cc_start: 0.8214 (Cg_endo) cc_final: 0.8004 (Cg_exo) REVERT: Q 201 ASP cc_start: 0.7225 (t0) cc_final: 0.6977 (t0) REVERT: R 26 PRO cc_start: 0.8225 (Cg_endo) cc_final: 0.8015 (Cg_exo) REVERT: R 201 ASP cc_start: 0.7209 (t0) cc_final: 0.6962 (t0) REVERT: S 26 PRO cc_start: 0.8181 (Cg_endo) cc_final: 0.7963 (Cg_exo) REVERT: S 201 ASP cc_start: 0.7228 (t0) cc_final: 0.6981 (t0) REVERT: T 26 PRO cc_start: 0.8185 (Cg_endo) cc_final: 0.7975 (Cg_exo) REVERT: T 201 ASP cc_start: 0.7225 (t0) cc_final: 0.6978 (t0) REVERT: U 26 PRO cc_start: 0.8184 (Cg_endo) cc_final: 0.7977 (Cg_exo) REVERT: U 201 ASP cc_start: 0.7248 (t0) cc_final: 0.7000 (t0) REVERT: V 201 ASP cc_start: 0.7259 (t0) cc_final: 0.7013 (t0) REVERT: W 26 PRO cc_start: 0.8191 (Cg_endo) cc_final: 0.7981 (Cg_exo) REVERT: W 201 ASP cc_start: 0.7234 (t0) cc_final: 0.6987 (t0) REVERT: X 26 PRO cc_start: 0.8185 (Cg_endo) cc_final: 0.7979 (Cg_exo) REVERT: X 201 ASP cc_start: 0.7245 (t0) cc_final: 0.6998 (t0) outliers start: 24 outliers final: 0 residues processed: 1448 average time/residue: 1.2881 time to fit residues: 2332.7300 Evaluate side-chains 980 residues out of total 5568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 980 time to evaluate : 4.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 506 optimal weight: 20.0000 chunk 454 optimal weight: 0.9980 chunk 252 optimal weight: 8.9990 chunk 155 optimal weight: 0.9980 chunk 306 optimal weight: 5.9990 chunk 242 optimal weight: 20.0000 chunk 470 optimal weight: 4.9990 chunk 181 optimal weight: 6.9990 chunk 285 optimal weight: 0.9990 chunk 350 optimal weight: 0.0000 chunk 544 optimal weight: 0.8980 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN A 88 HIS A 180 HIS A 187 GLN A 216 GLN A 248 HIS B 86 ASN B 88 HIS B 180 HIS B 187 GLN B 216 GLN B 248 HIS C 86 ASN C 88 HIS C 180 HIS C 187 GLN C 216 GLN ** C 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 86 ASN D 88 HIS D 180 HIS D 187 GLN D 216 GLN ** D 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 ASN E 88 HIS E 180 HIS E 187 GLN E 216 GLN E 248 HIS F 86 ASN F 88 HIS F 180 HIS F 187 GLN F 216 GLN F 248 HIS G 86 ASN G 88 HIS G 180 HIS G 187 GLN G 216 GLN ** G 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 86 ASN H 88 HIS H 180 HIS H 187 GLN H 216 GLN ** H 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 86 ASN I 88 HIS I 180 HIS I 187 GLN I 216 GLN ** I 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 86 ASN J 88 HIS J 180 HIS J 187 GLN J 216 GLN J 248 HIS K 86 ASN K 88 HIS K 180 HIS K 187 GLN K 216 GLN K 248 HIS L 86 ASN L 88 HIS L 180 HIS L 187 GLN L 216 GLN M 86 ASN M 88 HIS M 180 HIS M 187 GLN M 216 GLN ** M 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 86 ASN N 88 HIS N 180 HIS N 187 GLN N 216 GLN N 248 HIS O 86 ASN O 88 HIS O 180 HIS O 187 GLN O 216 GLN O 248 HIS P 86 ASN P 88 HIS P 180 HIS P 187 GLN P 216 GLN ** P 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 86 ASN Q 88 HIS Q 180 HIS Q 187 GLN Q 216 GLN Q 248 HIS R 86 ASN R 88 HIS R 180 HIS R 187 GLN R 216 GLN R 248 HIS S 86 ASN S 88 HIS S 180 HIS S 187 GLN S 216 GLN ** S 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 86 ASN T 88 HIS T 180 HIS T 187 GLN T 216 GLN ** T 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 86 ASN U 88 HIS U 180 HIS U 187 GLN U 216 GLN U 248 HIS V 86 ASN V 88 HIS V 180 HIS V 187 GLN V 216 GLN W 86 ASN W 88 HIS W 180 HIS W 187 GLN W 216 GLN X 86 ASN X 88 HIS X 180 HIS X 187 GLN X 216 GLN X 248 HIS Total number of N/Q/H flips: 132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 52800 Z= 0.190 Angle : 0.618 6.597 71064 Z= 0.321 Chirality : 0.037 0.161 7488 Planarity : 0.003 0.025 9264 Dihedral : 4.056 33.776 7104 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.10 % Favored : 94.51 % Rotamer: Outliers : 1.67 % Allowed : 18.14 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.11), residues: 6144 helix: 2.55 (0.07), residues: 4752 sheet: None (None), residues: 0 loop : -3.04 (0.15), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 168 HIS 0.010 0.001 HIS G 180 PHE 0.028 0.003 PHE F 207 TYR 0.025 0.002 TYR H 71 ARG 0.006 0.001 ARG G 118 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 891 residues out of total 5568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 797 time to evaluate : 4.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLN cc_start: 0.8830 (tp-100) cc_final: 0.8538 (mp10) REVERT: A 218 LYS cc_start: 0.8821 (mttp) cc_final: 0.8346 (mttm) REVERT: B 22 GLN cc_start: 0.8798 (tp-100) cc_final: 0.8535 (mp10) REVERT: B 218 LYS cc_start: 0.8820 (mttp) cc_final: 0.8346 (mttm) REVERT: C 22 GLN cc_start: 0.8805 (tp-100) cc_final: 0.8537 (mp10) REVERT: C 218 LYS cc_start: 0.8824 (mttp) cc_final: 0.8351 (mttm) REVERT: D 22 GLN cc_start: 0.8797 (tp-100) cc_final: 0.8533 (mp10) REVERT: D 218 LYS cc_start: 0.8819 (mttp) cc_final: 0.8346 (mttm) REVERT: E 22 GLN cc_start: 0.8804 (tp-100) cc_final: 0.8541 (mp10) REVERT: E 218 LYS cc_start: 0.8824 (mttp) cc_final: 0.8349 (mttm) REVERT: F 22 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8502 (mp10) REVERT: F 218 LYS cc_start: 0.8816 (mttp) cc_final: 0.8344 (mttm) REVERT: G 22 GLN cc_start: 0.8798 (tp-100) cc_final: 0.8538 (mp10) REVERT: G 218 LYS cc_start: 0.8817 (mttp) cc_final: 0.8348 (mttm) REVERT: H 22 GLN cc_start: 0.8803 (tp-100) cc_final: 0.8495 (mp10) REVERT: H 218 LYS cc_start: 0.8818 (mttp) cc_final: 0.8347 (mttm) REVERT: I 22 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8482 (mp10) REVERT: I 218 LYS cc_start: 0.8819 (mttp) cc_final: 0.8349 (mttm) REVERT: J 22 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8489 (mp10) REVERT: J 218 LYS cc_start: 0.8815 (mttp) cc_final: 0.8344 (mttm) REVERT: K 22 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8492 (mp10) REVERT: K 218 LYS cc_start: 0.8817 (mttp) cc_final: 0.8345 (mttm) REVERT: L 22 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8492 (mp10) REVERT: L 218 LYS cc_start: 0.8822 (mttp) cc_final: 0.8348 (mttm) REVERT: M 22 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8481 (mp10) REVERT: M 218 LYS cc_start: 0.8823 (mttp) cc_final: 0.8350 (mttm) REVERT: N 22 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8505 (mp10) REVERT: N 218 LYS cc_start: 0.8826 (mttp) cc_final: 0.8353 (mttm) REVERT: O 22 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8492 (mp10) REVERT: O 218 LYS cc_start: 0.8820 (mttp) cc_final: 0.8348 (mttm) REVERT: P 22 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8493 (mp10) REVERT: P 218 LYS cc_start: 0.8824 (mttp) cc_final: 0.8348 (mttm) REVERT: Q 22 GLN cc_start: 0.8804 (tp-100) cc_final: 0.8536 (mp10) REVERT: Q 218 LYS cc_start: 0.8821 (mttp) cc_final: 0.8347 (mttm) REVERT: R 22 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8497 (mp10) REVERT: R 218 LYS cc_start: 0.8824 (mttp) cc_final: 0.8348 (mttm) REVERT: S 22 GLN cc_start: 0.8810 (tp-100) cc_final: 0.8542 (mp10) REVERT: S 218 LYS cc_start: 0.8818 (mttp) cc_final: 0.8348 (mttm) REVERT: T 22 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8501 (mp10) REVERT: T 218 LYS cc_start: 0.8821 (mttp) cc_final: 0.8348 (mttm) REVERT: U 22 GLN cc_start: 0.8805 (tp-100) cc_final: 0.8491 (mp10) REVERT: U 218 LYS cc_start: 0.8821 (mttp) cc_final: 0.8351 (mttm) REVERT: V 22 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8487 (mp10) REVERT: V 218 LYS cc_start: 0.8820 (mttp) cc_final: 0.8347 (mttm) REVERT: W 22 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8483 (mp10) REVERT: W 218 LYS cc_start: 0.8820 (mttp) cc_final: 0.8348 (mttm) REVERT: X 22 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8489 (mp10) REVERT: X 218 LYS cc_start: 0.8819 (mttp) cc_final: 0.8347 (mttm) outliers start: 94 outliers final: 0 residues processed: 853 average time/residue: 1.3113 time to fit residues: 1399.1230 Evaluate side-chains 693 residues out of total 5568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 679 time to evaluate : 4.