Starting phenix.real_space_refine on Wed Mar 4 09:20:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oae_12775/03_2026/7oae_12775.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oae_12775/03_2026/7oae_12775.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7oae_12775/03_2026/7oae_12775.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oae_12775/03_2026/7oae_12775.map" model { file = "/net/cci-nas-00/data/ceres_data/7oae_12775/03_2026/7oae_12775.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oae_12775/03_2026/7oae_12775.cif" } resolution = 2.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 294 5.16 5 C 7980 2.51 5 N 2226 2.21 5 O 2268 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12768 Number of models: 1 Model: "" Number of chains: 42 Chain: "B" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "C" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "D" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "E" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "F" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "G" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "H" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "I" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "J" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "K" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "L" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "M" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "N" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "T" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "U" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "A" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "O" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "P" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "Q" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "R" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "S" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "V" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "W" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "X" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "Y" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "Z" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "0" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "1" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "2" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "3" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "4" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "5" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "6" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "7" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "8" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "9" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "a" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "b" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "c" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "d" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "e" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "f" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 304 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 38} Time building chain proxies: 2.67, per 1000 atoms: 0.21 Number of scatterers: 12768 At special positions: 0 Unit cell: (121.569, 126.531, 105.856, 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 294 16.00 O 2268 8.00 N 2226 7.00 C 7980 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=126, symmetry=0 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 30 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 37 " distance=2.03 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 39 " distance=2.03 Simple disulfide: pdb=" SG CYS C 4 " - pdb=" SG CYS C 30 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 37 " distance=2.03 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 39 " distance=2.03 Simple disulfide: pdb=" SG CYS D 4 " - pdb=" SG CYS D 30 " distance=2.03 Simple disulfide: pdb=" SG CYS D 15 " - pdb=" SG CYS D 37 " distance=2.03 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 39 " distance=2.03 Simple disulfide: pdb=" SG CYS E 4 " - pdb=" SG CYS E 30 " distance=2.03 Simple disulfide: pdb=" SG CYS E 15 " - pdb=" SG CYS E 37 " distance=2.03 Simple disulfide: pdb=" SG CYS E 19 " - pdb=" SG CYS E 39 " distance=2.03 Simple disulfide: pdb=" SG CYS F 4 " - pdb=" SG CYS F 30 " distance=2.03 Simple disulfide: pdb=" SG CYS F 15 " - pdb=" SG CYS F 37 " distance=2.03 Simple disulfide: pdb=" SG CYS F 19 " - pdb=" SG CYS F 39 " distance=2.03 Simple disulfide: pdb=" SG CYS G 4 " - pdb=" SG CYS G 30 " distance=2.03 Simple disulfide: pdb=" SG CYS G 15 " - pdb=" SG CYS G 37 " distance=2.03 Simple disulfide: pdb=" SG CYS G 19 " - pdb=" SG CYS G 39 " distance=2.03 Simple disulfide: pdb=" SG CYS H 4 " - pdb=" SG CYS H 30 " distance=2.03 Simple disulfide: pdb=" SG CYS H 15 " - pdb=" SG CYS H 37 " distance=2.03 Simple disulfide: pdb=" SG CYS H 19 " - pdb=" SG CYS H 39 " distance=2.03 Simple disulfide: pdb=" SG CYS I 4 " - pdb=" SG CYS I 30 " distance=2.03 Simple disulfide: pdb=" SG CYS I 15 " - pdb=" SG CYS I 37 " distance=2.03 Simple disulfide: pdb=" SG CYS I 19 " - pdb=" SG CYS I 39 " distance=2.03 Simple disulfide: pdb=" SG CYS J 4 " - pdb=" SG CYS J 30 " distance=2.03 Simple disulfide: pdb=" SG CYS J 15 " - pdb=" SG CYS J 37 " distance=2.03 Simple disulfide: pdb=" SG CYS J 19 " - pdb=" SG CYS J 39 " distance=2.03 Simple disulfide: pdb=" SG CYS K 4 " - pdb=" SG CYS K 30 " distance=2.03 Simple disulfide: pdb=" SG CYS K 15 " - pdb=" SG CYS K 37 " distance=2.03 Simple disulfide: pdb=" SG CYS K 19 " - pdb=" SG CYS K 39 " distance=2.03 Simple disulfide: pdb=" SG CYS L 4 " - pdb=" SG CYS L 30 " distance=2.03 Simple disulfide: pdb=" SG CYS L 15 " - pdb=" SG CYS L 37 " distance=2.03 Simple disulfide: pdb=" SG CYS L 19 " - pdb=" SG CYS L 39 " distance=2.03 Simple disulfide: pdb=" SG CYS M 4 " - pdb=" SG CYS M 30 " distance=2.03 Simple disulfide: pdb=" SG CYS M 15 " - pdb=" SG CYS M 37 " distance=2.03 Simple disulfide: pdb=" SG CYS M 19 " - pdb=" SG CYS M 39 " distance=2.03 Simple disulfide: pdb=" SG CYS N 4 " - pdb=" SG CYS N 30 " distance=2.03 Simple disulfide: pdb=" SG CYS N 15 " - pdb=" SG CYS N 37 " distance=2.03 Simple disulfide: pdb=" SG CYS N 19 " - pdb=" SG CYS N 39 " distance=2.03 Simple disulfide: pdb=" SG CYS T 4 " - pdb=" SG CYS T 30 " distance=2.03 Simple disulfide: pdb=" SG CYS T 15 " - pdb=" SG CYS T 37 " distance=2.03 Simple disulfide: pdb=" SG CYS T 19 " - pdb=" SG CYS T 39 " distance=2.03 Simple disulfide: pdb=" SG CYS U 4 " - pdb=" SG CYS U 30 " distance=2.03 Simple disulfide: pdb=" SG CYS U 15 " - pdb=" SG CYS U 37 " distance=2.03 Simple disulfide: pdb=" SG CYS U 19 " - pdb=" SG CYS U 39 " distance=2.03 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 30 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 37 " distance=2.03 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 39 " distance=2.03 Simple disulfide: pdb=" SG CYS O 4 " - pdb=" SG CYS O 30 " distance=2.03 Simple disulfide: pdb=" SG CYS O 15 " - pdb=" SG CYS O 37 " distance=2.03 Simple disulfide: pdb=" SG CYS O 19 " - pdb=" SG CYS O 39 " distance=2.03 Simple disulfide: pdb=" SG CYS P 4 " - pdb=" SG CYS P 30 " distance=2.03 Simple disulfide: pdb=" SG CYS P 15 " - pdb=" SG CYS P 37 " distance=2.03 Simple disulfide: pdb=" SG CYS P 19 " - pdb=" SG CYS P 39 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 4 " - pdb=" SG CYS Q 30 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 15 " - pdb=" SG CYS Q 37 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 19 " - pdb=" SG CYS Q 39 " distance=2.03 Simple disulfide: pdb=" SG CYS R 4 " - pdb=" SG CYS R 30 " distance=2.03 Simple disulfide: pdb=" SG CYS R 15 " - pdb=" SG CYS R 37 " distance=2.03 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 39 " distance=2.03 Simple disulfide: pdb=" SG CYS S 4 " - pdb=" SG CYS S 30 " distance=2.03 Simple disulfide: pdb=" SG CYS S 15 " - pdb=" SG CYS S 37 " distance=2.03 Simple disulfide: pdb=" SG CYS S 19 " - pdb=" SG CYS S 39 " distance=2.03 Simple disulfide: pdb=" SG CYS V 4 " - pdb=" SG CYS V 30 " distance=2.03 Simple disulfide: pdb=" SG CYS V 15 " - pdb=" SG CYS V 37 " distance=2.03 Simple disulfide: pdb=" SG CYS V 19 " - pdb=" SG CYS V 39 " distance=2.03 Simple disulfide: pdb=" SG CYS W 4 " - pdb=" SG CYS W 30 " distance=2.03 Simple disulfide: pdb=" SG CYS W 15 " - pdb=" SG CYS W 37 " distance=2.03 Simple disulfide: pdb=" SG CYS W 19 " - pdb=" SG CYS W 39 " distance=2.03 Simple disulfide: pdb=" SG CYS X 4 " - pdb=" SG CYS X 30 " distance=2.03 Simple disulfide: pdb=" SG CYS X 15 " - pdb=" SG CYS X 37 " distance=2.03 Simple disulfide: pdb=" SG CYS X 19 " - pdb=" SG CYS X 39 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 4 " - pdb=" SG CYS Y 30 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 15 " - pdb=" SG CYS Y 37 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 19 " - pdb=" SG CYS Y 39 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 4 " - pdb=" SG CYS Z 30 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 15 " - pdb=" SG CYS Z 37 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 19 " - pdb=" SG CYS Z 39 " distance=2.03 Simple disulfide: pdb=" SG CYS 0 4 " - pdb=" SG CYS 0 30 " distance=2.03 Simple disulfide: pdb=" SG CYS 0 15 " - pdb=" SG CYS 0 37 " distance=2.03 Simple disulfide: pdb=" SG CYS 0 19 " - pdb=" SG CYS 0 39 " distance=2.03 Simple disulfide: pdb=" SG CYS 1 4 " - pdb=" SG CYS 1 30 " distance=2.03 Simple disulfide: pdb=" SG CYS 1 15 " - pdb=" SG CYS 1 37 " distance=2.03 Simple disulfide: pdb=" SG CYS 1 19 " - pdb=" SG CYS 1 39 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 4 " - pdb=" SG CYS 2 30 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 15 " - pdb=" SG CYS 2 37 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 19 " - pdb=" SG CYS 2 39 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 4 " - pdb=" SG CYS 3 30 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 15 " - pdb=" SG CYS 3 37 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 19 " - pdb=" SG CYS 3 39 " distance=2.03 Simple disulfide: pdb=" SG CYS 4 4 " - pdb=" SG CYS 4 30 " distance=2.03 Simple disulfide: pdb=" SG CYS 4 15 " - pdb=" SG CYS 4 37 " distance=2.03 Simple disulfide: pdb=" SG CYS 4 19 " - pdb=" SG CYS 4 39 " distance=2.03 Simple disulfide: pdb=" SG CYS 5 4 " - pdb=" SG CYS 5 30 " distance=2.03 Simple disulfide: pdb=" SG CYS 5 15 " - pdb=" SG CYS 5 37 " distance=2.03 Simple disulfide: pdb=" SG CYS 5 19 " - pdb=" SG CYS 5 39 " distance=2.03 Simple disulfide: pdb=" SG CYS 6 4 " - pdb=" SG CYS 6 30 " distance=2.03 Simple disulfide: pdb=" SG CYS 6 15 " - pdb=" SG CYS 6 37 " distance=2.03 Simple disulfide: pdb=" SG CYS 6 19 " - pdb=" SG CYS 6 39 " distance=2.03 Simple disulfide: pdb=" SG CYS 7 4 " - pdb=" SG CYS 7 30 " distance=2.03 Simple disulfide: pdb=" SG CYS 7 15 " - pdb=" SG CYS 7 37 " distance=2.03 Simple disulfide: pdb=" SG CYS 7 19 " - pdb=" SG CYS 7 39 " distance=2.03 Simple disulfide: pdb=" SG CYS 8 4 " - pdb=" SG CYS 8 30 " distance=2.03 Simple disulfide: pdb=" SG CYS 8 15 " - pdb=" SG CYS 8 37 " distance=2.03 Simple disulfide: pdb=" SG CYS 8 19 " - pdb=" SG CYS 8 39 " distance=2.03 Simple disulfide: pdb=" SG CYS 9 4 " - pdb=" SG CYS 9 30 " distance=2.03 Simple disulfide: pdb=" SG CYS 9 15 " - pdb=" SG CYS 9 37 " distance=2.03 Simple disulfide: pdb=" SG CYS 9 19 " - pdb=" SG CYS 9 39 " distance=2.03 Simple disulfide: pdb=" SG CYS a 4 " - pdb=" SG CYS a 30 " distance=2.03 Simple disulfide: pdb=" SG CYS a 15 " - pdb=" SG CYS a 37 " distance=2.03 Simple disulfide: pdb=" SG CYS a 19 " - pdb=" SG CYS a 39 " distance=2.03 Simple disulfide: pdb=" SG CYS b 4 " - pdb=" SG CYS b 30 " distance=2.03 Simple disulfide: pdb=" SG CYS b 15 " - pdb=" SG CYS b 37 " distance=2.03 Simple disulfide: pdb=" SG CYS b 19 " - pdb=" SG CYS b 39 " distance=2.03 Simple disulfide: pdb=" SG CYS c 4 " - pdb=" SG CYS c 30 " distance=2.03 Simple disulfide: pdb=" SG CYS c 15 " - pdb=" SG CYS c 37 " distance=2.03 Simple disulfide: pdb=" SG CYS c 19 " - pdb=" SG CYS c 39 " distance=2.03 Simple disulfide: pdb=" SG CYS d 4 " - pdb=" SG CYS d 30 " distance=2.03 Simple disulfide: pdb=" SG CYS d 15 " - pdb=" SG CYS d 37 " distance=2.03 Simple disulfide: pdb=" SG CYS d 19 " - pdb=" SG CYS d 39 " distance=2.03 Simple disulfide: pdb=" SG CYS e 4 " - pdb=" SG CYS e 30 " distance=2.03 Simple disulfide: pdb=" SG CYS e 15 " - pdb=" SG CYS e 37 " distance=2.03 Simple disulfide: pdb=" SG CYS e 19 " - pdb=" SG CYS e 39 " distance=2.03 Simple disulfide: pdb=" SG CYS f 4 " - pdb=" SG CYS f 30 " distance=2.03 Simple disulfide: pdb=" SG CYS f 15 " - pdb=" SG CYS f 37 " distance=2.03 Simple disulfide: pdb=" SG CYS f 19 " - pdb=" SG CYS f 39 " 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: 0.90 Conformation dependent library (CDL) restraints added in 527.4 milliseconds 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2688 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 42 sheets defined 47.9% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'B' and resid 5 through 9 Processing helix chain 'B' and resid 13 through 22 removed outlier: 3.649A pdb=" N ILE B 22 " --> pdb=" O HIS B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 35 Processing helix chain 'C' and resid 5 through 9 Processing helix chain 'C' and resid 13 through 21 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'D' and resid 5 through 9 Processing helix chain 'D' and resid 13 through 21 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'E' and resid 5 through 9 Processing helix chain 'E' and resid 13 through 21 Processing helix chain 'E' and resid 31 through 35 Processing helix chain 'F' and resid 5 through 9 Processing helix chain 'F' and resid 13 through 21 Processing helix chain 'F' and resid 31 through 35 Processing helix chain 'G' and resid 5 through 9 Processing helix chain 'G' and resid 13 through 21 Processing helix chain 'G' and resid 31 through 35 Processing helix chain 'H' and resid 5 through 9 Processing helix chain 'H' and resid 13 through 21 Processing helix chain 'H' and resid 31 through 35 Processing helix chain 'I' and resid 5 through 9 Processing helix chain 'I' and resid 13 through 22 removed outlier: 3.649A pdb=" N ILE I 22 " --> pdb=" O HIS I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 31 through 35 Processing helix chain 'J' and resid 5 through 9 Processing helix chain 'J' and resid 13 through 21 Processing helix chain 'J' and resid 31 through 35 Processing helix chain 'K' and resid 5 through 9 Processing helix chain 'K' and resid 13 through 21 Processing helix chain 'K' and resid 31 through 35 Processing helix chain 'L' and resid 5 through 9 Processing helix chain 'L' and resid 13 through 21 Processing helix chain 'L' and resid 31 through 35 Processing helix chain 'M' and resid 5 through 9 Processing helix chain 'M' and resid 13 through 21 Processing helix chain 'M' and resid 31 through 35 Processing helix chain 'N' and resid 5 through 9 Processing helix chain 'N' and resid 13 through 21 Processing helix chain 'N' and resid 31 through 35 Processing helix chain 'T' and resid 5 through 9 Processing helix chain 'T' and resid 13 through 21 Processing helix chain 'T' and resid 31 through 35 Processing helix chain 'U' and resid 5 through 9 Processing helix chain 'U' and resid 13 through 22 removed outlier: 3.650A pdb=" N ILE U 22 " --> pdb=" O HIS U 18 " (cutoff:3.500A) Processing helix chain 'U' and resid 31 through 35 Processing helix