Starting phenix.real_space_refine on Sun Aug 9 16:15:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vwi_65397/08_2026/9vwi_65397.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vwi_65397/08_2026/9vwi_65397.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vwi_65397/08_2026/9vwi_65397.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vwi_65397/08_2026/9vwi_65397.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vwi_65397/08_2026/9vwi_65397.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vwi_65397/08_2026/9vwi_65397.map" } resolution = 1.82 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= 0.001 sd= 0.010 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: 4 Type Number sf(0) Gaussians S 384 5.16 5 C 21648 2.51 5 N 6336 2.21 5 O 7320 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 139 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35688 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1487 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain: "B" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1487 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain: "C" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1487 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain: "D" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1487 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain: "E" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1487 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain: "F" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1487 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain: "G" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1487 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain: "H" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1487 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain: "I" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1487 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain: "J" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1487 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain: "K" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1487 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain: "L" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1487 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain: "M" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1487 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain: "N" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1487 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain: "O" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1487 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain: "P" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1487 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain: "Q" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1487 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain: "R" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1487 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain: "S" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1487 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain: "T" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1487 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain: "U" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1487 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain: "V" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1487 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain: "W" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1487 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Chain: "X" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1487 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 6, 'TRANS': 188} Time building chain proxies: 7.14, per 1000 atoms: 0.20 Number of scatterers: 35688 At special positions: 0 Unit cell: (142.628, 142.628, 142.628, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 384 16.00 O 7320 8.00 N 6336 7.00 C 21648 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=192, symmetry=0 Simple disulfide: pdb=" SG CYS A 6 " - pdb=" SG CYS A 37 " distance=2.03 Simple disulfide: pdb=" SG CYS A 17 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 51 " - pdb=" SG CYS A 83 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 70 " distance=2.04 Simple disulfide: pdb=" SG CYS A 105 " - pdb=" SG CYS A 134 " distance=2.04 Simple disulfide: pdb=" SG CYS A 114 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS A 148 " - pdb=" SG CYS A 181 " distance=2.03 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 168 " distance=2.04 Simple disulfide: pdb=" SG CYS B 6 " - pdb=" SG CYS B 37 " distance=2.04 Simple disulfide: pdb=" SG CYS B 17 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 51 " - pdb=" SG CYS B 83 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 70 " distance=2.04 Simple disulfide: pdb=" SG CYS B 105 " - pdb=" SG CYS B 134 " distance=2.03 Simple disulfide: pdb=" SG CYS B 114 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 148 " - pdb=" SG CYS B 181 " distance=2.03 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 168 " distance=2.04 Simple disulfide: pdb=" SG CYS C 6 " - pdb=" SG CYS C 37 " distance=2.04 Simple disulfide: pdb=" SG CYS C 17 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 51 " - pdb=" SG CYS C 83 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 70 " distance=2.04 Simple disulfide: pdb=" SG CYS C 105 " - pdb=" SG CYS C 134 " distance=2.03 Simple disulfide: pdb=" SG CYS C 114 " - pdb=" SG CYS C 194 " distance=2.03 Simple disulfide: pdb=" SG CYS C 148 " - pdb=" SG CYS C 181 " distance=2.03 Simple disulfide: pdb=" SG CYS C 162 " - pdb=" SG CYS C 168 " distance=2.04 Simple disulfide: pdb=" SG CYS D 6 " - pdb=" SG CYS D 37 " distance=2.04 Simple disulfide: pdb=" SG CYS D 17 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 51 " - pdb=" SG CYS D 83 " distance=2.03 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 70 " distance=2.04 Simple disulfide: pdb=" SG CYS D 105 " - pdb=" SG CYS D 134 " distance=2.03 Simple disulfide: pdb=" SG CYS D 114 " - pdb=" SG CYS D 194 " distance=2.03 Simple disulfide: pdb=" SG CYS D 148 " - pdb=" SG CYS D 181 " distance=2.03 Simple disulfide: pdb=" SG CYS D 162 " - pdb=" SG CYS D 168 " distance=2.04 Simple disulfide: pdb=" SG CYS E 6 " - pdb=" SG CYS E 37 " distance=2.04 Simple disulfide: pdb=" SG CYS E 17 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 51 " - pdb=" SG CYS E 83 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 70 " distance=2.04 Simple disulfide: pdb=" SG CYS E 105 " - pdb=" SG CYS E 134 " distance=2.03 Simple disulfide: pdb=" SG CYS E 114 " - pdb=" SG CYS E 194 " distance=2.02 Simple disulfide: pdb=" SG CYS E 148 " - pdb=" SG CYS E 181 " distance=2.03 Simple disulfide: pdb=" SG CYS E 162 " - pdb=" SG CYS E 168 " distance=2.04 Simple disulfide: pdb=" SG CYS F 6 " - pdb=" SG CYS F 37 " distance=2.04 Simple disulfide: pdb=" SG CYS F 17 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 51 " - pdb=" SG CYS F 83 " distance=2.03 Simple disulfide: pdb=" SG CYS F 64 " - pdb=" SG CYS F 70 " distance=2.04 Simple disulfide: pdb=" SG CYS F 105 " - pdb=" SG CYS F 134 " distance=2.03 Simple disulfide: pdb=" SG CYS F 114 " - pdb=" SG CYS F 194 " distance=2.03 Simple disulfide: pdb=" SG CYS F 148 " - pdb=" SG CYS F 181 " distance=2.03 Simple disulfide: pdb=" SG CYS F 162 " - pdb=" SG CYS F 168 " distance=2.04 Simple disulfide: pdb=" SG CYS G 6 " - pdb=" SG CYS G 37 " distance=2.04 Simple disulfide: pdb=" SG CYS G 17 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 51 " - pdb=" SG CYS G 83 " distance=2.03 Simple disulfide: pdb=" SG CYS G 64 " - pdb=" SG CYS G 70 " distance=2.04 Simple disulfide: pdb=" SG CYS G 105 " - pdb=" SG CYS G 134 " distance=2.03 Simple disulfide: pdb=" SG CYS G 114 " - pdb=" SG CYS G 194 " distance=2.03 Simple disulfide: pdb=" SG CYS G 148 " - pdb=" SG CYS G 181 " distance=2.03 Simple disulfide: pdb=" SG CYS G 162 " - pdb=" SG CYS G 168 " distance=2.04 Simple disulfide: pdb=" SG CYS H 6 " - pdb=" SG CYS H 37 " distance=2.04 Simple disulfide: pdb=" SG CYS H 17 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 51 " - pdb=" SG CYS H 83 " distance=2.03 Simple disulfide: pdb=" SG CYS H 64 " - pdb=" SG CYS H 70 " distance=2.04 Simple disulfide: pdb=" SG CYS H 105 " - pdb=" SG CYS H 134 " distance=2.03 Simple disulfide: pdb=" SG CYS H 114 " - pdb=" SG CYS H 194 " distance=2.03 Simple disulfide: pdb=" SG CYS H 148 " - pdb=" SG CYS H 181 " distance=2.03 Simple disulfide: pdb=" SG CYS H 162 " - pdb=" SG CYS H 168 " distance=2.03 Simple disulfide: pdb=" SG CYS I 6 " - pdb=" SG CYS I 37 " distance=2.04 Simple disulfide: pdb=" SG CYS I 17 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 51 " - pdb=" SG CYS I 83 " distance=2.03 Simple disulfide: pdb=" SG CYS I 64 " - pdb=" SG CYS I 70 " distance=2.04 Simple disulfide: pdb=" SG CYS I 105 " - pdb=" SG CYS I 134 " distance=2.03 Simple disulfide: pdb=" SG CYS I 114 " - pdb=" SG CYS I 194 " distance=2.03 Simple disulfide: pdb=" SG CYS I 148 " - pdb=" SG CYS I 181 " distance=2.03 Simple disulfide: pdb=" SG CYS I 162 " - pdb=" SG CYS I 168 " distance=2.03 Simple disulfide: pdb=" SG CYS J 6 " - pdb=" SG CYS J 37 " distance=2.04 Simple disulfide: pdb=" SG CYS J 17 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 51 " - pdb=" SG CYS J 83 " distance=2.03 Simple disulfide: pdb=" SG CYS J 64 " - pdb=" SG CYS J 70 " distance=2.04 Simple disulfide: pdb=" SG CYS J 105 " - pdb=" SG CYS J 134 " distance=2.03 Simple disulfide: pdb=" SG CYS J 114 " - pdb=" SG CYS J 194 " distance=2.03 Simple disulfide: pdb=" SG CYS J 148 " - pdb=" SG CYS J 181 " distance=2.03 Simple disulfide: pdb=" SG CYS J 162 " - pdb=" SG CYS J 168 " distance=2.03 Simple disulfide: pdb=" SG CYS K 6 " - pdb=" SG CYS K 37 " distance=2.04 Simple disulfide: pdb=" SG CYS K 17 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 51 " - pdb=" SG CYS K 83 " distance=2.03 Simple disulfide: pdb=" SG CYS K 64 " - pdb=" SG CYS K 70 " distance=2.04 Simple disulfide: pdb=" SG CYS K 105 " - pdb=" SG CYS K 134 " distance=2.03 Simple disulfide: pdb=" SG CYS K 114 " - pdb=" SG CYS K 194 " distance=2.03 Simple disulfide: pdb=" SG CYS K 148 " - pdb=" SG CYS K 181 " distance=2.03 Simple disulfide: pdb=" SG CYS K 162 " - pdb=" SG CYS K 168 " distance=2.03 Simple disulfide: pdb=" SG CYS L 6 " - pdb=" SG CYS L 37 " distance=2.04 Simple disulfide: pdb=" SG CYS L 17 " - pdb=" SG CYS L 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 51 " - pdb=" SG CYS L 83 " distance=2.03 Simple disulfide: pdb=" SG CYS L 64 " - pdb=" SG CYS L 70 " distance=2.04 Simple disulfide: pdb=" SG CYS L 105 " - pdb=" SG CYS L 134 " distance=2.03 Simple disulfide: pdb=" SG CYS L 114 " - pdb=" SG CYS L 194 " distance=2.03 Simple disulfide: pdb=" SG CYS L 148 " - pdb=" SG CYS L 181 " distance=2.03 Simple disulfide: pdb=" SG CYS L 162 " - pdb=" SG CYS L 168 " distance=2.04 Simple disulfide: pdb=" SG CYS M 6 " - pdb=" SG CYS M 37 " distance=2.04 Simple disulfide: pdb=" SG CYS M 17 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS M 51 " - pdb=" SG CYS M 83 " distance=2.03 Simple disulfide: pdb=" SG CYS M 64 " - pdb=" SG CYS M 70 " distance=2.04 Simple disulfide: pdb=" SG CYS M 105 " - pdb=" SG CYS M 134 " distance=2.03 Simple disulfide: pdb=" SG CYS M 114 " - pdb=" SG CYS M 194 " distance=2.03 Simple disulfide: pdb=" SG CYS M 148 " - pdb=" SG CYS M 181 " distance=2.03 Simple disulfide: pdb=" SG CYS M 162 " - pdb=" SG CYS M 168 " distance=2.03 Simple disulfide: pdb=" SG CYS N 6 " - pdb=" SG CYS N 37 " distance=2.04 Simple disulfide: pdb=" SG CYS N 17 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 51 " - pdb=" SG CYS N 83 " distance=2.03 Simple disulfide: pdb=" SG CYS N 64 " - pdb=" SG CYS N 70 " distance=2.04 Simple disulfide: pdb=" SG CYS N 105 " - pdb=" SG CYS N 134 " distance=2.03 Simple disulfide: pdb=" SG CYS N 114 " - pdb=" SG CYS N 194 " distance=2.03 Simple disulfide: pdb=" SG CYS N 148 " - pdb=" SG CYS N 181 " distance=2.03 Simple disulfide: pdb=" SG CYS N 162 " - pdb=" SG CYS N 168 " distance=2.03 Simple disulfide: pdb=" SG CYS O 6 " - pdb=" SG CYS O 37 " distance=2.04 Simple disulfide: pdb=" SG CYS O 17 " - pdb=" SG CYS O 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 51 " - pdb=" SG CYS O 83 " distance=2.03 Simple disulfide: pdb=" SG CYS O 64 " - pdb=" SG CYS O 70 " distance=2.04 Simple disulfide: pdb=" SG CYS O 105 " - pdb=" SG CYS O 134 " distance=2.03 Simple disulfide: pdb=" SG CYS O 114 " - pdb=" SG CYS O 194 " distance=2.03 Simple disulfide: pdb=" SG CYS O 148 " - pdb=" SG CYS O 181 " distance=2.03 Simple disulfide: pdb=" SG CYS O 162 " - pdb=" SG CYS O 168 " distance=2.04 Simple disulfide: pdb=" SG CYS P 6 " - pdb=" SG CYS P 37 " distance=2.04 Simple disulfide: pdb=" SG CYS P 17 " - pdb=" SG CYS P 96 " distance=2.03 Simple disulfide: pdb=" SG CYS P 51 " - pdb=" SG CYS P 83 " distance=2.03 Simple disulfide: pdb=" SG CYS P 64 " - pdb=" SG CYS P 70 " distance=2.04 Simple disulfide: pdb=" SG CYS P 105 " - pdb=" SG CYS P 134 " distance=2.03 Simple disulfide: pdb=" SG CYS P 114 " - pdb=" SG CYS P 194 " distance=2.03 Simple disulfide: pdb=" SG CYS P 148 " - pdb=" SG CYS P 181 " distance=2.03 Simple disulfide: pdb=" SG CYS P 162 " - pdb=" SG CYS P 168 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 6 " - pdb=" SG CYS Q 37 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 17 " - pdb=" SG CYS Q 96 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 51 " - pdb=" SG CYS Q 83 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 64 " - pdb=" SG CYS Q 70 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 105 " - pdb=" SG CYS Q 134 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 114 " - pdb=" SG CYS Q 194 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 148 " - pdb=" SG CYS Q 181 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 162 " - pdb=" SG CYS Q 168 " distance=2.04 Simple disulfide: pdb=" SG CYS R 6 " - pdb=" SG CYS R 37 " distance=2.04 Simple disulfide: pdb=" SG CYS R 17 " - pdb=" SG CYS R 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 51 " - pdb=" SG CYS R 83 " distance=2.03 Simple disulfide: pdb=" SG CYS R 64 " - pdb=" SG CYS R 70 " distance=2.04 Simple disulfide: pdb=" SG CYS R 105 " - pdb=" SG CYS R 134 " distance=2.03 Simple disulfide: pdb=" SG CYS R 114 " - pdb=" SG CYS R 194 " distance=2.03 Simple disulfide: pdb=" SG CYS R 148 " - pdb=" SG CYS R 181 " distance=2.03 Simple disulfide: pdb=" SG CYS R 162 " - pdb=" SG CYS R 168 " distance=2.03 Simple disulfide: pdb=" SG CYS S 6 " - pdb=" SG CYS S 37 " distance=2.04 Simple disulfide: pdb=" SG CYS S 17 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 51 " - pdb=" SG CYS S 83 " distance=2.03 Simple disulfide: pdb=" SG CYS S 64 " - pdb=" SG CYS S 70 " distance=2.04 Simple disulfide: pdb=" SG CYS S 105 " - pdb=" SG CYS S 134 " distance=2.03 Simple disulfide: pdb=" SG CYS S 114 " - pdb=" SG CYS S 194 " distance=2.03 Simple disulfide: pdb=" SG CYS S 148 " - pdb=" SG CYS S 181 " distance=2.03 Simple disulfide: pdb=" SG CYS S 162 " - pdb=" SG CYS S 168 " distance=2.04 Simple disulfide: pdb=" SG CYS T 6 " - pdb=" SG CYS T 37 " distance=2.04 Simple disulfide: pdb=" SG CYS T 17 " - pdb=" SG CYS T 96 " distance=2.03 Simple disulfide: pdb=" SG CYS T 51 " - pdb=" SG CYS T 83 " distance=2.03 Simple disulfide: pdb=" SG CYS T 64 " - pdb=" SG CYS T 70 " distance=2.04 Simple disulfide: pdb=" SG CYS T 105 " - pdb=" SG CYS T 134 " distance=2.03 Simple disulfide: pdb=" SG CYS T 114 " - pdb=" SG CYS T 194 " distance=2.03 Simple disulfide: pdb=" SG CYS T 148 " - pdb=" SG CYS T 181 " distance=2.03 Simple disulfide: pdb=" SG CYS T 162 " - pdb=" SG CYS T 168 " distance=2.03 Simple disulfide: pdb=" SG CYS U 6 " - pdb=" SG CYS U 37 " distance=2.04 Simple disulfide: pdb=" SG CYS U 17 " - pdb=" SG CYS U 96 " distance=2.03 Simple disulfide: pdb=" SG CYS U 51 " - pdb=" SG CYS U 83 " distance=2.03 Simple disulfide: pdb=" SG CYS U 64 " - pdb=" SG CYS U 70 " distance=2.04 Simple disulfide: pdb=" SG CYS U 105 " - pdb=" SG CYS U 134 " distance=2.03 Simple disulfide: pdb=" SG CYS U 114 " - pdb=" SG CYS U 194 " distance=2.03 Simple disulfide: pdb=" SG CYS U 148 " - pdb=" SG CYS U 181 " distance=2.03 Simple disulfide: pdb=" SG CYS U 162 " - pdb=" SG CYS U 168 " distance=2.03 Simple disulfide: pdb=" SG CYS V 6 " - pdb=" SG CYS V 37 " distance=2.04 Simple disulfide: pdb=" SG CYS V 17 " - pdb=" SG CYS V 96 " distance=2.03 Simple disulfide: pdb=" SG CYS V 51 " - pdb=" SG CYS V 83 " distance=2.03 Simple disulfide: pdb=" SG CYS V 64 " - pdb=" SG CYS V 70 " distance=2.04 Simple disulfide: pdb=" SG CYS V 105 " - pdb=" SG CYS V 134 " distance=2.03 Simple disulfide: pdb=" SG CYS V 114 " - pdb=" SG CYS V 194 " distance=2.03 Simple disulfide: pdb=" SG CYS V 148 " - pdb=" SG CYS V 181 " distance=2.03 Simple disulfide: pdb=" SG CYS V 162 " - pdb=" SG CYS V 168 " distance=2.03 Simple disulfide: pdb=" SG CYS W 6 " - pdb=" SG CYS W 37 " distance=2.04 Simple disulfide: pdb=" SG CYS W 17 " - pdb=" SG CYS W 96 " distance=2.03 Simple disulfide: pdb=" SG CYS W 51 " - pdb=" SG CYS W 83 " distance=2.03 Simple disulfide: pdb=" SG CYS W 64 " - pdb=" SG CYS W 70 " distance=2.04 Simple disulfide: pdb=" SG CYS W 105 " - pdb=" SG CYS W 134 " distance=2.03 Simple disulfide: pdb=" SG CYS W 114 " - pdb=" SG CYS W 194 " distance=2.03 Simple disulfide: pdb=" SG CYS W 148 " - pdb=" SG CYS W 181 " distance=2.03 Simple disulfide: pdb=" SG CYS W 162 " - pdb=" SG CYS W 168 " distance=2.04 Simple disulfide: pdb=" SG CYS X 6 " - pdb=" SG CYS X 37 " distance=2.04 Simple disulfide: pdb=" SG CYS X 17 " - pdb=" SG CYS X 96 " distance=2.03 Simple disulfide: pdb=" SG CYS X 51 " - pdb=" SG CYS X 83 " distance=2.03 Simple disulfide: pdb=" SG CYS X 64 " - pdb=" SG CYS X 70 " distance=2.04 Simple disulfide: pdb=" SG CYS X 105 " - pdb=" SG CYS X 134 " distance=2.03 Simple disulfide: pdb=" SG CYS X 114 " - pdb=" SG CYS X 194 " distance=2.03 Simple disulfide: pdb=" SG CYS X 148 " - pdb=" SG CYS X 181 " distance=2.03 Simple disulfide: pdb=" SG CYS X 162 " - pdb=" SG CYS X 168 " 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: 2.46 Conformation dependent library (CDL) restraints added in 1.2 seconds 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8688 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 72 sheets defined 23.1% alpha, 31.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 42 through 46 Processing helix chain 'A' and resid 55 through 65 Processing helix chain 'A' and resid 75 through 78 Processing helix chain 'A' and resid 139 through 143 Processing helix chain 'A' and resid 150 through 163 Processing helix chain 'A' and resid 173 through 178 removed outlier: 3.502A pdb=" N TYR A 177 " --> pdb=" O SER A 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 46 Processing helix chain 'B' and resid 55 through 65 Processing helix chain 'B' and resid 75 through 78 Processing helix chain 'B' and resid 139 through 143 Processing helix chain 'B' and resid 150 through 163 Processing helix chain 'B' and resid 173 through 178 removed outlier: 3.502A pdb=" N TYR B 177 " --> pdb=" O SER B 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 46 Processing helix chain 'C' and resid 55 through 65 Processing helix chain 'C' and resid 75 through 78 Processing helix chain 'C' and resid 139 through 143 Processing helix chain 'C' and resid 150 through 163 Processing helix chain 'C' and resid 173 through 178 removed outlier: 3.502A pdb=" N TYR C 177 " --> pdb=" O SER C 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 46 Processing helix chain 'D' and resid 55 through 65 Processing helix chain 'D' and resid 75 through 78 Processing helix chain 'D' and resid 139 through 143 Processing helix chain 'D' and resid 150 through 163 Processing helix chain 'D' and resid 173 through 178 removed outlier: 3.502A pdb=" N TYR D 177 " --> pdb=" O SER D 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 46 Processing helix chain 'E' and resid 55 through 65 Processing helix chain 'E' and resid 75 through 78 Processing helix chain 'E' and resid 139 through 143 Processing helix chain 'E' and resid 150 through 163 Processing helix chain 'E' and resid 173 through 178 removed outlier: 3.502A pdb=" N TYR E 177 " --> pdb=" O SER E 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 46 Processing helix chain 'F' and resid 55 through 65 Processing helix chain 'F' and resid 75 through 78 Processing helix chain 'F' and resid 139 through 143 Processing helix chain 'F' and resid 150 through 163 Processing helix chain 'F' and resid 173 through 178 removed outlier: 3.502A pdb=" N TYR F 177 " --> pdb=" O SER F 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 46 Processing helix chain 'G' and resid 55 through 65 Processing helix chain 'G' and resid 75 through 78 Processing helix chain 'G' and resid 139 through 143 Processing helix chain 'G' and resid 150 through 163 Processing helix chain 'G' and resid 173 through 178 removed outlier: 3.502A pdb=" N TYR G 177 " --> pdb=" O SER G 173 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 46 Processing helix chain 'H' and resid 55 through 65 Processing helix chain 'H' and resid 75 through 78 Processing helix chain 'H' and resid 139 through 143 Processing helix chain 'H' and resid 150 through 163 Processing helix chain 'H' and resid 173 through 178 removed outlier: 3.502A pdb=" N TYR H 177 " --> pdb=" O SER H 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 46 Processing helix chain 'I' and resid 55 through 65 Processing helix chain 'I' and resid 75 through 78 Processing helix chain 'I' and resid 139 through 143 Processing helix chain 'I' and resid 150 through 163 Processing helix chain 'I' and resid 173 through 178 removed outlier: 3.502A pdb=" N TYR I 177 " --> pdb=" O SER I 173 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 46 Processing helix chain 'J' and resid 55 through 65 Processing helix chain 'J' and resid 75 through 78 Processing helix chain 'J' and resid 139 through 143 Processing helix chain 'J' and resid 150 through 163 Processing helix chain 'J' and resid 173 through 178 removed outlier: 3.502A pdb=" N TYR J 177 " --> pdb=" O SER J 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 42 through 46 Processing helix chain 'K' and resid 55 through 65 Processing helix chain 'K' and resid 75 through 78 Processing helix chain 'K' and resid 139 through 143 Processing helix chain 'K' and resid 150 through 163 Processing helix chain 'K' and resid 173 through 178 removed outlier: 3.502A pdb=" N TYR K 177 " --> pdb=" O SER K 173 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 46 Processing helix chain 'L' and resid 55 through 65 Processing helix chain 'L' and resid 75 through 78 Processing helix chain 'L' and resid 139 through 143 Processing helix chain 'L' and resid 150 through 163 Processing helix chain 'L' and resid 173 through 178 removed outlier: 3.502A pdb=" N TYR L 177 " --> pdb=" O SER L 173 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 46 Processing helix chain 'M' and resid 55 through 65 Processing helix chain 'M' and resid 75 through 78 Processing