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 22 GLN Chi-restraints excluded: chain I residue 22 GLN Chi-restraints excluded: chain J residue 22 GLN Chi-restraints excluded: chain K residue 22 GLN Chi-restraints excluded: chain L residue 22 GLN Chi-restraints excluded: chain M residue 22 GLN Chi-restraints excluded: chain N residue 22 GLN Chi-restraints excluded: chain O residue 22 GLN Chi-restraints excluded: chain P residue 22 GLN Chi-restraints excluded: chain R residue 22 GLN Chi-restraints excluded: chain T residue 22 GLN Chi-restraints excluded: chain V residue 22 GLN Chi-restraints excluded: chain W residue 22 GLN Chi-restraints excluded: chain X residue 22 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 302 optimal weight: 1.9990 chunk 169 optimal weight: 0.1980 chunk 453 optimal weight: 1.9990 chunk 371 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 545 optimal weight: 0.9990 chunk 589 optimal weight: 9.9990 chunk 486 optimal weight: 6.9990 chunk 541 optimal weight: 0.9990 chunk 186 optimal weight: 1.9990 chunk 437 optimal weight: 10.0000 overall best weight: 1.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN B 86 ASN C 86 ASN C 180 HIS D 86 ASN D 180 HIS E 86 ASN F 22 GLN F 86 ASN G 22 GLN G 86 ASN G 180 HIS H 86 ASN H 88 HIS H 180 HIS I 22 GLN I 86 ASN I 180 HIS J 22 GLN J 86 ASN J 88 HIS K 22 GLN K 86 ASN L 22 GLN L 86 ASN L 180 HIS M 22 GLN M 86 ASN M 180 HIS N 22 GLN N 86 ASN N 88 HIS O 22 GLN O 86 ASN O 88 HIS P 22 GLN P 86 ASN P 180 HIS Q 22 GLN Q 86 ASN R 22 GLN R 86 ASN S 22 GLN S 86 ASN S 180 HIS T 22 GLN T 86 ASN T 180 HIS U 22 GLN U 86 ASN V 22 GLN V 86 ASN V 180 HIS W 22 GLN W 86 ASN W 88 HIS W 180 HIS X 22 GLN X 86 ASN X 88 HIS X 158 GLN Total number of N/Q/H flips: 61 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 52800 Z= 0.192 Angle : 0.607 7.435 71064 Z= 0.313 Chirality : 0.037 0.143 7488 Planarity : 0.004 0.042 9264 Dihedral : 4.271 31.219 7104 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.24 % Allowed : 15.15 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.11), residues: 6144 helix: 2.66 (0.07), residues: 4776 sheet: None (None), residues: 0 loop : -2.62 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP S 168 HIS 0.009 0.001 HIS M 180 PHE 0.023 0.003 PHE N 207 TYR 0.031 0.002 TYR P 71 ARG 0.004 0.001 ARG H 154 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1012 residues out of total 5568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 238 poor density : 774 time to evaluate : 4.424 Fit side-chains REVERT: A 12 LEU cc_start: 0.7294 (OUTLIER) cc_final: 0.6933 (pp) REVERT: A 22 GLN cc_start: 0.8781 (tp-100) cc_final: 0.8438 (mp10) REVERT: A 52 MET cc_start: 0.1645 (OUTLIER) cc_final: 0.1380 (tmt) REVERT: A 218 LYS cc_start: 0.8912 (mttp) cc_final: 0.8438 (mttm) REVERT: B 12 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.6969 (pp) REVERT: B 22 GLN cc_start: 0.8745 (tp-100) cc_final: 0.8479 (mp10) REVERT: B 52 MET cc_start: 0.1730 (OUTLIER) cc_final: 0.1451 (tmt) REVERT: B 218 LYS cc_start: 0.8910 (mttp) cc_final: 0.8492 (mtpp) REVERT: C 12 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.6968 (pp) REVERT: C 22 GLN cc_start: 0.8755 (tp-100) cc_final: 0.8491 (mp10) REVERT: C 52 MET cc_start: 0.1711 (OUTLIER) cc_final: 0.1436 (tmt) REVERT: C 218 LYS cc_start: 0.8915 (mttp) cc_final: 0.8481 (mtpp) REVERT: D 12 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.6966 (pp) REVERT: D 22 GLN cc_start: 0.8745 (tp-100) cc_final: 0.8486 (mp10) REVERT: D 52 MET cc_start: 0.1726 (OUTLIER) cc_final: 0.1441 (tmt) REVERT: D 218 LYS cc_start: 0.8905 (mttp) cc_final: 0.8481 (mtpp) REVERT: E 12 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.6966 (pp) REVERT: E 22 GLN cc_start: 0.8750 (tp-100) cc_final: 0.8489 (mp10) REVERT: E 52 MET cc_start: 0.1728 (OUTLIER) cc_final: 0.1448 (tmt) REVERT: E 218 LYS cc_start: 0.8915 (mttp) cc_final: 0.8437 (mttm) REVERT: F 12 LEU cc_start: 0.7316 (OUTLIER) cc_final: 0.6963 (pp) REVERT: F 22 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8410 (mp10) REVERT: F 52 MET cc_start: 0.1643 (OUTLIER) cc_final: 0.1377 (tmt) REVERT: F 218 LYS cc_start: 0.8905 (mttp) cc_final: 0.8493 (mtpp) REVERT: G 12 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.6964 (pp) REVERT: G 22 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8464 (mp10) REVERT: G 52 MET cc_start: 0.1711 (OUTLIER) cc_final: 0.1436 (tmt) REVERT: G 218 LYS cc_start: 0.8907 (mttp) cc_final: 0.8432 (mttm) REVERT: H 12 LEU cc_start: 0.7316 (OUTLIER) cc_final: 0.6960 (pp) REVERT: H 22 GLN cc_start: 0.8756 (tp-100) cc_final: 0.8488 (mp10) REVERT: H 52 MET cc_start: 0.1678 (OUTLIER) cc_final: 0.1410 (tmt) REVERT: H 218 LYS cc_start: 0.8910 (mttp) cc_final: 0.8430 (mttm) REVERT: I 12 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.6963 (pp) REVERT: I 22 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8447 (mp10) REVERT: I 52 MET cc_start: 0.1711 (OUTLIER) cc_final: 0.1447 (tmt) REVERT: I 218 LYS cc_start: 0.8901 (mttp) cc_final: 0.8489 (mtpp) REVERT: J 12 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.6972 (pp) REVERT: J 22 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8443 (mp10) REVERT: J 52 MET cc_start: 0.1715 (OUTLIER) cc_final: 0.1437 (tmt) REVERT: J 218 LYS cc_start: 0.8900 (mttp) cc_final: 0.8488 (mtpp) REVERT: K 12 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.6973 (pp) REVERT: K 22 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.8448 (mp10) REVERT: K 52 MET cc_start: 0.1680 (OUTLIER) cc_final: 0.1417 (tmt) REVERT: K 218 LYS cc_start: 0.8910 (mttp) cc_final: 0.8428 (mttm) REVERT: L 12 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.6973 (pp) REVERT: L 22 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.8448 (mp10) REVERT: L 52 MET cc_start: 0.1680 (OUTLIER) cc_final: 0.1411 (tmt) REVERT: L 218 LYS cc_start: 0.8913 (mttp) cc_final: 0.8440 (mttm) REVERT: M 12 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.6966 (pp) REVERT: M 22 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8444 (mp10) REVERT: M 52 MET cc_start: 0.1604 (OUTLIER) cc_final: 0.1341 (tmt) REVERT: M 218 LYS cc_start: 0.8907 (mttp) cc_final: 0.8492 (mtpp) REVERT: N 12 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.6975 (pp) REVERT: N 22 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.8433 (mp10) REVERT: N 52 MET cc_start: 0.1731 (OUTLIER) cc_final: 0.1459 (tmt) REVERT: N 218 LYS cc_start: 0.8916 (mttp) cc_final: 0.8429 (mttm) REVERT: O 12 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.6978 (pp) REVERT: O 22 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8451 (mp10) REVERT: O 52 MET cc_start: 0.1692 (OUTLIER) cc_final: 0.1424 (tmt) REVERT: O 218 LYS cc_start: 0.8906 (mttp) cc_final: 0.8478 (mtpp) REVERT: P 12 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.6954 (pp) REVERT: P 22 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8407 (mp10) REVERT: P 52 MET cc_start: 0.1707 (OUTLIER) cc_final: 0.1437 (tmt) REVERT: P 218 LYS cc_start: 0.8909 (mttp) cc_final: 0.8433 (mttm) REVERT: Q 12 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.6967 (pp) REVERT: Q 22 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.8472 (mp10) REVERT: Q 52 MET cc_start: 0.1675 (OUTLIER) cc_final: 0.1403 (tmt) REVERT: Q 218 LYS cc_start: 0.8912 (mttp) cc_final: 0.8429 (mttm) REVERT: R 12 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.6968 (pp) REVERT: R 22 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.8454 (mp10) REVERT: R 52 MET cc_start: 0.1732 (OUTLIER) cc_final: 0.1459 (tmt) REVERT: R 218 LYS cc_start: 0.8915 (mttp) cc_final: 0.8492 (mtpp) REVERT: S 12 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.6970 (pp) REVERT: S 22 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8469 (mp10) REVERT: S 52 MET cc_start: 0.1686 (OUTLIER) cc_final: 0.1411 (tmt) REVERT: S 218 LYS cc_start: 0.8902 (mttp) cc_final: 0.8430 (mttm) REVERT: T 12 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.6951 (pp) REVERT: T 22 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.8410 (mp10) REVERT: T 52 MET cc_start: 0.1677 (OUTLIER) cc_final: 0.1396 (tmt) REVERT: T 218 LYS cc_start: 0.8912 (mttp) cc_final: 0.8479 (mtpp) REVERT: U 12 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.6963 (pp) REVERT: U 22 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8461 (mp10) REVERT: U 52 MET cc_start: 0.1666 (OUTLIER) cc_final: 0.1409 (tmt) REVERT: U 218 LYS cc_start: 0.8906 (mttp) cc_final: 0.8480 (mtpp) REVERT: V 12 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.6966 (pp) REVERT: V 22 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.8482 (mp10) REVERT: V 52 MET cc_start: 0.1718 (OUTLIER) cc_final: 0.1442 (tmt) REVERT: V 218 LYS cc_start: 0.8910 (mttp) cc_final: 0.8431 (mttm) REVERT: W 12 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.6975 (pp) REVERT: W 22 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8447 (mp10) REVERT: W 52 MET cc_start: 0.1615 (OUTLIER) cc_final: 0.1342 (tmt) REVERT: W 218 LYS cc_start: 0.8910 (mttp) cc_final: 0.8430 (mttm) REVERT: X 12 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.6965 (pp) REVERT: X 22 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8445 (mp10) REVERT: X 52 MET cc_start: 0.1703 (OUTLIER) cc_final: 0.1437 (tmt) REVERT: X 218 LYS cc_start: 0.8906 (mttp) cc_final: 0.8481 (mtpp) outliers start: 238 outliers final: 44 residues processed: 938 average time/residue: 1.3001 time to fit residues: 1527.6975 Evaluate side-chains 744 residues out of total 5568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 634 time to evaluate : 4.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 194 LYS Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 194 LYS Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 169 CYS Chi-restraints excluded: chain E residue 194 LYS Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 22 GLN Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 194 LYS Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 22 GLN Chi-restraints excluded: chain G residue 52 MET Chi-restraints excluded: chain G residue 169 CYS Chi-restraints excluded: chain G residue 194 LYS Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 52 MET Chi-restraints excluded: chain H residue 194 LYS Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 22 GLN Chi-restraints excluded: chain I residue 52 MET Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain I residue 169 CYS Chi-restraints excluded: chain I residue 194 LYS Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 22 GLN Chi-restraints excluded: chain J residue 52 MET Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain J residue 194 LYS Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 22 GLN Chi-restraints excluded: chain K residue 52 MET Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 194 LYS Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 22 GLN Chi-restraints excluded: chain L residue 52 MET Chi-restraints excluded: chain L residue 194 LYS Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 22 GLN Chi-restraints excluded: chain M residue 52 MET Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 169 CYS Chi-restraints excluded: chain M residue 194 LYS Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 22 GLN Chi-restraints excluded: chain N residue 52 MET Chi-restraints excluded: chain N residue 147 LEU Chi-restraints excluded: chain N residue 169 CYS Chi-restraints excluded: chain N residue 194 LYS Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 22 GLN Chi-restraints excluded: chain O residue 52 MET Chi-restraints excluded: chain O residue 147 LEU Chi-restraints excluded: chain O residue 169 CYS Chi-restraints excluded: chain O residue 194 LYS Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain P residue 22 GLN Chi-restraints excluded: chain P residue 52 MET Chi-restraints excluded: chain P residue 147 LEU Chi-restraints excluded: chain P residue 194 LYS Chi-restraints excluded: chain Q residue 12 LEU Chi-restraints excluded: chain Q residue 22 GLN Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain Q residue 194 LYS Chi-restraints excluded: chain R residue 12 LEU Chi-restraints excluded: chain R residue 22 GLN Chi-restraints excluded: chain R residue 52 MET Chi-restraints excluded: chain R residue 194 LYS Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain S residue 22 GLN Chi-restraints excluded: chain S residue 52 MET Chi-restraints excluded: chain S residue 194 LYS Chi-restraints excluded: chain T residue 12 LEU Chi-restraints excluded: chain T residue 22 GLN Chi-restraints excluded: chain T residue 52 MET Chi-restraints excluded: chain T residue 194 LYS Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 22 GLN Chi-restraints excluded: chain U residue 52 MET Chi-restraints excluded: chain U residue 147 LEU Chi-restraints excluded: chain U residue 169 CYS Chi-restraints excluded: chain U residue 194 LYS Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 22 GLN Chi-restraints excluded: chain V residue 52 MET Chi-restraints excluded: chain V residue 147 LEU Chi-restraints excluded: chain V residue 169 CYS Chi-restraints excluded: chain V residue 194 LYS Chi-restraints excluded: chain W residue 12 LEU Chi-restraints excluded: chain W residue 22 GLN Chi-restraints excluded: chain W residue 52 MET Chi-restraints excluded: chain W residue 147 LEU Chi-restraints excluded: chain W residue 194 LYS Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 22 GLN Chi-restraints excluded: chain X residue 52 MET Chi-restraints excluded: chain X residue 147 LEU Chi-restraints excluded: chain X residue 194 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 539 optimal weight: 0.9990 chunk 410 optimal weight: 8.9990 chunk 283 optimal weight: 0.0270 chunk 60 optimal weight: 6.9990 chunk 260 optimal weight: 6.9990 chunk 366 optimal weight: 0.5980 chunk 547 optimal weight: 0.9990 chunk 579 optimal weight: 9.9990 chunk 286 optimal weight: 0.0040 chunk 519 optimal weight: 2.9990 chunk 156 optimal weight: 6.9990 overall best weight: 0.5254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN A 88 HIS B 22 GLN B 88 HIS C 22 GLN C 88 HIS C 180 HIS D 22 GLN D 88 HIS D 180 HIS E 22 GLN E 88 HIS F 88 HIS G 88 HIS G 180 HIS H 22 GLN H 88 HIS H 180 HIS I 88 HIS I 180 HIS J 88 HIS K 88 HIS L 88 HIS L 180 HIS M 88 HIS M 180 HIS N 88 HIS O 88 HIS P 88 HIS P 180 HIS Q 88 HIS R 88 HIS S 88 HIS S 180 HIS T 88 HIS T 180 HIS U 88 HIS V 88 HIS V 180 HIS W 88 HIS W 180 HIS X 88 HIS Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 52800 Z= 0.165 Angle : 0.581 6.415 71064 Z= 0.303 Chirality : 0.036 0.138 7488 Planarity : 0.003 0.027 9264 Dihedral : 4.119 33.657 7104 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.24 % Allowed : 17.38 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.87 (0.11), residues: 6144 helix: 3.03 (0.07), residues: 4776 sheet: None (None), residues: 0 loop : -2.58 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 168 HIS 0.009 0.001 HIS L 180 PHE 0.019 0.002 PHE N 25 TYR 0.024 0.001 TYR P 71 ARG 0.005 0.000 ARG K 231 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 5568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 634 time to evaluate : 4.621 Fit side-chains REVERT: A 12 LEU cc_start: 0.7271 (OUTLIER) cc_final: 0.6908 (pp) REVERT: A 22 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.8515 (mp10) REVERT: B 12 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.6959 (pp) REVERT: C 12 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.6960 (pp) REVERT: D 12 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.6958 (pp) REVERT: E 12 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.6958 (pp) REVERT: F 12 LEU cc_start: 0.7301 (OUTLIER) cc_final: 0.6950 (pp) REVERT: F 22 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8289 (mp10) REVERT: G 12 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.6957 (pp) REVERT: G 22 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8270 (mp10) REVERT: G 218 LYS cc_start: 0.8776 (mttp) cc_final: 0.8536 (mtpp) REVERT: H 12 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.6952 (pp) REVERT: I 12 LEU cc_start: 0.7315 (OUTLIER) cc_final: 0.6956 (pp) REVERT: I 22 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8471 (mp10) REVERT: J 12 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.6964 (pp) REVERT: J 22 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8476 (mp10) REVERT: K 12 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.6959 (pp) REVERT: K 22 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8472 (mp10) REVERT: L 12 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.6965 (pp) REVERT: L 22 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8477 (mp10) REVERT: M 12 LEU cc_start: 0.7316 (OUTLIER) cc_final: 0.6957 (pp) REVERT: M 22 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.8469 (mp10) REVERT: N 12 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.6949 (pp) REVERT: N 22 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8476 (mp10) REVERT: O 12 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.6969 (pp) REVERT: O 22 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8475 (mp10) REVERT: P 12 LEU cc_start: 0.7308 (OUTLIER) cc_final: 0.6942 (pp) REVERT: P 22 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8474 (mp10) REVERT: Q 12 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.6960 (pp) REVERT: Q 22 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8284 (mp10) REVERT: R 12 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.6961 (pp) REVERT: R 22 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.8292 (mp10) REVERT: S 12 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.6961 (pp) REVERT: S 22 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8284 (mp10) REVERT: T 12 LEU cc_start: 0.7294 (OUTLIER) cc_final: 0.6925 (pp) REVERT: T 22 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.8286 (mp10) REVERT: U 12 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.6955 (pp) REVERT: U 22 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8437 (mp10) REVERT: V 12 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.6959 (pp) REVERT: V 22 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8464 (mp10) REVERT: W 12 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.6967 (pp) REVERT: W 22 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8469 (mp10) REVERT: X 12 LEU cc_start: 0.7315 (OUTLIER) cc_final: 0.6957 (pp) REVERT: X 22 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8470 (mp10) outliers start: 126 outliers final: 24 residues processed: 732 average time/residue: 1.1756 time to fit residues: 1104.1566 Evaluate side-chains 677 residues out of total 5568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 610 time to evaluate : 4.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 22 GLN Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 194 LYS Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 194 LYS Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 194 LYS Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 22 GLN Chi-restraints excluded: chain F residue 194 LYS Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 22 GLN Chi-restraints excluded: chain G residue 194 LYS Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 194 LYS Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 22 GLN Chi-restraints excluded: chain I residue 194 LYS Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 22 GLN Chi-restraints excluded: chain J residue 194 LYS Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 22 GLN Chi-restraints excluded: chain K residue 194 LYS Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 22 GLN Chi-restraints excluded: chain L residue 194 LYS Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 22 GLN Chi-restraints excluded: chain M residue 194 LYS Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 22 GLN Chi-restraints excluded: chain N residue 194 LYS Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 22 GLN Chi-restraints excluded: chain O residue 194 LYS Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain P residue 22 GLN Chi-restraints excluded: chain P residue 194 LYS Chi-restraints excluded: chain Q residue 12 LEU Chi-restraints excluded: chain Q residue 22 GLN Chi-restraints excluded: chain Q residue 194 LYS Chi-restraints excluded: chain R residue 12 LEU Chi-restraints excluded: chain R residue 22 GLN Chi-restraints excluded: chain R residue 194 LYS Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain S residue 22 GLN Chi-restraints excluded: chain S residue 194 LYS Chi-restraints excluded: chain T residue 12 LEU Chi-restraints excluded: chain T residue 22 GLN Chi-restraints excluded: chain T residue 194 LYS Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 22 GLN Chi-restraints excluded: chain U residue 194 LYS Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 22 GLN Chi-restraints excluded: chain V residue 194 LYS Chi-restraints excluded: chain W residue 12 LEU Chi-restraints excluded: chain W residue 22 GLN Chi-restraints excluded: chain W residue 194 LYS Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 22 GLN Chi-restraints excluded: chain X residue 194 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 483 optimal weight: 6.9990 chunk 329 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 431 optimal weight: 6.9990 chunk 239 optimal weight: 0.9980 chunk 494 optimal weight: 0.6980 chunk 400 optimal weight: 0.9990 chunk 0 optimal weight: 50.0000 chunk 296 optimal weight: 0.9990 chunk 520 optimal weight: 0.9990 chunk 146 optimal weight: 0.0030 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 HIS A 100 ASN B 88 HIS B 100 ASN C 88 HIS C 100 ASN D 88 HIS D 100 ASN E 88 HIS E 100 ASN F 22 GLN F 88 HIS F 100 ASN G 22 GLN G 88 HIS G 100 ASN H 88 HIS H 100 ASN I 22 GLN I 88 HIS I 100 ASN J 22 GLN J 88 HIS J 100 ASN K 22 GLN K 88 HIS K 100 ASN K 158 GLN L 22 GLN L 88 HIS L 100 ASN M 22 GLN M 88 HIS M 100 ASN N 22 GLN N 88 HIS N 100 ASN O 22 GLN O 88 HIS O 100 ASN P 22 GLN P 88 HIS P 100 ASN Q 22 GLN Q 88 HIS Q 100 ASN R 22 GLN R 88 HIS S 22 GLN S 88 HIS S 100 ASN T 22 GLN T 88 HIS T 100 ASN U 22 GLN U 88 HIS U 100 ASN V 22 GLN V 88 HIS V 100 ASN V 158 GLN W 22 GLN W 88 HIS W 100 ASN X 22 GLN X 88 HIS X 100 ASN Total number of N/Q/H flips: 67 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 52800 Z= 0.170 Angle : 0.582 6.203 71064 Z= 0.299 Chirality : 0.036 0.144 7488 Planarity : 0.003 0.064 9264 Dihedral : 4.213 36.538 7104 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.28 % Allowed : 19.27 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.06 (0.11), residues: 6144 helix: 3.08 (0.07), residues: 4824 sheet: None (None), residues: 0 loop : -2.35 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 168 HIS 0.007 0.001 HIS A 88 PHE 0.015 0.002 PHE N 25 TYR 0.021 0.002 TYR H 71 ARG 0.007 0.000 ARG T 165 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 853 residues out of total 5568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 725 time to evaluate : 4.