chain 'A' and resid 5 through 9 Processing helix chain 'A' and resid 13 through 21 Processing helix chain 'A' and resid 31 through 35 Processing helix chain 'O' and resid 5 through 9 Processing helix chain 'O' and resid 13 through 21 Processing helix chain 'O' and resid 31 through 35 Processing helix chain 'P' and resid 5 through 9 Processing helix chain 'P' and resid 13 through 21 Processing helix chain 'P' and resid 31 through 35 Processing helix chain 'Q' and resid 5 through 9 Processing helix chain 'Q' and resid 13 through 21 Processing helix chain 'Q' and resid 31 through 35 Processing helix chain 'R' and resid 5 through 9 Processing helix chain 'R' and resid 13 through 21 Processing helix chain 'R' and resid 31 through 35 Processing helix chain 'S' and resid 5 through 9 Processing helix chain 'S' and resid 13 through 21 Processing helix chain 'S' and resid 31 through 35 Processing helix chain 'V' and resid 5 through 9 Processing helix chain 'V' and resid 13 through 22 removed outlier: 3.650A pdb=" N ILE V 22 " --> pdb=" O HIS V 18 " (cutoff:3.500A) Processing helix chain 'V' and resid 31 through 35 Processing helix chain 'W' and resid 5 through 9 Processing helix chain 'W' and resid 13 through 21 Processing helix chain 'W' and resid 31 through 35 Processing helix chain 'X' and resid 5 through 9 Processing helix chain 'X' and resid 13 through 21 Processing helix chain 'X' and resid 31 through 35 Processing helix chain 'Y' and resid 5 through 9 Processing helix chain 'Y' and resid 13 through 21 Processing helix chain 'Y' and resid 31 through 35 Processing helix chain 'Z' and resid 5 through 9 Processing helix chain 'Z' and resid 13 through 21 Processing helix chain 'Z' and resid 31 through 35 Processing helix chain '0' and resid 5 through 9 Processing helix chain '0' and resid 13 through 21 Processing helix chain '0' and resid 31 through 35 Processing helix chain '1' and resid 5 through 9 Processing helix chain '1' and resid 13 through 21 Processing helix chain '1' and resid 31 through 35 Processing helix chain '2' and resid 5 through 9 Processing helix chain '2' and resid 13 through 22 removed outlier: 3.650A pdb=" N ILE 2 22 " --> pdb=" O HIS 2 18 " (cutoff:3.500A) Processing helix chain '2' and resid 31 through 35 Processing helix chain '3' and resid 5 through 9 Processing helix chain '3' and resid 13 through 21 Processing helix chain '3' and resid 31 through 35 Processing helix chain '4' and resid 5 through 9 Processing helix chain '4' and resid 13 through 21 Processing helix chain '4' and resid 31 through 35 Processing helix chain '5' and resid 5 through 9 Processing helix chain '5' and resid 13 through 21 Processing helix chain '5' and resid 31 through 35 Processing helix chain '6' and resid 5 through 9 Processing helix chain '6' and resid 13 through 21 Processing helix chain '6' and resid 31 through 35 Processing helix chain '7' and resid 5 through 9 Processing helix chain '7' and resid 13 through 21 Processing helix chain '7' and resid 31 through 35 Processing helix chain '8' and resid 5 through 9 Processing helix chain '8' and resid 13 through 21 Processing helix chain '8' and resid 31 through 35 Processing helix chain '9' and resid 5 through 9 Processing helix chain '9' and resid 13 through 22 removed outlier: 3.650A pdb=" N ILE 9 22 " --> pdb=" O HIS 9 18 " (cutoff:3.500A) Processing helix chain '9' and resid 31 through 35 Processing helix chain 'a' and resid 5 through 9 Processing helix chain 'a' and resid 13 through 21 Processing helix chain 'a' and resid 31 through 35 Processing helix chain 'b' and resid 5 through 9 Processing helix chain 'b' and resid 13 through 21 Processing helix chain 'b' and resid 31 through 35 Processing helix chain 'c' and resid 5 through 9 Processing helix chain 'c' and resid 13 through 21 Processing helix chain 'c' and resid 31 through 35 Processing helix chain 'd' and resid 5 through 9 Processing helix chain 'd' and resid 13 through 21 Processing helix chain 'd' and resid 31 through 35 Processing helix chain 'e' and resid 5 through 9 Processing helix chain 'e' and resid 13 through 21 Processing helix chain 'e' and resid 31 through 35 Processing helix chain 'f' and resid 5 through 9 Processing helix chain 'f' and resid 13 through 21 Processing helix chain 'f' and resid 31 through 35 Processing sheet with id=AA1, first strand: chain 'B' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'C' and resid 28 through 30 Processing sheet with id=AA3, first strand: chain 'D' and resid 28 through 30 Processing sheet with id=AA4, first strand: chain 'E' and resid 28 through 30 Processing sheet with id=AA5, first strand: chain 'F' and resid 28 through 30 Processing sheet with id=AA6, first strand: chain 'G' and resid 28 through 30 Processing sheet with id=AA7, first strand: chain 'H' and resid 28 through 30 Processing sheet with id=AA8, first strand: chain 'I' and resid 28 through 30 Processing sheet with id=AA9, first strand: chain 'J' and resid 28 through 30 Processing sheet with id=AB1, first strand: chain 'K' and resid 28 through 30 Processing sheet with id=AB2, first strand: chain 'L' and resid 28 through 30 Processing sheet with id=AB3, first strand: chain 'M' and resid 28 through 30 Processing sheet with id=AB4, first strand: chain 'N' and resid 28 through 30 Processing sheet with id=AB5, first strand: chain 'T' and resid 28 through 30 Processing sheet with id=AB6, first strand: chain 'U' and resid 28 through 30 Processing sheet with id=AB7, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AB8, first strand: chain 'O' and resid 28 through 30 Processing sheet with id=AB9, first strand: chain 'P' and resid 28 through 30 Processing sheet with id=AC1, first strand: chain 'Q' and resid 28 through 30 Processing sheet with id=AC2, first strand: chain 'R' and resid 28 through 30 Processing sheet with id=AC3, first strand: chain 'S' and resid 28 through 30 Processing sheet with id=AC4, first strand: chain 'V' and resid 28 through 30 Processing sheet with id=AC5, first strand: chain 'W' and resid 28 through 30 Processing sheet with id=AC6, first strand: chain 'X' and resid 28 through 30 Processing sheet with id=AC7, first strand: chain 'Y' and resid 28 through 30 Processing sheet with id=AC8, first strand: chain 'Z' and resid 28 through 30 Processing sheet with id=AC9, first strand: chain '0' and resid 28 through 30 Processing sheet with id=AD1, first strand: chain '1' and resid 28 through 30 Processing sheet with id=AD2, first strand: chain '2' and resid 28 through 30 Processing sheet with id=AD3, first strand: chain '3' and resid 28 through 30 Processing sheet with id=AD4, first strand: chain '4' and resid 28 through 30 Processing sheet with id=AD5, first strand: chain '5' and resid 28 through 30 Processing sheet with id=AD6, first strand: chain '6' and resid 28 through 30 Processing sheet with id=AD7, first strand: chain '7' and resid 28 through 30 Processing sheet with id=AD8, first strand: chain '8' and resid 28 through 30 Processing sheet with id=AD9, first strand: chain '9' and resid 28 through 30 Processing sheet with id=AE1, first strand: chain 'a' and resid 28 through 30 Processing sheet with id=AE2, first strand: chain 'b' and resid 28 through 30 Processing sheet with id=AE3, first strand: chain 'c' and resid 28 through 30 Processing sheet with id=AE4, first strand: chain 'd' and resid 28 through 30 Processing sheet with id=AE5, first strand: chain 'e' and resid 28 through 30 Processing sheet with id=AE6, first strand: chain 'f' and resid 28 through 30 420 hydrogen bonds defined for protein. 