Starting phenix.real_space_refine on Thu Jun 4 11:22:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r7m_53784/06_2026/9r7m_53784.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r7m_53784/06_2026/9r7m_53784.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9r7m_53784/06_2026/9r7m_53784.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r7m_53784/06_2026/9r7m_53784.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9r7m_53784/06_2026/9r7m_53784.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r7m_53784/06_2026/9r7m_53784.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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 25 5.49 5 S 336 5.16 5 C 7518 2.51 5 N 2208 2.21 5 O 2323 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12410 Number of models: 1 Model: "" Number of chains: 60 Chain: "A" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "B" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "C" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "D" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "E" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "F" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "G" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "H" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "I" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "J" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "K" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "L" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "M" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "N" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "O" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "P" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "Q" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "R" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "S" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "T" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "U" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "V" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "W" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "X" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "Y" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "Z" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "a" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "b" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "c" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "d" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "e" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "f" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "g" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "h" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "i" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "j" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "k" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "l" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "m" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "n" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "o" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "p" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "q" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "r" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "s" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "t" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "u" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "v" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 255 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Chain: "N" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Chain: "Q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "N" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "O" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 3.33, per 1000 atoms: 0.27 Number of scatterers: 12410 At special positions: 0 Unit cell: (100.552, 101.377, 126.927, 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 336 16.00 P 25 15.00 O 2323 8.00 N 2208 7.00 C 7518 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=144, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 31 " distance=2.03 Simple disulfide: pdb=" SG CYS A 6 " - pdb=" SG CYS A 20 " distance=2.03 Simple disulfide: pdb=" SG CYS A 10 " - pdb=" SG CYS A 30 " distance=2.03 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 31 " distance=2.03 Simple disulfide: pdb=" SG CYS B 6 " - pdb=" SG CYS B 20 " distance=2.03 Simple disulfide: pdb=" SG CYS B 10 " - pdb=" SG CYS B 30 " distance=2.03 Simple disulfide: pdb=" SG CYS C 4 " - pdb=" SG CYS C 31 " distance=2.03 Simple disulfide: pdb=" SG CYS C 6 " - pdb=" SG CYS C 20 " distance=2.03 Simple disulfide: pdb=" SG CYS C 10 " - pdb=" SG CYS C 30 " distance=2.03 Simple disulfide: pdb=" SG CYS D 4 " - pdb=" SG CYS D 31 " distance=2.03 Simple disulfide: pdb=" SG CYS D 6 " - pdb=" SG CYS D 20 " distance=2.03 Simple disulfide: pdb=" SG CYS D 10 " - pdb=" SG CYS D 30 " distance=2.03 Simple disulfide: pdb=" SG CYS E 4 " - pdb=" SG CYS E 31 " distance=2.03 Simple disulfide: pdb=" SG CYS E 6 " - pdb=" SG CYS E 20 " distance=2.03 Simple disulfide: pdb=" SG CYS E 10 " - pdb=" SG CYS E 30 " distance=2.03 Simple disulfide: pdb=" SG CYS F 4 " - pdb=" SG CYS F 31 " distance=2.03 Simple disulfide: pdb=" SG CYS F 6 " - pdb=" SG CYS F 20 " distance=2.03 Simple disulfide: pdb=" SG CYS F 10 " - pdb=" SG CYS F 30 " distance=2.03 Simple disulfide: pdb=" SG CYS G 4 " - pdb=" SG CYS G 31 " distance=2.03 Simple disulfide: pdb=" SG CYS G 6 " - pdb=" SG CYS G 20 " distance=2.03 Simple disulfide: pdb=" SG CYS G 10 " - pdb=" SG CYS G 30 " distance=2.03 Simple disulfide: pdb=" SG CYS H 4 " - pdb=" SG CYS H 31 " distance=2.03 Simple disulfide: pdb=" SG CYS H 6 " - pdb=" SG CYS H 20 " distance=2.03 Simple disulfide: pdb=" SG CYS H 10 " - pdb=" SG CYS H 30 " distance=2.03 Simple disulfide: pdb=" SG CYS I 4 " - pdb=" SG CYS I 31 " distance=2.02 Simple disulfide: pdb=" SG CYS I 6 " - pdb=" SG CYS I 20 " distance=2.03 Simple disulfide: pdb=" SG CYS I 10 " - pdb=" SG CYS I 30 " distance=2.03 Simple disulfide: pdb=" SG CYS J 4 " - pdb=" SG CYS J 31 " distance=2.03 Simple disulfide: pdb=" SG CYS J 6 " - pdb=" SG CYS J 20 " distance=2.03 Simple disulfide: pdb=" SG CYS J 10 " - pdb=" SG CYS J 30 " distance=2.03 Simple disulfide: pdb=" SG CYS K 4 " - pdb=" SG CYS K 31 " distance=2.03 Simple disulfide: pdb=" SG CYS K 6 " - pdb=" SG CYS K 20 " distance=2.03 Simple disulfide: pdb=" SG CYS K 10 " - pdb=" SG CYS K 30 " distance=2.03 Simple disulfide: pdb=" SG CYS L 4 " - pdb=" SG CYS L 31 " distance=2.03 Simple disulfide: pdb=" SG CYS L 6 " - pdb=" SG CYS L 20 " distance=2.03 Simple disulfide: pdb=" SG CYS L 10 " - pdb=" SG CYS L 30 " distance=2.03 Simple disulfide: pdb=" SG CYS M 4 " - pdb=" SG CYS M 31 " distance=2.03 Simple disulfide: pdb=" SG CYS M 6 " - pdb=" SG CYS M 20 " distance=2.03 Simple disulfide: pdb=" SG CYS M 10 " - pdb=" SG CYS M 30 " distance=2.03 Simple disulfide: pdb=" SG CYS N 4 " - pdb=" SG CYS N 31 " distance=2.03 Simple disulfide: pdb=" SG CYS N 6 " - pdb=" SG CYS N 20 " distance=2.03 Simple disulfide: pdb=" SG CYS N 10 " - pdb=" SG CYS N 30 " distance=2.03 Simple disulfide: pdb=" SG CYS O 4 " - pdb=" SG CYS O 31 " distance=2.03 Simple disulfide: pdb=" SG CYS O 6 " - pdb=" SG CYS O 20 " distance=2.03 Simple disulfide: pdb=" SG CYS O 10 " - pdb=" SG CYS O 30 " distance=2.03 Simple disulfide: pdb=" SG CYS P 4 " - pdb=" SG CYS P 31 " distance=2.03 Simple disulfide: pdb=" SG CYS P 6 " - pdb=" SG CYS P 20 " distance=2.03 Simple disulfide: pdb=" SG CYS P 10 " - pdb=" SG CYS P 30 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 4 " - pdb=" SG CYS Q 31 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 6 " - pdb=" SG CYS Q 20 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 10 " - pdb=" SG CYS Q 30 " distance=2.03 Simple disulfide: pdb=" SG CYS R 4 " - pdb=" SG CYS R 31 " distance=2.03 Simple disulfide: pdb=" SG CYS R 6 " - pdb=" SG CYS R 20 " distance=2.03 Simple disulfide: pdb=" SG CYS R 10 " - pdb=" SG CYS R 30 " distance=2.03 Simple disulfide: pdb=" SG CYS S 4 " - pdb=" SG CYS S 31 " distance=2.03 Simple disulfide: pdb=" SG CYS S 6 " - pdb=" SG CYS S 20 " distance=2.03 Simple disulfide: pdb=" SG CYS S 10 " - pdb=" SG CYS S 30 " distance=2.03 Simple disulfide: pdb=" SG CYS T 4 " - pdb=" SG CYS T 31 " distance=2.03 Simple disulfide: pdb=" SG CYS T 6 " - pdb=" SG CYS T 20 " distance=2.03 Simple disulfide: pdb=" SG CYS T 10 " - pdb=" SG CYS T 30 " distance=2.03 Simple disulfide: pdb=" SG CYS U 4 " - pdb=" SG CYS U 31 " distance=2.03 Simple disulfide: pdb=" SG CYS U 6 " - pdb=" SG CYS U 20 " distance=2.03 Simple disulfide: pdb=" SG CYS U 10 " - pdb=" SG CYS U 30 " distance=2.03 Simple disulfide: pdb=" SG CYS V 4 " - pdb=" SG CYS V 31 " distance=2.03 Simple disulfide: pdb=" SG CYS V 6 " - pdb=" SG CYS V 20 " distance=2.03 Simple disulfide: pdb=" SG CYS V 10 " - pdb=" SG CYS V 30 " distance=2.03 Simple disulfide: pdb=" SG CYS W 4 " - pdb=" SG CYS W 31 " distance=2.03 Simple disulfide: pdb=" SG CYS W 6 " - pdb=" SG CYS W 20 " distance=2.03 Simple disulfide: pdb=" SG CYS W 10 " - pdb=" SG CYS W 30 " distance=2.03 Simple disulfide: pdb=" SG CYS X 4 " - pdb=" SG CYS X 31 " distance=2.03 Simple disulfide: pdb=" SG CYS X 6 " - pdb=" SG CYS X 20 " distance=2.03 Simple disulfide: pdb=" SG CYS X 10 " - pdb=" SG CYS X 30 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 4 " - pdb=" SG CYS Y 31 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 6 " - pdb=" SG CYS Y 20 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 10 " - pdb=" SG CYS Y 30 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 4 " - pdb=" SG CYS Z 31 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 6 " - pdb=" SG CYS Z 20 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 10 " - pdb=" SG CYS Z 30 " distance=2.03 Simple disulfide: pdb=" SG CYS a 4 " - pdb=" SG CYS a 31 " distance=2.03 Simple disulfide: pdb=" SG CYS a 6 " - pdb=" SG CYS a 20 " distance=2.03 Simple disulfide: pdb=" SG CYS a 10 " - pdb=" SG CYS a 30 " distance=2.03 Simple disulfide: pdb=" SG CYS b 4 " - pdb=" SG CYS b 31 " distance=2.03 Simple disulfide: pdb=" SG CYS b 6 " - pdb=" SG CYS b 20 " distance=2.03 Simple disulfide: pdb=" SG CYS b 10 " - pdb=" SG CYS b 30 " distance=2.03 Simple disulfide: pdb=" SG CYS c 4 " - pdb=" SG CYS c 31 " distance=2.03 Simple disulfide: pdb=" SG CYS c 6 " - pdb=" SG CYS c 20 " distance=2.03 Simple disulfide: pdb=" SG CYS c 10 " - pdb=" SG CYS c 30 " distance=2.03 Simple disulfide: pdb=" SG CYS d 4 " - pdb=" SG CYS d 31 " distance=2.03 Simple disulfide: pdb=" SG CYS d 6 " - pdb=" SG CYS d 20 " distance=2.03 Simple disulfide: pdb=" SG CYS d 10 " - pdb=" SG CYS d 30 " distance=2.03 Simple disulfide: pdb=" SG CYS e 4 " - pdb=" SG CYS e 31 " distance=2.03 Simple disulfide: pdb=" SG CYS e 6 " - pdb=" SG CYS e 20 " distance=2.03 Simple disulfide: pdb=" SG CYS e 10 " - pdb=" SG CYS e 30 " distance=2.03 Simple disulfide: pdb=" SG CYS f 4 " - pdb=" SG CYS f 31 " distance=2.03 Simple disulfide: pdb=" SG CYS f 6 " - pdb=" SG CYS f 20 " distance=2.03 Simple disulfide: pdb=" SG CYS f 10 " - pdb=" SG CYS f 30 " distance=2.03 Simple disulfide: pdb=" SG CYS g 4 " - pdb=" SG CYS g 31 " distance=2.03 Simple disulfide: pdb=" SG CYS g 6 " - pdb=" SG CYS g 20 " distance=2.03 Simple disulfide: pdb=" SG CYS g 10 " - pdb=" SG CYS g 30 " distance=2.03 Simple disulfide: pdb=" SG CYS h 4 " - pdb=" SG CYS h 31 " distance=2.03 Simple disulfide: pdb=" SG CYS h 6 " - pdb=" SG CYS h 20 " distance=2.03 Simple disulfide: pdb=" SG CYS h 10 " - pdb=" SG CYS h 30 " distance=2.03 Simple disulfide: pdb=" SG CYS i 4 " - pdb=" SG CYS i 31 " distance=2.03 Simple disulfide: pdb=" SG CYS i 6 " - pdb=" SG CYS i 20 " distance=2.03 Simple disulfide: pdb=" SG CYS i 10 " - pdb=" SG CYS i 30 " distance=2.03 Simple disulfide: pdb=" SG CYS j 4 " - pdb=" SG CYS j 31 " distance=2.03 Simple disulfide: pdb=" SG CYS j 6 " - pdb=" SG CYS j 20 " distance=2.03 Simple disulfide: pdb=" SG CYS j 10 " - pdb=" SG CYS j 30 " distance=2.03 Simple disulfide: pdb=" SG CYS k 4 " - pdb=" SG CYS k 31 " distance=2.03 Simple disulfide: pdb=" SG CYS k 6 " - pdb=" SG CYS k 20 " distance=2.03 Simple disulfide: pdb=" SG CYS k 10 " - pdb=" SG CYS k 30 " distance=2.03 Simple disulfide: pdb=" SG CYS l 4 " - pdb=" SG CYS l 31 " distance=2.03 Simple disulfide: pdb=" SG CYS l 6 " - pdb=" SG CYS l 20 " distance=2.03 Simple disulfide: pdb=" SG CYS l 10 " - pdb=" SG CYS l 30 " distance=2.03 Simple disulfide: pdb=" SG CYS m 4 " - pdb=" SG CYS m 31 " distance=2.03 Simple disulfide: pdb=" SG CYS m 6 " - pdb=" SG CYS m 20 " distance=2.03 Simple disulfide: pdb=" SG CYS m 10 " - pdb=" SG CYS m 30 " distance=2.03 Simple disulfide: pdb=" SG CYS n 4 " - pdb=" SG CYS n 31 " distance=2.03 Simple disulfide: pdb=" SG CYS n 6 " - pdb=" SG CYS n 20 " distance=2.03 Simple disulfide: pdb=" SG CYS n 10 " - pdb=" SG CYS n 30 " distance=2.03 Simple disulfide: pdb=" SG CYS o 4 " - pdb=" SG CYS o 31 " distance=2.03 Simple disulfide: pdb=" SG CYS o 6 " - pdb=" SG CYS o 20 " distance=2.03 Simple disulfide: pdb=" SG CYS o 10 " - pdb=" SG CYS o 30 " distance=2.03 Simple disulfide: pdb=" SG CYS p 4 " - pdb=" SG CYS p 31 " distance=2.03 Simple disulfide: pdb=" SG CYS p 6 " - pdb=" SG CYS p 20 " distance=2.03 Simple disulfide: pdb=" SG CYS p 10 " - pdb=" SG CYS p 30 " distance=2.03 Simple disulfide: pdb=" SG CYS q 4 " - pdb=" SG CYS q 31 " distance=2.03 Simple disulfide: pdb=" SG CYS q 6 " - pdb=" SG CYS q 20 " distance=2.03 Simple disulfide: pdb=" SG CYS q 10 " - pdb=" SG CYS q 30 " distance=2.03 Simple disulfide: pdb=" SG CYS r 4 " - pdb=" SG CYS r 31 " distance=2.03 Simple disulfide: pdb=" SG CYS r 6 " - pdb=" SG CYS r 20 " distance=2.03 Simple disulfide: pdb=" SG CYS r 10 " - pdb=" SG CYS r 30 " distance=2.03 Simple disulfide: pdb=" SG CYS s 4 " - pdb=" SG CYS s 31 " distance=2.03 Simple disulfide: pdb=" SG CYS s 6 " - pdb=" SG CYS s 20 " distance=2.03 Simple disulfide: pdb=" SG CYS s 10 " - pdb=" SG CYS s 30 " distance=2.03 Simple disulfide: pdb=" SG CYS t 4 " - pdb=" SG CYS t 31 " distance=2.03 Simple disulfide: pdb=" SG CYS t 6 " - pdb=" SG CYS t 20 " distance=2.04 Simple disulfide: pdb=" SG CYS t 10 " - pdb=" SG CYS t 30 " distance=2.03 Simple disulfide: pdb=" SG CYS u 4 " - pdb=" SG CYS u 31 " distance=2.03 Simple disulfide: pdb=" SG CYS u 6 " - pdb=" SG CYS u 20 " distance=2.03 Simple disulfide: pdb=" SG CYS u 10 " - pdb=" SG CYS u 30 " distance=2.03 Simple disulfide: pdb=" SG CYS v 4 " - pdb=" SG CYS v 31 " distance=2.03 Simple disulfide: pdb=" SG CYS v 6 " - pdb=" SG CYS v 20 " distance=2.03 Simple disulfide: pdb=" SG CYS v 10 " - pdb=" SG CYS v 30 " 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: 1.03 Conformation dependent library (CDL) restraints added in 527.6 milliseconds 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2880 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 9 sheets defined 0.0% alpha, 72.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 removed outlier: 3.681A pdb=" N GLY A 18 " --> pdb=" O PHE A 29 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N CYS A 31 " --> pdb=" O SER A 16 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N SER A 16 " --> pdb=" O CYS A 31 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N SER B 16 " --> pdb=" O CYS B 31 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N CYS B 31 " --> pdb=" O SER B 16 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLY B 18 " --> pdb=" O PHE B 29 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE B 29 " --> pdb=" O GLY B 18 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N ILE E 25 " --> pdb=" O THR E 21 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N THR E 21 " --> pdb=" O ILE E 25 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N HIS E 27 " --> pdb=" O THR E 19 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N THR E 19 " --> pdb=" O HIS E 27 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N PHE E 29 " --> pdb=" O TYR E 17 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N SER F 16 " --> pdb=" O CYS F 31 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N CYS F 31 " --> pdb=" O SER F 16 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLY I 18 " --> pdb=" O PHE I 29 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N CYS I 31 " --> pdb=" O SER I 16 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N SER I 16 " --> pdb=" O CYS I 31 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N PHE J 29 " --> pdb=" O TYR J 17 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N THR J 19 " --> pdb=" O HIS J 27 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N HIS J 27 " --> pdb=" O THR J 19 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N THR J 21 " --> pdb=" O ILE J 25 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE J 25 " --> pdb=" O THR J 21 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 4 through 7 removed outlier: 3.681A pdb=" N GLY A 18 " --> pdb=" O PHE A 29 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N CYS A 31 " --> pdb=" O SER A 16 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N SER A 16 " --> pdb=" O CYS A 31 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N SER B 16 " --> pdb=" O CYS B 31 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N CYS B 31 " --> pdb=" O SER B 16 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLY B 18 " --> pdb=" O PHE B 29 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE B 29 " --> pdb=" O GLY B 18 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N ILE E 25 " --> pdb=" O THR E 21 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N THR E 21 " --> pdb=" O ILE E 25 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N HIS E 27 " --> pdb=" O THR E 19 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N THR E 19 " --> pdb=" O HIS E 27 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N PHE E 29 " --> pdb=" O TYR E 17 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N SER F 16 " --> pdb=" O CYS F 31 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N CYS F 31 " --> pdb=" O SER F 16 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLY I 18 " --> pdb=" O PHE I 29 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N CYS I 31 " --> pdb=" O SER I 16 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N SER I 16 " --> pdb=" O CYS I 31 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N PHE J 29 " --> pdb=" O TYR J 17 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N THR J 19 " --> pdb=" O HIS J 27 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N HIS J 27 " --> pdb=" O THR J 19 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N THR J 21 " --> pdb=" O ILE J 25 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE J 25 " --> pdb=" O THR J 21 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N SER N 16 " --> pdb=" O CYS N 31 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N CYS N 31 " --> pdb=" O SER N 16 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLY N 18 " --> pdb=" O PHE N 29 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE N 29 " --> pdb=" O GLY N 18 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ILE S 25 " --> pdb=" O THR S 21 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N THR S 21 " --> pdb=" O ILE S 25 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N HIS S 27 " --> pdb=" O THR S 19 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N THR S 19 " --> pdb=" O HIS S 27 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N PHE S 29 " --> pdb=" O TYR S 17 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR S 15 " --> pdb=" O CYS S 31 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N SER T 16 " --> pdb=" O CYS T 31 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N CYS T 31 " --> pdb=" O SER T 16 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY T 18 " --> pdb=" O PHE T 29 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE T 29 " --> pdb=" O GLY T 18 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.594A pdb=" N ILE C 25 " --> pdb=" O VAL C 22 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLY C 18 " --> pdb=" O PHE C 29 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N CYS C 31 " --> pdb=" O SER C 16 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N SER C 16 " --> pdb=" O CYS C 31 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N PHE D 29 " --> pdb=" O TYR D 17 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N THR D 19 " --> pdb=" O HIS D 27 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N HIS D 27 " --> pdb=" O THR D 19 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N THR D 21 " --> pdb=" O ILE D 25 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ILE D 25 " --> pdb=" O THR D 21 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLY G 18 " --> pdb=" O PHE G 29 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N CYS G 31 " --> pdb=" O SER G 16 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N SER G 16 " --> pdb=" O CYS G 31 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N SER H 16 " --> pdb=" O CYS H 31 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N CYS H 31 " --> pdb=" O SER H 16 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N GLY H 18 " --> pdb=" O PHE H 29 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N CYS K 31 " --> pdb=" O SER K 16 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N SER K 16 " --> pdb=" O CYS K 31 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N PHE L 29 " --> pdb=" O TYR L 17 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N THR L 19 " --> pdb=" O HIS L 27 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N HIS L 27 " --> pdb=" O THR L 19 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N THR L 21 " --> pdb=" O ILE L 25 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ILE L 25 " --> pdb=" O THR L 21 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY O 18 " --> pdb=" O PHE O 29 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N CYS O 31 " --> pdb=" O SER O 16 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N SER O 16 " --> pdb=" O CYS O 31 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N