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.6912 (pp) REVERT: A 22 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8686 (mp10) REVERT: B 12 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.6980 (pp) REVERT: C 12 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.6981 (pp) REVERT: D 12 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.6979 (pp) REVERT: D 214 SER cc_start: 0.9115 (OUTLIER) cc_final: 0.8685 (p) REVERT: E 12 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.6958 (pp) REVERT: F 12 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.6960 (pp) REVERT: F 22 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.8443 (mp10) REVERT: F 214 SER cc_start: 0.9112 (OUTLIER) cc_final: 0.8690 (p) REVERT: G 12 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.6947 (pp) REVERT: H 12 LEU cc_start: 0.7341 (OUTLIER) cc_final: 0.6973 (pp) REVERT: I 12 LEU cc_start: 0.7303 (OUTLIER) cc_final: 0.6933 (pp) REVERT: J 12 LEU cc_start: 0.7308 (OUTLIER) cc_final: 0.6941 (pp) REVERT: K 12 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.6949 (pp) REVERT: K 214 SER cc_start: 0.9112 (OUTLIER) cc_final: 0.8681 (p) REVERT: L 12 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.6949 (pp) REVERT: M 12 LEU cc_start: 0.7305 (OUTLIER) cc_final: 0.6936 (pp) REVERT: N 12 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.6952 (pp) REVERT: N 22 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8481 (mp10) REVERT: N 214 SER cc_start: 0.9113 (OUTLIER) cc_final: 0.8673 (p) REVERT: O 12 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.6947 (pp) REVERT: P 12 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.6930 (pp) REVERT: P 22 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8481 (mp10) REVERT: P 214 SER cc_start: 0.9117 (OUTLIER) cc_final: 0.8682 (p) REVERT: Q 12 LEU cc_start: 0.7323 (OUTLIER) cc_final: 0.6950 (pp) REVERT: R 12 LEU cc_start: 0.7323 (OUTLIER) cc_final: 0.6952 (pp) REVERT: R 214 SER cc_start: 0.9121 (OUTLIER) cc_final: 0.8683 (p) REVERT: S 12 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.6950 (pp) REVERT: S 214 SER cc_start: 0.9119 (OUTLIER) cc_final: 0.8709 (p) REVERT: T 12 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.6939 (pp) REVERT: T 22 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8461 (mp10) REVERT: T 214 SER cc_start: 0.9113 (OUTLIER) cc_final: 0.8683 (p) REVERT: U 12 LEU cc_start: 0.7302 (OUTLIER) cc_final: 0.6935 (pp) REVERT: V 12 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.6941 (pp) REVERT: V 22 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8485 (mp10) REVERT: W 12 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.6944 (pp) REVERT: W 214 SER cc_start: 0.9114 (OUTLIER) cc_final: 0.8683 (p) REVERT: X 12 LEU cc_start: 0.7303 (OUTLIER) cc_final: 0.6934 (pp) outliers start: 128 outliers final: 14 residues processed: 807 average time/residue: 1.0213 time to fit residues: 1087.5970 Evaluate side-chains 651 residues out of total 5568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 598 time to evaluate : 4.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 22 GLN Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 194 LYS Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 22 GLN Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 194 LYS Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 194 LYS Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 194 LYS Chi-restraints excluded: chain K residue 214 SER Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 194 LYS Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 194 LYS Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 22 GLN Chi-restraints excluded: chain N residue 194 LYS Chi-restraints excluded: chain N residue 214 SER Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 194 LYS Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain P residue 22 GLN Chi-restraints excluded: chain P residue 194 LYS Chi-restraints excluded: chain P residue 214 SER Chi-restraints excluded: chain Q residue 12 LEU Chi-restraints excluded: chain Q residue 194 LYS Chi-restraints excluded: chain R residue 12 LEU Chi-restraints excluded: chain R residue 214 SER Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain S residue 214 SER Chi-restraints excluded: chain T residue 12 LEU Chi-restraints excluded: chain T residue 22 GLN Chi-restraints excluded: chain T residue 214 SER Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 194 LYS Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 22 GLN Chi-restraints excluded: chain V residue 194 LYS Chi-restraints excluded: chain W residue 12 LEU Chi-restraints excluded: chain W residue 194 LYS Chi-restraints excluded: chain W residue 214 SER Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 194 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 195 optimal weight: 20.0000 chunk 522 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 chunk 340 optimal weight: 5.9990 chunk 143 optimal weight: 9.9990 chunk 580 optimal weight: 30.0000 chunk 481 optimal weight: 8.9990 chunk 268 optimal weight: 30.0000 chunk 48 optimal weight: 50.0000 chunk 192 optimal weight: 50.0000 chunk 304 optimal weight: 4.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 GLN ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 GLN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 GLN ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 GLN ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 GLN ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 GLN ** G 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 158 GLN ** H 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 158 GLN ** I 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 158 GLN ** J 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 158 GLN ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 158 GLN ** M 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 158 GLN ** N 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 158 GLN ** O 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 158 GLN ** P 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 158 GLN ** Q 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 158 GLN ** R 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 158 GLN ** S 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 158 GLN ** T 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 158 GLN ** U 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 158 GLN ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 158 GLN ** X 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.6175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 52800 Z= 0.478 Angle : 0.782 7.930 71064 Z= 0.404 Chirality : 0.046 0.202 7488 Planarity : 0.005 0.037 9264 Dihedral : 4.940 43.487 7104 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.14 % Favored : 96.47 % Rotamer: Outliers : 2.64 % Allowed : 17.95 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.11), residues: 6144 helix: 2.29 (0.07), residues: 4992 sheet: None (None), residues: 0 loop : -1.59 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.004 TRP J 168 HIS 0.006 0.002 HIS X 203 PHE 0.036 0.005 PHE K 116 TYR 0.022 0.002 TYR P 212 ARG 0.007 0.001 ARG Q 165 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 5568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 513 time to evaluate : 5.