1008 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: 1.86 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3948 1.34 - 1.46: 3478 1.46 - 1.58: 5384 1.58 - 1.69: 0 1.69 - 1.81: 336 Bond restraints: 13146 Sorted by residual: bond pdb=" CB TRP 2 8 " pdb=" CG TRP 2 8 " ideal model delta sigma weight residual 1.498 1.462 0.036 3.10e-02 1.04e+03 1.31e+00 bond pdb=" CB TRP I 8 " pdb=" CG TRP I 8 " ideal model delta sigma weight residual 1.498 1.463 0.035 3.10e-02 1.04e+03 1.31e+00 bond pdb=" CB TRP V 8 " pdb=" CG TRP V 8 " ideal model delta sigma weight residual 1.498 1.463 0.035 3.10e-02 1.04e+03 1.29e+00 bond pdb=" CB TRP U 8 " pdb=" CG TRP U 8 " ideal model delta sigma weight residual 1.498 1.463 0.035 3.10e-02 1.04e+03 1.27e+00 bond pdb=" CB TRP B 8 " pdb=" CG TRP B 8 " ideal model delta sigma weight residual 1.498 1.463 0.035 3.10e-02 1.04e+03 1.25e+00 ... (remaining 13141 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.70: 15053 0.70 - 1.40: 1937 1.40 - 2.10: 339 2.10 - 2.80: 59 2.80 - 3.50: 42 Bond angle restraints: 17430 Sorted by residual: angle pdb=" C MET a 13 " pdb=" CA MET a 13 " pdb=" CB MET a 13 " ideal model delta sigma weight residual 111.23 108.64 2.59 1.63e+00 3.76e-01 2.53e+00 angle pdb=" C MET W 13 " pdb=" CA MET W 13 " pdb=" CB MET W 13 " ideal model delta sigma weight residual 111.23 108.65 2.58 1.63e+00 3.76e-01 2.51e+00 angle pdb=" C MET 3 13 " pdb=" CA MET 3 13 " pdb=" CB MET 3 13 " ideal model delta sigma weight residual 111.23 108.65 2.58 1.63e+00 3.76e-01 2.51e+00 angle pdb=" C MET J 13 " pdb=" CA MET J 13 " pdb=" CB MET J 13 " ideal model delta sigma weight residual 111.23 108.66 2.57 1.63e+00 3.76e-01 2.49e+00 angle pdb=" C MET A 13 " pdb=" CA MET A 13 " pdb=" CB MET A 13 " ideal model delta sigma weight residual 111.23 108.66 2.57 1.63e+00 3.76e-01 2.49e+00 ... (remaining 17425 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.57: 6834 11.57 - 23.13: 714 23.13 - 34.70: 156 34.70 - 46.27: 42 46.27 - 57.83: 24 Dihedral angle restraints: 7770 sinusoidal: 3318 harmonic: 4452 Sorted by residual: dihedral pdb=" SG CYS I 19 " pdb=" CB CYS I 39 " pdb=" SG CYS I 39 " pdb=" CA CYS I 39 " ideal model delta sinusoidal sigma weight residual 79.00 40.53 38.47 1 2.00e+01 2.50e-03 5.21e+00 dihedral pdb=" SG CYS 2 19 " pdb=" CB CYS 2 39 " pdb=" SG CYS 2 39 " pdb=" CA CYS 2 39 " ideal model delta sinusoidal sigma weight residual 79.00 40.54 38.46 1 2.00e+01 2.50e-03 5.21e+00 dihedral pdb=" SG CYS 9 19 " pdb=" CB CYS 9 39 " pdb=" SG CYS 9 39 " pdb=" CA CYS 9 39 " ideal model delta sinusoidal sigma weight residual 79.00 40.54 38.46 1 2.00e+01 2.50e-03 5.21e+00 ... (remaining 7767 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 681 0.024 - 0.048: 289 0.048 - 0.073: 236 0.073 - 0.097: 100 0.097 - 0.121: 122 Chirality restraints: 1428 Sorted by residual: chirality pdb=" CA PRO N 7 " pdb=" N PRO N 7 " pdb=" C PRO N 7 " pdb=" CB PRO N 7 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.67e-01 chirality pdb=" CA PRO R 7 " pdb=" N PRO R 7 " pdb=" C PRO R 7 " pdb=" CB PRO R 7 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.67e-01 chirality pdb=" CA PRO T 7 " pdb=" N PRO T 7 " pdb=" C PRO T 7 " pdb=" CB PRO T 7 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.64e-01 ... (remaining 1425 not shown) Planarity restraints: 2268 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY 9 6 " 0.016 5.00e-02 4.00e+02 2.37e-02 9.01e-01 pdb=" N PRO 9 7 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO 9 7 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO 9 7 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY 2 6 " 0.016 5.00e-02 4.00e+02 2.36e-02 8.93e-01 pdb=" N PRO 2 7 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO 2 7 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO 2 7 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY I 6 " 0.016 5.00e-02 4.00e+02 2.36e-02 8.91e-01 pdb=" N PRO I 7 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO I 7 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO I 7 " 0.013 5.00e-02 4.00e+02 ... (remaining 2265 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 5512 2.93 - 3.42: 11385 3.42 - 3.92: 23277 3.92 - 4.41: 25147 4.41 - 4.90: 42143 Nonbonded interactions: 107464 Sorted by model distance: nonbonded pdb=" NZ LYS E 14 " pdb=" OD2 ASP G 11 " model vdw 2.440 3.120 nonbonded pdb=" N ASP U 12 " pdb=" OD1 ASP U 12 " model vdw 2.445 3.120 nonbonded pdb=" N ASP 2 12 " pdb=" OD1 ASP 2 12 " model vdw 2.445 3.120 nonbonded pdb=" N ASP V 12 " pdb=" OD1 ASP V 12 " model vdw 2.446 3.120 nonbonded pdb=" N ASP B 12 " pdb=" OD1 ASP B 12 " model vdw 2.446 3.120 ... (remaining 107459 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' } 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: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 11.640 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 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:6.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 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 0.041 13272 Z= 0.350 Angle : 0.530 3.501 17682 Z= 0.314 Chirality : 0.049 0.121 1428 Planarity : 0.003 0.024 2268 Dihedral : 9.441 57.834 4704 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.22 (0.21), residues: 1596 helix: 1.78 (0.28), residues: 378 sheet: -0.91 (0.31), residues: 378 loop : 0.02 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR U 25 PHE 0.007 0.001 PHE P 35 TRP 0.010 0.002 TRP 1 8 HIS 0.004 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00760 (13146) covalent geometry : angle 0.52609 (17430) SS BOND : bond 0.00138 ( 126) SS BOND : angle 0.74154 ( 252) hydrogen bonds : bond 0.12159 ( 420) hydrogen bonds : angle 5.15067 ( 1008) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 385 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 8 32 LYS cc_start: 0.9052 (mmtt) cc_final: 0.8023 (mtpt) REVERT: e 32 LYS cc_start: 0.9282 (mmtt) cc_final: 0.8273 (mtmt) outliers start: 0 outliers final: 1 residues processed: 385 average time/residue: 0.8323 time to fit residues: 339.0967 Evaluate side-chains 309 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 308 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 22 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.1980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.0370 overall best weight: 1.4464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 16 HIS F 16 HIS ** L 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 16 HIS S 17 ASN 0 16 HIS 4 16 HIS 5 16 HIS a 17 ASN c 16 HIS e 17 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.102780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.060916 restraints weight = 19305.462| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 3.22 r_work: 0.2630 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2509 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9142 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 13272 Z= 0.100 Angle : 0.441 6.380 17682 Z= 0.239 Chirality : 0.042 0.122 1428 Planarity : 0.003 0.029 2268 Dihedral : 3.250 24.434 1808 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.46 % Allowed : 15.98 % Favored : 82.57 % 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: 0.20 (0.22), residues: 1596 helix: 1.10 (0.27), residues: 420 sheet: -0.81 (0.31), residues: 378 loop : 0.27 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR N 25 PHE 0.004 0.001 PHE H 2 TRP 0.011 0.002 TRP L 8 HIS 0.007 0.001 HIS 6 16 Details of bonding type rmsd covalent geometry : bond 0.00222 (13146) covalent geometry : angle 0.43938 (17430) SS BOND : bond 0.00092 ( 126) SS BOND : angle 0.54943 ( 252) hydrogen bonds : bond 0.02535 ( 420) hydrogen bonds : angle 4.85279 ( 1008) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 317 time to evaluate : 0.542 Fit side-chains REVERT: N 26 LYS cc_start: 0.8716 (mppt) cc_final: 0.8485 (mppt) REVERT: P 14 LYS cc_start: 0.8870 (mtpp) cc_final: 0.8614 (mtpt) REVERT: P 20 LYS cc_start: 0.8650 (mtmm) cc_final: 