PHE P 29 " --> pdb=" O TYR P 17 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N THR P 19 " --> pdb=" O HIS P 27 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N HIS P 27 " --> pdb=" O THR P 19 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N THR P 21 " --> pdb=" O ILE P 25 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ILE P 25 " --> pdb=" O THR P 21 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N THR P 3 " --> pdb=" O LEU P 32 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY Q 18 " --> pdb=" O PHE Q 29 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N CYS Q 31 " --> pdb=" O SER Q 16 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N SER Q 16 " --> pdb=" O CYS Q 31 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N PHE R 29 " --> pdb=" O TYR R 17 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N THR R 19 " --> pdb=" O HIS R 27 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N HIS R 27 " --> pdb=" O THR R 19 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N THR R 21 " --> pdb=" O ILE R 25 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE R 25 " --> pdb=" O THR R 21 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'U' and resid 3 through 7 removed outlier: 4.208A pdb=" N GLY U 18 " --> pdb=" O PHE U 29 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N CYS U 31 " --> pdb=" O SER U 16 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N SER U 16 " --> pdb=" O CYS U 31 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N PHE V 29 " --> pdb=" O TYR V 17 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N THR V 19 " --> pdb=" O HIS V 27 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N HIS V 27 " --> pdb=" O THR V 19 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N THR V 21 " --> pdb=" O ILE V 25 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE V 25 " --> pdb=" O THR V 21 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY Y 18 " --> pdb=" O PHE Y 29 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N CYS Y 31 " --> pdb=" O SER Y 16 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N SER Y 16 " --> pdb=" O CYS Y 31 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N PHE Z 29 " --> pdb=" O TYR Z 17 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N THR Z 19 " --> pdb=" O HIS Z 27 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N HIS Z 27 " --> pdb=" O THR Z 19 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR Z 21 " --> pdb=" O ILE Z 25 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ILE Z 25 " --> pdb=" O THR Z 21 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLY c 18 " --> pdb=" O PHE c 29 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N CYS c 31 " --> pdb=" O SER c 16 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N SER c 16 " --> pdb=" O CYS c 31 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'U' and resid 3 through 7 removed outlier: 4.208A pdb=" N GLY U 18 " --> pdb=" O PHE U 29 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N CYS U 31 " --> pdb=" O SER U 16 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N SER U 16 " --> pdb=" O CYS U 31 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N PHE V 29 " --> pdb=" O TYR V 17 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N THR V 19 " --> pdb=" O HIS V 27 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N HIS V 27 " --> pdb=" O THR V 19 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N THR V 21 " --> pdb=" O ILE V 25 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE V 25 " --> pdb=" O THR V 21 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY Y 18 " --> pdb=" O PHE Y 29 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N CYS Y 31 " --> pdb=" O SER Y 16 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N SER Y 16 " --> pdb=" O CYS Y 31 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N PHE Z 29 " --> pdb=" O TYR Z 17 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N THR Z 19 " --> pdb=" O HIS Z 27 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N HIS Z 27 " --> pdb=" O THR Z 19 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR Z 21 " --> pdb=" O ILE Z 25 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ILE Z 25 " --> pdb=" O THR Z 21 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLY c 18 " --> pdb=" O PHE c 29 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N CYS c 31 " --> pdb=" O SER c 16 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N SER c 16 " --> pdb=" O CYS c 31 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N ILE g 25 " --> pdb=" O THR g 21 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N THR g 21 " --> pdb=" O ILE g 25 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N HIS g 27 " --> pdb=" O THR g 19 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N THR g 19 " --> pdb=" O HIS g 27 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N PHE g 29 " --> pdb=" O TYR g 17 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N SER h 16 " --> pdb=" O CYS h 31 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N CYS h 31 " --> pdb=" O SER h 16 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY h 18 " --> pdb=" O PHE h 29 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY k 18 " --> pdb=" O PHE k 29 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N CYS k 31 " --> pdb=" O SER k 16 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N SER k 16 " --> pdb=" O CYS k 31 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N SER l 16 " --> pdb=" O CYS l 31 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N CYS l 31 " --> pdb=" O SER l 16 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLY l 18 " --> pdb=" O PHE l 29 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY o 18 " --> pdb=" O PHE o 29 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N CYS o 31 " --> pdb=" O SER o 16 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N SER o 16 " --> pdb=" O CYS o 31 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N SER p 16 " --> pdb=" O CYS p 31 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N CYS p 31 " --> pdb=" O SER p 16 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLY p 18 " --> pdb=" O PHE p 29 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ILE s 25 " --> pdb=" O THR s 21 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N THR s 21 " --> pdb=" O ILE s 25 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N HIS s 27 " --> pdb=" O THR s 19 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N THR s 19 " --> pdb=" O HIS s 27 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N PHE s 29 " --> pdb=" O TYR s 17 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N SER t 16 " --> pdb=" O CYS t 31 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N CYS t 31 " --> pdb=" O SER t 16 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY t 18 " --> pdb=" O PHE t 29 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE t 29 " --> pdb=" O GLY t 18 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE t 25 " --> pdb=" O VAL t 22 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'W' and resid 3 through 7 removed outlier: 3.928A pdb=" N GLY W 18 " --> pdb=" O PHE W 29 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N CYS W 31 " --> pdb=" O SER W 16 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N SER W 16 " --> pdb=" O CYS W 31 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N PHE X 29 " --> pdb=" O TYR X 17 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N THR X 19 " --> pdb=" O HIS X 27 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N HIS X 27 " --> pdb=" O THR X 19 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR X 21 " --> pdb=" O ILE X 25 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ILE X 25 " --> pdb=" O THR X 21 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE a 25 " --> pdb=" O THR a 21 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N THR a 21 " --> pdb=" O ILE a 25 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N HIS a 27 " --> pdb=" O THR a 19 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N THR a 19 " --> pdb=" O HIS a 27 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N PHE a 29 " --> pdb=" O TYR a 17 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ILE e 25 " --> pdb=" O THR e 21 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N THR e 21 " --> pdb=" O ILE e 25 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N HIS e 27 " --> pdb=" O THR e 19 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N THR e 19 " --> pdb=" O HIS e 27 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N PHE e 29 " --> pdb=" O TYR e 17 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'b' and resid 15 through 16 removed outlier: 6.193A pdb=" N ILE e 25 " --> pdb=" O THR e 21 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N THR e 21 " --> pdb=" O ILE e 25 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N HIS e 27 " --> pdb=" O THR e 19 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N THR e 19 " --> pdb=" O HIS e 27 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N PHE e 29 " --> pdb=" O TYR e 17 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLY i 18 " --> pdb=" O PHE i 29 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N CYS i 31 " --> pdb=" O SER i 16 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N SER i 16 " --> pdb=" O CYS i 31 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N PHE j 29 " --> pdb=" O TYR j 17 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N THR j 19 " --> pdb=" O HIS j 27 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N HIS j 27 " --> pdb=" O THR j 19 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N THR j 21 " --> pdb=" O ILE j 25 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ILE j 25 " --> pdb=" O THR j 21 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'm' and resid 4 through 7 removed outlier: 4.269A pdb=" N GLY m 18 " --> pdb=" O PHE m 29 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N CYS m 31 " --> pdb=" O SER m 16 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N SER m 16 " --> pdb=" O CYS m 31 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N PHE n 29 " --> pdb=" O TYR n 17 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N THR n 19 " --> pdb=" O HIS n 27 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N HIS n 27 " --> pdb=" O THR n 19 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N THR n 21 " --> pdb=" O ILE n 25 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ILE n 25 " --> pdb=" O THR n 21 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N GLY q 18 " --> pdb=" O PHE q 29 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N CYS q 31 " --> pdb=" O SER q 16 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N SER q 16 " --> pdb=" O CYS q 31 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N SER r 16 " --> pdb=" O CYS r 31 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N CYS r 31 " --> pdb=" O SER r 16 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY r 18 " --> pdb=" O PHE r 29 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR r 3 " --> pdb=" O LEU r 32 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE u 29 " --> pdb=" O GLY u 18 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY u 18 " --> pdb=" O PHE u 29 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N CYS u 31 " --> pdb=" O SER u 16 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N SER u 16 " --> pdb=" O CYS u 31 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'v' and resid 3 through 4 removed outlier: 3.930A pdb=" N THR v 3 " --> pdb=" O LEU v 32 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR v 15 " --> pdb=" O CYS v 31 " (cutoff:3.500A) 727 hydrogen bonds defined for protein. 