Starting phenix.real_space_refine on Wed Jul 30 14:56:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oae_12775/07_2025/7oae_12775.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oae_12775/07_2025/7oae_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_12775/07_2025/7oae_12775.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oae_12775/07_2025/7oae_12775.map" model { file = "/net/cci-nas-00/data/ceres_data/7oae_12775/07_2025/7oae_12775.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oae_12775/07_2025/7oae_12775.cif" } resolution = 2.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.00, per 1000 atoms: 0.63 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: 2.83 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.61 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: 3.26 Time building geometry restraints manager: 3.47 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: 1.570 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: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 29.980 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.090 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:12.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.950 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (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 TRP 0.010 0.002 TRP 1 8 HIS 0.004 0.001 HIS A 18 PHE 0.007 0.001 PHE P 35 TYR 0.007 0.001 TYR U 25 Details of bonding type rmsd hydrogen bonds : bond 0.12159 ( 420) hydrogen bonds : angle 5.15067 ( 1008) SS BOND : bond 0.00138 ( 126) SS BOND : angle 0.74154 ( 252) covalent geometry : bond 0.00760 (13146) covalent geometry : angle 0.52609 (17430) *********************** 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 : 1.547 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: 1.6314 time to fit residues: 668.1451 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 : 1.509 ------------------------------------------------------------------------------- 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 141 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 80 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 ** Y 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 16 HIS 5 16 HIS a 17 ASN c 16 HIS e 17 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.102259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.060342 restraints weight = 19109.873| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 3.21 r_work: 0.2616 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2493 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9154 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 13272 Z= 0.119 Angle : 0.448 6.207 17682 Z= 0.244 Chirality : 0.043 0.121 1428 Planarity : 0.004 0.031 2268 Dihedral : 3.362 24.462 1808 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.31 % Allowed : 16.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.22), residues: 1596 helix: 1.11 (0.27), residues: 420 sheet: -0.82 (0.31), residues: 378 loop : 0.22 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 8 HIS 0.006 0.001 HIS 6 16 PHE 0.005 0.001 PHE 3 35 TYR 0.004 0.001 TYR N 25 Details of bonding type rmsd hydrogen bonds : bond 0.02618 ( 420) hydrogen bonds : angle 4.90508 ( 1008) SS BOND : bond 0.00099 ( 126) SS BOND : angle 0.55710 ( 252) covalent geometry : bond 0.00262 (13146) covalent geometry : angle 0.44623 (17430) *********************** 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 332 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 315 time to evaluate : 1.433 Fit side-chains REVERT: N 26 LYS cc_start: 0.8734 (mppt) cc_final: 0.8496 (mppt) REVERT: O 14 LYS cc_start: 0.9114 (mtpt) cc_final: 0.8884 (mtpp) REVERT: P 14 LYS cc_start: 0.8879 (mtpp) cc_final: 0.8650 (mtpt) REVERT: P 20 LYS cc_start: 0.8698 (mtmm) cc_final: 0.8418 (mtmm) REVERT: P 26 LYS cc_start: 0.8940 (ptpp) cc_final: 0.8733 (pttp) REVERT: W 14 LYS cc_start: 0.9148 (mttp) cc_final: 0.8917 (mtpt) REVERT: 1 38 LYS cc_start: 0.9115 (tttm) cc_final: 0.8870 (ttmp) REVERT: 4 14 LYS cc_start: 0.9039 (ttpp) cc_final: 0.8777 (ttmp) REVERT: 5 20 LYS cc_start: 0.8882 (mtmm) cc_final: 0.8448 (mtmm) REVERT: 6 20 LYS cc_start: 0.9278 (mtmt) cc_final: 0.8900 (mtmt) REVERT: 8 20 LYS cc_start: 0.9092 (mtpp) cc_final: 0.8762 (mmmm) REVERT: 8 32 LYS cc_start: 0.9522 (mmtt) cc_final: 0.8453 (mtpt) REVERT: b 14 LYS cc_start: 0.8977 (ttpp) cc_final: 0.8717 (ttmp) REVERT: b 38 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8827 (ttmm) REVERT: c 20 LYS cc_start: 0.8846 (mtmm) cc_final: 0.8265 (mtmm) REVERT: e 32 LYS cc_start: 0.9552 (mmtt) cc_final: 0.8366 (mtpt) REVERT: f 20 LYS cc_start: 0.9003 (mtpp) cc_final: 0.8770 (mtpp) outliers start: 17 outliers final: 4 residues processed: 316 average time/residue: 1.8357 time to fit residues: 613.8052 Evaluate side-chains 308 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 303 time to evaluate : 1.399 ------------------------------------------------------------------------------- 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 22 ILE Chi-restraints excluded: chain b residue 38 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 68 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 119 optimal weight: 0.8980 chunk 65 optimal weight: 10.0000 chunk 135 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 6 optimal weight: 8.9990 chunk 79 optimal weight: 0.7980 chunk 87 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 9 optimal weight: 0.3980 overall best weight: 2.8184 ------------------------------------------------------------------------------- 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** ** 7 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 17 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.101360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.059522 restraints weight = 19398.179| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 3.22 r_work: 0.2593 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2472 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9157 moved from start: 0.2450 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= 0.153 Angle : 0.437 4.699 17682 Z= 0.241 Chirality : 0.044 0.120 1428 Planarity : 0.004 0.031 2268 Dihedral : 3.368 25.202 1808 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.69 % Allowed : 15.44 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.22), residues: 1596 helix: 1.09 (0.27), residues: 420 sheet: -0.79 (0.31), residues: 378 loop : 0.24 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP 0 8 HIS 0.006 0.001 HIS 7 16 PHE 0.005 0.001 PHE a 35 TYR 0.006 0.001 TYR E 25 Details of bonding type rmsd hydrogen bonds : bond 0.02794 ( 420) hydrogen bonds : angle 4.97484 ( 1008) SS BOND : bond 0.00086 ( 126) SS BOND : angle 0.48712 ( 252) covalent geometry : bond 0.00338 (13146) covalent geometry : angle 0.43580 (17430) *********************** 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 330 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 308 time to evaluate : 1.581 Fit side-chains revert: symmetry clash REVERT: R 20 LYS cc_start: 0.9172 (mtpt) cc_final: 0.8964 (ttmt) REVERT: W 14 LYS cc_start: 0.9144 (mttp) cc_final: 0.8908 (mtpt) REVERT: X 20 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8763 (mtmm) REVERT: 1 26 LYS cc_start: 0.8940 (mtmm) cc_final: 0.8687 (mppt) REVERT: 4 14 LYS cc_start: 0.9024 (ttpp) cc_final: 0.8798 (ttmp) REVERT: 6 20 LYS cc_start: 0.9286 (mtmt) cc_final: 0.9063 (mtmt) REVERT: 8 32 LYS cc_start: 0.9532 (mmtt) cc_final: 0.8528 (mtpt) REVERT: b 14 LYS cc_start: 0.8936 (ttpp) cc_final: 0.8614 (ttmm) REVERT: b 20 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8477 (mtmm) REVERT: c 20 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8446 (mtmm) REVERT: e 32 LYS cc_start: 0.9554 (mmtt) cc_final: 0.8387 (mtpt) REVERT: f 20 LYS cc_start: 0.9027 (mtpp) cc_final: 0.8807 (mtpp) REVERT: f 32 LYS cc_start: 0.9587 (mmtp) cc_final: 0.8696 (mtpt) outliers start: 22 outliers final: 3 residues processed: 308 average time/residue: 1.7468 time to fit residues: 570.3779 Evaluate side-chains 313 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 307 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 20 LYS Chi-restraints excluded: chain b residue 22 ILE Chi-restraints excluded: chain c residue 20 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 120 optimal weight: 6.9990 chunk 102 optimal weight: 0.9980 chunk 115 optimal weight: 8.9990 chunk 51 optimal weight: 6.9990 chunk 123 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 88 optimal weight: 0.7980 chunk 74 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 167 optimal weight: 6.