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.7206 (OUTLIER) cc_final: 0.6856 (pp) REVERT: A 22 GLN cc_start: 0.8791 (tp40) cc_final: 0.8534 (mp10) REVERT: B 12 LEU cc_start: 0.7329 (OUTLIER) cc_final: 0.6978 (pp) REVERT: C 12 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.7011 (pp) REVERT: D 12 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.7018 (pp) REVERT: E 12 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.7009 (pp) REVERT: F 12 LEU cc_start: 0.7124 (OUTLIER) cc_final: 0.6813 (pp) REVERT: G 12 LEU cc_start: 0.7285 (OUTLIER) cc_final: 0.6932 (pp) REVERT: H 12 LEU cc_start: 0.7323 (OUTLIER) cc_final: 0.6972 (pp) REVERT: I 12 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.6898 (pp) REVERT: J 12 LEU cc_start: 0.7213 (OUTLIER) cc_final: 0.6878 (pp) REVERT: K 12 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.6913 (pp) REVERT: L 12 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6914 (pp) REVERT: L 194 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.8815 (tppp) REVERT: M 12 LEU cc_start: 0.7243 (OUTLIER) cc_final: 0.6899 (pp) REVERT: N 12 LEU cc_start: 0.7162 (OUTLIER) cc_final: 0.6852 (pp) REVERT: N 22 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8677 (mp10) REVERT: O 12 LEU cc_start: 0.7261 (OUTLIER) cc_final: 0.6915 (pp) REVERT: P 12 LEU cc_start: 0.7152 (OUTLIER) cc_final: 0.6833 (pp) REVERT: P 22 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.8687 (mp10) REVERT: Q 12 LEU cc_start: 0.7295 (OUTLIER) cc_final: 0.6934 (pp) REVERT: R 12 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.6914 (pp) REVERT: S 12 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.6914 (pp) REVERT: T 12 LEU cc_start: 0.7149 (OUTLIER) cc_final: 0.6840 (pp) REVERT: U 12 LEU cc_start: 0.7195 (OUTLIER) cc_final: 0.6861 (pp) REVERT: V 12 LEU cc_start: 0.7164 (OUTLIER) cc_final: 0.6841 (pp) REVERT: W 12 LEU cc_start: 0.7250 (OUTLIER) cc_final: 0.6908 (pp) REVERT: X 12 LEU cc_start: 0.7197 (OUTLIER) cc_final: 0.6861 (pp) outliers start: 148 outliers final: 24 residues processed: 653 average time/residue: 1.1408 time to fit residues: 961.9338 Evaluate side-chains 525 residues out of total 5568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 474 time to evaluate : 4.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 147 LEU Chi-restraints excluded: chain L residue 194 LYS Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 22 GLN Chi-restraints excluded: chain N residue 147 LEU Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 147 LEU Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain P residue 22 GLN Chi-restraints excluded: chain P residue 147 LEU Chi-restraints excluded: chain Q residue 12 LEU Chi-restraints excluded: chain Q residue 147 LEU Chi-restraints excluded: chain R residue 12 LEU Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain T residue 12 LEU Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 147 LEU Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 147 LEU Chi-restraints excluded: chain W residue 12 LEU Chi-restraints excluded: chain W residue 147 LEU Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 147 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 559 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 330 optimal weight: 0.9990 chunk 423 optimal weight: 9.9990 chunk 328 optimal weight: 3.9990 chunk 488 optimal weight: 0.9990 chunk 324 optimal weight: 3.9990 chunk 578 optimal weight: 0.0980 chunk 361 optimal weight: 0.8980 chunk 352 optimal weight: 3.9990 chunk 266 optimal weight: 40.0000 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 HIS A 98 GLN B 88 HIS B 98 GLN C 88 HIS C 98 GLN D 88 HIS D 98 GLN E 88 HIS E 98 GLN F 88 HIS F 98 GLN G 88 HIS G 98 GLN H 88 HIS H 98 GLN I 88 HIS I 98 GLN J 88 HIS J 98 GLN K 88 HIS K 98 GLN L 88 HIS L 98 GLN M 88 HIS M 98 GLN N 88 HIS N 98 GLN O 88 HIS O 98 GLN P 88 HIS P 98 GLN Q 88 HIS Q 98 GLN R 88 HIS R 98 GLN S 88 HIS S 98 GLN T 88 HIS T 98 GLN U 88 HIS U 98 GLN V 88 HIS V 98 GLN W 88 HIS W 98 GLN X 88 HIS X 98 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.6094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 52800 Z= 0.217 Angle : 0.637 7.735 71064 Z= 0.331 Chirality : 0.038 0.204 7488 Planarity : 0.004 0.030 9264 Dihedral : 4.656 43.847 7104 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.39 % Allowed : 2.37 % Favored : 97.24 % Rotamer: Outliers : 1.42 % Allowed : 19.11 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.85 (0.11), residues: 6144 helix: 2.57 (0.07), residues: 4992 sheet: None (None), residues: 0 loop : -1.35 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP T 168 HIS 0.008 0.001 HIS K 88 PHE 0.025 0.003 PHE H 116 TYR 0.035 0.002 TYR C 211 ARG 0.006 0.000 ARG H 165 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 5568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 531 time to evaluate : 4.370 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: A 12 LEU cc_start: 0.7184 (OUTLIER) cc_final: 0.6851 (pp) REVERT: B 12 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.6962 (pp) REVERT: C 12 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.6998 (pp) REVERT: D 12 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.6984 (pp) REVERT: E 12 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.6993 (pp) REVERT: F 12 LEU cc_start: 0.7232 (OUTLIER) cc_final: 0.6895 (pp) REVERT: G 12 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.7003 (pp) REVERT: H 12 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.6954 (pp) REVERT: I 12 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.6905 (pp) REVERT: J 12 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.6913 (pp) REVERT: K 12 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.6968 (pp) REVERT: L 12 LEU cc_start: 0.7288 (OUTLIER) cc_final: 0.6945 (pp) REVERT: M 12 LEU cc_start: 0.7243 (OUTLIER) cc_final: 0.6907 (pp) REVERT: N 12 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.6857 (pp) REVERT: N 22 GLN cc_start: 0.8901 (tp-100) cc_final: 0.8673 (mp10) REVERT: O 12 LEU cc_start: 0.7295 (OUTLIER) cc_final: 0.6949 (pp) REVERT: P 12 LEU cc_start: 0.7161 (OUTLIER) cc_final: 0.6839 (pp) REVERT: P 22 GLN cc_start: 0.8901 (tp-100) cc_final: 0.8680 (mp10) REVERT: Q 12 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.6962 (pp) REVERT: R 12 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.6964 (pp) REVERT: S 12 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.7006 (pp) REVERT: T 12 LEU cc_start: 0.7290 (OUTLIER) cc_final: 0.6938 (pp) REVERT: U 12 LEU cc_start: 0.7276 (OUTLIER) cc_final: 0.6936 (pp) REVERT: V 12 LEU cc_start: 0.7259 (OUTLIER) cc_final: 0.6909 (pp) REVERT: W 12 LEU cc_start: 0.7252 (OUTLIER) cc_final: 0.6915 (pp) REVERT: X 12 LEU cc_start: 0.7280 (OUTLIER) cc_final: 0.6937 (pp) outliers start: 80 outliers final: 12 residues processed: 590 average time/residue: 1.1613 time to fit residues: 880.9602 Evaluate side-chains 470 residues out of total 5568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 434 time to evaluate : 4.