1803 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.32 Time building geometry restraints manager: 1.43 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: 3888 1.35 - 1.47: 3913 1.47 - 1.59: 4478 1.59 - 1.71: 25 1.71 - 1.83: 384 Bond restraints: 12688 Sorted by residual: bond pdb=" O32 IHP Q 101 " pdb=" P2 IHP Q 101 " ideal model delta sigma weight residual 1.537 1.507 0.030 2.00e-02 2.50e+03 2.21e+00 bond pdb=" O32 IHP N 101 " pdb=" P2 IHP N 101 " ideal model delta sigma weight residual 1.537 1.507 0.030 2.00e-02 2.50e+03 2.18e+00 bond pdb=" O32 IHP K 101 " pdb=" P2 IHP K 101 " ideal model delta sigma weight residual 1.537 1.508 0.029 2.00e-02 2.50e+03 2.17e+00 bond pdb=" O32 IHP C 101 " pdb=" P2 IHP C 101 " ideal model delta sigma weight residual 1.537 1.508 0.029 2.00e-02 2.50e+03 2.17e+00 bond pdb=" O32 IHP F 101 " pdb=" P2 IHP F 101 " ideal model delta sigma weight residual 1.537 1.508 0.029 2.00e-02 2.50e+03 2.14e+00 ... (remaining 12683 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 16720 1.96 - 3.91: 307 3.91 - 5.87: 55 5.87 - 7.82: 11 7.82 - 9.78: 20 Bond angle restraints: 17113 Sorted by residual: angle pdb=" CB MET U 23 " pdb=" CG MET U 23 " pdb=" SD MET U 23 " ideal model delta sigma weight residual 112.70 122.48 -9.78 3.00e+00 1.11e-01 1.06e+01 angle pdb=" CB MET s 23 " pdb=" CG MET s 23 " pdb=" SD MET s 23 " ideal model delta sigma weight residual 112.70 122.32 -9.62 3.00e+00 1.11e-01 1.03e+01 angle pdb=" O12 IHP K 101 " pdb=" P2 IHP K 101 " pdb=" O32 IHP K 101 " ideal model delta sigma weight residual 100.47 109.88 -9.41 3.00e+00 1.11e-01 9.84e+00 angle pdb=" O12 IHP F 101 " pdb=" P2 IHP F 101 " pdb=" O32 IHP F 101 " ideal model delta sigma weight residual 100.47 109.80 -9.33 3.00e+00 1.11e-01 9.67e+00 angle pdb=" CB MET Y 23 " pdb=" CG MET Y 23 " pdb=" SD MET Y 23 " ideal model delta sigma weight residual 112.70 122.00 -9.30 3.00e+00 1.11e-01 9.61e+00 ... (remaining 17108 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.04: 6426 17.04 - 34.07: 995 34.07 - 51.11: 324 51.11 - 68.15: 73 68.15 - 85.19: 9 Dihedral angle restraints: 7827 sinusoidal: 3315 harmonic: 4512 Sorted by residual: dihedral pdb=" CB CYS I 6 " pdb=" SG CYS I 6 " pdb=" SG CYS I 20 " pdb=" CB CYS I 20 " ideal model delta sinusoidal sigma weight residual 93.00 176.44 -83.44 1 1.00e+01 1.00e-02 8.50e+01 dihedral pdb=" CB CYS j 10 " pdb=" SG CYS j 10 " pdb=" SG CYS j 30 " pdb=" CB CYS j 30 " ideal model delta sinusoidal sigma weight residual -86.00 -165.36 79.36 1 1.00e+01 1.00e-02 7.83e+01 dihedral pdb=" CB CYS p 6 " pdb=" SG CYS p 6 " pdb=" SG CYS p 20 " pdb=" CB CYS p 20 " ideal model delta sinusoidal sigma weight residual -86.00 -161.15 75.15 1 1.00e+01 1.00e-02 7.14e+01 ... (remaining 7824 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1337 0.039 - 0.078: 348 0.078 - 0.118: 90 0.118 - 0.157: 21 0.157 - 0.196: 10 Chirality restraints: 1806 Sorted by residual: chirality pdb=" C1 IHP K 101 " pdb=" C2 IHP K 101 " pdb=" C6 IHP K 101 " pdb=" O11 IHP K 101 " both_signs ideal model delta sigma weight residual False 2.32 2.51 -0.20 2.00e-01 2.50e+01 9.63e-01 chirality pdb=" C1 IHP C 101 " pdb=" C2 IHP C 101 " pdb=" C6 IHP C 101 " pdb=" O11 IHP C 101 " both_signs ideal model delta sigma weight residual False 2.32 2.51 -0.19 2.00e-01 2.50e+01 9.37e-01 chirality pdb=" C3 IHP F 101 " pdb=" C2 IHP F 101 " pdb=" C4 IHP F 101 " pdb=" O13 IHP F 101 " both_signs ideal model delta sigma weight residual False -2.34 -2.52 0.19 2.00e-01 2.50e+01 8.73e-01 ... (remaining 1803 not shown) Planarity restraints: 2112 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR c 15 " -0.008 2.00e-02 2.50e+03 1.03e-02 2.13e+00 pdb=" CG TYR c 15 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR c 15 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR c 15 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR c 15 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR c 15 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR c 15 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR c 15 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE m 2 " -0.007 2.00e-02 2.50e+03 1.41e-02 1.98e+00 pdb=" C PHE m 2 " 0.024 2.00e-02 2.50e+03 pdb=" O PHE m 2 " -0.009 2.00e-02 2.50e+03 pdb=" N THR m 3 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG V 7 " 0.094 9.50e-02 1.11e+02 4.23e-02 1.34e+00 pdb=" NE ARG V 7 " -0.009 2.00e-02 2.50e+03 pdb=" CZ ARG V 7 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG V 7 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG V 7 " 0.001 2.00e-02 2.50e+03 ... (remaining 2109 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 313 2.69 - 3.24: 10548 3.24 - 3.80: 18357 3.80 - 4.35: 25371 4.35 - 4.90: 45439 Nonbonded interactions: 100028 Sorted by model distance: nonbonded pdb=" OG1 THR Y 21 " pdb=" OG1 THR Z 21 " model vdw 2.139 3.040 nonbonded pdb=" OH TYR J 17 " pdb=" NE2 HIS N 27 " model vdw 2.221 3.120 nonbonded pdb=" OH TYR B 17 " pdb=" NE2 HIS F 27 " model vdw 2.235 3.120 nonbonded pdb=" OH TYR r 17 " pdb=" NE2 HIS v 27 " model vdw 2.270 3.120 nonbonded pdb=" O SER K 16 " pdb=" OG SER K 16 " model vdw 2.274 3.040 ... (remaining 100023 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' selection = chain 'B' selection = (chain 'C' and resid 1 through 32) selection = chain 'D' selection = chain 'E' selection = (chain 'F' and resid 1 through 32) selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = (chain 'K' and resid 1 through 32) selection = chain 'L' selection = chain 'M' selection = (chain 'N' and resid 1 through 32) selection = chain 'O' selection = chain 'P' selection = (chain 'Q' and resid 1 through 32) selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = 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' } 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=1.00 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: 11.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.870 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.020 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:7.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 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 : 0.004 0.033 12832 Z= 0.176 Angle : 0.733 9.781 17401 Z= 0.361 Chirality : 0.042 0.196 1806 Planarity : 0.003 0.042 2112 Dihedral : 17.027 85.185 4515 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.46 % Favored : 98.40 % Rotamer: Outliers : 4.17 % Allowed : 26.87 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.21), residues: 1440 helix: None (None), residues: 0 sheet: -1.19 (0.18), residues: 774 loop : -1.42 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG O 8 TYR 0.025 0.001 TYR c 15 PHE 0.016 0.002 PHE I 29 HIS 0.007 0.001 HIS d 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.18 (12688) covalent geometry : angle 0.72886 / 0.36 (17113) SS BOND : bond 0.00234 / 0.16 ( 144) SS BOND : angle 0.94593 / 0.63 ( 288) hydrogen bonds : bond 0.14988 / 9.74 ( 561) hydrogen bonds : angle 8.06743 / 5.63 ( 1803) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 331 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: A 15 TYR cc_start: 0.7917 (m-80) cc_final: 0.7631 (m-80) REVERT: g 7 ARG cc_start: 0.8366 (mtt-85) cc_final: 0.8119 (mtt-85) REVERT: m 28 ARG cc_start: 0.7668 (mtm180) cc_final: 0.7457 (mtm180) outliers start: 58 outliers final: 49 residues processed: 378 average time/residue: 0.5360 time to fit residues: 221.5495 Evaluate side-chains 366 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 317 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain F residue 20 CYS Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain N residue 12 SER Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 32 LEU Chi-restraints excluded: chain S residue 7 ARG Chi-restraints excluded: chain S residue 19 THR Chi-restraints excluded: chain T residue 19 THR Chi-restraints excluded: chain U residue 10 CYS Chi-restraints excluded: chain X residue 12 SER Chi-restraints excluded: chain Y residue 5 HIS Chi-restraints excluded: chain Y residue 12 SER Chi-restraints excluded: chain a residue 32 LEU Chi-restraints excluded: chain b residue 2 PHE Chi-restraints excluded: chain b residue 7 ARG Chi-restraints excluded: chain b residue 9 SER Chi-restraints excluded: chain b residue 25 ILE Chi-restraints excluded: chain c residue 13 THR Chi-restraints excluded: chain c residue 20 CYS Chi-restraints excluded: chain d residue 10 CYS Chi-restraints excluded: chain d residue 13 THR Chi-restraints excluded: chain d residue 19 THR Chi-restraints excluded: chain e residue 7 ARG Chi-restraints excluded: chain e residue 16 SER Chi-restraints excluded: chain f residue 10 CYS Chi-restraints excluded: chain f residue 19 THR Chi-restraints excluded: chain i residue 7 ARG Chi-restraints excluded: chain i residue 16 SER Chi-restraints excluded: chain i residue 31 CYS Chi-restraints excluded: chain i residue 32 LEU Chi-restraints excluded: chain j residue 20 CYS Chi-restraints excluded: chain k residue 9 SER Chi-restraints excluded: chain k residue 20 CYS Chi-restraints excluded: chain l residue 14 GLU Chi-restraints excluded: chain l residue 20 CYS Chi-restraints excluded: chain l residue 25 ILE Chi-restraints excluded: chain m residue 13 THR Chi-restraints excluded: chain m residue 16 SER Chi-restraints excluded: chain m residue 22 VAL Chi-restraints excluded: chain q residue 3 THR Chi-restraints excluded: chain s residue 14 GLU Chi-restraints excluded: chain t residue 21 THR Chi-restraints excluded: chain v residue 19 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 26 ASN C 27 HIS F 5 HIS P 26 ASN T 27 HIS ** U 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 26 ASN k 26 ASN ** k 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 5 HIS ** p 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.115630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.096227 restraints weight = 17216.430| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.63 r_work: 0.3174 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 12832 Z= 0.333 Angle : 0.671 7.047 17401 Z= 0.370 Chirality : 0.044 0.156 1806 Planarity : 0.005 0.055 2112 Dihedral : 9.959 88.298 2092 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.88 % Favored : 97.99 % Rotamer: Outliers : 8.69 % Allowed : 21.19 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.21), residues: 