0.8380 (mtmm) REVERT: P 26 LYS cc_start: 0.8919 (ptpp) cc_final: 0.8717 (pttp) REVERT: W 14 LYS cc_start: 0.9138 (mttp) cc_final: 0.8899 (mtpt) REVERT: Z 20 LYS cc_start: 0.8963 (mtpt) cc_final: 0.8665 (mtmt) REVERT: 1 38 LYS cc_start: 0.9105 (tttm) cc_final: 0.8861 (ttmp) REVERT: 4 14 LYS cc_start: 0.9042 (ttpp) cc_final: 0.8785 (ttmp) REVERT: 5 20 LYS cc_start: 0.8880 (mtmm) cc_final: 0.8470 (mtmm) REVERT: 6 20 LYS cc_start: 0.9275 (mtmt) cc_final: 0.8887 (mtmt) REVERT: 7 20 LYS cc_start: 0.9165 (mtmt) cc_final: 0.8908 (mtmm) REVERT: 8 32 LYS cc_start: 0.9499 (mmtt) cc_final: 0.8405 (mtpt) REVERT: b 14 LYS cc_start: 0.8965 (ttpp) cc_final: 0.8701 (ttmp) REVERT: b 20 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8574 (mtmm) REVERT: b 38 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8830 (ttmm) REVERT: c 20 LYS cc_start: 0.8812 (mtmm) cc_final: 0.8211 (mtmm) REVERT: d 20 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8756 (mttp) REVERT: e 32 LYS cc_start: 0.9544 (mmtt) cc_final: 0.8450 (mtmt) REVERT: f 20 LYS cc_start: 0.8996 (mtpp) cc_final: 0.8766 (mtpp) outliers start: 19 outliers final: 4 residues processed: 318 average time/residue: 0.8706 time to fit residues: 292.3680 Evaluate side-chains 311 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 304 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 22 ILE Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain b residue 20 LYS Chi-restraints excluded: chain b residue 22 ILE Chi-restraints excluded: chain b residue 38 LYS Chi-restraints excluded: chain d residue 20 LYS Chi-restraints excluded: chain d residue 38 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 38 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 120 optimal weight: 10.0000 chunk 5 optimal weight: 0.6980 chunk 58 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 118 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 16 HIS L 17 ASN ** Y 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 16 HIS e 17 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.101358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.059440 restraints weight = 19509.675| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 3.23 r_work: 0.2588 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2465 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9157 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13272 Z= 0.157 Angle : 0.441 4.697 17682 Z= 0.243 Chirality : 0.044 0.120 1428 Planarity : 0.004 0.030 2268 Dihedral : 3.343 25.094 1808 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.07 % Allowed : 14.82 % Favored : 83.10 % 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: 0.19 (0.22), residues: 1596 helix: 1.07 (0.27), residues: 420 sheet: -0.80 (0.31), residues: 378 loop : 0.25 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR E 25 PHE 0.005 0.001 PHE a 35 TRP 0.011 0.002 TRP 0 8 HIS 0.005 0.001 HIS d 16 Details of bonding type rmsd covalent geometry : bond 0.00347 (13146) covalent geometry : angle 0.44028 (17430) SS BOND : bond 0.00082 ( 126) SS BOND : angle 0.48310 ( 252) hydrogen bonds : bond 0.02822 ( 420) hydrogen bonds : angle 4.97819 ( 1008) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 309 time to evaluate : 0.560 Fit side-chains revert: symmetry clash REVERT: O 20 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8728 (mtmm) REVERT: R 20 LYS cc_start: 0.9177 (mtpt) cc_final: 0.8951 (ttmt) REVERT: W 14 LYS cc_start: 0.9134 (mttp) cc_final: 0.8902 (mtpt) REVERT: X 20 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8740 (mtmm) REVERT: 1 26 LYS cc_start: 0.8942 (mtmm) cc_final: 0.8678 (mppt) REVERT: 4 14 LYS cc_start: 0.9022 (ttpp) cc_final: 0.8796 (ttmp) REVERT: 6 20 LYS cc_start: 0.9290 (mtmt) cc_final: 0.9076 (mtmt) REVERT: 8 20 LYS cc_start: 0.9079 (mtpp) cc_final: 0.8875 (mmmm) REVERT: 8 32 LYS cc_start: 0.9536 (mmtt) cc_final: 0.8594 (mtpt) REVERT: b 14 LYS cc_start: 0.8934 (ttpp) cc_final: 0.8708 (ttmp) REVERT: c 20 LYS cc_start: 0.8794 (mtmm) cc_final: 0.8455 (mtmm) REVERT: d 20 LYS cc_start: 0.9177 (OUTLIER) cc_final: 0.8798 (mttp) REVERT: e 32 LYS cc_start: 0.9565 (mmtt) cc_final: 0.8339 (mtpt) REVERT: f 32 LYS cc_start: 0.9591 (mmtp) cc_final: 0.8696 (mtpt) outliers start: 27 outliers final: 3 residues processed: 309 average time/residue: 0.8778 time to fit residues: 286.1445 Evaluate side-chains 309 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 303 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 20 LYS Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain X residue 20 LYS Chi-restraints excluded: chain 2 residue 20 LYS Chi-restraints excluded: chain b residue 22 ILE Chi-restraints excluded: chain d residue 20 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 8 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 105 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 chunk 99 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 16 HIS ** Y 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 17 ASN b 16 HIS e 17 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.101138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.059263 restraints weight = 19437.588| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 3.23 r_work: 0.2587 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2463 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9159 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 13272 Z= 0.170 Angle : 0.457 5.059 17682 Z= 0.249 Chirality : 0.044 0.120 1428 Planarity : 0.004 0.031 2268 Dihedral : 3.343 16.048 1806 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.77 % Allowed : 15.59 % Favored : 82.64 % 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: 0.16 (0.22), residues: 1596 helix: 1.06 (0.27), residues: 420 sheet: -0.82 (0.31), residues: 378 loop : 0.24 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR E 25 PHE 0.006 0.001 PHE D 2 TRP 0.011 0.002 TRP 0 8 HIS 0.005 0.001 HIS d 16 Details of bonding type rmsd covalent geometry : bond 0.00378 (13146) covalent geometry : angle 0.45652 (17430) SS BOND : bond 0.00095 ( 126) SS BOND : angle 0.48732 ( 252) hydrogen bonds : bond 0.02785 ( 420) hydrogen bonds : angle 4.99614 ( 1008) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 307 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 20 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8741 (mtmm) REVERT: R 20 LYS cc_start: 0.9171 (mtpt) cc_final: 0.8892 (ttmt) REVERT: W 14 LYS cc_start: 0.9132 (mttp) cc_final: 0.8897 (mtpt) REVERT: X 20 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8758 (mtmm) REVERT: 1 26 LYS cc_start: 0.8926 (mtmm) cc_final: 0.8685 (mppt) REVERT: 1 38 LYS cc_start: 0.9179 (ttmm) cc_final: 0.8911 (ttmp) REVERT: 4 14 LYS cc_start: 0.9005 (ttpp) cc_final: 0.8780 (ttmp) REVERT: 4 20 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8694 (mtmm) REVERT: 8 20 LYS cc_start: 0.9084 (mtpp) cc_final: 0.8867 (mmmm) REVERT: 8 32 LYS cc_start: 0.9529 (mmtt) cc_final: 0.8587 (mtpt) REVERT: b 14 LYS cc_start: 0.8917 (ttpp) cc_final: 0.8693 (ttmp) REVERT: b 20 LYS cc_start: 0.8894 (mtmm) cc_final: 0.8610 (mtmm) REVERT: e 32 LYS cc_start: 0.9571 (mmtt) cc_final: 0.8346 (mtpt) REVERT: f 32 LYS cc_start: 0.9596 (mmtp) cc_final: 0.8687 (mtpt) outliers start: 23 outliers final: 7 residues processed: 307 average time/residue: 0.8772 time to fit residues: 284.4481 Evaluate side-chains 312 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 302 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 20 LYS Chi-restraints excluded: chain O residue 22 ILE Chi-restraints excluded: chain R residue 22 ILE Chi-restraints excluded: chain X residue 20 LYS Chi-restraints excluded: chain X residue 22 ILE Chi-restraints excluded: chain 0 residue 20 LYS Chi-restraints excluded: chain 2 residue 20 LYS Chi-restraints excluded: chain 4 residue 20 LYS Chi-restraints excluded: chain 9 residue 20 LYS Chi-restraints excluded: chain c residue 20 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 91 optimal weight: 0.9980 chunk 70 optimal weight: 0.2980 chunk 134 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 59 optimal weight: 7.9990 chunk 141 optimal weight: 20.0000 chunk 57 optimal weight: 0.9990 chunk 82 optimal weight: 10.0000 chunk 67 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 17 ASN e 17 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.102801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.061245 restraints weight = 19370.303| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 3.23 r_work: 0.2637 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2518 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9122 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13272 Z= 0.073 Angle : 0.411 5.656 17682 Z= 0.218 Chirality : 0.041 0.121 1428 Planarity : 0.003 0.026 2268 Dihedral : 2.838 15.369 1806 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 1.54 % Allowed : 15.82 % Favored : 82.64 % 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: 0.30 (0.22), residues: 1596 helix: 1.07 (0.27), residues: 420 sheet: -0.77 (0.32), residues: 378 loop : 0.41 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR f 29 PHE 0.003 0.000 PHE e 2 TRP 0.009 0.001 TRP H 8 HIS 0.005 0.001 HIS F 16 Details of bonding type rmsd covalent geometry : bond 0.00159 (13146) covalent geometry : angle 0.41062 (17430) SS BOND : bond 0.00073 ( 126) SS BOND : angle 0.41925 ( 252) hydrogen bonds : bond 0.01936 ( 420) hydrogen bonds : angle 4.66134 ( 1008) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 310 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 26 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8700 (mtmm) REVERT: O 14 LYS cc_start: 0.9063 (mtpt) cc_final: 0.8814 (mtpp) REVERT: O 20 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8754 (mtmm) REVERT: Q 20 LYS cc_start: 0.9048 (mtpt) cc_final: 0.8549 (mtmt) REVERT: R 20 LYS cc_start: 0.9211 (mtpt) cc_final: 0.8942 (ttmt) REVERT: 1 26 LYS cc_start: 0.8964 (mtmm) cc_final: 0.8688 (mppt) REVERT: 4 14 LYS cc_start: 0.8969 (ttpp) cc_final: 0.8751 (ttmp) REVERT: 4 20 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8624 (mtmm) REVERT: 5 20 LYS cc_start: 0.8951 (mtmm) cc_final: 0.8469 (mtmm) REVERT: 7 20 LYS cc_start: 0.9202 (ttmm) cc_final: 0.8704 (mtmm) REVERT: 8 32 LYS cc_start: 0.9483 (mmtt) cc_final: 0.8554 (mtpt) REVERT: b 14 LYS cc_start: 0.8901 (ttpp) cc_final: 0.8620 (ttmm) REVERT: b 20 LYS cc_start: 0.8938 (mtmm) cc_final: 0.8649 (mtmm) REVERT: c 20 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8544 (mtmm) REVERT: e 32 LYS cc_start: 0.9551 (mmtt) cc_final: 0.8396 (mtpt) REVERT: f 20 LYS cc_start: 0.9047 (mmmm) cc_final: 0.8794 (mmmm) REVERT: f 32 LYS cc_start: 0.9551 (mmtp) cc_final: 0.8650 (mtpt) outliers start: 20 outliers final: 4 residues processed: 311 average time/residue: 0.8559 time to fit residues: 281.2701 Evaluate side-chains 313 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 305 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 26 LYS Chi-restraints excluded: chain O residue 20 LYS Chi-restraints excluded: chain O residue 22 ILE Chi-restraints excluded: chain 0 residue 20 LYS Chi-restraints excluded: chain 4 residue 20 LYS Chi-restraints excluded: chain 9 residue 20 LYS Chi-restraints excluded: chain b residue 22 ILE Chi-restraints excluded: chain c residue 20 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 10 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 161 optimal weight: 0.0060 chunk 72 optimal weight: 0.0070 chunk 132 optimal weight: 8.9990 chunk 18 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 overall best weight: 1.3618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 16 HIS 7 17 ASN e 17 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.102465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.060543 restraints weight = 19298.716| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 3.24 r_work: 0.2621 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2500 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9134 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13272 Z= 0.092 Angle : 0.447 7.815 17682 Z= 0.235 Chirality : 0.042 0.124 1428 Planarity : 0.003 0.025 2268 Dihedral : 2.756 10.259 1806 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.23 % Allowed : 16.51 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.34 (0.22), residues: 1596 helix: 1.12 (0.27), residues: 420 sheet: -0.75 (0.32), residues: 378 loop : 0.43 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR Z 40 PHE 0.006 0.000 PHE e 2 TRP 0.010 0.002 TRP H 8 HIS 0.006 0.001 HIS G 16 Details of bonding type rmsd covalent geometry : bond 0.00209 (13146) covalent geometry : angle 0.44749 (17430) SS BOND : bond 0.00069 ( 126) SS BOND : angle 0.37797 ( 252) hydrogen bonds : bond 0.02151 ( 420) hydrogen bonds : angle 4.68212 ( 1008) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 310 time to evaluate : 0.426 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: G 20 LYS cc_start: 0.9070 (ttmm) cc_final: 0.8477 (mtmm) REVERT: G 26 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8763 (mtmm) REVERT: O 14 LYS cc_start: 0.9064 (mtpt) cc_final: 0.8811 (mtpp) REVERT: O 20 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8759 (mtmm) REVERT: R 20 LYS cc_start: 0.9224 (mtpt) cc_final: 0.8954 (ttmt) REVERT: X 20 LYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8771 (mtmm) REVERT: 1 26 LYS cc_start: 0.8967 (mtmm) cc_final: 0.8694 (mppt) REVERT: 4 14 LYS cc_start: 0.8946 (ttpp) cc_final: 0.8736 (ttmp) REVERT: 4 20 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8629 (mtmm) REVERT: 7 20 LYS cc_start: 0.9215 (ttmm) cc_final: 0.8785 (mtmm) REVERT: 8 20 LYS cc_start: 0.9057 (mmmm) cc_final: 0.8854 (mmmm) REVERT: 8 32 LYS cc_start: 0.9507 (mmtt) cc_final: 0.8592 (mtpt) REVERT: b 14 LYS cc_start: 0.8881 (ttpp) cc_final: 0.8612 (ttmm) REVERT: b 20 LYS cc_start: 0.8982 (mtmm) cc_final: 0.8633 (mtmm) REVERT: e 26 LYS cc_start: 0.8916 (mtmm) cc_final: 0.8683 (mppt) REVERT: e 32 LYS cc_start: 0.9562 (mmtt) cc_final: 0.8430 (mtpt) REVERT: f 20 LYS cc_start: 0.9095 (mmmm) cc_final: 0.8866 (mmtp) REVERT: f 32 LYS cc_start: 0.9572 (mmtp) cc_final: 0.8673 (mtpt) outliers start: 16 outliers final: 7 residues processed: 310 average time/residue: 0.8206 time to fit residues: 269.1250 Evaluate side-chains 316 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 305 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 26 LYS Chi-restraints excluded: chain O residue 20 LYS Chi-restraints excluded: chain O residue 22 ILE Chi-restraints excluded: chain X residue 20 LYS Chi-restraints excluded: chain X residue 22 ILE Chi-restraints excluded: chain 0 residue 20 LYS Chi-restraints excluded: chain 4 residue 20 LYS Chi-restraints excluded: chain 9 residue 20 LYS Chi-restraints excluded: chain b residue 22 ILE Chi-restraints excluded: chain c residue 20 LYS Chi-restraints excluded: chain f residue 38 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 79 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 120 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 124 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 141 optimal weight: 9.9990 chunk 122 optimal weight: 7.9990 chunk 135 optimal weight: 7.