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- 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 = 0.3681 r_free = 0.3681 target = 0.101155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.059360 restraints weight = 19143.098| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 3.21 r_work: 0.2590 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2468 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9157 moved from start: 0.2536 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= 0.168 Angle : 0.455 5.007 17682 Z= 0.248 Chirality : 0.044 0.119 1428 Planarity : 0.004 0.032 2268 Dihedral : 3.351 15.896 1806 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.00 % Allowed : 15.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.22), residues: 1596 helix: 1.09 (0.27), residues: 420 sheet: -0.81 (0.31), residues: 378 loop : 0.22 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP L 8 HIS 0.004 0.001 HIS 7 16 PHE 0.006 0.001 PHE a 35 TYR 0.006 0.001 TYR E 25 Details of bonding type rmsd hydrogen bonds : bond 0.02800 ( 420) hydrogen bonds : angle 5.00679 ( 1008) SS BOND : bond 0.00087 ( 126) SS BOND : angle 0.48465 ( 252) covalent geometry : bond 0.00372 (13146) covalent geometry : angle 0.45459 (17430) *********************** 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 334 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 308 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 26 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8663 (mtmm) REVERT: L 14 LYS cc_start: 0.8959 (mtpp) cc_final: 0.8732 (mtpt) REVERT: O 20 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8761 (mtmm) REVERT: R 20 LYS cc_start: 0.9174 (mtpt) cc_final: 0.8893 (ttmt) REVERT: W 14 LYS cc_start: 0.9118 (mttp) cc_final: 0.8880 (mtpt) REVERT: X 20 LYS cc_start: 0.9101 (OUTLIER) cc_final: 0.8757 (mtmm) REVERT: 1 26 LYS cc_start: 0.8930 (mtmm) cc_final: 0.8701 (mppt) REVERT: 1 38 LYS cc_start: 0.9186 (ttmm) cc_final: 0.8916 (ttmp) REVERT: 4 14 LYS cc_start: 0.9008 (ttpp) cc_final: 0.8784 (ttmp) REVERT: 7 38 LYS cc_start: 0.9393 (OUTLIER) cc_final: 0.8851 (tttm) REVERT: 8 20 LYS cc_start: 0.9045 (mmmm) cc_final: 0.8752 (mmmm) REVERT: 8 32 LYS cc_start: 0.9533 (mmtt) cc_final: 0.8595 (mtpt) REVERT: b 10 GLU cc_start: 0.8225 (mt-10) cc_final: 0.8022 (mt-10) REVERT: b 14 LYS cc_start: 0.8908 (ttpp) cc_final: 0.8687 (ttmp) REVERT: b 38 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8753 (ttmm) 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: 0.8689 (mtpt) outliers start: 26 outliers final: 6 residues processed: 309 average time/residue: 1.8920 time to fit residues: 619.7295 Evaluate side-chains 315 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 304 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 26 LYS Chi-restraints excluded: chain I residue 13 MET 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 4 residue 20 LYS Chi-restraints excluded: chain 7 residue 38 LYS Chi-restraints excluded: chain 9 residue 20 LYS Chi-restraints excluded: chain b residue 38 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 108 optimal weight: 0.4980 chunk 113 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 126 optimal weight: 9.9990 chunk 140 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 138 optimal weight: 0.7980 chunk 151 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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** 1 17 ASN 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 = 0.102541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.060839 restraints weight = 19158.523| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 3.22 r_work: 0.2629 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2508 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9131 moved from start: 0.2678 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= 0.080 Angle : 0.414 7.065 17682 Z= 0.222 Chirality : 0.042 0.120 1428 Planarity : 0.003 0.027 2268 Dihedral : 2.911 13.129 1806 