Starting phenix.real_space_refine (version: 1.21rc1) on Thu Jul 20 17:11:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tbh_25799/07_2023/7tbh_25799_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tbh_25799/07_2023/7tbh_25799.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tbh_25799/07_2023/7tbh_25799.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tbh_25799/07_2023/7tbh_25799.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tbh_25799/07_2023/7tbh_25799_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tbh_25799/07_2023/7tbh_25799_updated.pdb" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 312 5.16 5 C 32424 2.51 5 N 9168 2.21 5 O 9840 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H GLU 68": "OE1" <-> "OE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 51768 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "B" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "C" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "D" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "E" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "F" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "G" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "H" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "I" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "J" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "K" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "L" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "M" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "N" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "O" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "P" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "Q" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "R" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "S" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "T" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "U" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "V" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "W" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "X" Number of atoms: 2000 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 243, 1992 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 236} bond proxies already assigned to first conformer: 2023 Chain: "a" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 157 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 2, 'TRANS': 16} Chain: "b" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 157 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 2, 'TRANS': 16} Chain: "c" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 157 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 2, 'TRANS': 16} Chain: "d" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 157 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 2, 'TRANS': 16} Chain: "e" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 157 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 2, 'TRANS': 16} Chain: "f" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 157 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 2, 'TRANS': 16} Chain: "g" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 157 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 2, 'TRANS': 16} Chain: "h" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 157 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 2, 'TRANS': 16} Chain: "i" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 157 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 2, 'TRANS': 16} Chain: "j" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 157 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 2, 'TRANS': 16} Chain: "k" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 157 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 2, 'TRANS': 16} Chain: "l" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 157 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 2, 'TRANS': 16} Chain: "m" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 157 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 2, 'TRANS': 16} Chain: "n" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 157 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 2, 'TRANS': 16} Chain: "o" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 157 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 2, 'TRANS': 16} Chain: "p" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 157 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 2, 'TRANS': 16} Chain: "q" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 157 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 2, 'TRANS': 16} Chain: "r" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 157 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 2, 'TRANS': 16} Chain: "s" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 157 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 2, 'TRANS': 16} Chain: "t" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 157 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 2, 'TRANS': 16} Chain: "u" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 157 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 2, 'TRANS': 16} Chain: "v" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 157 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 2, 'TRANS': 16} Chain: "w" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 157 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 2, 'TRANS': 16} Chain: "x" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 157 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 2, 'TRANS': 16} Time building chain proxies: 39.88, per 1000 atoms: 0.77 Number of scatterers: 51768 At special positions: 0 Unit cell: (173.02, 173.02, 173.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 312 16.00 P 24 15.00 O 9840 8.00 N 9168 7.00 C 32424 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 27 " - pdb=" SG CYS J 169 " distance=2.04 Simple disulfide: pdb=" SG CYS A 31 " - pdb=" SG CYS J 237 " distance=2.04 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS J 27 " distance=2.02 Simple disulfide: pdb=" SG CYS A 237 " - pdb=" SG CYS J 31 " distance=2.01 Simple disulfide: pdb=" SG CYS B 27 " - pdb=" SG CYS I 169 " distance=2.04 Simple disulfide: pdb=" SG CYS B 31 " - pdb=" SG CYS I 237 " distance=2.04 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS I 27 " distance=2.02 Simple disulfide: pdb=" SG CYS B 237 " - pdb=" SG CYS I 31 " distance=2.02 Simple disulfide: pdb=" SG CYS C 27 " - pdb=" SG CYS L 169 " distance=2.04 Simple disulfide: pdb=" SG CYS C 31 " - pdb=" SG CYS L 237 " distance=2.04 Simple disulfide: pdb=" SG CYS C 169 " - pdb=" SG CYS L 27 " distance=2.02 Simple disulfide: pdb=" SG CYS C 237 " - pdb=" SG CYS L 31 " distance=2.02 Simple disulfide: pdb=" SG CYS D 27 " - pdb=" SG CYS K 169 " distance=2.04 Simple disulfide: pdb=" SG CYS D 31 " - pdb=" SG CYS K 237 " distance=2.04 Simple disulfide: pdb=" SG CYS D 169 " - pdb=" SG CYS K 27 " distance=2.02 Simple disulfide: pdb=" SG CYS D 237 " - pdb=" SG CYS K 31 " distance=2.03 