1440 helix: None (None), residues: 0 sheet: -1.26 (0.17), residues: 804 loop : -1.27 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 8 TYR 0.020 0.002 TYR I 17 PHE 0.020 0.003 PHE e 29 HIS 0.009 0.002 HIS d 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00765 / 0.33 (12688) covalent geometry : angle 0.65399 / 0.36 (17113) SS BOND : bond 0.00611 / 0.43 ( 144) SS BOND : angle 1.35056 / 0.86 ( 288) hydrogen bonds : bond 0.04375 / 2.92 ( 561) hydrogen bonds : angle 6.80285 / 4.69 ( 1803) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 310 time to evaluate : 0.519 Fit side-chains revert: symmetry clash REVERT: H 28 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7987 (mmp-170) REVERT: L 28 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.7793 (mpp80) REVERT: M 28 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.7897 (mtp85) REVERT: N 8 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8049 (ttp80) REVERT: g 7 ARG cc_start: 0.8543 (mtt-85) cc_final: 0.8298 (mtt-85) REVERT: h 28 ARG cc_start: 0.8000 (mmt180) cc_final: 0.7775 (mpt90) REVERT: i 7 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.7887 (mtp180) REVERT: j 23 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.6850 (mtp) REVERT: m 7 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8086 (ptp-170) REVERT: n 15 TYR cc_start: 0.8146 (t80) cc_final: 0.7926 (t80) REVERT: q 28 ARG cc_start: 0.7306 (mtt180) cc_final: 0.7091 (mtp180) REVERT: r 14 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.6981 (pp20) outliers start: 121 outliers final: 61 residues processed: 379 average time/residue: 0.5820 time to fit residues: 239.0603 Evaluate side-chains 362 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 293 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 28 ARG Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 28 ARG Chi-restraints excluded: chain M residue 12 SER Chi-restraints excluded: chain M residue 28 ARG Chi-restraints excluded: chain N residue 8 ARG Chi-restraints excluded: chain O residue 16 SER Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain S residue 19 THR Chi-restraints excluded: chain T residue 19 THR Chi-restraints excluded: chain U residue 21 THR Chi-restraints excluded: chain W residue 8 ARG Chi-restraints excluded: chain W residue 16 SER Chi-restraints excluded: chain X residue 16 SER Chi-restraints excluded: chain Y residue 5 HIS Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 16 SER Chi-restraints excluded: chain a residue 22 VAL Chi-restraints excluded: chain a residue 32 LEU Chi-restraints excluded: chain b residue 7 ARG Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain c residue 8 ARG Chi-restraints excluded: chain c residue 13 THR Chi-restraints excluded: chain c residue 16 SER Chi-restraints excluded: chain c residue 20 CYS Chi-restraints excluded: chain c residue 21 THR Chi-restraints excluded: chain d residue 3 THR Chi-restraints excluded: chain d residue 19 THR Chi-restraints excluded: chain d residue 32 LEU Chi-restraints excluded: chain e residue 7 ARG Chi-restraints excluded: chain e residue 10 CYS Chi-restraints excluded: chain e residue 32 LEU Chi-restraints excluded: chain f residue 21 THR Chi-restraints excluded: chain f residue 32 LEU Chi-restraints excluded: chain g residue 12 SER Chi-restraints excluded: chain h residue 13 THR Chi-restraints excluded: chain i residue 7 ARG Chi-restraints excluded: chain i residue 19 THR Chi-restraints excluded: chain i residue 21 THR Chi-restraints excluded: chain i residue 32 LEU Chi-restraints excluded: chain j residue 16 SER Chi-restraints excluded: chain j residue 20 CYS Chi-restraints excluded: chain j residue 23 MET Chi-restraints excluded: chain k residue 20 CYS Chi-restraints excluded: chain l residue 19 THR Chi-restraints excluded: chain l residue 20 CYS Chi-restraints excluded: chain l residue 21 THR Chi-restraints excluded: chain m residue 7 ARG Chi-restraints excluded: chain m residue 9 SER Chi-restraints excluded: chain m residue 22 VAL Chi-restraints excluded: chain n residue 28 ARG Chi-restraints excluded: chain q residue 3 THR Chi-restraints excluded: chain q residue 19 THR Chi-restraints excluded: chain q residue 23 MET Chi-restraints excluded: chain r residue 13 THR Chi-restraints excluded: chain r residue 14 GLU Chi-restraints excluded: chain s residue 7 ARG Chi-restraints excluded: chain t residue 11 TYR Chi-restraints excluded: chain t residue 30 CYS Chi-restraints excluded: chain v residue 21 THR Chi-restraints excluded: chain v residue 26 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 90 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 26 ASN P 26 ASN k 26 ASN ** k 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.119324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.100178 restraints weight = 17727.837| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.65 r_work: 0.3245 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12832 Z= 0.121 Angle : 0.511 7.158 17401 Z= 0.284 Chirality : 0.038 0.154 1806 Planarity : 0.003 0.035 2112 Dihedral : 8.489 89.388 2051 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.46 % Favored : 98.47 % Rotamer: Outliers : 5.53 % Allowed : 23.49 % Favored : 70.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.21), residues: 1440 helix: None (None), residues: 0 sheet: -1.10 (0.18), residues: 774 loop : -1.16 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 8 TYR 0.012 0.001 TYR I 17 PHE 0.014 0.002 PHE I 29 HIS 0.005 0.001 HIS d 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (12688) covalent geometry : angle 0.50415 / 0.28 (17113) SS BOND : bond 0.00275 / 0.19 ( 144) SS BOND : angle 0.81782 / 0.53 ( 288) hydrogen bonds : bond 0.03368 / 2.24 ( 561) hydrogen bonds : angle 6.01677 / 4.16 ( 1803) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 334 time to evaluate : 0.499 Fit side-chains REVERT: A 15 TYR cc_start: 0.8203 (m-80) cc_final: 0.7946 (m-80) REVERT: C 8 ARG cc_start: 0.8396 (ttm-80) cc_final: 0.8048 (ptm160) REVERT: M 28 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.7636 (mtp85) REVERT: N 8 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.8094 (ttp80) REVERT: T 7 ARG cc_start: 0.9265 (OUTLIER) cc_final: 0.8287 (ptp-170) REVERT: W 8 ARG cc_start: 0.7313 (OUTLIER) cc_final: 0.7099 (tpp80) REVERT: a 32 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8033 (pp) REVERT: e 7 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.7944 (mtp180) REVERT: h 28 ARG cc_start: 0.8035 (mmt180) cc_final: 0.7807 (mpt180) REVERT: i 7 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.8132 (mtp180) REVERT: n 15 TYR cc_start: 0.8041 (t80) cc_final: 0.7737 (t80) REVERT: n 28 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7445 (mmt90) outliers start: 77 outliers final: 42 residues processed: 380 average time/residue: 0.5829 time to fit residues: 240.2753 Evaluate side-chains 357 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 307 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 CYS Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain M residue 12 SER Chi-restraints excluded: chain M residue 28 ARG Chi-restraints excluded: chain N residue 8 ARG Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 32 LEU Chi-restraints excluded: chain S residue 7 ARG Chi-restraints excluded: chain S residue 19 THR Chi-restraints excluded: chain T residue 7 ARG Chi-restraints excluded: chain W residue 8 ARG Chi-restraints excluded: chain W residue 16 SER Chi-restraints excluded: chain Y residue 5 HIS Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 22 VAL Chi-restraints excluded: chain a residue 32 LEU Chi-restraints excluded: chain b residue 7 ARG Chi-restraints excluded: chain b residue 32 LEU Chi-restraints excluded: chain c residue 16 SER Chi-restraints excluded: chain c residue 19 THR Chi-restraints excluded: chain c residue 20 CYS Chi-restraints excluded: chain c residue 21 THR Chi-restraints excluded: chain d residue 3 THR Chi-restraints excluded: chain e residue 7 ARG Chi-restraints excluded: chain e residue 10 CYS Chi-restraints excluded: chain e residue 23 MET Chi-restraints excluded: chain f residue 21 THR Chi-restraints excluded: chain f residue 32 LEU Chi-restraints excluded: chain h residue 13 THR Chi-restraints excluded: chain i residue 7 ARG Chi-restraints excluded: chain i residue 19 THR Chi-restraints excluded: chain i residue 21 THR Chi-restraints excluded: chain i residue 32 LEU Chi-restraints excluded: chain j residue 16 SER Chi-restraints excluded: chain j residue 20 CYS Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain k residue 11 TYR Chi-restraints excluded: chain k residue 20 CYS Chi-restraints excluded: chain l residue 21 THR Chi-restraints excluded: chain m residue 22 VAL Chi-restraints excluded: chain m residue 31 CYS Chi-restraints excluded: chain n residue 28 ARG Chi-restraints excluded: chain q residue 19 THR Chi-restraints excluded: chain r residue 13 THR Chi-restraints excluded: chain t residue 11 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 17 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 135 optimal weight: 0.0770 chunk 99 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 overall best weight: 1.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 26 ASN P 26 ASN ** U 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 26 ASN ** k 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.118889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.099774 restraints weight = 17648.809| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.63 r_work: 0.3234 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12832 Z= 0.148 Angle : 0.524 7.661 17401 Z= 0.291 Chirality : 0.039 0.145 1806 Planarity : 0.003 0.057 2112 Dihedral : 8.310 87.847 2044 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.39 % Favored : 98.54 % Rotamer: Outliers : 7.47 % Allowed : 22.49 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.21), residues: 1440 helix: None (None), residues: 0 sheet: -1.11 (0.18), residues: 774 loop : -1.06 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG J 8 TYR 0.019 0.001 TYR c 15 PHE 0.014 0.002 PHE m 29 HIS 0.005 0.001 HIS d 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (12688) covalent geometry : angle 0.51626 / 0.29 (17113) SS BOND : bond 0.00289 / 0.20 ( 144) SS BOND : angle 0.84989 / 0.55 ( 288) hydrogen bonds : bond 0.03383 / 2.25 ( 561) hydrogen bonds : angle 5.97193 / 4.12 ( 1803) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 317 time to evaluate : 0.531 Fit side-chains REVERT: C 8 ARG cc_start: 0.8413 (ttm-80) cc_final: 0.8060 (ptm160) REVERT: C 32 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7867 (pt) REVERT: H 28 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.7973 (mmp-170) REVERT: L 23 MET cc_start: 0.9062 (OUTLIER) cc_final: 0.8687 (mpp) REVERT: M 28 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.7655 (mtp85) REVERT: S 28 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8190 (mtp180) REVERT: T 7 ARG cc_start: 0.9269 (OUTLIER) cc_final: 0.8605 (ptp-170) REVERT: W 8 ARG cc_start: 0.7302 (OUTLIER) cc_final: 0.7094 (tpp80) REVERT: X 7 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.8571 (ptp90) REVERT: X 13 THR cc_start: 0.9000 (p) cc_final: 0.8543 (t) REVERT: b 7 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.7444 (ptp-170) REVERT: h 28 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7863 (mpt180) REVERT: i 7 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7987 (mtp180) REVERT: j 23 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.6689 (mtp) REVERT: n 15 TYR cc_start: 0.8027 (t80) cc_final: 0.7795 (t80) REVERT: n 28 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7457 (mmt90) REVERT: r 14 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7716 (pp20) outliers start: 104 outliers final: 59 residues processed: 375 average time/residue: 0.5691 time to fit residues: 232.0578 Evaluate side-chains 380 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 307 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ARG Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 30 CYS Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 28 ARG Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 23 MET Chi-restraints excluded: chain M residue 12 SER Chi-restraints excluded: chain M residue 28 ARG Chi-restraints excluded: chain N residue 12 SER Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain S residue 7 ARG Chi-restraints excluded: chain S residue 19 THR Chi-restraints excluded: chain S residue 28 ARG Chi-restraints excluded: chain T residue 7 ARG Chi-restraints excluded: chain U residue 10 CYS Chi-restraints excluded: chain U residue 20 CYS Chi-restraints excluded: chain V residue 20 CYS Chi-restraints excluded: chain W residue 8 ARG Chi-restraints excluded: chain W residue 16 SER Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain X residue 7 ARG Chi-restraints excluded: chain Y residue 5 HIS Chi-restraints excluded: chain Y residue 30 CYS Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 16 SER Chi-restraints excluded: chain a residue 22 VAL Chi-restraints excluded: chain b residue 7 ARG Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 32 LEU Chi-restraints excluded: chain c residue 13 THR Chi-restraints excluded: chain c residue 16 SER Chi-restraints excluded: chain c residue 19 THR Chi-restraints excluded: chain c residue 20 CYS Chi-restraints excluded: chain c residue 21 THR Chi-restraints excluded: chain d residue 3 THR Chi-restraints excluded: chain d residue 19 THR Chi-restraints excluded: chain d residue 32 LEU Chi-restraints excluded: chain e residue 7 ARG Chi-restraints excluded: chain e residue 10 CYS Chi-restraints excluded: chain e residue 32 LEU Chi-restraints excluded: chain f residue 21 THR Chi-restraints excluded: chain f residue 32 LEU Chi-restraints excluded: chain g residue 12 SER Chi-restraints excluded: chain h residue 13 THR Chi-restraints excluded: chain h residue 28 ARG Chi-restraints excluded: chain i residue 7 ARG Chi-restraints excluded: chain i residue 19 THR Chi-restraints excluded: chain i residue 21 THR Chi-restraints excluded: chain j residue 16 SER Chi-restraints excluded: chain j residue 20 CYS Chi-restraints excluded: chain j residue 23 MET Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain k residue 11 TYR Chi-restraints excluded: chain k residue 19 THR Chi-restraints excluded: chain k residue 20 CYS Chi-restraints excluded: chain l residue 21 THR Chi-restraints excluded: chain m residue 22 VAL Chi-restraints excluded: chain m residue 31 CYS Chi-restraints excluded: chain n residue 9 SER Chi-restraints excluded: chain n residue 28 ARG Chi-restraints excluded: chain q residue 3 THR Chi-restraints excluded: chain q residue 19 THR Chi-restraints excluded: chain r residue 13 THR Chi-restraints excluded: chain r residue 14 GLU Chi-restraints excluded: chain s residue 7 ARG Chi-restraints excluded: chain s residue 13 THR Chi-restraints excluded: chain t residue 11 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 78 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 106 optimal weight: 6.9990 chunk 104 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 26 ASN P 26 ASN ** U 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.117907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.098831 restraints weight = 17808.377| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.63 r_work: 0.3211 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12832 Z= 0.174 Angle : 0.547 9.326 17401 Z= 0.301 Chirality : 0.039 0.143 1806 Planarity : 0.003 0.066 2112 Dihedral : 8.279 86.021 2040 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.53 % Favored : 98.40 % Rotamer: Outliers : 7.40 % Allowed : 22.99 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.21), residues: 1440 helix: None (None), residues: 0 sheet: -1.16 (0.17), residues: 804 loop : -0.88 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG J 8 TYR 0.011 0.001 TYR I 17 PHE 0.014 0.002 PHE m 29 HIS 0.006 0.001 HIS d 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (12688) covalent geometry : angle 0.53821 / 0.30 (17113) SS BOND : bond 0.00329 / 0.23 ( 144) SS BOND : angle 0.91345 / 0.59 ( 288) hydrogen bonds : bond 0.03442 / 2.29 ( 561) hydrogen bonds : angle 6.02093 / 4.15 ( 1803) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 316 time to evaluate : 0.529 Fit side-chains REVERT: C 32 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7854 (pt) REVERT: H 28 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7931 (mmp-170) REVERT: M 28 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.7670 (mtp85) REVERT: S 28 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8162 (mtp180) REVERT: T 7 ARG cc_start: 0.9282 (OUTLIER) cc_final: 0.8734 (ptp-170) REVERT: W 8 ARG cc_start: 0.7331 (OUTLIER) cc_final: 0.6975 (tpp80) REVERT: X 13 THR cc_start: 0.9006 (p) cc_final: 0.8559 (t) REVERT: h 28 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7842 (mpt180) REVERT: n 15 TYR cc_start: 0.8131 (t80) cc_final: 0.7850 (t80) REVERT: n 28 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7523 (mmt90) outliers start: 103 outliers final: 64 residues processed: 376 average time/residue: 0.5875 time to fit residues: 239.7498 Evaluate side-chains 380 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 308 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ARG Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 28 ARG Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain M residue 12 SER Chi-restraints excluded: chain M residue 28 ARG Chi-restraints excluded: chain N residue 12 SER Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain S residue 7 ARG Chi-restraints excluded: chain S residue 19 THR Chi-restraints excluded: chain S residue 28 ARG Chi-restraints excluded: chain T residue 7 ARG Chi-restraints excluded: chain U residue 10 CYS Chi-restraints excluded: chain U residue 15 TYR Chi-restraints excluded: chain U residue 20 CYS Chi-restraints excluded: chain V residue 20 CYS Chi-restraints excluded: chain W residue 8 ARG Chi-restraints excluded: chain W residue 16 SER Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain Y residue 5 HIS Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 16 SER Chi-restraints excluded: chain a residue 22 VAL Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 25 ILE Chi-restraints excluded: chain b residue 32 LEU Chi-restraints excluded: chain c residue 13 THR Chi-restraints excluded: chain c residue 16 SER Chi-restraints excluded: chain c residue 19 THR Chi-restraints excluded: chain c residue 20 CYS Chi-restraints excluded: chain c residue 21 THR Chi-restraints excluded: chain d residue 3 THR Chi-restraints excluded: chain d residue 19 THR Chi-restraints excluded: chain d residue 32 LEU Chi-restraints excluded: chain e residue 7 ARG Chi-restraints excluded: chain e residue 10 CYS Chi-restraints excluded: chain e residue 32 LEU Chi-restraints excluded: chain f residue 21 THR Chi-restraints excluded: chain f residue 32 LEU Chi-restraints excluded: chain g residue 12 SER Chi-restraints excluded: chain h residue 13 THR Chi-restraints excluded: chain h residue 16 SER Chi-restraints excluded: chain h residue 28 ARG Chi-restraints excluded: chain i residue 19 THR Chi-restraints excluded: chain i residue 21 THR Chi-restraints excluded: chain j residue 16 SER Chi-restraints excluded: chain j residue 20 CYS Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain k residue 11 TYR Chi-restraints excluded: chain k residue 19 THR Chi-restraints excluded: chain k residue 20 CYS Chi-restraints excluded: chain l residue 19 THR Chi-restraints excluded: chain l residue 21 THR Chi-restraints excluded: chain m residue 22 VAL Chi-restraints excluded: chain m residue 31 CYS Chi-restraints excluded: chain n residue 9 SER Chi-restraints excluded: chain n residue 28 ARG Chi-restraints excluded: chain q residue 3 THR Chi-restraints excluded: chain q residue 19 THR Chi-restraints excluded: chain r residue 13 THR Chi-restraints excluded: chain s residue 7 ARG Chi-restraints excluded: chain s residue 13 THR Chi-restraints excluded: chain t residue 11 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 16 optimal weight: 4.9990 chunk 49 optimal weight: 0.4980 chunk 109 optimal weight: 0.3980 chunk 47 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 85 optimal weight: 0.0980 chunk 18 optimal weight: 2.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 26 ASN P 26 ASN ** k 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.121204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.102101 restraints weight = 17727.311| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.65 r_work: 0.3281 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12832 Z= 0.093 Angle : 0.495 9.338 17401 Z= 0.272 Chirality : 0.037 0.143 1806 Planarity : 0.003 0.034 2112 Dihedral : 7.396 82.320 2032 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.25 % Favored : 98.68 % Rotamer: Outliers : 4.96 % Allowed : 25.57 % Favored : 69.