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.92 % Allowed : 15.28 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.22), residues: 1596 helix: 1.12 (0.27), residues: 420 sheet: -0.75 (0.32), residues: 378 loop : 0.37 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP T 8 HIS 0.006 0.001 HIS b 16 PHE 0.004 0.000 PHE D 2 TYR 0.003 0.001 TYR Z 40 Details of bonding type rmsd hydrogen bonds : bond 0.02097 ( 420) hydrogen bonds : angle 4.72165 ( 1008) SS BOND : bond 0.00074 ( 126) SS BOND : angle 0.41847 ( 252) covalent geometry : bond 0.00176 (13146) covalent geometry : angle 0.41425 (17430) *********************** 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 334 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 309 time to evaluate : 1.541 Fit side-chains revert: symmetry clash REVERT: O 14 LYS cc_start: 0.9000 (mtpt) cc_final: 0.8796 (mtpp) REVERT: R 20 LYS cc_start: 0.9215 (mtpt) cc_final: 0.8975 (ttmt) REVERT: S 26 LYS cc_start: 0.8917 (mtmm) cc_final: 0.8694 (mppt) REVERT: W 14 LYS cc_start: 0.9103 (mttp) cc_final: 0.8894 (mtpt) REVERT: X 20 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8773 (mtmm) REVERT: 0 20 LYS cc_start: 0.9181 (ttmt) cc_final: 0.8968 (mtmm) REVERT: 1 26 LYS cc_start: 0.8961 (mtmm) cc_final: 0.8698 (mppt) REVERT: 4 14 LYS cc_start: 0.8972 (ttpp) cc_final: 0.8752 (ttmp) REVERT: 4 20 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8648 (mtmm) REVERT: 5 20 LYS cc_start: 0.8934 (mtmm) cc_final: 0.8439 (mtmm) REVERT: 8 32 LYS cc_start: 0.9496 (mmtt) cc_final: 0.8564 (mtpt) REVERT: b 14 LYS cc_start: 0.8870 (ttpp) cc_final: 0.8600 (ttmm) REVERT: b 38 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8746 (ttmm) REVERT: e 32 LYS cc_start: 0.9559 (mmtt) cc_final: 0.8440 (mtpt) REVERT: f 20 LYS cc_start: 0.9079 (mmmm) cc_final: 0.8785 (mmmm) REVERT: f 32 LYS cc_start: 0.9558 (mmtp) cc_final: 0.8662 (mtpt) outliers start: 25 outliers final: 3 residues processed: 310 average time/residue: 1.7843 time to fit residues: 585.6215 Evaluate side-chains 310 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 304 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 20 LYS Chi-restraints excluded: chain O residue 22 ILE Chi-restraints excluded: chain X 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 38 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 96 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 106 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 26 optimal weight: 0.8980 chunk 132 optimal weight: 8.9990 chunk 23 optimal weight: 0.5980 chunk 36 optimal weight: 5.9990 chunk 141 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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** 6 16 HIS 7 17 ASN b 16 HIS e 17 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.102693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.060878 restraints weight = 19414.279| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 3.24 r_work: 0.2628 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2507 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9129 moved from start: 0.2766 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= 0.082 Angle : 0.436 7.223 17682 Z= 0.229 Chirality : 0.041 0.125 1428 Planarity : 0.003 0.025 2268 Dihedral : 2.714 9.951 1806 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.23 % Allowed : 16.74 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.22), residues: 1596 helix: 1.12 (0.27), residues: 420 sheet: -0.73 (0.32), residues: 378 loop : 0.43 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP T 8 HIS 0.004 0.001 HIS 7 16 PHE 0.005 0.000 PHE e 2 TYR 0.003 0.001 TYR Z 40 Details of bonding type rmsd hydrogen bonds : bond 0.02040 ( 420) hydrogen bonds : angle 4.64428 ( 1008) SS BOND : bond 0.00068 ( 126) SS BOND : angle 0.38290 ( 252) covalent geometry : bond 0.00185 (13146) covalent geometry : angle 0.43647 (17430) *********************** 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 324 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 308 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 26 LYS cc_start: 0.9040 (mtmm) cc_final: 0.8804 (mtmm) REVERT: O 20 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8752 (mtmm) REVERT: R 20 LYS cc_start: 0.9224 (mtpt) cc_final: 0.8982 (ttmt) REVERT: S 26 LYS cc_start: 0.8946 (mtmm) cc_final: 0.8709 (mppt) REVERT: 1 26 LYS cc_start: 0.8971 (mtmm) cc_final: 0.8701 (mppt) REVERT: 4 14 LYS cc_start: 0.8939 (ttpp) cc_final: 0.8733 (ttmp) REVERT: 4 20 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8580 (mtmm) REVERT: 5 20 LYS cc_start: 0.8960 (mtmm) cc_final: 0.8480 (mtmm) REVERT: 7 20 LYS cc_start: 0.9252 (OUTLIER) cc_final: 0.8979 (mtmm) REVERT: 8 20 LYS cc_start: 0.8979 (mmmm) cc_final: 0.8685 (mmtp) REVERT: 8 32 LYS cc_start: 0.9502 (mmtt) cc_final: 0.8597 (mtpt) REVERT: b 14 LYS cc_start: 0.8870 (ttpp) cc_final: 0.8603 (ttmm) REVERT: b 38 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8737 (ttmm) REVERT: e 26 LYS cc_start: 0.8907 (mtmm) cc_final: 0.8679 (mppt) REVERT: e 32 LYS cc_start: 0.9560 (mmtt) cc_final: 0.8423 (mtpt) REVERT: f 20 LYS cc_start: 0.9149 (mmmm) cc_final: 0.8920 (mmtp) REVERT: f 32 LYS cc_start: 0.9564 (mmtp) cc_final: 0.8680 (mtpt) outliers start: 16 outliers final: 5 residues processed: 308 average time/residue: 1.8233 time to fit residues: 594.4718 Evaluate side-chains 312 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 303 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 20 LYS Chi-restraints excluded: chain O residue 22 ILE Chi-restraints excluded: chain 1 residue 20 LYS Chi-restraints excluded: chain 4 residue 20 LYS Chi-restraints excluded: chain 7 residue 20 LYS Chi-restraints excluded: chain 9 residue 20 LYS Chi-restraints excluded: chain b residue 38 LYS Chi-restraints excluded: chain c residue 20 LYS Chi-restraints excluded: chain c residue 22 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 79 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 chunk 147 optimal weight: 9.9990 chunk 24 optimal weight: 0.7980 chunk 125 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 37 optimal weight: 0.0870 chunk 97 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 93 optimal weight: 8.9990 overall best weight: 1.0960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 17 ASN Q 16 HIS ** Y 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 16 HIS 6 16 HIS d 16 HIS e 17 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.102686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.060976 restraints weight = 19229.105| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 3.23 r_work: 0.2632 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2510 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9128 moved from start: 0.2808 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= 0.082 Angle : 0.438 6.997 17682 Z= 0.227 Chirality : 0.041 0.120 1428 Planarity : 0.003 0.025 2268 Dihedral : 2.621 10.658 1806 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.23 % Allowed : 16.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.22), residues: 1596 helix: 1.17 (0.27), residues: 420 sheet: -0.74 (0.32), residues: 378 loop : 0.47 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 8 HIS 0.005 0.001 HIS e 16 PHE 0.005 0.000 PHE e 2 TYR 0.003 0.001 TYR Z 40 Details of bonding type rmsd hydrogen bonds : bond 0.02024 ( 420) hydrogen bonds : angle 4.60870 ( 1008) SS BOND : bond 0.00066 ( 126) SS BOND : angle 0.36353 ( 252) covalent geometry : bond 0.00186 (13146) covalent geometry : angle 0.43852 (17430) *********************** 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 321 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 305 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 26 LYS cc_start: 0.9053 (mtmm) cc_final: 0.8817 (mtmm) REVERT: N 20 LYS cc_start: 0.9103 (ttmm) cc_final: 0.8446 (mtmm) REVERT: O 20 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8769 (mtmm) REVERT: S 26 LYS cc_start: 0.8945 (mtmm) cc_final: 0.8715 (mppt) REVERT: X 20 LYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8760 (mtmm) REVERT: 1 26 LYS cc_start: 0.8970 (mtmm) cc_final: 0.8698 (mppt) REVERT: 4 14 LYS cc_start: 0.8932 (ttpp) cc_final: 0.8731 (ttmp) REVERT: 4 20 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8632 (mtmm) REVERT: 6 20 LYS cc_start: 0.9231 (ttpt) cc_final: 0.8957 (mtmt) REVERT: 7 20 LYS cc_start: 0.9248 (OUTLIER) cc_final: 0.8992 (mtmt) REVERT: 8 