Simple disulfide: pdb=" SG CYS E 27 " - pdb=" SG CYS N 169 " distance=2.04 Simple disulfide: pdb=" SG CYS E 31 " - pdb=" SG CYS N 237 " distance=2.03 Simple disulfide: pdb=" SG CYS E 169 " - pdb=" SG CYS N 27 " distance=2.03 Simple disulfide: pdb=" SG CYS E 237 " - pdb=" SG CYS N 31 " distance=2.03 Simple disulfide: pdb=" SG CYS F 27 " - pdb=" SG CYS M 169 " distance=2.03 Simple disulfide: pdb=" SG CYS F 31 " - pdb=" SG CYS M 237 " distance=2.03 Simple disulfide: pdb=" SG CYS F 169 " - pdb=" SG CYS M 27 " distance=2.02 Simple disulfide: pdb=" SG CYS F 237 " - pdb=" SG CYS M 31 " distance=2.02 Simple disulfide: pdb=" SG CYS G 27 " - pdb=" SG CYS P 169 " distance=2.04 Simple disulfide: pdb=" SG CYS G 31 " - pdb=" SG CYS P 237 " distance=2.04 Simple disulfide: pdb=" SG CYS G 169 " - pdb=" SG CYS P 27 " distance=2.02 Simple disulfide: pdb=" SG CYS G 237 " - pdb=" SG CYS P 31 " distance=2.03 Simple disulfide: pdb=" SG CYS H 27 " - pdb=" SG CYS O 169 " distance=2.03 Simple disulfide: pdb=" SG CYS H 31 " - pdb=" SG CYS O 237 " distance=2.04 Simple disulfide: pdb=" SG CYS H 169 " - pdb=" SG CYS O 27 " distance=2.02 Simple disulfide: pdb=" SG CYS H 237 " - pdb=" SG CYS O 31 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 27 " - pdb=" SG CYS X 169 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 31 " - pdb=" SG CYS X 237 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 169 " - pdb=" SG CYS X 27 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 237 " - pdb=" SG CYS X 31 " distance=2.02 Simple disulfide: pdb=" SG CYS R 27 " - pdb=" SG CYS W 169 " distance=2.04 Simple disulfide: pdb=" SG CYS R 31 " - pdb=" SG CYS W 237 " distance=2.04 Simple disulfide: pdb=" SG CYS R 169 " - pdb=" SG CYS W 27 " distance=2.02 Simple disulfide: pdb=" SG CYS R 237 " - pdb=" SG CYS W 31 " distance=2.03 Simple disulfide: pdb=" SG CYS S 27 " - pdb=" SG CYS V 169 " distance=2.04 Simple disulfide: pdb=" SG CYS S 31 " - pdb=" SG CYS V 237 " distance=2.04 Simple disulfide: pdb=" SG CYS S 169 " - pdb=" SG CYS V 27 " distance=2.02 Simple disulfide: pdb=" SG CYS S 237 " - pdb=" SG CYS V 31 " distance=2.02 Simple disulfide: pdb=" SG CYS T 27 " - pdb=" SG CYS U 169 " distance=2.03 Simple disulfide: pdb=" SG CYS T 31 " - pdb=" SG CYS U 237 " distance=2.04 Simple disulfide: pdb=" SG CYS T 169 " - pdb=" SG CYS U 27 " distance=2.02 Simple disulfide: pdb=" SG CYS T 237 " - pdb=" SG CYS U 31 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 17.91 Conformation dependent library (CDL) restraints added in 12.5 seconds 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12240 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 240 helices and 0 sheets defined 71.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.87 Creating SS restraints... Processing helix chain 'A' and resid 10 through 24 removed outlier: 3.536A pdb=" N LEU A 20 " --> pdb=" O LEU A 16 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL A 21 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLN A 22 " --> pdb=" O HIS A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 54 Processing helix chain 'A' and resid 60 through 76 removed outlier: 4.100A pdb=" N GLU A 76 " --> pdb=" O LYS A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 116 Processing helix chain 'A' and resid 124 through 151 Processing helix chain 'A' and resid 172 through 198 Processing helix chain 'A' and resid 202 through 211 Processing helix chain 'A' and resid 213 through 233 Processing helix chain 'A' and resid 239 through 248 Processing helix chain 'B' and resid 10 through 24 removed outlier: 3.536A pdb=" N LEU B 20 " --> pdb=" O LEU B 16 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL B 21 " --> pdb=" O VAL B 17 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLN B 22 " --> pdb=" O HIS B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 54 Processing helix chain 'B' and resid 60 through 76 removed outlier: 4.100A pdb=" N GLU B 76 " --> pdb=" O LYS B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 116 Processing helix chain 'B' and resid 124 through 151 Processing helix chain 'B' and resid 172 through 198 Processing helix chain 'B' and resid 202 through 211 Processing helix chain 'B' and resid 213 through 233 Processing helix chain 'B' and resid 239 through 248 Processing helix chain 'C' and resid 10 through 24 removed outlier: 3.536A pdb=" N LEU C 20 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL C 21 " --> pdb=" O VAL C 17 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN C 22 " --> pdb=" O HIS C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 54 Processing helix chain 'C' and resid 60 through 76 removed outlier: 4.100A pdb=" N GLU C 76 " --> pdb=" O LYS C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 116 Processing helix chain 'C' and resid 124 through 151 Processing helix chain 'C' and resid 172 through 198 Processing helix chain 'C' and resid 202 through 211 Processing helix chain 'C' and resid 213 through 233 Processing helix chain 'C' and resid 239 through 248 Processing helix chain 'D' and resid 10 through 24 removed outlier: 3.535A pdb=" N LEU D 20 " --> pdb=" O LEU D 16 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL D 21 " --> pdb=" O VAL D 17 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLN D 22 " --> pdb=" O HIS D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 54 Processing helix chain 'D' and resid 60 through 76 removed outlier: 4.099A pdb=" N GLU D 76 " --> pdb=" O LYS D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 116 Processing helix chain 'D' and resid 124 through 151 Processing helix chain 'D' and resid 172 through 198 Processing helix chain 'D' and resid 202 through 211 Processing helix chain 'D' and resid 213 through 233 Processing helix chain 'D' and resid 239 through 248 Processing helix chain 'E' and resid 10 through 24 removed outlier: 3.536A pdb=" N LEU E 20 " --> pdb=" O LEU E 16 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL E 21 " --> pdb=" O VAL E 17 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLN E 22 " --> pdb=" O HIS E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 54 Processing helix chain 'E' and resid 60 through 76 removed outlier: 4.099A pdb=" N GLU E 76 " --> pdb=" O LYS E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 116 Processing helix chain 'E' and resid 124 through 151 Processing helix chain 'E' and resid 172 through 198 Processing helix chain 'E' and resid 202 through 211 Processing helix chain 'E' and resid 213 through 233 Processing helix chain 'E' and resid 239 through 248 Processing helix chain 'F' and resid 10 through 24 removed outlier: 3.536A pdb=" N LEU F 20 " --> pdb=" O LEU F 16 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL F 21 " --> pdb=" O VAL F 17 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLN F 22 " --> pdb=" O HIS F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 54 Processing helix chain 'F' and resid 60 through 76 removed outlier: 4.099A pdb=" N GLU F 76 " --> pdb=" O LYS F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 116 Processing