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.21), residues: 1440 helix: None (None), residues: 0 sheet: -1.03 (0.18), residues: 774 loop : -0.97 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG X 8 TYR 0.021 0.001 TYR c 15 PHE 0.012 0.002 PHE m 29 HIS 0.005 0.001 HIS k 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.09 (12688) covalent geometry : angle 0.49102 / 0.27 (17113) SS BOND : bond 0.00187 / 0.13 ( 144) SS BOND : angle 0.67556 / 0.45 ( 288) hydrogen bonds : bond 0.02972 / 1.97 ( 561) hydrogen bonds : angle 5.59932 / 3.88 ( 1803) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 334 time to evaluate : 0.467 Fit side-chains REVERT: C 8 ARG cc_start: 0.8391 (ttm-80) cc_final: 0.8006 (ptm160) REVERT: C 32 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7821 (pt) REVERT: T 7 ARG cc_start: 0.9223 (OUTLIER) cc_final: 0.8198 (ptp-170) REVERT: U 28 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.7249 (mtp85) REVERT: W 8 ARG cc_start: 0.7320 (OUTLIER) cc_final: 0.6807 (tpp80) REVERT: X 13 THR cc_start: 0.8888 (p) cc_final: 0.8437 (t) REVERT: e 7 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.7967 (mtp180) REVERT: g 8 ARG cc_start: 0.8282 (ttp-110) cc_final: 0.8067 (mtm-85) REVERT: h 21 THR cc_start: 0.9006 (m) cc_final: 0.8604 (p) REVERT: h 28 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7764 (mpt180) REVERT: n 15 TYR cc_start: 0.8082 (t80) cc_final: 0.7845 (t80) REVERT: p 7 ARG cc_start: 0.8453 (mtp85) cc_final: 0.8251 (mtp85) REVERT: r 14 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7755 (pp20) outliers start: 69 outliers final: 39 residues processed: 380 average time/residue: 0.5999 time to fit residues: 246.9246 Evaluate side-chains 357 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 311 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 CYS Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain S residue 19 THR Chi-restraints excluded: chain T residue 7 ARG Chi-restraints excluded: chain U residue 20 CYS Chi-restraints excluded: chain U residue 28 ARG Chi-restraints excluded: chain V residue 20 CYS Chi-restraints excluded: chain W residue 8 ARG Chi-restraints excluded: chain W residue 10 CYS Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain Y residue 5 HIS Chi-restraints excluded: chain Y residue 30 CYS Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 16 SER Chi-restraints excluded: chain a residue 22 VAL Chi-restraints excluded: chain b residue 32 LEU Chi-restraints excluded: chain c residue 8 ARG Chi-restraints excluded: chain c residue 13 THR Chi-restraints excluded: chain c residue 20 CYS Chi-restraints excluded: chain d residue 19 THR Chi-restraints excluded: chain e residue 7 ARG Chi-restraints excluded: chain e residue 10 CYS Chi-restraints excluded: chain f residue 21 THR Chi-restraints excluded: chain f residue 32 LEU Chi-restraints excluded: chain h residue 13 THR Chi-restraints excluded: chain h residue 28 ARG Chi-restraints excluded: chain i residue 19 THR Chi-restraints excluded: chain i residue 21 THR Chi-restraints excluded: chain j residue 16 SER Chi-restraints excluded: chain j residue 20 CYS Chi-restraints excluded: chain k residue 11 TYR Chi-restraints excluded: chain k residue 20 CYS Chi-restraints excluded: chain m residue 22 VAL Chi-restraints excluded: chain m residue 31 CYS Chi-restraints excluded: chain n residue 9 SER Chi-restraints excluded: chain r residue 13 THR Chi-restraints excluded: chain r residue 14 GLU Chi-restraints excluded: chain t residue 11 TYR Chi-restraints excluded: chain t residue 30 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 5 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 46 optimal weight: 0.0470 chunk 14 optimal weight: 8.9990 chunk 58 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.1284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 26 ASN J 26 ASN P 26 ASN ** U 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 26 ASN k 27 HIS ** p 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.118729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.099357 restraints weight = 17756.558| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.65 r_work: 0.3230 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12832 Z= 0.145 Angle : 0.548 10.554 17401 Z= 0.303 Chirality : 0.039 0.144 1806 Planarity : 0.004 0.071 2112 Dihedral : 7.547 80.189 2032 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.46 % Favored : 98.47 % Rotamer: Outliers : 5.03 % Allowed : 25.93 % Favored : 69.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.21), residues: 1440 helix: None (None), residues: 0 sheet: -1.01 (0.18), residues: 774 loop : -0.97 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG J 8 TYR 0.015 0.001 TYR b 11 PHE 0.014 0.002 PHE m 29 HIS 0.008 0.001 HIS k 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (12688) covalent geometry : angle 0.53925 / 0.30 (17113) SS BOND : bond 0.00267 / 0.19 ( 144) SS BOND : angle 0.94186 / 0.61 ( 288) hydrogen bonds : bond 0.03293 / 2.20 ( 561) hydrogen bonds : angle 5.82264 / 4.02 ( 1803) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 322 time to evaluate : 0.500 Fit side-chains REVERT: C 8 ARG cc_start: 0.8418 (ttm-80) cc_final: 0.8010 (ptm160) REVERT: C 32 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7877 (pt) REVERT: D 28 ARG cc_start: 0.8615 (mmm160) cc_final: 0.8390 (mmp-170) REVERT: T 7 ARG cc_start: 0.9265 (OUTLIER) cc_final: 0.8379 (ptp-170) REVERT: X 13 THR cc_start: 0.8916 (p) cc_final: 0.8500 (t) REVERT: d 28 ARG cc_start: 0.7925 (mmm160) cc_final: 0.7681 (mmm160) REVERT: h 28 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.7753 (mpt180) REVERT: m 23 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.7237 (mpt) REVERT: n 15 TYR cc_start: 0.8094 (t80) cc_final: 0.7778 (t80) REVERT: n 28 ARG cc_start: 0.7936 (mmm160) cc_final: 0.7392 (mmt90) REVERT: p 7 ARG cc_start: 0.8426 (mtp85) cc_final: 0.8187 (mtp85) REVERT: p 23 MET cc_start: 0.8149 (mmm) cc_final: 0.7898 (mtp) REVERT: r 14 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7742 (pp20) REVERT: u 23 MET cc_start: 0.8298 (mmt) cc_final: 0.7944 (mmt) outliers start: 70 outliers final: 50 residues processed: 365 average time/residue: 0.5477 time to fit residues: 218.0331 Evaluate side-chains 368 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 313 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 CYS Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain M residue 12 SER Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain S residue 19 THR Chi-restraints excluded: chain T residue 7 ARG Chi-restraints excluded: chain U residue 20 CYS Chi-restraints excluded: chain V residue 20 CYS Chi-restraints excluded: chain W residue 8 ARG Chi-restraints excluded: chain W residue 10 CYS Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain Y residue 5 HIS Chi-restraints excluded: chain Y residue 30 CYS Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 22 VAL Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 32 LEU Chi-restraints excluded: chain c residue 13 THR Chi-restraints excluded: chain c residue 19 THR Chi-restraints excluded: chain c residue 20 CYS Chi-restraints excluded: chain d residue 19 THR Chi-restraints excluded: chain d residue 32 LEU Chi-restraints excluded: chain e residue 7 ARG Chi-restraints excluded: chain e residue 10 CYS Chi-restraints excluded: chain e residue 32 LEU Chi-restraints excluded: chain f residue 21 THR Chi-restraints excluded: chain f residue 32 LEU Chi-restraints excluded: chain g residue 12 SER Chi-restraints excluded: chain h residue 13 THR Chi-restraints excluded: chain h residue 28 ARG Chi-restraints excluded: chain i residue 7 ARG Chi-restraints excluded: chain i residue 19 THR Chi-restraints excluded: chain i residue 21 THR Chi-restraints excluded: chain j residue 16 SER Chi-restraints excluded: chain j residue 20 CYS Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain k residue 11 TYR Chi-restraints excluded: chain m residue 22 VAL Chi-restraints excluded: chain m residue 23 MET Chi-restraints excluded: chain m residue 31 CYS Chi-restraints excluded: chain n residue 9 SER Chi-restraints excluded: chain r residue 13 THR Chi-restraints excluded: chain r residue 14 GLU Chi-restraints excluded: chain t residue 11 TYR Chi-restraints excluded: chain t residue 16 SER Chi-restraints excluded: chain t residue 30 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 84 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 126 optimal weight: 0.1980 chunk 39 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 26 ASN P 26 ASN ** U 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 26 ASN p 5 HIS ** p 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.120750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.101463 restraints weight = 17694.775| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.64 r_work: 0.3269 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12832 Z= 0.108 Angle : 0.519 11.295 17401 Z= 0.285 Chirality : 0.038 0.133 1806 Planarity : 0.003 0.077 2112 Dihedral : 7.221 76.633 2031 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.32 % Favored : 98.61 % Rotamer: Outliers : 4.45 % Allowed : 26.94 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.21), residues: 1440 helix: None (None), residues: 0 sheet: -0.98 (0.18), residues: 774 loop : -0.96 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG J 8 TYR 0.022 0.001 TYR c 15 PHE 0.013 0.002 PHE m 29 HIS 0.007 0.001 HIS k 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (12688) covalent geometry : angle 0.51229 / 0.28 (17113) SS BOND : bond 0.00207 / 0.14 ( 144) SS BOND : angle 0.81695 / 0.53 ( 288) hydrogen bonds : bond 0.03018 / 2.01 ( 561) hydrogen bonds : angle 5.65430 / 3.91 ( 1803) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 315 time to evaluate : 0.511 Fit side-chains REVERT: C 8 ARG cc_start: 0.8396 (ttm-80) cc_final: 0.8020 (ptm160) REVERT: C 32 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7853 (pt) REVERT: D 28 ARG cc_start: 0.8610 (mmm160) cc_final: 0.8399 (mmp-170) REVERT: T 7 ARG cc_start: 0.9241 (OUTLIER) cc_final: 0.8430 (ptp-170) REVERT: V 7 ARG cc_start: 0.8625 (mtp85) cc_final: 0.8289 (mtt-85) REVERT: W 8 ARG cc_start: 0.7279 (OUTLIER) cc_final: 0.6978 (tpp80) REVERT: X 13 THR cc_start: 0.8793 (p) cc_final: 0.8356 (t) REVERT: d 28 ARG cc_start: 0.7897 (mmm160) cc_final: 0.7644 (mmm160) REVERT: g 8 ARG cc_start: 0.8252 (ttp-110) cc_final: 0.8044 (mtm-85) REVERT: h 21 THR cc_start: 0.9001 (m) cc_final: 0.8585 (p) REVERT: h 28 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7701 (mpt180) REVERT: n 15 TYR cc_start: 0.8102 (t80) cc_final: 0.7770 (t80) REVERT: n 28 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7423 (mmt90) REVERT: r 14 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7765 (pp20) outliers start: 62 outliers final: 41 residues processed: 354 average time/residue: 0.5532 time to fit residues: 213.4476 Evaluate side-chains 356 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 309 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 CYS Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain S residue 19 THR Chi-restraints excluded: chain T residue 7 ARG Chi-restraints excluded: chain U residue 20 CYS Chi-restraints excluded: chain V residue 20 CYS Chi-restraints excluded: chain W residue 8 ARG Chi-restraints excluded: chain W residue 10 CYS Chi-restraints excluded: chain W residue 16 SER Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain Y residue 30 CYS Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 22 VAL Chi-restraints excluded: chain b residue 32 LEU Chi-restraints excluded: chain c residue 13 THR Chi-restraints excluded: chain c residue 19 THR Chi-restraints excluded: chain c residue 20 CYS Chi-restraints excluded: chain d residue 19 THR Chi-restraints excluded: chain d residue 32 LEU Chi-restraints excluded: chain e residue 7 ARG Chi-restraints excluded: chain e residue 10 CYS Chi-restraints excluded: chain f residue 21 THR Chi-restraints excluded: chain f residue 32 LEU Chi-restraints excluded: chain h residue 28 ARG Chi-restraints excluded: chain i residue 19 THR Chi-restraints excluded: chain i residue 21 THR Chi-restraints excluded: chain j residue 16 SER Chi-restraints excluded: chain j residue 20 CYS Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain k residue 11 TYR Chi-restraints excluded: chain l residue 20 CYS Chi-restraints excluded: chain m residue 22 VAL Chi-restraints excluded: chain m residue 31 CYS Chi-restraints excluded: chain n residue 9 SER Chi-restraints excluded: chain n residue 28 ARG Chi-restraints excluded: chain q residue 3 THR Chi-restraints excluded: chain r residue 14 GLU Chi-restraints excluded: chain t residue 16 SER Chi-restraints excluded: chain t residue 30 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 116 optimal weight: 0.3980 chunk 29 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 103 optimal weight: 0.5980 chunk 118 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 109 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 3 optimal weight: 0.0870 chunk 114 optimal weight: 0.