20 LYS cc_start: 0.9068 (mmmm) cc_final: 0.8786 (mmmm) REVERT: 8 32 LYS cc_start: 0.9505 (mmtt) cc_final: 0.8627 (mtpt) REVERT: b 14 LYS cc_start: 0.8865 (ttpp) cc_final: 0.8613 (ttmm) REVERT: b 38 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8747 (ttmm) REVERT: e 20 LYS cc_start: 0.9270 (ttmm) cc_final: 0.8783 (mtmm) REVERT: e 26 LYS cc_start: 0.8907 (mtmm) cc_final: 0.8659 (mppt) REVERT: e 32 LYS cc_start: 0.9557 (mmtt) cc_final: 0.8432 (mtpt) REVERT: f 20 LYS cc_start: 0.9153 (mmmm) cc_final: 0.8912 (mmmm) REVERT: f 32 LYS cc_start: 0.9572 (mmtp) cc_final: 0.8696 (mtpt) outliers start: 16 outliers final: 6 residues processed: 305 average time/residue: 1.7871 time to fit residues: 576.8597 Evaluate side-chains 315 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 304 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 20 LYS Chi-restraints excluded: chain O residue 20 LYS Chi-restraints excluded: chain O residue 22 ILE Chi-restraints excluded: chain R residue 26 LYS Chi-restraints excluded: chain X residue 20 LYS Chi-restraints excluded: chain 1 residue 20 LYS Chi-restraints excluded: chain 4 residue 20 LYS Chi-restraints excluded: chain 7 residue 20 LYS Chi-restraints excluded: chain 9 residue 20 LYS Chi-restraints excluded: chain b residue 38 LYS Chi-restraints excluded: chain c residue 22 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 112 optimal weight: 6.9990 chunk 120 optimal weight: 6.9990 chunk 139 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 109 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 17 ASN ** Y 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 16 HIS 7 17 ASN b 16 HIS d 16 HIS e 17 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.100583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.058708 restraints weight = 19359.912| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 3.22 r_work: 0.2578 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2456 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9166 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 13272 Z= 0.268 Angle : 0.532 7.579 17682 Z= 0.282 Chirality : 0.047 0.120 1428 Planarity : 0.004 0.028 2268 Dihedral : 3.499 20.914 1806 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.22), residues: 1596 helix: 1.08 (0.27), residues: 420 sheet: -0.88 (0.30), residues: 378 loop : 0.19 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP E 8 HIS 0.008 0.001 HIS 6 16 PHE 0.009 0.001 PHE D 2 TYR 0.009 0.001 TYR E 25 Details of bonding type rmsd hydrogen bonds : bond 0.03289 ( 420) hydrogen bonds : angle 5.12059 ( 1008) SS BOND : bond 0.00137 ( 126) SS BOND : angle 0.53831 ( 252) covalent geometry : bond 0.00595 (13146) covalent geometry : angle 0.53212 (17430) *********************** 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 314 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 299 time to evaluate : 1.344 Fit side-chains revert: symmetry clash REVERT: G 26 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8732 (mtmm) REVERT: H 26 LYS cc_start: 0.8810 (mtmm) cc_final: 0.8584 (mppt) REVERT: O 20 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8753 (mtmm) REVERT: X 20 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8747 (mtmm) REVERT: 0 20 LYS cc_start: 0.9099 (mtmm) cc_final: 0.8861 (mtmm) REVERT: 1 26 LYS cc_start: 0.8934 (mtmm) cc_final: 0.8717 (mppt) REVERT: 4 14 LYS cc_start: 0.8980 (ttpp) cc_final: 0.8768 (ttmp) REVERT: 4 26 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8560 (ptpp) REVERT: 5 20 LYS cc_start: 0.8893 (mtmm) cc_final: 0.8426 (mtmm) REVERT: 8 32 LYS cc_start: 0.9553 (mmtt) cc_final: 0.8594 (mtpt) REVERT: b 14 LYS cc_start: 0.8929 (ttpp) cc_final: 0.8664 (ttmm) outliers start: 15 outliers final: 7 residues processed: 299 average time/residue: 1.8008 time to fit residues: 569.8672 Evaluate side-chains 309 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 298 time to evaluate : 1.387 ------------------------------------------------------------------------------- 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 R residue 26 LYS Chi-restraints excluded: chain X residue 20 LYS Chi-restraints excluded: chain X residue 22 ILE Chi-restraints excluded: chain 4 residue 