helix chain 'F' and resid 124 through 151 Processing helix chain 'F' and resid 172 through 198 Processing helix chain 'F' and resid 202 through 211 Processing helix chain 'F' and resid 213 through 233 Processing helix chain 'F' and resid 239 through 248 Processing helix chain 'G' and resid 10 through 24 removed outlier: 3.536A pdb=" N LEU G 20 " --> pdb=" O LEU G 16 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL G 21 " --> pdb=" O VAL G 17 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN G 22 " --> pdb=" O HIS G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 54 Processing helix chain 'G' and resid 60 through 76 removed outlier: 4.100A pdb=" N GLU G 76 " --> pdb=" O LYS G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 116 Processing helix chain 'G' and resid 124 through 151 Processing helix chain 'G' and resid 172 through 198 Processing helix chain 'G' and resid 202 through 211 Processing helix chain 'G' and resid 213 through 233 Processing helix chain 'G' and resid 239 through 248 Processing helix chain 'H' and resid 10 through 24 removed outlier: 3.535A pdb=" N LEU H 20 " --> pdb=" O LEU H 16 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL H 21 " --> pdb=" O VAL H 17 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLN H 22 " --> pdb=" O HIS H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 54 Processing helix chain 'H' and resid 60 through 76 removed outlier: 4.100A pdb=" N GLU H 76 " --> pdb=" O LYS H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 116 Processing helix chain 'H' and resid 124 through 151 Processing helix chain 'H' and resid 172 through 198 Processing helix chain 'H' and resid 202 through 211 Processing helix chain 'H' and resid 213 through 233 Processing helix chain 'H' and resid 239 through 248 Processing helix chain 'I' and resid 10 through 24 removed outlier: 3.535A pdb=" N LEU I 20 " --> pdb=" O LEU I 16 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL I 21 " --> pdb=" O VAL I 17 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN I 22 " --> pdb=" O HIS I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 36 through 54 Processing helix chain 'I' and resid 60 through 76 removed outlier: 4.100A pdb=" N GLU I 76 " --> pdb=" O LYS I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 89 through 116 Processing helix chain 'I' and resid 124 through 151 Processing helix chain 'I' and resid 172 through 198 Processing helix chain 'I' and resid 202 through 211 Processing helix chain 'I' and resid 213 through 233 Processing helix chain 'I' and resid 239 through 248 Processing helix chain 'J' and resid 10 through 24 removed outlier: 3.535A pdb=" N LEU J 20 " --> pdb=" O LEU J 16 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL J 21 " --> pdb=" O VAL J 17 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN J 22 " --> pdb=" O HIS J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 54 Processing helix chain 'J' and resid 60 through 76 removed outlier: 4.100A pdb=" N GLU J 76 " --> pdb=" O LYS J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 116 Processing helix chain 'J' and resid 124 through 151 Processing helix chain 'J' and resid 172 through 198 Processing helix chain 'J' and resid 202 through 211 Processing helix chain 'J' and resid 213 through 233 Processing helix chain 'J' and resid 239 through 248 Processing helix chain 'K' and resid 10 through 24 removed outlier: 3.536A pdb=" N LEU K 20 " --> pdb=" O LEU K 16 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL K 21 " --> pdb=" O VAL K 17 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN K 22 " --> pdb=" O HIS K 18 " (cutoff:3.500A) Processing helix chain 'K' and resid 36 through 54 Processing helix chain 'K' and resid 60 through 76 removed outlier: 4.099A pdb=" N GLU K 76 " --> pdb=" O LYS K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 116 Processing helix chain 'K' and resid 124 through 151 Processing helix chain 'K' and resid 172 through 198 Processing helix chain 'K' and resid 202 through 211 Processing helix chain 'K' and resid 213 through 233 Processing helix chain 'K' and resid 239 through 248 Processing helix chain 'L' and resid 10 through 24 removed outlier: 3.536A pdb=" N LEU L 20 " --> pdb=" O LEU L 16 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL L 21 " --> pdb=" O VAL L 17 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN L 22 " --> pdb=" O HIS L 18 " (cutoff:3.500A) Processing helix chain 'L' and resid 36 through 54 Processing helix chain 'L' and resid 60 through 76 removed outlier: 4.099A pdb=" N GLU L 76 " --> pdb=" O LYS L 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 89 through 116 Processing helix chain 'L' and resid 124 through 151 Processing helix chain 'L' and resid 172 through 198 Processing helix chain 'L' and resid 202 through 211 Processing helix chain 'L' and resid 213 through 233 Processing helix chain 'L' and resid 239 through 248 Processing helix chain 'M' and resid 10 through 24 removed outlier: 3.535A pdb=" N LEU M 20 " --> pdb=" O LEU M 16 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL M 21 " --> pdb=" O VAL M 17 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN M 22 " --> pdb=" O HIS M 18 " (cutoff:3.500A) Processing helix chain 'M' and resid 36 through 54 Processing helix chain 'M' and resid 60 through 76 removed outlier: 4.099A pdb=" N GLU M 76 " --> pdb=" O LYS M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 116 Processing helix chain 'M' and resid 124 through 151 Processing helix chain 'M' and resid 172 through 198 Processing helix chain 'M' and resid 202 through 211 Processing helix chain 'M' and resid 213 through 233 Processing helix chain 'M' and resid 239 through 248 Processing helix chain 'N' and resid 10 through 24 removed outlier: 3.536A pdb=" N LEU N 20 " --> pdb=" O LEU N 16 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL N 21 " --> pdb=" O VAL N 17 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN N 22 " --> pdb=" O HIS N 18 " (cutoff:3.500A) Processing helix chain 'N' and resid 36 through 54 Processing helix chain 'N' and resid 60 through 76 removed outlier: 4.100A pdb=" N GLU N 76 " --> pdb=" O LYS N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 89 through 116 Processing helix chain 'N' and resid 124 through 151 Processing helix chain 'N' and resid 172 through 198 Processing helix chain 'N' and resid 202 through 211 Processing helix chain 'N' and resid 213 through 233 Processing helix chain 'N' and resid 239 through 248 Processing helix chain 'O' and resid 10 through 24 removed outlier: 3.535A pdb=" N LEU O 20 " --> pdb=" O LEU O 16 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL O 21 " --> pdb=" O VAL O 17 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN O 22 " --> pdb=" O HIS O 18 " (cutoff:3.500A) Processing helix chain 'O' and resid 36 through 54 Processing helix chain 'O' and resid 60 through 76 removed outlier: 4.100A pdb=" N GLU O 76 " --> pdb=" O LYS O 72 " (cutoff:3.500A) Processing helix chain 'O' and resid 89 through 116 Processing helix chain 'O' and resid 124 