helix chain 'M' and resid 139 through 143 Processing helix chain 'M' and resid 150 through 163 Processing helix chain 'M' and resid 173 through 178 removed outlier: 3.502A pdb=" N TYR M 177 " --> pdb=" O SER M 173 " (cutoff:3.500A) Processing helix chain 'N' and resid 42 through 46 Processing helix chain 'N' and resid 55 through 65 Processing helix chain 'N' and resid 75 through 78 Processing helix chain 'N' and resid 139 through 143 Processing helix chain 'N' and resid 150 through 163 Processing helix chain 'N' and resid 173 through 178 removed outlier: 3.502A pdb=" N TYR N 177 " --> pdb=" O SER N 173 " (cutoff:3.500A) Processing helix chain 'O' and resid 42 through 46 Processing helix chain 'O' and resid 55 through 65 Processing helix chain 'O' and resid 75 through 78 Processing helix chain 'O' and resid 139 through 143 Processing helix chain 'O' and resid 150 through 163 Processing helix chain 'O' and resid 173 through 178 removed outlier: 3.502A pdb=" N TYR O 177 " --> pdb=" O SER O 173 " (cutoff:3.500A) Processing helix chain 'P' and resid 42 through 46 Processing helix chain 'P' and resid 55 through 65 Processing helix chain 'P' and resid 75 through 78 Processing helix chain 'P' and resid 139 through 143 Processing helix chain 'P' and resid 150 through 163 Processing helix chain 'P' and resid 173 through 178 removed outlier: 3.502A pdb=" N TYR P 177 " --> pdb=" O SER P 173 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 46 Processing helix chain 'Q' and resid 55 through 65 Processing helix chain 'Q' and resid 75 through 78 Processing helix chain 'Q' and resid 139 through 143 Processing helix chain 'Q' and resid 150 through 163 Processing helix chain 'Q' and resid 173 through 178 removed outlier: 3.502A pdb=" N TYR Q 177 " --> pdb=" O SER Q 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 46 Processing helix chain 'R' and resid 55 through 65 Processing helix chain 'R' and resid 75 through 78 Processing helix chain 'R' and resid 139 through 143 Processing helix chain 'R' and resid 150 through 163 removed outlier: 3.521A pdb=" N SER R 156 " --> pdb=" O SER R 152 " (cutoff:3.500A) Processing helix chain 'R' and resid 173 through 178 removed outlier: 3.502A pdb=" N TYR R 177 " --> pdb=" O SER R 173 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 46 Processing helix chain 'S' and resid 55 through 65 Processing helix chain 'S' and resid 75 through 78 Processing helix chain 'S' and resid 139 through 143 Processing helix chain 'S' and resid 150 through 163 Processing helix chain 'S' and resid 173 through 178 removed outlier: 3.502A pdb=" N TYR S 177 " --> pdb=" O SER S 173 " (cutoff:3.500A) Processing helix chain 'T' and resid 42 through 46 Processing helix chain 'T' and resid 55 through 65 Processing helix chain 'T' and resid 75 through 78 Processing helix chain 'T' and resid 139 through 143 Processing helix chain 'T' and resid 150 through 163 Processing helix chain 'T' and resid 173 through 178 removed outlier: 3.502A pdb=" N TYR T 177 " --> pdb=" O SER T 173 " (cutoff:3.500A) Processing helix chain 'U' and resid 42 through 46 Processing helix chain 'U' and resid 55 through 65 Processing helix chain 'U' and resid 75 through 78 Processing helix chain 'U' and resid 139 through 143 Processing helix chain 'U' and resid 150 through 163 Processing helix chain 'U' and resid 173 through 178 removed outlier: 3.502A pdb=" N TYR U 177 " --> pdb=" O SER U 173 " (cutoff:3.500A) Processing helix chain 'V' and resid 42 through 46 Processing helix chain 'V' and resid 55 through 65 Processing helix chain 'V' and resid 75 through 78 Processing helix chain 'V' and resid 139 through 143 Processing helix chain 'V' and resid 150 through 163 Processing helix chain 'V' and resid 173 through 178 removed outlier: 3.502A pdb=" N TYR V 177 " --> pdb=" O SER V 173 " (cutoff:3.500A) Processing helix chain 'W' and resid 42 through 46 Processing helix chain 'W' and resid 55 through 65 Processing helix chain 'W' and resid 75 through 78 Processing helix chain 'W' and resid 139 through 143 Processing helix chain 'W' and resid 150 through 163 Processing helix chain 'W' and resid 173 through 178 removed outlier: 3.502A pdb=" N TYR W 177 " --> pdb=" O SER W 173 " (cutoff:3.500A) Processing helix chain 'X' and resid 42 through 46 Processing helix chain 'X' and resid 55 through 65 Processing helix chain 'X' and resid 75 through 78 Processing helix chain 'X' and resid 139 through 143 Processing helix chain 'X' and resid 150 through 163 Processing helix chain 'X' and resid 173 through 178 removed outlier: 3.502A pdb=" N TYR X 177 " --> pdb=" O SER X 173 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 52 removed outlier: 5.616A pdb=" N ILE A 22 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU A 97 " --> pdb=" O ILE A 22 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ILE A 24 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THR A 95 " --> pdb=" O ILE A 24 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ARG A 2 " --> pdb=" O LEU N 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 12 through 16 Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 105 removed outlier: 6.486A pdb=" N THR A 193 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ILE A 121 " --> pdb=" O THR A 193 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLY A 195 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ILE A 119 " --> pdb=" O GLY A 195 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 167 through 171 removed outlier: 3.561A pdb=" N LEU A 111 " --> pdb=" O ARG P 2 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ARG P 2 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THR P 95 " --> pdb=" O ILE P 24 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ILE P 24 " --> pdb=" O THR P 95 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU P 97 " --> pdb=" O ILE P 22 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ILE P 22 " --> pdb=" O LEU P 97 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 52 removed outlier: 5.650A pdb=" N ILE B 22 " --> pdb=" O LEU B 97 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU B 97 " --> pdb=" O ILE B 22 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ILE B 24 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THR B 95 " --> pdb=" O ILE B 24 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N ARG B 2 " --> pdb=" O LEU Q 111 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 12 through 16 Processing sheet with id=AA7, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.220A pdb=" N TYR B 187 " --> pdb=" O TYR B 126 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N TYR B 126 " --> pdb=" O TYR B 187 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ASP B 189 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA B 124 " --> pdb=" O ASP B 189 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ALA B 191 " --> pdb=" O HIS B 122 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 167 through 171 removed outlier: 5.005A pdb=" N ARG X 2 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THR X 95 " --> pdb=" O ILE X 24 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ILE X 24 " --> pdb=" O THR X 95 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU X 97 " --> pdb=" O ILE X 22 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ILE X 22 " --> pdb=" O LEU X 97 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 51 through 52 removed outlier: 5.650A pdb=" N ILE C 22 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU C 97 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ILE C 24 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THR C 95 " --> pdb=" O ILE C 24 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ARG C 2 " --> pdb=" O LEU O 111 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 12 through 16 Processing sheet with id=AB2, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.486A pdb=" N THR C 193 " --> pdb=" O ILE C 121 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ILE C 121 " --> pdb=" O THR C 193 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLY C 195 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ILE C 119 " --> pdb=" O GLY C 195 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 167 through 171 removed outlier: 4.998A pdb=" N ARG G 2 " --> pdb=" O LEU C 111 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THR G 95 " --> pdb=" O ILE G 24 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ILE G 24 " --> pdb=" O THR G 95 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU G 97 " --> pdb=" O ILE G 22 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ILE G 22 " --> pdb=" O LEU G 97 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 51 through 52 removed outlier: 5.650A pdb=" N ILE D 22 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU D 97 " --> pdb=" O ILE D 22 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ILE D 24 " --> pdb=" O THR D 95 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THR D 95 " --> pdb=" O ILE D 24 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N ARG D 2 " --> pdb=" O LEU U 111 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU U 111 " --> pdb=" O ARG D 2 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 12 through 16 Processing sheet with id=AB6, first strand: chain 'D' and resid 100 through 105 removed outlier: 6.220A pdb=" N TYR D 187 " --> pdb=" O TYR D 126 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N TYR D 126 " --> pdb=" O TYR D 187 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ASP D 189 " --> pdb=" O ALA D 124 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA D 124 " --> pdb=" O ASP D 189 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ALA D 191 " --> pdb=" O HIS D 122 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 167 through 171 removed outlier: 4.996A pdb=" N ARG R 2 " --> pdb=" O LEU D 111 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THR R 95 " --> pdb=" O ILE R 24 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ILE R 24 " --> pdb=" O THR R 95 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU R 97 " --> pdb=" O ILE R 22 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ILE R 22 " --> pdb=" O LEU R 97 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 51 through 52 removed outlier: 5.650A pdb=" N ILE E 22 " --> pdb=" O LEU E 97 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU E 97 " --> pdb=" O ILE E 22 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ILE E 24 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THR E 95 " --> pdb=" O ILE E 24 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ARG E 2 " --> pdb=" O LEU V 111 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU V 111 " --> pdb=" O ARG E 2 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 12 through 16 Processing sheet with id=AC1, first strand: chain 'E' and resid 100 through 105 removed outlier: 6.486A pdb=" N THR E 193 " --> pdb=" O ILE E 121 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ILE E 121 " --> pdb=" O THR E 193 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLY E 195 " --> pdb=" O ILE E 119 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N ILE E 119 " --> pdb=" O GLY E 195 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 167 through 171 removed outlier: 4.994A pdb=" N ARG J 2 " --> pdb=" O LEU E 111 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THR J 95 " --> pdb=" O ILE J 24 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ILE J 24 " --> pdb=" O THR J 95 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU J 97 " --> pdb=" O ILE J 22 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ILE J 22 " --> pdb=" O LEU J 97 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 51 through 52 removed outlier: 5.650A pdb=" N ILE F 22 " --> pdb=" O LEU F 97 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU F 97 " --> pdb=" O ILE F 22 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ILE F 24 " --> pdb=" O THR F 95 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THR F 95 " --> pdb=" O ILE F 24 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ARG F 2 " --> pdb=" O LEU K 111 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 12 through 16 Processing sheet with id=AC5, first strand: chain 'F' and resid 100 through 105 removed outlier: 6.486A pdb=" N THR F 193 " --> pdb=" O ILE F 121 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ILE F 121 " --> pdb=" O THR F 193 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N GLY F 195 " --> pdb=" O ILE F 119 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ILE F 119 " --> pdb=" O GLY F 195 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 167 through 171 removed outlier: 4.985A pdb=" N ARG S 2 " --> pdb=" O LEU F 111 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THR S 95 " --> pdb=" O ILE S 24 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ILE S 24 " --> pdb=" O THR S 95 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU S 97 " --> pdb=" O ILE S 22 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ILE S 22 " --> pdb=" O LEU S 97 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 12 through 16 Processing sheet with id=AC8, first strand: chain 'G' and resid 100 through 105 removed outlier: 6.486A pdb=" N THR G 193 " --> pdb=" O ILE G 121 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ILE G 121 " --> pdb=" O THR G 193 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLY G 195 " --> pdb=" O ILE G 119 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ILE G 119 " --> pdb=" O GLY G 195 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 167 through 171 removed outlier: 4.989A pdb=" N ARG O 2 " --> pdb=" O LEU G 111 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THR O 95 " --> pdb=" O ILE O 24 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ILE O 24 " --> pdb=" O THR O 95 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU O 97 " --> pdb=" O ILE O 22 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ILE O 22 " --> pdb=" O LEU O 97 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 51 through 52 removed outlier: 5.650A pdb=" N ILE H 22 " --> pdb=" O LEU H 97 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU H 97 " --> pdb=" O ILE H 22 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ILE H 24 " --> pdb=" O THR H 95 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THR H 95 " --> pdb=" O ILE H 24 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ARG H 2 " --> pdb=" O LEU W 111 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU W 111 " --> pdb=" O ARG H 2 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 12 through 16 Processing sheet with id=AD3, first strand: chain 'H' and resid 100 through 105 removed outlier: 6.486A pdb=" N THR H 193 " --> pdb=" O ILE H 121 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ILE H 121 " --> pdb=" O THR H 193 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N GLY H 195 " --> pdb=" O ILE H 119 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ILE H 119 " --> pdb=" O GLY H 195 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 167 through 171 removed outlier: 4.917A pdb=" N ARG M 2 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THR M 95 " --> pdb=" O ILE M 24 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ILE M 24 " --> pdb=" O THR M 95 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU M 97 " --> pdb=" O ILE M 22 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ILE M 22 " --> pdb=" O LEU M 97 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 51 through 52 removed outlier: 5.650A pdb=" N ILE I 22 " --> pdb=" O LEU I 97 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU I 97 " --> pdb=" O ILE I 22 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ILE I 24 " --> pdb=" O THR I 95 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THR I 95 " --> pdb=" O ILE I 24 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ARG I 2 " --> pdb=" O LEU L 111 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 12 through 16 Processing sheet with id=AD7, first strand: chain 'I' and resid 100 through 105 removed outlier: 6.486A pdb=" N THR I 193 " --> pdb=" O ILE I 121 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ILE I 121 " --> pdb=" O THR I 193 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLY I 195 " --> pdb=" O ILE I 119 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ILE I 119 " --> pdb=" O GLY I 195 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 167 through 171 removed outlier: 4.923A pdb=" N ARG T 2 " --> pdb=" O LEU I 111 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THR T 95 " --> pdb=" O ILE T 24 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ILE T 24 " --> pdb=" O THR T 95 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU T 97 " --> pdb=" O ILE T 22 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ILE T 22 " --> pdb=" O LEU T 97 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 12 through 16 Processing sheet with id=AE1, first strand: chain 'J' and resid 100 through 105 removed outlier: 6.486A pdb=" N THR J 193 " --> pdb=" O ILE J 121 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ILE J 121 " --> pdb=" O THR J 193 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLY J 195 " --> pdb=" O ILE J 119 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ILE J 119 " --> pdb=" O GLY J 195 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 167 through 171 removed outlier: 4.927A pdb=" N ARG V 2 " --> pdb=" O LEU J 111 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THR V 95 " --> pdb=" O ILE V 24 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ILE V 24 " --> pdb=" O THR V 95 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU V 97 " --> pdb=" O ILE V 22 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ILE V 22 " --> pdb=" O LEU V 97 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 51 through 52 removed outlier: 5.650A pdb=" N ILE K 22 " --> pdb=" O LEU K 97 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU K 97 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ILE K 24 " --> pdb=" O THR K 95 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THR K 95 " --> pdb=" O ILE K 24 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ARG K 2 " --> pdb=" O LEU S 111 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU S 111 " --> pdb=" O ARG K 2 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 12 through 16 Processing sheet with id=AE5, first strand: chain 'K' and resid 100 through 105 removed outlier: 6.185A pdb=" N TYR K 187 " --> pdb=" O TYR K 126 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N TYR K 126 " --> pdb=" O TYR K 187 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASP K 189 " --> pdb=" O ALA K 124 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA K 124 " --> pdb=" O ASP K 189 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA K 191 " --> pdb=" O HIS K 122 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 51 through 52 removed outlier: 5.650A pdb=" N ILE L 22 " --> pdb=" O LEU L 97 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU L 97 " --> pdb=" O ILE L 22 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ILE L 24 " --> pdb=" O THR L 95 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THR L 95 " --> pdb=" O ILE L 24 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ARG L 2 " --> pdb=" O LEU T 111 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU T 111 " --> pdb=" O ARG L 2 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 12 through 16 Processing sheet with id=AE8, first strand: chain 'L' and resid 100 through 105 removed outlier: 6.486A pdb=" N THR L 193 " --> pdb=" O ILE L 121 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ILE L 121 " --> pdb=" O THR L 193 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLY L 195 " --> pdb=" O ILE L 119 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ILE L 119 " --> pdb=" O GLY L 195 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 12 through 16 Processing sheet with id=AF1, first strand: chain 'M' and resid 100 through 105 removed outlier: 6.486A pdb=" N THR M 193 " --> pdb=" O ILE M 121 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ILE M 121 " --> pdb=" O THR M 193 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLY M 195 " --> pdb=" O ILE M 119 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ILE M 119 " --> pdb=" O GLY M 195 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 167 through 171 removed outlier: 4.924A pdb=" N ARG W 2 " --> pdb=" O LEU M 111 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THR W 95 " --> pdb=" O ILE W 24 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ILE W 24 " --> pdb=" O THR W 95 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU W 97 " --> pdb=" O ILE W 22 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ILE W 22 " --> pdb=" O LEU W 97 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'N' and resid 51 through 52 removed outlier: 5.650A pdb=" N ILE N 22 " --> pdb=" O LEU N 97 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU N 97 " --> pdb=" O ILE N 22 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ILE N 24 " --> pdb=" O THR N 95 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THR N 95 " --> pdb=" O ILE N 24 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ARG N 2 " --> pdb=" O LEU P 111 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'N' and resid 12 through 16 Processing sheet with id=AF5, first strand: chain 'N' and resid 100 through 105 removed outlier: 6.486A pdb=" N THR N 193 " --> pdb=" O ILE N 121 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ILE N 121 " --> pdb=" O THR N 193 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLY N 195 " --> pdb=" O ILE N 119 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N ILE N 119 " --> pdb=" O GLY N 195 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'O' and resid 12 through 16 Processing sheet with id=AF7, first strand: chain 'O' and resid 100 through 105 removed outlier: 6.486A pdb=" N THR O 193 " --> pdb=" O ILE O 121 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ILE O 121 " --> pdb=" O THR O 193 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLY O 195 " --> pdb=" O ILE O 119 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ILE O 119 " --> pdb=" O GLY O 195 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'P' and resid 12 through 16 Processing sheet with id=AF9, first strand: chain 'P' and resid 100 through 105 removed outlier: 6.486A pdb=" N THR P 193 " --> pdb=" O ILE P 121 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ILE P 121 " --> pdb=" O THR P 193 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLY P 195 " --> pdb=" O ILE P 119 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ILE P 119 " --> pdb=" O GLY P 195 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Q' and resid 51 through 52 removed outlier: 5.650A pdb=" N ILE Q 22 " --> pdb=" O LEU Q 97 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU Q 97 " --> pdb=" O ILE Q 22 