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 147 LEU Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 147 LEU Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain Q residue 12 LEU Chi-restraints excluded: chain R residue 12 LEU Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain T residue 12 LEU Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 147 LEU Chi-restraints excluded: chain W residue 12 LEU Chi-restraints excluded: chain W residue 147 LEU Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 147 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 357 optimal weight: 7.9990 chunk 230 optimal weight: 0.9990 chunk 345 optimal weight: 2.9990 chunk 174 optimal weight: 6.9990 chunk 113 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 367 optimal weight: 7.9990 chunk 393 optimal weight: 2.9990 chunk 285 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 454 optimal weight: 6.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 HIS E 193 HIS F 193 HIS ** H 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 193 HIS R 193 HIS T 193 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.6169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 52800 Z= 0.233 Angle : 0.625 7.668 71064 Z= 0.328 Chirality : 0.039 0.174 7488 Planarity : 0.004 0.031 9264 Dihedral : 4.583 43.604 7104 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.39 % Allowed : 2.94 % Favored : 96.67 % Rotamer: Outliers : 1.78 % Allowed : 19.59 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.98 (0.11), residues: 6144 helix: 2.88 (0.07), residues: 4824 sheet: None (None), residues: 0 loop : -1.78 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP M 168 HIS 0.003 0.001 HIS J 203 PHE 0.022 0.003 PHE O 116 TYR 0.036 0.002 TYR N 211 ARG 0.007 0.001 ARG E 165 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 5568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 477 time to evaluate : 4.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.7238 (OUTLIER) cc_final: 0.6893 (pp) REVERT: B 12 LEU cc_start: 0.7341 (OUTLIER) cc_final: 0.6945 (pp) REVERT: C 12 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.6958 (pp) REVERT: D 12 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.6964 (pp) REVERT: E 12 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.6955 (pp) REVERT: F 12 LEU cc_start: 0.7304 (OUTLIER) cc_final: 0.6945 (pp) REVERT: G 12 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.7008 (pp) REVERT: G 22 GLN cc_start: 0.8813 (pm20) cc_final: 0.8602 (pm20) REVERT: H 12 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.6939 (pp) REVERT: H 201 ASP cc_start: 0.8586 (t0) cc_final: 0.8355 (t0) REVERT: I 12 LEU cc_start: 0.7294 (OUTLIER) cc_final: 0.6941 (pp) REVERT: J 12 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.6937 (pp) REVERT: K 12 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.6963 (pp) REVERT: L 12 LEU cc_start: 0.7303 (OUTLIER) cc_final: 0.6949 (pp) REVERT: L 201 ASP cc_start: 0.8583 (t0) cc_final: 0.8353 (t0) REVERT: M 12 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.6947 (pp) REVERT: N 12 LEU cc_start: 0.7190 (OUTLIER) cc_final: 0.6865 (pp) REVERT: O 12 LEU cc_start: 0.7308 (OUTLIER) cc_final: 0.6952 (pp) REVERT: P 12 LEU cc_start: 0.7177 (OUTLIER) cc_final: 0.6846 (pp) REVERT: Q 12 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.7011 (pp) REVERT: Q 22 GLN cc_start: 0.8808 (pm20) cc_final: 0.8600 (pm20) REVERT: R 12 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.6970 (pp) REVERT: R 22 GLN cc_start: 0.8814 (pm20) cc_final: 0.8593 (pm20) REVERT: S 12 LEU cc_start: 0.7380 (OUTLIER) cc_final: 0.7011 (pp) REVERT: S 22 GLN cc_start: 0.8812 (pm20) cc_final: 0.8599 (pm20) REVERT: T 12 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.6989 (pp) REVERT: U 12 LEU cc_start: 0.7290 (OUTLIER) cc_final: 0.6939 (pp) REVERT: V 12 LEU cc_start: 0.7253 (OUTLIER) cc_final: 0.6910 (pp) REVERT: W 12 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.6939 (pp) REVERT: X 12 LEU cc_start: 0.7294 (OUTLIER) cc_final: 0.6941 (pp) outliers start: 100 outliers final: 27 residues processed: 561 average time/residue: 1.0373 time to fit residues: 768.2699 Evaluate side-chains 521 residues out of total 5568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 470 time to evaluate : 4.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 214 SER Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 147 LEU Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain M residue 214 SER Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 214 SER Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain P residue 214 SER Chi-restraints excluded: chain Q residue 12 LEU Chi-restraints excluded: chain Q residue 214 SER Chi-restraints excluded: chain R residue 12 LEU Chi-restraints excluded: chain R residue 214 SER Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain T residue 12 LEU Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 21 VAL Chi-restraints excluded: chain U residue 214 SER Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain W residue 12 LEU Chi-restraints excluded: chain W residue 21 VAL Chi-restraints excluded: chain W residue 214 SER Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 214 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 526 optimal weight: 6.9990 chunk 554 optimal weight: 50.0000 chunk 505 optimal weight: 8.9990 chunk 538 optimal weight: 0.8980 chunk 553 optimal weight: 10.0000 chunk 324 optimal weight: 2.9990 chunk 234 optimal weight: 2.9990 chunk 423 optimal weight: 0.3980 chunk 165 optimal weight: 2.9990 chunk 486 optimal weight: 0.0970 chunk 509 optimal weight: 6.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 HIS C 193 HIS G 193 HIS I 193 HIS L 193 HIS M 193 HIS N 193 HIS Q 193 HIS S 193 HIS U 193 HIS W 193 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.6201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 52800 Z= 0.216 Angle : 0.613 7.939 71064 Z= 0.322 Chirality : 0.038 0.163 7488 Planarity : 0.004 0.031 9264 Dihedral : 4.582 43.995 7104 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.39 % Allowed : 2.78 % Favored : 96.83 % Rotamer: Outliers : 0.87 % Allowed : 19.82 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.01 (0.11), residues: 6144 helix: 2.87 (0.07), residues: 4848 sheet: None (None), residues: 0 loop : -1.73 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP M 168 HIS 0.002 0.000 HIS D 203 PHE 0.020 0.003 PHE O 116 TYR 0.018 0.001 TYR H 71 ARG 0.006 0.000 ARG G 165 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 5568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 504 time to evaluate : 4.486 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 12 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.6920 (pp) REVERT: B 12 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.6940 (pp) REVERT: C 12 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.6961 (pp) REVERT: D 12 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.6958 (pp) REVERT: E 12 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.6958 (pp) REVERT: F 12 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.6950 (pp) REVERT: G 12 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.6923 (pp) REVERT: H 12 LEU cc_start: 0.7380 (OUTLIER) cc_final: 0.6988 (pp) REVERT: H 201 ASP cc_start: 0.8564 (t0) cc_final: 0.8340 (t0) REVERT: I 12 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.6906 (pp) REVERT: J 12 LEU cc_start: 0.7280 (OUTLIER) cc_final: 0.6914 (pp) REVERT: K 12 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.6970 (pp) REVERT: L 12 LEU cc_start: 0.7283 (OUTLIER) cc_final: 0.6915 (pp) REVERT: L 201 ASP cc_start: 0.8560 (t0) cc_final: 0.8347 (t0) REVERT: M 12 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.6923 (pp) REVERT: N 12 LEU cc_start: 0.7288 (OUTLIER) cc_final: 0.6942 (pp) REVERT: O 12 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.6917 (pp) REVERT: P 12 LEU cc_start: 0.7211 (OUTLIER) cc_final: 0.6876 (pp) REVERT: Q 12 LEU cc_start: 0.7280 (OUTLIER) cc_final: 0.6924 (pp) REVERT: R 12 LEU cc_start: 0.7279 (OUTLIER) cc_final: 0.6940 (pp) REVERT: S 12 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.6939 (pp) REVERT: T 12 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.6913 (pp) REVERT: U 12 LEU cc_start: 0.7271 (OUTLIER) cc_final: 0.6906 (pp) REVERT: V 12 LEU cc_start: 0.7299 (OUTLIER) cc_final: 0.6947 (pp) REVERT: W 12 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.6916 (pp) REVERT: X 12 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.6906 (pp) outliers start: 49 outliers final: 15 residues processed: 532 average time/residue: 1.0985 time to fit residues: 763.6037 Evaluate side-chains 514 residues out of total 5568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 475 time to evaluate : 4.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 147 LEU Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain Q residue 12 LEU Chi-restraints excluded: chain R residue 12 LEU Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain T residue 12 LEU Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 21 VAL Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain W residue 12 LEU Chi-restraints excluded: chain W residue 21 VAL Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 21 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 537 optimal weight: 0.9980 chunk 353 optimal weight: 3.9990 chunk 569 optimal weight: 1.9990 chunk 347 optimal weight: 0.9980 chunk 270 optimal weight: 5.9990 chunk 396 optimal weight: 0.6980 chunk 597 optimal weight: 5.9990 chunk 550 optimal weight: 2.9990 chunk 475 optimal weight: 0.9990 chunk 49 optimal weight: 9.9990 chunk 367 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 HIS J 193 HIS K 193 HIS O 193 HIS P 193 HIS V 193 HIS X 193 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.6183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 52800 Z= 0.187 Angle : 0.612 8.496 71064 Z= 0.324 Chirality : 0.037 0.157 7488 Planarity : 0.004 0.040 9264 Dihedral : 4.565 43.734 7104 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.01 % Favored : 96.60 % Rotamer: Outliers : 0.73 % Allowed : 19.50 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.91 (0.11), residues: 6144 helix: 2.85 (0.07), residues: 4824 sheet: None (None), residues: 0 loop : -1.90 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 168 HIS 0.002 0.000 HIS L 203 PHE 0.018 0.002 PHE O 116 TYR 0.018 0.001 TYR H 71 ARG 0.006 0.000 ARG S 165 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 5568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 544 time to evaluate : 4.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 12 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.6938 (pp) REVERT: A 211 TYR cc_start: 0.8584 (m-80) cc_final: 0.8267 (m-80) REVERT: B 12 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.6994 (pp) REVERT: B 211 TYR cc_start: 0.8595 (m-80) cc_final: 0.8279 (m-80) REVERT: C 12 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.6961 (pp) REVERT: D 12 LEU cc_start: 0.7329 (OUTLIER) cc_final: 0.6959 (pp) REVERT: E 12 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.6961 (pp) REVERT: F 12 LEU cc_start: 0.7301 (OUTLIER) cc_final: 0.6940 (pp) REVERT: G 12 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.6970 (pp) REVERT: H 12 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.7007 (pp) REVERT: H 201 ASP cc_start: 0.8539 (t0) cc_final: 0.8314 (t0) REVERT: H 211 TYR cc_start: 0.8600 (m-80) cc_final: 0.8288 (m-80) REVERT: I 12 LEU cc_start: 0.7276 (OUTLIER) cc_final: 0.6921 (pp) REVERT: J 12 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.6916 (pp) REVERT: K 12 LEU cc_start: 0.7341 (OUTLIER) cc_final: 0.6941 (pp) REVERT: L 12 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.6941 (pp) REVERT: L 201 ASP cc_start: 0.8537 (t0) cc_final: 0.8317 (t0) REVERT: M 12 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.6918 (pp) REVERT: N 12 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.6939 (pp) REVERT: O 12 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.6927 (pp) REVERT: P 12 LEU cc_start: 0.7283 (OUTLIER) cc_final: 0.6927 (pp) REVERT: Q 12 LEU cc_start: 0.7334 (OUTLIER) cc_final: 0.6965 (pp) REVERT: R 12 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.6967 (pp) REVERT: S 12 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.6958 (pp) REVERT: T 12 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.6948 (pp) REVERT: U 12 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.6917 (pp) REVERT: V 12 LEU cc_start: 0.7304 (OUTLIER) cc_final: 0.6935 (pp) REVERT: W 12 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.6931 (pp) REVERT: X 12 LEU cc_start: 0.7276 (OUTLIER) cc_final: 0.6908 (pp) outliers start: 41 outliers final: 12 residues processed: 572 average time/residue: 1.1251 time to fit residues: 837.5629 Evaluate side-chains 510 residues out of total 5568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 474 time to evaluate : 4.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain Q residue 12 LEU Chi-restraints excluded: chain R residue 12 LEU Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain T residue 12 LEU Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 21 VAL Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain W residue 12 LEU Chi-restraints excluded: chain W residue 21 VAL Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 21 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 291 optimal weight: 30.0000 chunk 378 optimal weight: 0.7980 chunk 507 optimal weight: 5.9990 chunk 145 optimal weight: 7.9990 chunk 438 optimal weight: 7.9990 chunk 70 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 chunk 476 optimal weight: 0.7980 chunk 199 optimal weight: 0.0170 chunk 489 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 22 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 = 0.4181 r_free = 0.4181 target = 0.128956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.082853 restraints weight = 262754.750| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 4.48 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3273 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3273 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.6189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 52800 Z= 0.187 Angle : 0.622 8.280 71064 Z= 0.326 Chirality : 0.036 0.164 7488 Planarity : 0.004 0.042 9264 Dihedral : 4.575 43.641 7104 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.39 % Allowed : 2.89 % Favored : 96.72 % Rotamer: Outliers : 0.73 % Allowed : 19.62 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.92 (0.11), residues: 6144 helix: 2.87 (0.07), residues: 4824 sheet: None (None), residues: 0 loop : -1.94 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP S 168 HIS 0.002 0.000 HIS Q 140 PHE 0.017 0.002 PHE O 116 TYR 0.018 0.001 TYR H 71 ARG 0.006 0.000 ARG E 165 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17716.71 seconds wall clock time: 307 minutes 14.15 seconds (18434.15 seconds total)