through 151 Processing helix chain 'O' and resid 172 through 198 Processing helix chain 'O' and resid 202 through 211 Processing helix chain 'O' and resid 213 through 233 Processing helix chain 'O' and resid 239 through 248 Processing helix chain 'P' and resid 10 through 24 removed outlier: 3.536A pdb=" N LEU P 20 " --> pdb=" O LEU P 16 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL P 21 " --> pdb=" O VAL P 17 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLN P 22 " --> pdb=" O HIS P 18 " (cutoff:3.500A) Processing helix chain 'P' and resid 36 through 54 Processing helix chain 'P' and resid 60 through 76 removed outlier: 4.100A pdb=" N GLU P 76 " --> pdb=" O LYS P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 89 through 116 Processing helix chain 'P' and resid 124 through 151 Processing helix chain 'P' and resid 172 through 198 Processing helix chain 'P' and resid 202 through 211 Processing helix chain 'P' and resid 213 through 233 Processing helix chain 'P' and resid 239 through 248 Processing helix chain 'Q' and resid 10 through 24 removed outlier: 3.535A pdb=" N LEU Q 20 " --> pdb=" O LEU Q 16 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL Q 21 " --> pdb=" O VAL Q 17 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLN Q 22 " --> pdb=" O HIS Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 36 through 54 Processing helix chain 'Q' and resid 60 through 76 removed outlier: 4.100A pdb=" N GLU Q 76 " --> pdb=" O LYS Q 72 " (cutoff:3.500A) Processing helix chain 'Q' and resid 89 through 116 Processing helix chain 'Q' and resid 124 through 151 Processing helix chain 'Q' and resid 172 through 198 Processing helix chain 'Q' and resid 202 through 211 Processing helix chain 'Q' and resid 213 through 233 Processing helix chain 'Q' and resid 239 through 248 Processing helix chain 'R' and resid 10 through 24 removed outlier: 3.536A pdb=" N LEU R 20 " --> pdb=" O LEU R 16 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL R 21 " --> pdb=" O VAL R 17 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN R 22 " --> pdb=" O HIS R 18 " (cutoff:3.500A) Processing helix chain 'R' and resid 36 through 54 Processing helix chain 'R' and resid 60 through 76 removed outlier: 4.099A pdb=" N GLU R 76 " --> pdb=" O LYS R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 89 through 116 Processing helix chain 'R' and resid 124 through 151 Processing helix chain 'R' and resid 172 through 198 Processing helix chain 'R' and resid 202 through 211 Processing helix chain 'R' and resid 213 through 233 Processing helix chain 'R' and resid 239 through 248 Processing helix chain 'S' and resid 10 through 24 removed outlier: 3.536A pdb=" N LEU S 20 " --> pdb=" O LEU S 16 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL S 21 " --> pdb=" O VAL S 17 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN S 22 " --> pdb=" O HIS S 18 " (cutoff:3.500A) Processing helix chain 'S' and resid 36 through 54 Processing helix chain 'S' and resid 60 through 76 removed outlier: 4.100A pdb=" N GLU S 76 " --> pdb=" O LYS S 72 " (cutoff:3.500A) Processing helix chain 'S' and resid 89 through 116 Processing helix chain 'S' and resid 124 through 151 Processing helix chain 'S' and resid 172 through 198 Processing helix chain 'S' and resid 202 through 211 Processing helix chain 'S' and resid 213 through 233 Processing helix chain 'S' and resid 239 through 248 Processing helix chain 'T' and resid 10 through 24 removed outlier: 3.536A pdb=" N LEU T 20 " --> pdb=" O LEU T 16 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL T 21 " --> pdb=" O VAL T 17 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN T 22 " --> pdb=" O HIS T 18 " (cutoff:3.500A) Processing helix chain 'T' and resid 36 through 54 Processing helix chain 'T' and resid 60 through 76 removed outlier: 4.100A pdb=" N GLU T 76 " --> pdb=" O LYS T 72 " (cutoff:3.500A) Processing helix chain 'T' and resid 89 through 116 Processing helix chain 'T' and resid 124 through 151 Processing helix chain 'T' and resid 172 through 198 Processing helix chain 'T' and resid 202 through 211 Processing helix chain 'T' and resid 213 through 233 Processing helix chain 'T' and resid 239 through 248 Processing helix chain 'U' and resid 10 through 24 removed outlier: 3.536A pdb=" N LEU U 20 " --> pdb=" O LEU U 16 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL U 21 " --> pdb=" O VAL U 17 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLN U 22 " --> pdb=" O HIS U 18 " (cutoff:3.500A) Processing helix chain 'U' and resid 36 through 54 Processing helix chain 'U' and resid 60 through 76 removed outlier: 4.101A pdb=" N GLU U 76 " --> pdb=" O LYS U 72 " (cutoff:3.500A) Processing helix chain 'U' and resid 89 through 116 Processing helix chain 'U' and resid 124 through 151 Processing helix chain 'U' and resid 172 through 198 Processing helix chain 'U' and resid 202 through 211 Processing helix chain 'U' and resid 213 through 233 Processing helix chain 'U' and resid 239 through 248 Processing helix chain 'V' and resid 10 through 24 removed outlier: 3.535A pdb=" N LEU V 20 " --> pdb=" O LEU V 16 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL V 21 " --> pdb=" O VAL V 17 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN V 22 " --> pdb=" O HIS V 18 " (cutoff:3.500A) Processing helix chain 'V' and resid 36 through 54 Processing helix chain 'V' and resid 60 through 76 removed outlier: 4.100A pdb=" N GLU V 76 " --> pdb=" O LYS V 72 " (cutoff:3.500A) Processing helix chain 'V' and resid 89 through 116 Processing helix chain 'V' and resid 124 through 151 Processing helix chain 'V' and resid 172 through 198 Processing helix chain 'V' and resid 202 through 211 Processing helix chain 'V' and resid 213 through 233 Processing helix chain 'V' and resid 239 through 248 Processing helix chain 'W' and resid 10 through 24 removed outlier: 3.536A pdb=" N LEU W 20 " --> pdb=" O LEU W 16 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL W 21 " --> pdb=" O VAL W 17 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN W 22 " --> pdb=" O HIS W 18 " (cutoff:3.500A) Processing helix chain 'W' and resid 36 through 54 Processing helix chain 'W' and resid 60 through 76 removed outlier: 4.100A pdb=" N GLU W 76 " --> pdb=" O LYS W 72 " (cutoff:3.500A) Processing helix chain 'W' and resid 89 through 116 Processing helix chain 'W' and resid 124 through 151 Processing helix chain 'W' and resid 172 through 198 Processing helix chain 'W' and resid 202 through 211 Processing helix chain 'W' and resid 213 through 233 Processing helix chain 'W' and resid 239 through 248 Processing helix chain 'X' and resid 10 through 24 removed outlier: 3.535A pdb=" N LEU X 20 " --> pdb=" O LEU X 16 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL X 21 " --> pdb=" O VAL X 17 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN X 22 " --> pdb=" O HIS X 18 " (cutoff:3.500A) Processing helix chain 'X' and resid 36 through 54 Processing helix chain 'X' and resid 60 through 76 removed outlier: 4.100A pdb=" N GLU X 76 " --> pdb=" O LYS X 72 " (cutoff:3.500A) Processing helix chain 'X' and resid 89 through 116 Processing helix chain 'X' and resid 124 through 151 Processing helix chain 'X' and resid 172 through 198 Processing helix chain 'X' and resid 202 through 211 Processing helix chain 'X' and resid 213 through 233 Processing helix chain 'X' and resid 239 through 248 Processing helix chain 'a' and resid 5 through 17 removed outlier: 3.723A pdb=" N ASP a 17 " --> pdb=" O LEU a 14 " (cutoff:3.500A) Processing helix chain 'b' and resid 5 through 17 removed outlier: 3.723A pdb=" N ASP b 17 " --> pdb=" O LEU b 14 " (cutoff:3.500A) Processing helix chain 'c' and resid 5 through 17 removed outlier: 3.723A pdb=" N ASP c 17 " --> pdb=" O LEU c 14 " (cutoff:3.500A) Processing helix chain 'd' and resid 5 through 17 removed outlier: 3.723A pdb=" N ASP d 17 " --> pdb=" O LEU d 14 " (cutoff:3.500A) Processing helix chain 'e' and resid 5 through 17 removed outlier: 3.723A pdb=" N ASP e 17 " --> pdb=" O LEU e 14 " (cutoff:3.500A) Processing helix chain 'f' and resid 5 through 17 removed outlier: 3.723A pdb=" N ASP f 17 " --> pdb=" O LEU f 14 " (cutoff:3.500A) Processing helix chain 'g' and resid 5 through 17 removed outlier: 3.723A pdb=" N ASP g 17 " --> pdb=" O LEU g 14 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 17 removed outlier: 3.723A pdb=" N ASP h 17 " --> pdb=" O LEU h 14 " (cutoff:3.500A) Processing helix chain 'i' and resid 5 through 17 removed outlier: 3.723A pdb=" N ASP i 17 " --> pdb=" O LEU i 14 " (cutoff:3.500A) Processing helix chain 'j' and resid 5 through 17 removed outlier: 3.723A pdb=" N ASP j 17 " --> pdb=" O LEU j 14 " (cutoff:3.500A) Processing helix chain 'k' and resid 5 through 17 removed outlier: 3.723A pdb=" N ASP k 17 " --> pdb=" O LEU k 14 " (cutoff:3.500A) Processing helix chain 'l' and resid 5 through 17 removed outlier: 3.723A pdb=" N ASP l 17 " --> pdb=" O LEU l 14 " (cutoff:3.500A) Processing helix chain 'm' and resid 5 through 17 removed outlier: 3.723A pdb=" N ASP m 17 " --> pdb=" O LEU m 14 " (cutoff:3.500A) Processing helix chain 'n' and resid 5 through 17 removed outlier: 3.723A pdb=" N ASP n 17 " --> pdb=" O LEU n 14 " (cutoff:3.500A) Processing helix chain 'o' and resid 5 through 17 removed outlier: 3.723A pdb=" N ASP o 17 " --> pdb=" O LEU o 14 " (cutoff:3.500A) Processing helix chain 'p' and resid 5 through 17 removed outlier: 3.723A pdb=" N ASP p 17 " --> pdb=" O LEU p 14 " (cutoff:3.500A) Processing helix chain 'q' and resid 5 through 17 removed outlier: 3.723A pdb=" N ASP q 17 " --> pdb=" O LEU q 14 " (cutoff:3.500A) Processing helix chain 'r' and resid 5 through 17 removed outlier: 3.723A pdb=" N ASP r 17 " --> pdb=" O LEU r 14 " (cutoff:3.500A) Processing helix chain 's' and resid 5 through 17 removed outlier: 3.723A pdb=" N ASP s 17 " --> pdb=" O LEU s 14 " (cutoff:3.500A) Processing helix chain 't' and resid 5 through 17 removed outlier: 3.723A pdb=" N ASP t 17 " --> pdb=" O LEU t 14 " (cutoff:3.500A) Processing helix chain 'u' and resid 5 through 17 removed outlier: 3.723A pdb=" N ASP u 17 " --> pdb=" O LEU u 14 " (cutoff:3.500A) Processing helix chain 'v' and resid 5 through 17 removed outlier: 3.723A pdb=" N ASP v 17 " --> pdb=" O LEU v 14 " (cutoff:3.500A) Processing helix chain 'w' and resid 5 through 17 removed outlier: 3.723A pdb=" N ASP w 17 " --> pdb=" O LEU w 14 " (cutoff:3.500A) Processing helix chain 'x' and resid 5 through 17 removed outlier: 3.723A pdb=" N ASP x 17 " --> pdb=" O LEU x 14 " (cutoff:3.500A) 3456 hydrogen bonds defined for protein. 9696 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: 14.63 Time building geometry restraints manager: 19.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 17424 1.35 - 1.46: 11516 1.46 - 1.58: 23284 1.58 - 1.69: 96 1.69 - 1.81: 480 Bond restraints: 52800 Sorted by residual: bond pdb=" CA LEU W 77 " pdb=" CB LEU W 77 " ideal model delta sigma weight residual 1.524 1.505 0.019 1.41e-02 5.03e+03 1.75e+00 bond pdb=" CA LEU V 77 " pdb=" CB LEU V 77 " ideal model delta sigma weight residual 1.524 1.505 0.019 1.41e-02 5.03e+03 1.75e+00 bond pdb=" CA LEU A 77 " pdb=" CB LEU A 77 " ideal model delta sigma weight residual 1.524 1.505 0.019 1.41e-02 5.03e+03 1.75e+00 bond pdb=" CA LEU C 77 " pdb=" CB LEU C 77 " ideal model delta sigma weight residual 1.524 1.505 0.018 1.41e-02 5.03e+03 1.70e+00 bond pdb=" CA LEU S 77 " pdb=" CB LEU S 77 " ideal model delta sigma weight residual 1.524 1.505 0.018 1.41e-02 5.03e+03 1.70e+00 ... (remaining 52795 not shown) Histogram of bond angle deviations from ideal: 100.69 - 107.34: 1560 107.34 - 114.00: 29200 114.00 - 120.65: 25271 120.65 - 127.31: 14579 127.31 - 133.97: 454 Bond angle restraints: 71064 Sorted by residual: angle pdb=" CA LEU A 33 " pdb=" C LEU A 33 " pdb=" O LEU A 33 " ideal model delta sigma weight residual 117.94 121.55 -3.61 5.80e-01 2.97e+00 3.87e+01 angle pdb=" CA LEU Q 33 " pdb=" C LEU Q 33 " pdb=" O LEU Q 33 " ideal model delta sigma weight residual 117.94 121.52 -3.58 5.80e-01 2.97e+00 3.82e+01 angle pdb=" CA LEU R 33 " pdb=" C LEU R 33 " pdb=" O LEU R 33 " ideal model delta sigma weight residual 117.94 121.52 -3.58 5.80e-01 2.97e+00 3.82e+01 angle pdb=" CA LEU B 33 " pdb=" C LEU B 33 " pdb=" O LEU B 33 " ideal model delta sigma weight residual 117.94 121.51 -3.57 5.80e-01 2.97e+00 3.80e+01 angle pdb=" CA LEU N 33 " pdb=" C LEU N 33 " pdb=" O LEU N 33 " ideal model delta sigma weight residual 117.94 121.51 -3.57 5.80e-01 2.97e+00 3.80e+01 ... (remaining 71059 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.52: 31400 14.52 - 29.03: 1068 29.03 - 43.55: 292 43.55 - 58.06: 24 58.06 - 72.58: 24 Dihedral angle restraints: 32808 sinusoidal: 13920 harmonic: 18888 Sorted by residual: dihedral pdb=" CA AARG X 138 " pdb=" CB AARG X 138 " pdb=" CG AARG X 138 " pdb=" CD AARG X 138 " ideal model delta sinusoidal sigma weight residual -180.00 -122.95 -57.05 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" CA AARG I 138 " pdb=" CB AARG I 138 " pdb=" CG AARG I 138 " pdb=" CD AARG I 138 " ideal model delta sinusoidal sigma weight residual -180.00 -122.98 -57.02 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" CA AARG K 138 " pdb=" CB AARG K 138 " pdb=" CG AARG K 138 " pdb=" CD AARG K 138 " ideal model delta sinusoidal sigma weight residual -180.00 -122.98 -57.02 3 1.50e+01 4.44e-03 9.42e+00 ... (remaining 32805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 5567 0.028 - 0.056: 1537 0.056 - 0.085: 288 0.085 - 0.113: 68 0.113 - 0.141: 28 Chirality restraints: 7488 Sorted by residual: chirality pdb=" CG LEU A 77 " pdb=" CB LEU A 77 " pdb=" CD1 LEU A 77 " pdb=" CD2 LEU A 77 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 4.98e-01 chirality pdb=" CG LEU V 77 " pdb=" CB LEU V 77 " pdb=" CD1 LEU V 77 " pdb=" CD2 LEU V 77 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 4.94e-01 chirality pdb=" CG LEU W 77 " pdb=" CB LEU W 77 " pdb=" CD1 LEU W 77 " pdb=" CD2 LEU W 77 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 4.94e-01 ... (remaining 7485 not shown) Planarity restraints: 9264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SEP