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 26 ASN P 26 ASN b 26 ASN k 26 ASN ** p 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.122583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.103265 restraints weight = 17706.147| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.64 r_work: 0.3286 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12832 Z= 0.094 Angle : 0.511 12.828 17401 Z= 0.280 Chirality : 0.037 0.131 1806 Planarity : 0.003 0.082 2112 Dihedral : 6.800 71.271 2029 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.32 % Favored : 98.61 % Rotamer: Outliers : 4.02 % Allowed : 27.66 % Favored : 68.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.21), residues: 1440 helix: None (None), residues: 0 sheet: -0.96 (0.18), residues: 774 loop : -0.92 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG J 8 TYR 0.013 0.001 TYR Q 15 PHE 0.013 0.001 PHE m 29 HIS 0.007 0.001 HIS k 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.09 (12688) covalent geometry : angle 0.50642 / 0.28 (17113) SS BOND : bond 0.00184 / 0.13 ( 144) SS BOND : angle 0.75296 / 0.49 ( 288) hydrogen bonds : bond 0.02888 / 1.92 ( 561) hydrogen bonds : angle 5.51202 / 3.82 ( 1803) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 317 time to evaluate : 0.499 Fit side-chains REVERT: C 8 ARG cc_start: 0.8346 (ttm-80) cc_final: 0.8010 (ptm160) REVERT: C 32 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7813 (pt) REVERT: D 28 ARG cc_start: 0.8599 (mmm160) cc_final: 0.8352 (mmp-170) REVERT: T 7 ARG cc_start: 0.9217 (OUTLIER) cc_final: 0.7738 (ptp-170) REVERT: V 7 ARG cc_start: 0.8582 (mtp85) cc_final: 0.8267 (mtt-85) REVERT: X 13 THR cc_start: 0.8601 (p) cc_final: 0.8227 (t) REVERT: f 32 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7175 (pt) REVERT: h 21 THR cc_start: 0.9008 (m) cc_final: 0.8604 (p) REVERT: n 15 TYR cc_start: 0.8087 (t80) cc_final: 0.7788 (t80) REVERT: n 28 ARG cc_start: 0.7899 (mmm160) cc_final: 0.7379 (mmt90) REVERT: q 14 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8215 (mt-10) REVERT: r 14 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7786 (pp20) outliers start: 56 outliers final: 40 residues processed: 355 average time/residue: 0.5316 time to fit residues: 206.1989 Evaluate side-chains 351 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 306 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 CYS Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain N residue 12 SER Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain S residue 19 THR Chi-restraints excluded: chain T residue 7 ARG Chi-restraints excluded: chain U residue 20 CYS Chi-restraints excluded: chain V residue 20 CYS Chi-restraints excluded: chain W residue 10 CYS Chi-restraints excluded: chain W residue 16 SER Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain Y residue 30 CYS Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 22 VAL Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 32 LEU Chi-restraints excluded: chain c residue 13 THR Chi-restraints excluded: chain c residue 19 THR Chi-restraints excluded: chain c residue 20 CYS Chi-restraints excluded: chain d residue 19 THR Chi-restraints excluded: chain d residue 32 LEU Chi-restraints excluded: chain e residue 7 ARG Chi-restraints excluded: chain e residue 10 CYS Chi-restraints excluded: chain f residue 21 THR Chi-restraints excluded: chain f residue 32 LEU Chi-restraints excluded: chain i residue 7 ARG Chi-restraints excluded: chain i residue 19 THR Chi-restraints excluded: chain j residue 20 CYS Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain l residue 20 CYS Chi-restraints excluded: chain m residue 22 VAL Chi-restraints excluded: chain m residue 31 CYS Chi-restraints excluded: chain n residue 9 SER Chi-restraints excluded: chain q residue 14 GLU Chi-restraints excluded: chain r residue 14 GLU Chi-restraints excluded: chain s residue 7 ARG Chi-restraints excluded: chain t residue 16 SER Chi-restraints excluded: chain t residue 23 MET Chi-restraints excluded: chain t residue 30 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 41 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 137 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 114 optimal weight: 0.9980 chunk 116 optimal weight: 8.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 26 ASN P 26 ASN ** U 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 26 ASN k 26 ASN ** p 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.120841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.101482 restraints weight = 17655.190| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.64 r_work: 0.3254 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12832 Z= 0.123 Angle : 0.535 11.778 17401 Z= 0.292 Chirality : 0.038 0.137 1806 Planarity : 0.003 0.044 2112 Dihedral : 6.947 68.111 2029 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.39 % Favored : 98.54 % Rotamer: Outliers : 3.88 % Allowed : 28.30 % Favored : 67.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.21), residues: 1440 helix: None (None), residues: 0 sheet: -0.93 (0.18), residues: 774 loop : -0.86 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG O 8 TYR 0.022 0.001 TYR c 15 PHE 0.016 0.002 PHE W 29 HIS 0.007 0.001 HIS k 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (12688) covalent geometry : angle 0.52880 / 0.29 (17113) SS BOND : bond 0.00230 / 0.16 ( 144) SS BOND : angle 0.84080 / 0.54 ( 288) hydrogen bonds : bond 0.03068 / 2.03 ( 561) hydrogen bonds : angle 5.61748 / 3.89 ( 1803) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2880 Ramachandran restraints generated. 1440 Oldfield, 0 Emsley, 1440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 311 time to evaluate : 0.553 Fit side-chains REVERT: A 14 GLU cc_start: 0.9031 (mt-10) cc_final: 0.8795 (mt-10) REVERT: C 8 ARG cc_start: 0.8413 (ttm-80) cc_final: 0.8045 (ptm160) REVERT: C 32 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7840 (pt) REVERT: D 28 ARG cc_start: 0.8630 (mmm160) cc_final: 0.8422 (mmp-170) REVERT: Q 23 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.7512 (mtp) REVERT: T 7 ARG cc_start: 0.9249 (OUTLIER) cc_final: 0.8444 (ptp-170) REVERT: W 8 ARG cc_start: 0.7231 (OUTLIER) cc_final: 0.6824 (tpp80) REVERT: X 13 THR cc_start: 0.8571 (p) cc_final: 0.8184 (t) REVERT: Z 17 TYR cc_start: 0.8930 (m-80) cc_final: 0.8706 (m-80) REVERT: n 15 TYR cc_start: 0.8108 (t80) cc_final: 0.7765 (t80) REVERT: n 28 ARG cc_start: 0.7950 (mmm160) cc_final: 0.7429 (mmt90) REVERT: r 14 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7768 (pp20) REVERT: u 23 MET cc_start: 0.8140 (mmt) cc_final: 0.7850 (mmt) outliers start: 54 outliers final: 43 residues processed: 347 average time/residue: 0.5401 time to fit residues: 204.5116 Evaluate side-chains 353 residues out of total 1392 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 305 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 CYS Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain N residue 12 SER Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain Q residue 23 MET Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain S residue 19 THR Chi-restraints excluded: chain T residue 7 ARG Chi-restraints excluded: chain U residue 20 CYS Chi-restraints excluded: chain V residue 20 CYS Chi-restraints excluded: chain W residue 8 ARG Chi-restraints excluded: chain W residue 10 CYS Chi-restraints excluded: chain W residue 16 SER Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain Y residue 30 CYS Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 22 VAL Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 32 LEU Chi-restraints excluded: chain c residue 13 THR Chi-restraints excluded: chain c residue 19 THR Chi-restraints excluded: chain c residue 20 CYS Chi-restraints excluded: chain d residue 19 THR Chi-restraints excluded: chain d residue 32 LEU Chi-restraints excluded: chain e residue 7 ARG Chi-restraints excluded: chain e residue 10 CYS Chi-restraints excluded: chain f residue 21 THR Chi-restraints excluded: chain f residue 32 LEU Chi-restraints excluded: chain i residue 7 ARG Chi-restraints excluded: chain i residue 19 THR Chi-restraints excluded: chain j residue 20 CYS Chi-restraints excluded: chain j residue 32 LEU Chi-restraints excluded: chain k residue 11 TYR Chi-restraints excluded: chain l residue 20 CYS Chi-restraints excluded: chain m residue 22 VAL Chi-restraints excluded: chain m residue 31 CYS Chi-restraints excluded: chain n residue 9 SER Chi-restraints excluded: chain r residue 14 GLU Chi-restraints excluded: chain s residue 7 ARG Chi-restraints excluded: chain t residue 16 SER Chi-restraints excluded: chain t residue 30 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 7 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 19 optimal weight: 0.4980 chunk 34 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 26 ASN P 26 ASN ** U 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 26 ASN k 26 ASN ** p 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.120001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.100636 restraints weight = 17632.907| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.66 r_work: 0.3236 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12832 Z= 0.137 Angle : 0.553 13.227 17401 Z= 0.300 Chirality : 0.039 0.142 1806 Planarity : 0.004 0.081 2112 Dihedral : 7.073 65.042 2029 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.46 % Favored : 98.47 % Rotamer: Outliers : 3.88 % Allowed : 28.09 % Favored : 68.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.21), residues: 1440 helix: None (None), residues: 0 sheet: -0.90 (0.18), residues: 774 loop : -0.85 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG J 8 TYR 0.011 0.001 TYR d 11 PHE 0.014 0.002 PHE m 29 HIS 0.007 0.001 HIS k 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (12688) covalent geometry : angle 0.54569 / 0.30 (17113) SS BOND : bond 0.00251 / 0.17 ( 144) SS BOND : angle 0.88590 / 0.57 ( 288) hydrogen bonds : bond 0.03157 / 2.09 ( 561) hydrogen bonds : angle 5.69789 / 3.93 ( 1803) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5128.15 seconds wall clock time: 88 minutes 16.86 seconds (5296.86 seconds total)