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ILE Q 24 " --> pdb=" O THR Q 95 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THR Q 95 " --> pdb=" O ILE Q 24 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ARG Q 2 " --> pdb=" O LEU X 111 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU X 111 " --> pdb=" O ARG Q 2 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Q' and resid 12 through 16 Processing sheet with id=AG3, first strand: chain 'Q' and resid 100 through 105 removed outlier: 6.486A pdb=" N THR Q 193 " --> pdb=" O ILE Q 121 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ILE Q 121 " --> pdb=" O THR Q 193 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLY Q 195 " --> pdb=" O ILE Q 119 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ILE Q 119 " --> pdb=" O GLY Q 195 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'R' and resid 12 through 16 Processing sheet with id=AG5, first strand: chain 'R' and resid 100 through 105 removed outlier: 6.486A pdb=" N THR R 193 " --> pdb=" O ILE R 121 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ILE R 121 " --> pdb=" O THR R 193 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLY R 195 " --> pdb=" O ILE R 119 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ILE R 119 " --> pdb=" O GLY R 195 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'R' and resid 167 through 171 removed outlier: 3.619A pdb=" N LEU R 111 " --> pdb=" O ARG U 2 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ARG U 2 " --> pdb=" O LEU R 111 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THR U 95 " --> pdb=" O ILE U 24 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ILE U 24 " --> pdb=" O THR U 95 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU U 97 " --> pdb=" O ILE U 22 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N ILE U 22 " --> pdb=" O LEU U 97 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'S' and resid 12 through 16 Processing sheet with id=AG8, first strand: chain 'S' and resid 100 through 105 removed outlier: 6.486A pdb=" N THR S 193 " --> pdb=" O ILE S 121 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ILE S 121 " --> pdb=" O THR S 193 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLY S 195 " --> pdb=" O ILE S 119 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ILE S 119 " --> pdb=" O GLY S 195 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'T' and resid 12 through 16 Processing sheet with id=AH1, first strand: chain 'T' and resid 100 through 105 removed outlier: 6.185A pdb=" N TYR T 187 " --> pdb=" O TYR T 126 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N TYR T 126 " --> pdb=" O TYR T 187 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ASP T 189 " --> pdb=" O ALA T 124 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ALA T 124 " --> pdb=" O ASP T 189 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ALA T 191 " --> pdb=" O HIS T 122 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'U' and resid 12 through 16 Processing sheet with id=AH3, first strand: chain 'U' and resid 100 through 105 removed outlier: 6.486A pdb=" N THR U 193 " --> pdb=" O ILE U 121 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ILE U 121 " --> pdb=" O THR U 193 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLY U 195 " --> pdb=" O ILE U 119 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ILE U 119 " --> pdb=" O GLY U 195 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'V' and resid 12 through 16 Processing sheet with id=AH5, first strand: chain 'V' and resid 100 through 105 removed outlier: 6.486A pdb=" N THR V 193 " --> pdb=" O ILE V 121 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ILE V 121 " --> pdb=" O THR V 193 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLY V 195 " --> pdb=" O ILE V 119 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ILE V 119 " --> pdb=" O GLY V 195 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'W' and resid 12 through 16 Processing sheet with id=AH7, first strand: chain 'W' and resid 100 through 105 removed outlier: 6.486A pdb=" N THR W 193 " --> pdb=" O ILE W 121 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ILE W 121 " --> pdb=" O THR W 193 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLY W 195 " --> pdb=" O ILE W 119 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ILE W 119 " --> pdb=" O GLY W 195 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'X' and resid 12 through 16 Processing sheet with id=AH9, first strand: chain 'X' and resid 100 through 105 removed outlier: 6.486A pdb=" N THR X 193 " --> pdb=" O ILE X 121 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ILE X 121 " --> pdb=" O THR X 193 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLY X 195 " --> pdb=" O ILE X 119 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ILE X 119 " --> pdb=" O GLY X 195 " (cutoff:3.500A) 1379 hydrogen bonds defined for protein. 3489 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: 6.87 Time building geometry restraints manager: 3.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 8409 1.33 - 1.45: 7426 1.45 - 1.57: 19949 1.57 - 1.70: 0 1.70 - 1.82: 384 Bond restraints: 36168 Sorted by residual: bond pdb=" CA SER N 135 " pdb=" CB SER N 135 " ideal model delta sigma weight residual 1.537 1.484 0.053 1.41e-02 5.03e+03 1.41e+01 bond pdb=" N VAL I 72 " pdb=" CA VAL I 72 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.11e-02 8.12e+03 1.24e+01 bond pdb=" N VAL N 72 " pdb=" CA VAL N 72 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.11e-02 8.12e+03 1.24e+01 bond pdb=" N VAL U 72 " pdb=" CA VAL U 72 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.11e-02 8.12e+03 1.24e+01 bond pdb=" N VAL X 72 " pdb=" CA VAL X 72 " ideal model delta sigma weight residual 1.456 1.494 -0.039 1.11e-02 8.12e+03 1.22e+01 ... (remaining 36163 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 42957 1.47 - 2.94: 5227 2.94 - 4.40: 776 4.40 - 5.87: 140 5.87 - 7.34: 4 Bond angle restraints: 49104 Sorted by residual: angle pdb=" C LYS H 165 " pdb=" N SER H 166 " pdb=" CA SER H 166 " ideal model delta sigma weight residual 120.44 125.58 -5.14 1.30e+00 5.92e-01 1.56e+01 angle pdb=" N ASN A 8 " pdb=" CA ASN A 8 " pdb=" C ASN A 8 " ideal model delta sigma weight residual 114.39 108.72 5.67 1.45e+00 4.76e-01 1.53e+01 angle pdb=" C ASP A 179 " pdb=" CA ASP A 179 " pdb=" CB ASP A 179 " ideal model delta sigma weight residual 110.33 114.32 -3.99 1.02e+00 9.61e-01 1.53e+01 angle pdb=" CA VAL F 72 " pdb=" C VAL F 72 " pdb=" O VAL F 72 " ideal model delta sigma weight residual 121.63 117.81 3.82 9.90e-01 1.02e+00 1.49e+01 angle pdb=" CA VAL A 72 " pdb=" C VAL A 72 " pdb=" O VAL A 72 " ideal model delta sigma weight residual 121.63 117.81 3.82 9.90e-01 1.02e+00 1.49e+01 ... (remaining 49099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 20450 17.74 - 35.47: 1641 35.47 - 53.21: 236 53.21 - 70.94: 141 70.94 - 88.68: 92 Dihedral angle restraints: 22560 sinusoidal: 9000 harmonic: 13560 Sorted by residual: dihedral pdb=" CA ASP Q 130 " pdb=" CB ASP Q 130 " pdb=" CG ASP Q 130 " pdb=" OD1 ASP Q 130 " ideal model delta sinusoidal sigma weight residual -30.00 -87.14 57.14 1 2.00e+01 2.50e-03 1.10e+01 dihedral pdb=" CB CYS P 162 " pdb=" SG CYS P 162 " pdb=" SG CYS P 168 " pdb=" CB CYS P 168 " ideal model delta sinusoidal sigma weight residual -86.00 -58.33 -27.67 1 1.00e+01 1.00e-02 1.10e+01 dihedral pdb=" CB CYS G 162 " pdb=" SG CYS G 162 " pdb=" SG CYS G 168 " pdb=" CB CYS G 168 " ideal model delta sinusoidal sigma weight residual -86.00 -58.38 -27.62 1 1.00e+01 1.00e-02 1.09e+01 ... (remaining 22557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 4049 0.063 - 0.125: 1394 0.125 - 0.187: 232 0.187 - 0.250: 37 0.250 - 0.312: 24 Chirality restraints: 5736 Sorted by residual: chirality pdb=" CB VAL A 76 " pdb=" CA VAL A 76 " pdb=" CG1 VAL A 76 " pdb=" CG2 VAL A 76 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CB VAL E 76 " pdb=" CA VAL E 76 " pdb=" CG1 VAL E 76 " pdb=" CG2 VAL E 76 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CB VAL T 76 " pdb=" CA VAL T 76 " pdb=" CG1 VAL T 76 " pdb=" CG2 VAL T 76 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 5733 not shown) Planarity restraints: 6504 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 76 " -0.016 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C VAL A 76 " 0.058 2.00e-02 2.50e+03 pdb=" O VAL A 76 " -0.022 2.00e-02 2.50e+03 pdb=" N PHE A 77 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 31 " 0.258 9.50e-02 1.11e+02 1.16e-01 8.27e+00 pdb=" NE ARG A 31 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 31 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 31 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 31 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 78 " -0.243 9.50e-02 1.11e+02 1.09e-01 7.27e+00 pdb=" NE ARG A 78 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 78 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 78 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 78 " -0.009 2.00e-02 2.50e+03 ... (remaining 6501 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.96: 17180 2.96 - 3.44: 34048 3.44 - 3.93: 66403 3.93 - 4.41: 73196 4.41 - 4.90: 118948 Nonbonded interactions: 309775 Sorted by model distance: nonbonded pdb=" NH2 ARG P 2 " pdb=" OE2 GLU P 91 " model vdw 2.473 3.120 nonbonded pdb=" OE1 GLN G 151 " pdb=" OG1 THR G 155 " model vdw 2.481 3.040 nonbonded pdb=" OG SER D 123 " pdb=" OE1 GLN D 151 " model vdw 2.492 3.040 nonbonded pdb=" OD2 ASP O 7 " pdb=" OH TYR O 29 " model vdw 2.523 3.040 nonbonded pdb=" OD2 ASP T 7 " pdb=" OH TYR T 29 " model vdw 2.523 3.040 ... (remaining 309770 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 4.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.710 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 29.280 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 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 : 0.008 0.053 36360 Z= 0.605 Angle : 1.003 7.339 49488 Z= 0.707 Chirality : 0.063 0.312 5736 Planarity : 0.008 0.116 6504 Dihedral : 14.672 88.676 13296 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.02 % Allowed : 6.92 % Favored : 93.06 % 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: -1.55 (0.11), residues: 4632 helix: -1.38 (0.18), residues: 648 sheet: -0.60 (0.13), residues: 1608 loop : -1.15 (0.11), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 138 TYR 0.010 0.001 TYR C 94 PHE 0.012 0.003 PHE U 77 HIS 0.005 0.001 HIS G 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00836 / 0.61 (36168) covalent geometry : angle 1.00407 / 0.71 (49104) SS BOND : bond 0.00402 / 0.27 ( 192) SS BOND : angle 0.82970 / 0.57 ( 384) hydrogen bonds : bond 0.15499 / 10.34 ( 1379) hydrogen bonds : angle 6.88718 / 4.85 ( 3489) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 725 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 725 average time/residue: 0.8284 time to fit residues: 698.9697 Evaluate side-chains 601 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 601 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 432 optimal weight: 1.9990 chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 1.9990 chunk 455 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.2980 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 131 GLN E 131 GLN F 120 GLN O 120 GLN R 120 GLN R 151 GLN S 120 GLN X 120 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.079667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.066354 restraints weight = 47287.398| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 