x 6 " -0.006 2.00e-02 2.50e+03 1.24e-02 1.53e+00 pdb=" C SEP x 6 " 0.021 2.00e-02 2.50e+03 pdb=" O SEP x 6 " -0.008 2.00e-02 2.50e+03 pdb=" N TYR x 7 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SEP d 6 " -0.006 2.00e-02 2.50e+03 1.24e-02 1.53e+00 pdb=" C SEP d 6 " 0.021 2.00e-02 2.50e+03 pdb=" O SEP d 6 " -0.008 2.00e-02 2.50e+03 pdb=" N TYR d 7 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SEP e 6 " 0.006 2.00e-02 2.50e+03 1.24e-02 1.53e+00 pdb=" C SEP e 6 " -0.021 2.00e-02 2.50e+03 pdb=" O SEP e 6 " 0.008 2.00e-02 2.50e+03 pdb=" N TYR e 7 " 0.007 2.00e-02 2.50e+03 ... (remaining 9261 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 888 2.69 - 3.24: 51180 3.24 - 3.80: 85787 3.80 - 4.35: 104815 4.35 - 4.90: 173288 Nonbonded interactions: 415958 Sorted by model distance: nonbonded pdb=" O ALA B 67 " pdb=" CD2 TYR B 71 " model vdw 2.141 3.340 nonbonded pdb=" O ALA V 67 " pdb=" CD2 TYR V 71 " model vdw 2.142 3.340 nonbonded pdb=" O ALA M 67 " pdb=" CD2 TYR M 71 " model vdw 2.143 3.340 nonbonded pdb=" O ALA H 67 " pdb=" CD2 TYR H 71 " model vdw 2.143 3.340 nonbonded pdb=" O ALA A 67 " pdb=" CD2 TYR A 71 " model vdw 2.143 3.340 ... (remaining 415953 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'B' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'C' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'D' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'E' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'F' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'G' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'H' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'I' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'J' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'K' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'L' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'M' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'N' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'O' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'P' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'Q' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'R' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'S' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'T' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'U' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'V' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'W' and (resid 9 through 137 or resid 139 through 251)) selection = (chain 'X' and (resid 9 through 137 or resid 139 through 251)) } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.220 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: 0.030 Extract box with map and model: 15.060 Check model and map are aligned: 0.780 Set scattering table: 0.440 Process input model: 133.460 Find NCS groups from input model: 3.380 Set up NCS constraints: 0.650 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 168.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.001 0.019 52800 Z= 0.092 Angle : 0.427 6.212 71064 Z= 0.291 Chirality : 0.029 0.141 7488 Planarity : 0.002 0.021 9264 Dihedral : 8.124 72.580 20424 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.78 % Allowed : 7.84 % Favored : 91.37 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.10), residues: 6144 helix: 1.67 (0.07), residues: 4704 sheet: None (None), residues: 0 loop : -3.53 (0.14), residues: 1440 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1448 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1424 time to evaluate : 4.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 0 residues processed: 1448 average time/residue: 1.4750 time to fit residues: 2665.6748 Evaluate side-chains 957 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 957 time to evaluate : 4.587 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.2804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 506 optimal weight: 30.0000 chunk 454 optimal weight: 0.8980 chunk 252 optimal weight: 8.9990 chunk 155 optimal weight: 1.9990 chunk 306 optimal weight: 3.9990 chunk 242 optimal weight: 40.0000 chunk 470 optimal weight: 3.9990 chunk 181 optimal weight: 7.9990 chunk 285 optimal weight: 0.8980 chunk 350 optimal weight: 0.9980 chunk 544 optimal weight: 0.3980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN A 88 HIS A 180 HIS A 187 GLN A 248 HIS B 86 ASN B 88 HIS B 180 HIS B 187 GLN B 248 HIS C 86 ASN C 88 HIS C 180 HIS C 187 GLN ** C 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 86 ASN D 88 HIS D 180 HIS D 187 GLN ** D 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 ASN E 88 HIS E 180 HIS E 187 GLN E 248 HIS F 86 ASN F 88 HIS F 180 HIS F 187 GLN F 248 HIS G 86 ASN G 88 HIS G 180 HIS G 187 GLN ** G 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 86 ASN H 88 HIS H 180 HIS H 187 GLN ** H 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 86 ASN I 88 HIS I 180 HIS I 187 GLN ** I 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 86 ASN J 88 HIS J 180 HIS J 187 GLN J 248 HIS K 86 ASN K 88 HIS K 180 HIS K 187 GLN K 248 HIS L 86 ASN L 88 HIS L 180 HIS L 187 GLN ** L 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 86 ASN M 88 HIS M 180 HIS M 187 GLN ** M 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 86 ASN N 88 HIS N 180 HIS N 187 GLN N 248 HIS O 86 ASN O 88 HIS O 180 HIS O 187 GLN O 248 HIS P 86 ASN P 88 HIS P 180 HIS P 187 GLN ** P 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 86 ASN Q 88 HIS Q 180 HIS Q 187 GLN Q 248 HIS R 86 ASN R 88 HIS R 180 HIS R 187 GLN R 248 HIS S 86 ASN S 88 HIS S 180 HIS S 187 GLN ** S 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 86 ASN T 88 HIS T 180 HIS T 187 GLN ** T 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 86 ASN U 88 HIS U 180 HIS U 187 GLN U 248 HIS V 86 ASN V 88 HIS V 180 HIS V 187 GLN ** V 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 86 ASN W 88 HIS W 180 HIS W 187 GLN ** W 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 86 ASN X 88 HIS X 180 HIS X 187 GLN X 248 HIS Total number of N/Q/H flips: 108 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 52800 Z= 0.196 Angle : 0.607 7.086 71064 Z= 0.313 Chirality : 0.036 0.151 7488 Planarity : 0.004 0.042 9264 Dihedral : 4.147 36.648 7104 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.65 % Allowed : 3.33 % Favored : 96.01 % Rotamer Outliers : 2.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.11), residues: 6144 helix: 2.26 (0.08), residues: 4776 sheet: None (None), residues: 0 loop : -3.02 (0.16), residues: 1368 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 879 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 748 time to evaluate : 4.