20 LYS Chi-restraints excluded: chain 4 residue 26 LYS Chi-restraints excluded: chain 9 residue 20 LYS Chi-restraints excluded: chain c residue 20 LYS Chi-restraints excluded: chain f residue 38 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 45 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 131 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 150 optimal weight: 0.7980 chunk 153 optimal weight: 20.0000 chunk 128 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 17 ASN b 16 HIS e 17 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.101992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.060206 restraints weight = 19263.289| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 3.22 r_work: 0.2611 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2489 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9142 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13272 Z= 0.112 Angle : 0.490 8.450 17682 Z= 0.252 Chirality : 0.043 0.120 1428 Planarity : 0.003 0.028 2268 Dihedral : 3.090 15.983 1806 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.84 % Allowed : 16.97 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.22), residues: 1596 helix: 1.16 (0.27), residues: 420 sheet: -0.84 (0.31), residues: 378 loop : 0.33 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 8 HIS 0.007 0.001 HIS 6 16 PHE 0.007 0.001 PHE e 2 TYR 0.005 0.001 TYR E 25 Details of bonding type rmsd hydrogen bonds : bond 0.02400 ( 420) hydrogen bonds : angle 4.84331 ( 1008) SS BOND : bond 0.00079 ( 126) SS BOND : angle 0.42398 ( 252) covalent geometry : bond 0.00256 (13146) covalent geometry : angle 0.49114 (17430) *********************** 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 320 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 309 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 26 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8857 (mtmm) REVERT: H 26 LYS cc_start: 0.8825 (mtmm) cc_final: 0.8601 (mppt) REVERT: N 20 LYS cc_start: 0.9084 (ttmm) cc_final: 0.8421 (mtmm) REVERT: O 20 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8776 (mtmm) REVERT: R 20 LYS cc_start: 0.9314 (ttpp) cc_final: 0.8884 (ttmt) REVERT: X 20 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8753 (mtmm) REVERT: 1 26 LYS cc_start: 0.8955 (mtmm) cc_final: 0.8719 (mppt) REVERT: 4 14 LYS cc_start: 0.8929 (ttpp) cc_final: 0.8713 (ttmp) REVERT: 4 20 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8645 (mtmm) REVERT: 8 20 LYS cc_start: 0.9003 (mmmm) cc_final: 0.8663 (mmmm) REVERT: 8 32 LYS cc_start: 0.9525 (mmtt) cc_final: 0.8577 (mtpt) REVERT: b 10 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7862 (mt-10) REVERT: b 14 LYS cc_start: 0.8908 (ttpp) cc_final: 0.8640 (ttmm) REVERT: d 20 LYS cc_start: 0.9237 (ttpt) cc_final: 0.8685 (mtmt) REVERT: e 20 LYS cc_start: 0.9228 (ttmm) cc_final: 0.8746 (mtmm) REVERT: e 26 LYS cc_start: 0.8871 (mtmm) cc_final: 0.8634 (mppt) REVERT: e 32 LYS cc_start: 0.9572 (mmtt) cc_final: 0.8416 (mtpt) REVERT: f 20 LYS cc_start: 0.9045 (mmmm) cc_final: 0.8729 (mmmm) REVERT: f 32 LYS cc_start: 0.9583 (mmtp) cc_final: 0.8672 (mtpt) REVERT: f 38 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8957 (ttmm) outliers start: 11 outliers final: 4 residues processed: 309 average time/residue: 1.9201 time to fit residues: 627.3450 Evaluate side-chains 315 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 306 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 26 LYS Chi-restraints excluded: chain O residue 20 LYS Chi-restraints excluded: chain R residue 26 LYS Chi-restraints excluded: chain X residue 20 LYS Chi-restraints excluded: chain X residue 22 ILE Chi-restraints excluded: chain 1 residue 20 LYS Chi-restraints excluded: chain 4 residue 20 LYS Chi-restraints excluded: chain 9 residue 20 LYS 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 93 optimal weight: 10.0000 chunk 155 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 151 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 139 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 153 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 17 ASN ** 0 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 = 0.3666 r_free = 0.3666 