1.90 r_work: 0.2727 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9388 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 36360 Z= 0.123 Angle : 0.457 4.165 49488 Z= 0.268 Chirality : 0.043 0.128 5736 Planarity : 0.003 0.022 6504 Dihedral : 4.654 20.230 5160 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.07 % Allowed : 11.60 % Favored : 88.33 % 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: -1.02 (0.11), residues: 4632 helix: 0.04 (0.20), residues: 648 sheet: -0.33 (0.13), residues: 1608 loop : -1.07 (0.11), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 128 TYR 0.006 0.001 TYR A 94 PHE 0.012 0.002 PHE L 14 HIS 0.003 0.001 HIS W 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (36168) covalent geometry : angle 0.45693 / 0.27 (49104) SS BOND : bond 0.00180 / 0.12 ( 192) SS BOND : angle 0.41462 / 0.29 ( 384) hydrogen bonds : bond 0.04517 / 3.05 ( 1379) hydrogen bonds : angle 5.79328 / 4.02 ( 3489) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 602 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.7674 (pm20) cc_final: 0.7427 (pm20) REVERT: C 120 GLN cc_start: 0.8874 (tt0) cc_final: 0.8622 (tt0) REVERT: D 120 GLN cc_start: 0.8828 (tt0) cc_final: 0.8621 (tt0) REVERT: E 116 GLU cc_start: 0.7582 (pm20) cc_final: 0.7357 (pm20) REVERT: F 116 GLU cc_start: 0.7735 (pm20) cc_final: 0.7509 (pm20) REVERT: H 120 GLN cc_start: 0.8892 (tt0) cc_final: 0.8654 (tt0) REVERT: J 120 GLN cc_start: 0.8895 (tt0) cc_final: 0.8656 (tt0) REVERT: K 116 GLU cc_start: 0.7724 (pm20) cc_final: 0.7488 (pm20) REVERT: K 120 GLN cc_start: 0.8861 (tt0) cc_final: 0.8645 (tt0) REVERT: L 120 GLN cc_start: 0.8894 (tt0) cc_final: 0.8648 (tt0) REVERT: M 120 GLN cc_start: 0.8893 (tt0) cc_final: 0.8644 (tt0) REVERT: P 120 GLN cc_start: 0.8881 (tt0) cc_final: 0.8630 (tt0) REVERT: Q 116 GLU cc_start: 0.7702 (pm20) cc_final: 0.7495 (pm20) REVERT: Q 120 GLN cc_start: 0.8899 (tt0) cc_final: 0.8658 (tt0) REVERT: R 116 GLU cc_start: 0.7680 (pm20) cc_final: 0.7451 (pm20) REVERT: T 116 GLU cc_start: 0.7660 (pm20) cc_final: 0.7439 (pm20) REVERT: U 116 GLU cc_start: 0.7690 (pm20) cc_final: 0.7458 (pm20) REVERT: V 116 GLU cc_start: 0.7658 (pm20) cc_final: 0.7433 (pm20) REVERT: W 116 GLU cc_start: 0.7682 (pm20) cc_final: 0.7447 (pm20) outliers start: 3 outliers final: 0 residues processed: 602 average time/residue: 0.7676 time to fit residues: 543.9110 Evaluate side-chains 598 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 598 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 358 optimal weight: 10.0000 chunk 380 optimal weight: 10.0000 chunk 253 optimal weight: 6.9990 chunk 193 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 321 optimal weight: 4.9990 chunk 382 optimal weight: 5.9990 chunk 265 optimal weight: 0.9990 chunk 376 optimal weight: 9.9990 chunk 452 optimal weight: 10.0000 chunk 112 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 120 GLN F 120 GLN N 120 GLN O 120 GLN R 120 GLN S 120 GLN T 120 GLN X 120 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.073774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.060374 restraints weight = 47518.943| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 1.88 r_work: 0.2606 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2479 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9458 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.052 36360 Z= 0.343 Angle : 0.566 4.572 49488 Z= 0.324 Chirality : 0.050 0.124 5736 Planarity : 0.004 0.027 6504 Dihedral : 5.190 18.766 5160 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 0.78 % Allowed : 12.38 % Favored : 86.84 % 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: -0.90 (0.11), residues: 4632 helix: 0.43 (0.20), residues: 648 sheet: -0.45 (0.13), residues: 1608 loop : -0.93 (0.11), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 128 TYR 0.009 0.001 TYR D 94 PHE 0.015 0.003 PHE A 77 HIS 0.007 0.002 HIS W 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00769 / 0.34 (36168) covalent geometry : angle 0.56469 / 0.32 (49104) SS BOND : bond 0.00504 / 0.33 ( 192) SS BOND : angle 0.71266 / 0.49 ( 384) hydrogen bonds : bond 0.05748 / 3.84 ( 1379) hydrogen bonds : angle 6.12262 / 4.25 ( 3489) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 550 time to evaluate : 1.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 167 GLN cc_start: 0.8745 (pt0) cc_final: 0.8310 (mt0) REVERT: H 113 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8200 (tt0) REVERT: I 120 GLN cc_start: 0.8942 (tt0) cc_final: 0.8703 (tt0) REVERT: J 113 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8190 (tt0) REVERT: K 113 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8135 (tt0) REVERT: L 113 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8324 (tt0) REVERT: N 10 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8484 (pt0) REVERT: S 113 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8146 (tt0) REVERT: W 120 GLN cc_start: 0.8943 (tt0) cc_final: 0.8729 (tt0) REVERT: X 113 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7860 (tt0) outliers start: 32 outliers final: 0 residues processed: 576 average time/residue: 0.8398 time to fit residues: 568.3624 Evaluate side-chains 553 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 547 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain J residue 113 GLU Chi-restraints excluded: chain K residue 113 GLU Chi-restraints excluded: chain L residue 113 GLU Chi-restraints excluded: chain S residue 113 GLU Chi-restraints excluded: chain X residue 113 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 260 optimal weight: 3.9990 chunk 316 optimal weight: 5.9990 chunk 438 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 240 optimal weight: 9.9990 chunk 329 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 308 optimal weight: 3.9990 chunk 268 optimal weight: 2.9990 chunk 200 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 GLN B 120 GLN C 120 GLN D 120 GLN E 120 GLN G 120 GLN H 120 GLN J 120 GLN K 120 GLN L 120 GLN M 120 GLN N 120 GLN O 120 GLN O 167 GLN P 120 GLN Q 120 GLN R 120 GLN S 120 GLN T 120 GLN U 120 GLN V 120 GLN X 120 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.075372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.062066 restraints weight = 45445.857| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 1.82 r_work: 0.2645 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2521 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9432 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 36360 Z= 0.143 Angle : 0.461 4.078 49488 Z= 0.267 Chirality : 0.043 0.123 5736 Planarity : 0.003 0.025 6504 Dihedral : 4.779 18.400 5160 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 0.27 % Allowed : 12.38 % Favored : 87.35 % 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: -0.87 (0.11), residues: 4632 helix: 0.54 (0.20), residues: 648 sheet: -0.38 (0.12), residues: 1608 loop : -0.98 (0.11), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 164 TYR 0.006 0.001 TYR D 94 PHE 0.011 0.002 PHE L 14 HIS 0.002 0.001 HIS W 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (36168) covalent geometry : angle 0.46100 / 0.27 (49104) SS BOND : bond 0.00176 / 0.12 ( 192) SS BOND : angle 0.40898 / 0.28 ( 384) hydrogen bonds : bond 0.04413 / 2.97 ( 1379) hydrogen bonds : angle 5.96918 / 4.15 ( 3489) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 570 time to evaluate : 1.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8231 (pt0) REVERT: A 116 GLU cc_start: 0.7821 (pm20) cc_final: 0.7595 (pm20) REVERT: B 10 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8335 (pt0) REVERT: C 10 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8345 (pt0) REVERT: D 10 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8362 (pt0) REVERT: E 10 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8421 (pt0) REVERT: F 10 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8355 (pt0) REVERT: G 10 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8343 (pt0) REVERT: I 10 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8356 (pt0) REVERT: I 120 GLN cc_start: 0.8902 (tt0) cc_final: 0.8655 (tt0) REVERT: J 10 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8407 (pt0) REVERT: L 10 GLU cc_start: 0.8868 (mt-10) cc_final: 0.8370 (pt0) REVERT: M 10 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8357 (pt0) REVERT: N 10 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8426 (pt0) REVERT: O 10 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8366 (pt0) REVERT: P 10 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8359 (pt0) REVERT: R 10 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8343 (pt0) REVERT: S 10 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8351 (pt0) REVERT: S 113 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8151 (tt0) REVERT: T 10 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8344 (pt0) REVERT: U 10 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8363 (pt0) REVERT: V 10 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8345 (pt0) REVERT: W 10 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8383 (pt0) REVERT: W 116 GLU cc_start: 0.7750 (pm20) cc_final: 0.7543 (pm20) REVERT: W 120 GLN cc_start: 0.8850 (tt0) cc_final: 0.8609 (tt0) REVERT: X 10 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8351 (pt0) outliers start: 11 outliers final: 0 residues processed: 579 average time/residue: 0.8409 time to fit residues: 570.3586 Evaluate side-chains 565 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 564 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 113 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 16 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 285 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 298 optimal weight: 5.9990 chunk 255 optimal weight: 0.8980 chunk 312 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 299 optimal weight: 1.9990 chunk 388 optimal weight: 0.8980 chunk 348 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 GLN B 120 GLN C 120 GLN D 120 GLN E 120 GLN F 120 GLN G 120 GLN H 120 GLN J 120 GLN K 120 GLN L 120 GLN M 120 GLN N 120 GLN O 120 GLN O 167 GLN P 120 GLN Q 120 GLN R 120 GLN S 120 GLN T 120 GLN U 120 GLN V 120 GLN X 120 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.076401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.063189 restraints weight = 45733.939| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 1.83 r_work: 0.2676 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2551 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9420 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 36360 Z= 0.111 Angle : 0.437 4.961 49488 Z= 0.253 Chirality : 0.042 0.124 5736 Planarity : 0.003 0.027 6504 Dihedral : 4.511 17.675 5160 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.44 % Allowed : 12.74 % Favored : 86.82 % 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: -0.75 (0.12), residues: 4632 helix: 0.61 (0.20), residues: 648 sheet: -0.14 (0.13), residues: 1656 loop : -1.05 (0.11), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 164 TYR 0.005 0.001 TYR Q 94 PHE 0.011 0.002 PHE L 14 HIS 0.001 0.000 HIS W 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (36168) covalent geometry : angle 0.43719 / 0.25 (49104) SS BOND : bond 0.00123 / 0.08 ( 192) SS BOND : angle 0.34149 / 0.24 ( 384) hydrogen bonds : bond 0.03968 / 2.67 ( 1379) hydrogen bonds : angle 5.95336 / 4.13 ( 3489) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 575 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8252 (pt0) REVERT: B 10 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8357 (pt0) REVERT: C 10 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8379 (pt0) REVERT: D 10 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8378 (pt0) REVERT: E 10 GLU cc_start: 0.8863 (mt-10) cc_final: 0.8406 (pt0) REVERT: F 10 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8379 (pt0) REVERT: G 10 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8367 (pt0) REVERT: I 10 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8395 (pt0) REVERT: I 164 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.7403 (mtt180) REVERT: J 10 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8414 (pt0) REVERT: L 10 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8405 (pt0) REVERT: M 10 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8365 (pt0) REVERT: N 10 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8428 (pt0) REVERT: O 10 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8412 (pt0) REVERT: P 10 GLU cc_start: 0.8855 (mt-10) cc_final: 0.8396 (pt0) REVERT: R 10 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8378 (pt0) REVERT: S 10 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8362 (pt0) REVERT: T 10 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8377 (pt0) REVERT: U 10 GLU cc_start: 0.8865 (mt-10) cc_final: 0.8390 (pt0) REVERT: V 10 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8365 (pt0) REVERT: W 10 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8407 (pt0) REVERT: X 10 GLU cc_start: 0.8855 (mt-10) cc_final: 0.8395 (pt0) outliers start: 18 outliers final: 0 residues processed: 591 average time/residue: 0.8468 time to fit residues: 586.1737 Evaluate side-chains 537 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 536 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 164 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 288 optimal weight: 8.9990 chunk 175 optimal weight: 10.0000 chunk 349 optimal weight: 3.9990 chunk 430 optimal weight: 10.0000 chunk 274 optimal weight: 0.5980 chunk 223 optimal weight: 9.9990 chunk 1 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 405 optimal weight: 7.9990 chunk 49 optimal weight: 9.9990 chunk 237 optimal weight: 5.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 GLN B 120 GLN C 120 GLN D 120 GLN E 120 GLN F 120 GLN G 120 GLN H 120 GLN J 120 GLN K 120 GLN L 120 GLN M 120 GLN N 120 GLN O 120 GLN O 167 GLN P 120 GLN Q 120 GLN R 120 GLN S 120 GLN T 120 GLN U 120 GLN V 120 GLN X 120 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.074276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.060524 restraints weight = 45997.888| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 1.87 r_work: 0.2599 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2474 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9458 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 36360 Z= 0.284 Angle : 0.527 5.169 49488 Z= 0.302 Chirality : 0.047 0.120 5736 Planarity : 0.003 0.025 6504 Dihedral : 5.042 17.505 5160 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 0.12 % Allowed : 12.74 % Favored : 87.13 % 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: -0.77 (0.12), residues: 4632 helix: 0.46 (0.20), residues: 648 sheet: -0.29 (0.13), residues: 1608 loop : -0.88 (0.11), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 164 TYR 0.007 0.001 TYR P 94 PHE 0.014 0.003 PHE Q 77 HIS 0.004 0.001 HIS W 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00632 / 0.28 (36168) covalent geometry : angle 0.52702 / 0.30 (49104) SS BOND : bond 0.00392 / 0.26 ( 192) SS BOND : angle 0.55580 / 0.39 ( 384) hydrogen bonds : bond 0.05263 / 3.52 ( 1379) hydrogen bonds : angle 6.12674 / 4.25 ( 3489) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 516 time to evaluate : 1.547 Fit side-chains revert: symmetry clash REVERT: B 10 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8500 (pt0) REVERT: C 10 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8515 (pt0) REVERT: D 10 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8541 (pt0) REVERT: E 10 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8555 (pt0) REVERT: F 10 GLU cc_start: 0.8910 (mt-10) cc_final: 0.8524 (pt0) REVERT: G 10 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8511 (pt0) REVERT: I 10 GLU cc_start: 0.8882 (mt-10) cc_final: 0.8458 (pt0) REVERT: I 120 GLN cc_start: 0.8878 (tt0) cc_final: 0.8642 (tt0) REVERT: L 10 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8448 (pt0) REVERT: M 10 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8517 (pt0) REVERT: N 10 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8535 (pt0) REVERT: P 10 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8469 (pt0) REVERT: R 10 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8517 (pt0) REVERT: S 10 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8495 (pt0) REVERT: U 10 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8523 (pt0) REVERT: V 10 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8514 (pt0) REVERT: W 10 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8557 (pt0) REVERT: W 120 GLN cc_start: 0.8879 (tt0) cc_final: 0.8642 (tt0) REVERT: X 10 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8454 (pt0) REVERT: X 113 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7993 (tt0) outliers start: 5 outliers final: 0 residues processed: 519 average time/residue: 0.8750 time to fit residues: 530.2675 Evaluate side-chains 504 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 503 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 113 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 53 optimal weight: 6.9990 chunk 448 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 363 optimal weight: 2.9990 chunk 261 optimal weight: 0.9990 chunk 232 optimal weight: 2.9990 chunk 440 optimal weight: 6.9990 chunk 441 optimal weight: 4.9990 chunk 180 optimal weight: 6.9990 chunk 66 optimal weight: 0.5980 chunk 190 optimal weight: 5.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 GLN B 120 GLN C 120 GLN D 120 GLN E 120 GLN F 120 GLN G 120 GLN H 120 GLN J 120 GLN K 120 GLN L 120 GLN M 120 GLN N 120 GLN O 120 GLN P 120 GLN Q 120 GLN R 120 GLN S 120 GLN T 120 GLN U 120 GLN V 120 GLN X 120 GLN X 167 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.074806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.061517 restraints weight = 46064.880| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 1.84 r_work: 0.2638 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2510 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9437 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 36360 Z= 0.152 Angle : 0.460 5.289 49488 Z= 0.266 Chirality : 0.043 0.122 5736 Planarity : 0.003 0.026 6504 Dihedral : 4.777 17.725 5160 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 0.07 % Allowed : 12.74 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.12), residues: 4632 helix: 0.57 (0.20), residues: 648 sheet: -0.15 (0.13), residues: 1656 loop : -0.98 (0.12), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 164 TYR 0.005 0.001 TYR K 94 PHE 0.012 0.002 PHE L 14 HIS 0.002 0.001 HIS W 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (36168) covalent geometry : angle 0.46057 / 0.27 (49104) SS BOND : bond 0.00180 / 0.12 ( 192) SS BOND : angle 0.38774 / 0.27 ( 384) hydrogen bonds : bond 0.04419 / 2.97 ( 1379) hydrogen bonds : angle 6.04442 / 4.19 ( 3489) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 521 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8334 (pt0) REVERT: B 10 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8393 (pt0) REVERT: C 10 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8416 (pt0) REVERT: D 10 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8414 (pt0) REVERT: E 10 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8448 (pt0) REVERT: E 113 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8260 (tt0) REVERT: F 10 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8423 (pt0) REVERT: G 10 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8410 (pt0) REVERT: I 10 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8419 (pt0) REVERT: J 10 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8431 (pt0) REVERT: L 10 GLU cc_start: 0.8871 (mt-10) cc_final: 0.8428 (pt0) REVERT: M 10 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8415 (pt0) REVERT: N 10 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8524 (pt0) REVERT: P 10 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8425 (pt0) REVERT: Q 113 GLU cc_start: 0.8596 (tt0) cc_final: 0.8381 (tt0) REVERT: R 10 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8408 (pt0) REVERT: S 10 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8392 (pt0) REVERT: T 10 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8415 (pt0) REVERT: U 10 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8436 (pt0) REVERT: V 10 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8409 (pt0) REVERT: W 10 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8438 (pt0) REVERT: W 120 GLN cc_start: 0.8863 (tt0) cc_final: 0.8609 (tt0) REVERT: X 10 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8414 (pt0) outliers start: 3 outliers final: 0 residues processed: 523 average time/residue: 0.8351 time to fit residues: 511.2479 Evaluate side-chains 510 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 509 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 113 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 102 optimal weight: 5.9990 chunk 158 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 202 optimal weight: 9.9990 chunk 303 optimal weight: 1.9990 chunk 178 optimal weight: 0.7980 chunk 436 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 429 optimal weight: 5.9990 chunk 210 optimal weight: 5.