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 131 outliers final: 32 residues processed: 831 average time/residue: 1.4760 time to fit residues: 1527.7529 Evaluate side-chains 718 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 686 time to evaluate : 4.592 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 8 residues processed: 32 average time/residue: 0.7214 time to fit residues: 40.6077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 302 optimal weight: 5.9990 chunk 169 optimal weight: 8.9990 chunk 453 optimal weight: 0.8980 chunk 371 optimal weight: 0.1980 chunk 150 optimal weight: 6.9990 chunk 545 optimal weight: 0.9980 chunk 589 optimal weight: 6.9990 chunk 486 optimal weight: 5.9990 chunk 541 optimal weight: 1.9990 chunk 186 optimal weight: 7.9990 chunk 437 optimal weight: 40.0000 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 158 GLN B 98 GLN B 158 GLN C 98 GLN C 158 GLN ** C 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN D 158 GLN ** D 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN E 158 GLN F 86 ASN F 98 GLN F 158 GLN G 98 GLN G 158 GLN ** G 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 GLN H 158 GLN ** H 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 98 GLN I 158 GLN ** I 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 GLN J 158 GLN K 98 GLN K 158 GLN L 98 GLN L 158 GLN ** L 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 98 GLN M 158 GLN ** M 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 98 GLN N 158 GLN O 98 GLN O 158 GLN P 98 GLN P 158 GLN ** P 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 98 GLN Q 158 GLN R 86 ASN R 98 GLN R 158 GLN S 98 GLN S 158 GLN ** S 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 86 ASN T 98 GLN T 158 GLN ** T 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 98 GLN U 158 GLN V 86 ASN V 98 GLN V 158 GLN ** V 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 98 GLN W 158 GLN ** W 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 98 GLN X 158 GLN Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 52800 Z= 0.239 Angle : 0.623 9.691 71064 Z= 0.323 Chirality : 0.039 0.143 7488 Planarity : 0.004 0.042 9264 Dihedral : 4.734 44.573 7104 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.14 % Favored : 96.47 % Rotamer Outliers : 3.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.11), residues: 6144 helix: 2.31 (0.08), residues: 4776 sheet: None (None), residues: 0 loop : -2.57 (0.18), residues: 1368 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 840 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 662 time to evaluate : 4.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 178 outliers final: 64 residues processed: 813 average time/residue: 1.3358 time to fit residues: 1380.0010 Evaluate side-chains 544 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 480 time to evaluate : 4.859 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 64 residues processed: 0 time to fit residues: 6.7264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 539 optimal weight: 0.0970 chunk 410 optimal weight: 7.9990 chunk 283 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 260 optimal weight: 0.8980 chunk 366 optimal weight: 8.9990 chunk 547 optimal weight: 4.9990 chunk 579 optimal weight: 20.0000 chunk 286 optimal weight: 0.9990 chunk 519 optimal weight: 2.9990 chunk 156 optimal weight: 4.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN B 86 ASN C 86 ASN D 86 ASN E 86 ASN G 86 ASN H 86 ASN I 86 ASN J 86 ASN K 86 ASN L 86 ASN L 100 ASN M 86 ASN N 86 ASN O 86 ASN P 86 ASN P 100 ASN Q 86 ASN S 86 ASN U 86 ASN W 86 ASN X 86 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.5134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 52800 Z= 0.197 Angle : 0.593 8.689 71064 Z= 0.303 Chirality : 0.037 0.158 7488 Planarity : 0.003 0.024 9264 Dihedral : 4.758 53.039 7104 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.46 % Favored : 96.14 % Rotamer Outliers : 2.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.11), residues: 6144 helix: 2.69 (0.08), residues: 4680 sheet: None (None), residues: 0 loop : -2.58 (0.17), residues: 1464 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 559 time to evaluate : 5.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 141 outliers final: 62 residues processed: 672 average time/residue: 1.3258 time to fit residues: 1130.0345 Evaluate side-chains 602 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 540 time to evaluate : 4.535 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 62 residues processed: 0 time to fit residues: 6.3847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 483 optimal weight: 10.0000 chunk 329 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 431 optimal weight: 3.9990 chunk 239 optimal weight: 6.9990 chunk 494 optimal weight: 6.9990 chunk 400 optimal weight: 0.8980 chunk 0 optimal weight: 50.0000 chunk 296 optimal weight: 2.9990 chunk 520 optimal weight: 6.9990 chunk 146 optimal weight: 50.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.5530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 52800 Z= 0.223 Angle : 0.583 7.751 71064 Z= 0.297 Chirality : 0.036 0.169 7488 Planarity : 0.003 0.029 9264 Dihedral : 4.849 57.379 7104 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.09 % Favored : 96.52 % Rotamer Outliers : 2.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.12), residues: 6144 helix: 2.68 (0.08), residues: 4800 sheet: None (None), residues: 0 loop : -2.32 (0.18), residues: 1344 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 496 time to evaluate : 4.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 126 outliers final: 56 residues processed: 612 average time/residue: 1.2914 time to fit residues: 1007.9501 Evaluate side-chains 501 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 445 time to evaluate : 4.573 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 52 residues processed: 4 average time/residue: 0.3886 time to fit residues: 9.1951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 195 optimal weight: 10.0000 chunk 522 optimal weight: 0.9990 chunk 114 optimal weight: 0.6980 chunk 340 optimal weight: 30.0000 chunk 143 optimal weight: 0.9990 chunk 580 optimal weight: 10.0000 chunk 481 optimal weight: 20.0000 chunk 268 optimal weight: 50.0000 chunk 48 optimal weight: 50.0000 chunk 192 optimal weight: 50.0000 chunk 304 optimal weight: 5.9990 overall best weight: 3.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 GLN ** J 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 98 GLN ** M 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 98 GLN P 98 GLN U 98 GLN ** U 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 98 GLN W 98 GLN X 98 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.6461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.062 52800 Z= 0.348 Angle : 0.651 7.544 71064 Z= 0.330 Chirality : 0.040 0.191 7488 Planarity : 0.004 0.032 9264 Dihedral : 4.702 43.268 7104 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.17 % Favored : 96.44 % Rotamer Outliers : 2.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.11), residues: 6144 helix: 2.63 (0.08), residues: 4752 sheet: None (None), residues: 0 loop : -2.05 (0.17), residues: 1392 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 435 time to evaluate : 4.