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 16 HIS 7 17 ASN e 17 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.101960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.059985 restraints weight = 19241.925| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 3.23 r_work: 0.2607 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2485 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9145 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13272 Z= 0.123 Angle : 0.456 7.074 17682 Z= 0.240 Chirality : 0.043 0.120 1428 Planarity : 0.003 0.026 2268 Dihedral : 2.881 11.789 1806 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.15 % Allowed : 16.36 % Favored : 82.49 % 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: 0.30 (0.22), residues: 1596 helix: 1.12 (0.27), residues: 420 sheet: -0.79 (0.31), residues: 378 loop : 0.39 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR E 25 PHE 0.007 0.001 PHE K 2 TRP 0.010 0.002 TRP T 8 HIS 0.005 0.001 HIS e 16 Details of bonding type rmsd covalent geometry : bond 0.00276 (13146) covalent geometry : angle 0.45701 (17430) SS BOND : bond 0.00078 ( 126) SS BOND : angle 0.39161 ( 252) hydrogen bonds : bond 0.02437 ( 420) hydrogen bonds : angle 4.79464 ( 1008) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 310 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 20 LYS cc_start: 0.8844 (mtmm) cc_final: 0.8598 (mttp) REVERT: G 26 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8836 (mtmm) REVERT: O 20 LYS cc_start: 0.9101 (OUTLIER) cc_final: 0.8761 (mtmm) REVERT: R 20 LYS cc_start: 0.9222 (mtpt) cc_final: 0.8909 (ttmt) REVERT: X 20 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8763 (mtmm) REVERT: 1 26 LYS cc_start: 0.8963 (mtmm) cc_final: 0.8698 (mppt) REVERT: 4 14 LYS cc_start: 0.8935 (ttpp) cc_final: 0.8726 (ttmp) REVERT: 4 20 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8627 (mtmm) REVERT: 6 20 LYS cc_start: 0.9235 (ttpt) cc_final: 0.8959 (mtmt) REVERT: 7 20 LYS cc_start: 0.9221 (ttmm) cc_final: 0.8618 (mtmm) REVERT: 7 38 LYS cc_start: 0.9388 (OUTLIER) cc_final: 0.8850 (tttm) REVERT: 8 20 LYS cc_start: 0.9075 (mmmm) cc_final: 0.8860 (mmmm) REVERT: 8 32 LYS cc_start: 0.9532 (mmtt) cc_final: 0.8629 (mtpt) REVERT: b 14 LYS cc_start: 0.8894 (ttpp) cc_final: 0.8637 (ttmm) REVERT: b 20 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8798 (mtmm) REVERT: e 26 LYS cc_start: 0.8897 (mtmm) cc_final: 0.8674 (mppt) REVERT: e 32 LYS cc_start: 0.9567 (mmtt) cc_final: 0.8410 (mtpt) REVERT: f 32 LYS cc_start: 0.9592 (mmtp) cc_final: 0.8686 (mtpt) outliers start: 15 outliers final: 7 residues processed: 310 average time/residue: 0.8774 time to fit residues: 287.2248 Evaluate side-chains 320 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 307 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 26 LYS Chi-restraints excluded: chain O residue 20 LYS Chi-restraints excluded: chain O residue 22 ILE Chi-restraints excluded: chain X residue 20 LYS Chi-restraints excluded: chain X residue 22 ILE Chi-restraints excluded: chain 0 residue 20 LYS Chi-restraints excluded: chain 4 residue 20 LYS Chi-restraints excluded: chain 4 residue 38 LYS Chi-restraints excluded: chain 7 residue 38 LYS Chi-restraints excluded: chain 9 residue 20 LYS Chi-restraints excluded: chain b residue 20 LYS Chi-restraints excluded: chain b residue 22 ILE Chi-restraints excluded: chain f residue 38 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 82 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 145 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 120 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 17 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.101863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.059940 restraints weight = 19212.717| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 3.23 r_work: 0.2607 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2485 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9145 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13272 Z= 0.126 Angle : 0.469 7.802 17682 Z= 0.244 Chirality : 0.043 0.121 1428 Planarity : 0.003 0.027 2268 Dihedral : 2.914 12.735 1806 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.77 % Allowed : 16.90 % Favored : 82.33 % 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: 0.30 (0.22), residues: 1596 helix: 1.14 (0.27), residues: 420 sheet: -0.80 (0.31), residues: 378 loop : 0.38 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR E 25 PHE 0.006 0.001 PHE e 2 TRP 0.010 0.002 TRP H 8 HIS 0.007 0.001 HIS 6 16 Details of bonding type rmsd covalent geometry : bond 0.00283 (13146) covalent geometry : angle 0.47031 (17430) SS BOND : bond 0.00080 ( 126) SS BOND : angle 0.39666 ( 252) hydrogen bonds : bond 0.02462 ( 420) hydrogen bonds : angle 4.79680 ( 1008) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 309 time to evaluate : 0.517 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: E 20 LYS cc_start: 0.8830 (mtmm) cc_final: 0.8592 (mttp) REVERT: G 20 LYS cc_start: 0.9034 (ttmm) cc_final: 0.8465 (mtmm) REVERT: G 26 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8801 (mtmm) REVERT: O 20 LYS cc_start: 0.9101 (OUTLIER) cc_final: 0.8761 (mtmm) REVERT: R 20 LYS cc_start: 0.9220 (mtpt) cc_final: 0.8909 (ttmt) REVERT: X 20 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8755 (mtmm) REVERT: 1 26 LYS cc_start: 0.8948 (mtmm) cc_final: 0.8702 (mppt) REVERT: 4 14 LYS cc_start: 0.8935 (ttpp) cc_final: 0.8728 (ttmp) REVERT: 4 20 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8614 (mtmm) REVERT: 8 20 LYS cc_start: 0.9116 (mmmm) cc_final: 0.8910 (mmmm) REVERT: 8 32 LYS cc_start: 0.9528 (mmtt) cc_final: 0.8605 (mtpt) REVERT: b 14 LYS cc_start: 0.8912 (ttpp) cc_final: 0.8634 (ttmm) REVERT: b 20 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8859 (mtmm) REVERT: e 20 LYS cc_start: 0.9234 (ttmm) cc_final: 0.8758 (mtmm) REVERT: e 26 LYS cc_start: 0.8893 (mtmm) cc_final: 0.8655 (mppt) REVERT: e 32 LYS cc_start: 0.9569 (mmtt) cc_final: 0.8409 (mtpt) REVERT: f 20 LYS cc_start: 0.9065 (mmmm) cc_final: 0.8829 (mmmm) REVERT: f 32 LYS cc_start: 0.9592 (mmtp) cc_final: 0.8677 (mtpt) outliers start: 10 outliers final: 7 residues processed: 309 average time/residue: 0.8449 time to fit residues: 275.7346 Evaluate side-chains 320 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 308 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 26 LYS Chi-restraints excluded: chain O residue 20 LYS Chi-restraints excluded: chain O residue 22 ILE Chi-restraints excluded: chain X residue 20 LYS Chi-restraints excluded: chain 0 residue 20 LYS Chi-restraints excluded: chain 4 residue 20 LYS Chi-restraints excluded: chain 4 residue 38 LYS Chi-restraints excluded: chain 9 residue 20 LYS Chi-restraints excluded: chain b residue 20 LYS Chi-restraints excluded: chain b residue 22 ILE Chi-restraints excluded: chain c residue 20 LYS Chi-restraints excluded: chain c residue 22 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 37 optimal weight: 0.3980 chunk 123 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 145 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 104 optimal weight: 0.0570 chunk 139 optimal weight: 8.9990 chunk 52 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 29 optimal weight: 0.0370 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 17 ASN e 17 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.103270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.061632 restraints weight = 19363.469| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 3.24 r_work: 0.2650 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2531 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9114 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13272 Z= 0.075 Angle : 0.448 8.381 17682 Z= 0.228 Chirality : 0.041 0.120 1428 Planarity : 0.003 0.025 2268 Dihedral : 2.631 18.158 1806 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 0.92 % Allowed : 16.59 % Favored : 82.49 % 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: 0.41 (0.22), residues: 1596 helix: 1.13 (0.27), residues: 420 sheet: -0.74 (0.32), residues: 378 loop : 0.51 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR 2 29 PHE 0.007 0.000 PHE e 2 TRP 0.008 0.001 TRP H 8 HIS 0.008 0.001 HIS 7 16 Details of bonding type rmsd covalent geometry : bond 0.00173 (13146) covalent geometry : angle 0.44848 (17430) SS BOND : bond 0.00070 ( 126) SS BOND : angle 0.38639 ( 252) hydrogen bonds : bond 0.01845 ( 420) hydrogen bonds : angle 4.57646 ( 1008) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 310 time to evaluate : 0.450 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: E 20 LYS cc_start: 0.8819 (mtmm) cc_final: 0.8568 (mtmp) REVERT: G 20 LYS cc_start: 0.9036 (ttmm) cc_final: 0.8494 (mtmm) REVERT: G 26 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8795 (mtmm) REVERT: T 26 LYS cc_start: 0.8826 (mtmm) cc_final: 0.8587 (mppt) REVERT: R 20 LYS cc_start: 0.9223 (mtpt) cc_final: 0.8955 (ttmt) REVERT: X 20 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8771 (mtmm) REVERT: 1 26 LYS cc_start: 0.8960 (mtmm) cc_final: 0.8663 (mppt) REVERT: 4 14 LYS cc_start: 0.8887 (ttpp) cc_final: 0.8653 (ttmm) REVERT: 4 20 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8621 (mtmm) REVERT: 6 20 LYS cc_start: 0.9231 (ttpt) cc_final: 0.8831 (mtmt) REVERT: 8 32 LYS cc_start: 0.9488 (mmtt) cc_final: 0.8601 (mtpt) REVERT: b 14 LYS cc_start: 0.8886 (ttpp) cc_final: 0.8614 (ttmm) REVERT: e 20 LYS cc_start: 0.9244 (ttmm) cc_final: 0.8689 (mtmm) REVERT: e 26 LYS cc_start: 0.8878 (mtmm) cc_final: 0.8652 (mppt) REVERT: e 32 LYS cc_start: 0.9535 (mmtt) cc_final: 0.8430 (mtpt) REVERT: f 20 LYS cc_start: 0.9094 (mmmm) cc_final: 0.8850 (mmmm) REVERT: f 32 LYS cc_start: 0.9554 (mmtp) cc_final: 0.8675 (mtpt) outliers start: 12 outliers final: 5 residues processed: 310 average time/residue: 0.8923 time to fit residues: 291.8027 Evaluate side-chains 317 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 309 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 26 LYS Chi-restraints excluded: chain O residue 22 ILE Chi-restraints excluded: chain X residue 20 LYS Chi-restraints excluded: chain 0 residue 20 LYS Chi-restraints excluded: chain 4 residue 20 LYS Chi-restraints excluded: chain 9 residue 20 LYS Chi-restraints excluded: chain b residue 22 ILE Chi-restraints excluded: chain c residue 22 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 106 optimal weight: 4.9990 chunk 133 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 46 optimal weight: 0.3980 chunk 7 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 148 optimal weight: 0.0770 chunk 56 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 51 optimal weight: 0.3980 chunk 149 optimal weight: 6.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 ASN ** Y 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 17 ASN e 17 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.103553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.061933 restraints weight = 19368.968| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 3.24 r_work: 0.2660 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2539 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9110 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13272 Z= 0.076 Angle : 0.467 9.132 17682 Z= 0.236 Chirality : 0.041 0.126 1428 Planarity : 0.003 0.024 2268 Dihedral : 2.455 12.708 1806 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 0.54 % Allowed : 17.20 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.47 (0.22), residues: 1596 helix: 1.16 (0.27), residues: 420 sheet: -0.73 (0.32), residues: 378 loop : 0.59 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR 1 29 PHE 0.007 0.000 PHE e 2 TRP 0.008 0.001 TRP T 8 HIS 0.008 0.001 HIS 7 16 Details of bonding type rmsd covalent geometry : bond 0.00181 (13146) covalent geometry : angle 0.46828 (17430) SS BOND : bond 0.00067 ( 126) SS BOND : angle 0.35594 ( 252) hydrogen bonds : bond 0.01817 ( 420) hydrogen bonds : angle 4.51355 ( 1008) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3192 Ramachandran restraints generated. 1596 Oldfield, 0 Emsley, 1596 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 311 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 20 LYS cc_start: 0.9041 (ttmm) cc_final: 0.8530 (mtmm) REVERT: G 26 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8800 (mtmm) REVERT: N 20 LYS cc_start: 0.9102 (ttmm) cc_final: 0.8475 (mtmm) REVERT: T 26 LYS cc_start: 0.8855 (mtmm) cc_final: 0.8609 (mppt) REVERT: Q 20 LYS cc_start: 0.9076 (mtpt) cc_final: 0.8621 (mtmt) REVERT: R 20 LYS cc_start: 0.9224 (mtpt) cc_final: 0.8952 (ttmt) REVERT: Z 20 LYS cc_start: 0.9057 (mtpt) cc_final: 0.8593 (mtmt) REVERT: 1 26 LYS cc_start: 0.8989 (mtmm) cc_final: 0.8704 (mppt) REVERT: 4 14 LYS cc_start: 0.8899 (ttpp) cc_final: 0.8661 (ttmm) REVERT: 8 20 LYS cc_start: 0.9001 (mmmm) cc_final: 0.8678 (mmmm) REVERT: 8 32 LYS cc_start: 0.9490 (mmtt) cc_final: 0.8669 (mtpt) REVERT: b 14 LYS cc_start: 0.8894 (ttpp) cc_final: 0.8610 (ttmm) REVERT: b 20 LYS cc_start: 0.9109 (mtmm) cc_final: 0.8705 (mtmm) REVERT: e 20 LYS cc_start: 0.9234 (ttmm) cc_final: 0.8691 (mtmm) REVERT: e 26 LYS cc_start: 0.8903 (mtmm) cc_final: 0.8666 (mppt) REVERT: e 32 LYS cc_start: 0.9539 (mmtt) cc_final: 0.8448 (mtpt) REVERT: f 20 LYS cc_start: 0.9104 (mmmm) cc_final: 0.8880 (mmmm) REVERT: f 32 LYS cc_start: 0.9559 (mmtp) cc_final: 0.8697 (mtpt) outliers start: 7 outliers final: 8 residues processed: 311 average time/residue: 0.8226 time to fit residues: 270.0584 Evaluate side-chains 319 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 310 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 26 LYS Chi-restraints excluded: chain O residue 22 ILE Chi-restraints excluded: chain X residue 22 ILE Chi-restraints excluded: chain 0 residue 20 LYS Chi-restraints excluded: chain 4 residue 38 LYS Chi-restraints excluded: chain 9 residue 20 LYS Chi-restraints excluded: chain b residue 22 ILE Chi-restraints excluded: chain c residue 22 ILE Chi-restraints excluded: chain f residue 38 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 49 optimal weight: 9.9990 chunk 104 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 94 optimal weight: 8.9990 chunk 143 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 120 optimal weight: 0.7980 chunk 22 optimal weight: 7.9990 chunk 127 optimal weight: 4.9990 chunk 148 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 17 ASN 4 16 HIS 7 16 HIS 7 17 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.101381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.059509 restraints weight = 19304.084| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 3.23 r_work: 0.2597 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2475 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9154 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13272 Z= 0.180 Angle : 0.524 8.588 17682 Z= 0.268 Chirality : 0.045 0.127 1428 Planarity : 0.003 0.026 2268 Dihedral : 2.939 12.579 1806 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.69 % Allowed : 17.20 % Favored : 82.10 % 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: 0.35 (0.22), residues: 1596 helix: 1.20 (0.27), residues: 420 sheet: -0.81 (0.31), residues: 378 loop : 0.42 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR U 25 PHE 0.011 0.001 PHE T 2 TRP 0.011 0.002 TRP E 8 HIS 0.014 0.001 HIS 7 16 Details of bonding type rmsd covalent geometry : bond 0.00407 (13146) covalent geometry : angle 0.52520 (17430) SS BOND : bond 0.00108 ( 126) SS BOND : angle 0.41720 ( 252) hydrogen bonds : bond 0.02815 ( 420) hydrogen bonds : angle 4.90990 ( 1008) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9441.38 seconds wall clock time: 160 minutes 23.35 seconds (9623.35 seconds total)