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 GLN B 120 GLN C 120 GLN D 120 GLN E 120 GLN F 120 GLN G 120 GLN H 120 GLN J 120 GLN K 120 GLN L 120 GLN M 120 GLN N 120 GLN O 120 GLN P 120 GLN Q 120 GLN R 120 GLN S 120 GLN T 120 GLN U 120 GLN V 120 GLN X 120 GLN X 167 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.075767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.062618 restraints weight = 45943.721| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 1.82 r_work: 0.2665 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2539 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9424 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 36360 Z= 0.118 Angle : 0.437 5.249 49488 Z= 0.252 Chirality : 0.042 0.124 5736 Planarity : 0.003 0.026 6504 Dihedral : 4.585 17.660 5160 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.17 % Allowed : 12.60 % Favored : 87.23 % 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: -0.65 (0.12), residues: 4632 helix: 0.60 (0.20), residues: 648 sheet: -0.05 (0.13), residues: 1656 loop : -0.97 (0.12), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 164 TYR 0.005 0.001 TYR V 87 PHE 0.011 0.002 PHE L 14 HIS 0.001 0.000 HIS W 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (36168) covalent geometry : angle 0.43785 / 0.25 (49104) SS BOND : bond 0.00131 / 0.09 ( 192) SS BOND : angle 0.34913 / 0.25 ( 384) hydrogen bonds : bond 0.04024 / 2.71 ( 1379) hydrogen bonds : angle 6.00332 / 4.17 ( 3489) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 528 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8287 (pt0) REVERT: B 10 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8393 (pt0) REVERT: C 10 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8418 (pt0) REVERT: D 10 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8414 (pt0) REVERT: E 10 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8433 (pt0) REVERT: F 10 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8412 (pt0) REVERT: G 10 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8407 (pt0) REVERT: H 113 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8062 (mt-10) REVERT: I 10 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8423 (pt0) REVERT: J 10 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8442 (pt0) REVERT: L 10 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8417 (pt0) REVERT: M 10 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8407 (pt0) REVERT: N 10 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8441 (pt0) REVERT: P 10 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8410 (pt0) REVERT: R 10 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8411 (pt0) REVERT: S 10 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8400 (pt0) REVERT: T 10 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8403 (pt0) REVERT: U 10 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8414 (pt0) REVERT: V 10 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8406 (pt0) REVERT: W 10 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8435 (pt0) REVERT: X 10 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8412 (pt0) outliers start: 7 outliers final: 1 residues processed: 534 average time/residue: 0.8267 time to fit residues: 518.4939 Evaluate side-chains 519 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 517 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain X residue 111 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 134 optimal weight: 0.0010 chunk 289 optimal weight: 0.6980 chunk 437 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 424 optimal weight: 6.9990 chunk 270 optimal weight: 0.0970 chunk 207 optimal weight: 0.6980 chunk 209 optimal weight: 10.0000 chunk 153 optimal weight: 0.0470 chunk 26 optimal weight: 8.9990 chunk 299 optimal weight: 9.9990 overall best weight: 0.3082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 GLN B 120 GLN C 120 GLN D 120 GLN E 120 GLN F 120 GLN G 120 GLN H 120 GLN J 120 GLN K 120 GLN L 120 GLN M 120 GLN N 120 GLN O 120 GLN P 120 GLN Q 120 GLN R 120 GLN S 120 GLN T 120 GLN U 120 GLN V 120 GLN X 120 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.079430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.066534 restraints weight = 45790.992| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 1.82 r_work: 0.2763 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9368 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 36360 Z= 0.075 Angle : 0.391 6.572 49488 Z= 0.227 Chirality : 0.041 0.128 5736 Planarity : 0.003 0.026 6504 Dihedral : 4.222 18.010 5160 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 0.19 % Allowed : 11.92 % Favored : 87.89 % 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: -0.43 (0.12), residues: 4632 helix: 1.05 (0.21), residues: 648 sheet: -0.01 (0.13), residues: 1656 loop : -0.83 (0.12), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 164 TYR 0.007 0.001 TYR X 87 PHE 0.008 0.001 PHE U 14 HIS 0.001 0.000 HIS A 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00153 / 0.07 (36168) covalent geometry : angle 0.39105 / 0.23 (49104) SS BOND : bond 0.00081 / 0.05 ( 192) SS BOND : angle 0.38043 / 0.26 ( 384) hydrogen bonds : bond 0.03263 / 2.20 ( 1379) hydrogen bonds : angle 5.86149 / 4.07 ( 3489) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 524 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8271 (pt0) REVERT: B 10 GLU cc_start: 0.8782 (mt-10) cc_final: 0.8329 (pt0) REVERT: C 10 GLU cc_start: 0.8812 (mt-10) cc_final: 0.8361 (pt0) REVERT: D 10 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8351 (pt0) REVERT: E 10 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8387 (pt0) REVERT: F 10 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8342 (pt0) REVERT: F 167 GLN cc_start: 0.8711 (pt0) cc_final: 0.8336 (mt0) REVERT: G 10 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8346 (pt0) REVERT: I 10 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8362 (pt0) REVERT: J 10 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8389 (pt0) REVERT: L 10 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8378 (pt0) REVERT: M 10 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8340 (pt0) REVERT: N 10 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8452 (pt0) REVERT: O 10 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8353 (pt0) REVERT: P 10 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8362 (pt0) REVERT: R 10 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8343 (pt0) REVERT: S 10 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8366 (pt0) REVERT: T 10 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8358 (pt0) REVERT: U 10 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8380 (pt0) REVERT: V 10 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8357 (pt0) REVERT: W 10 GLU cc_start: 0.8815 (mt-10) cc_final: 0.8393 (pt0) REVERT: X 10 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8365 (pt0) REVERT: X 113 GLU cc_start: 0.8320 (tt0) cc_final: 0.7993 (tt0) REVERT: X 167 GLN cc_start: 0.8558 (pt0) cc_final: 0.8101 (mt0) outliers start: 8 outliers final: 3 residues processed: 532 average time/residue: 0.7073 time to fit residues: 448.2341 Evaluate side-chains 512 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 509 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 170 VAL Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain N residue 170 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 198 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 227 optimal weight: 3.9990 chunk 232 optimal weight: 5.9990 chunk 250 optimal weight: 0.0570 chunk 220 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 347 optimal weight: 9.9990 chunk 397 optimal weight: 3.9990 chunk 251 optimal weight: 0.8980 chunk 258 optimal weight: 5.9990 overall best weight: 2.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 120 GLN C 120 GLN D 120 GLN E 120 GLN F 120 GLN G 120 GLN H 120 GLN J 120 GLN K 120 GLN L 120 GLN M 120 GLN N 120 GLN O 120 GLN P 120 GLN Q 120 GLN R 120 GLN S 120 GLN T 120 GLN U 120 GLN V 120 GLN X 120 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.076171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.062426 restraints weight = 45609.472| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 1.87 r_work: 0.2645 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2517 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9436 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 36360 Z= 0.165 Angle : 0.456 5.385 49488 Z= 0.262 Chirality : 0.043 0.124 5736 Planarity : 0.003 0.029 6504 Dihedral : 4.711 17.662 5160 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.17 % Allowed : 11.62 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.60 (0.12), residues: 4632 helix: 0.42 (0.20), residues: 648 sheet: 0.06 (0.13), residues: 1656 loop : -0.94 (0.12), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 164 TYR 0.012 0.001 TYR B 87 PHE 0.011 0.002 PHE N 14 HIS 0.002 0.001 HIS W 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 (36168) covalent geometry : angle 0.45666 / 0.26 (49104) SS BOND : bond 0.00209 / 0.14 ( 192) SS BOND : angle 0.35087 / 0.25 ( 384) hydrogen bonds : bond 0.04402 / 2.95 ( 1379) hydrogen bonds : angle 5.99270 / 4.16 ( 3489) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 531 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8357 (pt0) REVERT: A 120 GLN cc_start: 0.8863 (tt0) cc_final: 0.8662 (tt0) REVERT: B 10 GLU cc_start: 0.8865 (mt-10) cc_final: 0.8430 (pt0) REVERT: C 10 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8439 (pt0) REVERT: D 10 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8439 (pt0) REVERT: E 10 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8446 (pt0) REVERT: F 10 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8454 (pt0) REVERT: F 167 GLN cc_start: 0.8877 (pt0) cc_final: 0.8314 (mt0) REVERT: G 10 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8452 (pt0) REVERT: I 10 GLU cc_start: 0.8863 (mt-10) cc_final: 0.8439 (pt0) REVERT: J 10 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8460 (pt0) REVERT: M 10 GLU cc_start: 0.8868 (mt-10) cc_final: 0.8437 (pt0) REVERT: N 10 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8518 (pt0) REVERT: O 10 GLU cc_start: 0.8863 (mt-10) cc_final: 0.8434 (pt0) REVERT: P 10 GLU cc_start: 0.8868 (mt-10) cc_final: 0.8434 (pt0) REVERT: R 10 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8438 (pt0) REVERT: T 10 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8427 (pt0) REVERT: U 10 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8448 (pt0) REVERT: V 10 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8447 (pt0) REVERT: W 10 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8462 (pt0) REVERT: X 10 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8434 (pt0) outliers start: 7 outliers final: 5 residues processed: 537 average time/residue: 0.7519 time to fit residues: 476.1107 Evaluate side-chains 523 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 518 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 167 GLN Chi-restraints excluded: chain O residue 166 SER Chi-restraints excluded: chain P residue 166 SER Chi-restraints excluded: chain Q residue 166 SER Chi-restraints excluded: chain X residue 111 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 57 optimal weight: 10.0000 chunk 361 optimal weight: 2.9990 chunk 412 optimal weight: 0.8980 chunk 339 optimal weight: 3.9990 chunk 300 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 183 optimal weight: 9.9990 chunk 246 optimal weight: 0.9980 chunk 117 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 chunk 228 optimal weight: 10.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 120 GLN C 120 GLN D 120 GLN E 120 GLN F 120 GLN G 120 GLN H 120 GLN J 120 GLN K 120 GLN L 120 GLN M 120 GLN N 120 GLN O 120 GLN P 120 GLN Q 120 GLN R 120 GLN S 120 GLN T 120 GLN U 120 GLN V 120 GLN X 120 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.076827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.063192 restraints weight = 45355.136| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 1.86 r_work: 0.2659 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2535 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9431 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 36360 Z= 0.129 Angle : 0.434 5.861 49488 Z= 0.252 Chirality : 0.042 0.127 5736 Planarity : 0.003 0.024 6504 Dihedral : 4.641 17.339 5160 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 0.12 % Allowed : 12.13 % Favored : 87.74 % 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: -0.58 (0.12), residues: 4632 helix: 0.47 (0.20), residues: 648 sheet: 0.06 (0.13), residues: 1656 loop : -0.91 (0.12), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 164 TYR 0.011 0.001 TYR U 87 PHE 0.011 0.002 PHE L 14 HIS 0.001 0.000 HIS W 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (36168) covalent geometry : angle 0.43494 / 0.25 (49104) SS BOND : bond 0.00152 / 0.10 ( 192) SS BOND : angle 0.35101 / 0.24 ( 384) hydrogen bonds : bond 0.04105 / 2.76 ( 1379) hydrogen bonds : angle 5.96001 / 4.14 ( 3489) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16517.42 seconds wall clock time: 281 minutes 1.99 seconds (16861.99 seconds total)