target = 0.100251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.058381 restraints weight = 19329.630| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 3.21 r_work: 0.2569 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2446 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9172 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 13272 Z= 0.306 Angle : 0.580 9.049 17682 Z= 0.303 Chirality : 0.049 0.122 1428 Planarity : 0.004 0.029 2268 Dihedral : 3.691 19.824 1806 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.84 % Allowed : 17.20 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.21), residues: 1596 helix: 1.07 (0.27), residues: 420 sheet: -0.95 (0.30), residues: 378 loop : 0.07 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP E 8 HIS 0.006 0.001 HIS 6 16 PHE 0.012 0.001 PHE e 2 TYR 0.012 0.002 TYR G 25 Details of bonding type rmsd hydrogen bonds : bond 0.03478 ( 420) hydrogen bonds : angle 5.23927 ( 1008) SS BOND : bond 0.00156 ( 126) SS BOND : angle 0.59617 ( 252) covalent geometry : bond 0.00680 (13146) covalent geometry : angle 0.57968 (17430) ********************** 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 310 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 299 time to evaluate : 1.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 26 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8755 (mtmm) REVERT: O 20 LYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8761 (mtmm) REVERT: X 20 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8743 (mtmm) REVERT: 0 20 LYS cc_start: 0.9109 (mtmm) cc_final: 0.8823 (mtmm) REVERT: 4 14 LYS cc_start: 0.8974 (ttpp) cc_final: 0.8761 (ttmp) REVERT: 4 26 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8557 (ptpp) REVERT: 5 20 LYS cc_start: 0.8897 (mtmm) cc_final: 0.8424 (mtmm) REVERT: 8 32 LYS cc_start: 0.9558 (mmtt) cc_final: 0.8606 (mtpt) REVERT: e 26 LYS cc_start: 0.8871 (mtmm) cc_final: 0.8653 (mppt) REVERT: f 20 LYS cc_start: 0.9050 (mmmm) cc_final: 0.8697 (mmmm) outliers start: 11 outliers final: 6 residues processed: 299 average time/residue: 1.8189 time to fit residues: 575.0958 Evaluate side-chains 306 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 296 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 26 LYS Chi-restraints excluded: chain O residue 20 LYS Chi-restraints excluded: chain R residue 26 LYS Chi-restraints excluded: chain X residue 20 LYS Chi-restraints excluded: chain X residue 22 ILE Chi-restraints excluded: chain 4 residue 20 LYS Chi-restraints excluded: chain 4 residue 26 LYS Chi-restraints excluded: chain 9 residue 20 LYS Chi-restraints excluded: chain c residue 20 LYS 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 162 optimal weight: 0.9990 chunk 147 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 2 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 113 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 9 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3702 r_free = 0.3702 target = 0.102755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.061235 restraints weight = 19211.632| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 3.22 r_work: 0.2636 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2515 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9126 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13272 Z= 0.089 Angle : 0.504 8.917 17682 Z= 0.254 Chirality : 0.042 0.121 1428 Planarity : 0.003 0.026 2268 Dihedral : 3.029 13.156 1806 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.61 % Allowed : 17.67 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.22), residues: 1596 helix: 1.12 (0.27), residues: 420 sheet: -0.87 (0.31), residues: 378 loop : 0.38 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 8 HIS 0.006 0.001 HIS 6 16 PHE 0.007 0.000 PHE e 2 TYR 0.005 0.001 TYR X 25 Details of bonding type rmsd hydrogen bonds : bond 0.02084 ( 420) hydrogen bonds : angle 4.76188 ( 1008) SS BOND : bond 0.00082 ( 126) SS BOND : angle 0.44398 ( 252) covalent geometry : bond 0.00210 (13146) covalent geometry : angle 0.50489 (17430) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22179.80 seconds wall clock time: 384 minutes 47.04 seconds (23087.04 seconds total)