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 115 outliers final: 31 residues processed: 547 average time/residue: 1.1533 time to fit residues: 822.3147 Evaluate side-chains 454 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 423 time to evaluate : 4.487 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 31 residues processed: 0 time to fit residues: 6.1467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 559 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 330 optimal weight: 2.9990 chunk 423 optimal weight: 1.9990 chunk 328 optimal weight: 2.9990 chunk 488 optimal weight: 1.9990 chunk 324 optimal weight: 7.9990 chunk 578 optimal weight: 20.0000 chunk 361 optimal weight: 8.9990 chunk 352 optimal weight: 0.9980 chunk 266 optimal weight: 30.0000 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 193 HIS B 98 GLN B 193 HIS C 98 GLN C 193 HIS D 193 HIS E 98 GLN E 193 HIS F 98 GLN ** F 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN G 193 HIS H 98 GLN H 193 HIS ** I 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 GLN ** J 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 98 GLN K 216 GLN L 193 HIS M 98 GLN ** M 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 193 HIS M 216 GLN ** N 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 193 HIS O 98 GLN ** O 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 193 HIS O 216 GLN P 98 GLN P 193 HIS P 216 GLN Q 98 GLN R 98 GLN R 193 HIS S 98 GLN T 98 GLN T 193 HIS U 98 GLN ** U 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 193 HIS U 216 GLN V 98 GLN ** V 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 193 HIS W 98 GLN ** W 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 98 GLN ** X 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 193 HIS Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.6450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 52800 Z= 0.197 Angle : 0.586 8.173 71064 Z= 0.294 Chirality : 0.038 0.188 7488 Planarity : 0.004 0.027 9264 Dihedral : 4.573 46.232 7104 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.39 % Allowed : 2.32 % Favored : 97.29 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.90 (0.11), residues: 6144 helix: 2.82 (0.08), residues: 4776 sheet: None (None), residues: 0 loop : -1.62 (0.18), residues: 1368 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 445 time to evaluate : 4.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 31 residues processed: 476 average time/residue: 1.2242 time to fit residues: 746.1950 Evaluate side-chains 441 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 410 time to evaluate : 4.440 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 24 residues processed: 7 average time/residue: 0.3894 time to fit residues: 11.1591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 357 optimal weight: 7.9990 chunk 230 optimal weight: 3.9990 chunk 345 optimal weight: 3.9990 chunk 174 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 367 optimal weight: 7.9990 chunk 393 optimal weight: 2.9990 chunk 285 optimal weight: 0.9990 chunk 53 optimal weight: 8.9990 chunk 454 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 200 ASN ** I 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 98 GLN ** M 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 200 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.6715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.064 52800 Z= 0.296 Angle : 0.622 8.647 71064 Z= 0.314 Chirality : 0.038 0.156 7488 Planarity : 0.004 0.028 9264 Dihedral : 4.567 42.870 7104 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.02 % Favored : 96.58 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.86 (0.11), residues: 6144 helix: 2.76 (0.08), residues: 4776 sheet: None (None), residues: 0 loop : -1.47 (0.18), residues: 1368 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 434 time to evaluate : 4.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 25 residues processed: 458 average time/residue: 1.1647 time to fit residues: 690.1196 Evaluate side-chains 440 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 415 time to evaluate : 4.322 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 24 residues processed: 1 average time/residue: 0.3807 time to fit residues: 6.7299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 526 optimal weight: 1.9990 chunk 554 optimal weight: 0.8980 chunk 505 optimal weight: 8.9990 chunk 538 optimal weight: 0.9990 chunk 553 optimal weight: 3.9990 chunk 324 optimal weight: 7.9990 chunk 234 optimal weight: 2.9990 chunk 423 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 486 optimal weight: 8.9990 chunk 509 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN B 200 ASN C 200 ASN D 98 GLN H 200 ASN I 98 GLN ** I 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 200 ASN J 98 GLN ** J 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 98 GLN L 98 GLN M 98 GLN ** M 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 98 GLN ** N 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 98 GLN ** O 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 98 GLN U 98 GLN ** U 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 98 GLN W 98 GLN X 98 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.6750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.069 52800 Z= 0.229 Angle : 0.582 7.228 71064 Z= 0.296 Chirality : 0.037 0.143 7488 Planarity : 0.004 0.026 9264 Dihedral : 4.566 43.840 7104 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.39 % Allowed : 1.73 % Favored : 97.88 % Rotamer Outliers : 0.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.85 (0.11), residues: 6144 helix: 2.76 (0.08), residues: 4776 sheet: None (None), residues: 0 loop : -1.46 (0.18), residues: 1368 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 450 time to evaluate : 4.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 29 residues processed: 484 average time/residue: 1.0987 time to fit residues: 696.9397 Evaluate side-chains 455 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 426 time to evaluate : 4.361 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 24 residues processed: 5 average time/residue: 0.3914 time to fit residues: 9.6463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 537 optimal weight: 1.9990 chunk 353 optimal weight: 1.9990 chunk 569 optimal weight: 1.9990 chunk 347 optimal weight: 4.9990 chunk 270 optimal weight: 5.9990 chunk 396 optimal weight: 2.9990 chunk 597 optimal weight: 30.0000 chunk 550 optimal weight: 0.9990 chunk 475 optimal weight: 3.9990 chunk 49 optimal weight: 20.0000 chunk 367 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 98 GLN F 193 HIS I 193 HIS J 98 GLN ** J 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 193 HIS J 248 HIS K 193 HIS K 200 ASN ** M 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 200 ASN N 98 GLN Q 193 HIS S 193 HIS S 200 ASN U 98 GLN U 200 ASN ** V 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 98 GLN W 193 HIS W 200 ASN ** X 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.6766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 52800 Z= 0.198 Angle : 0.574 9.822 71064 Z= 0.289 Chirality : 0.037 0.181 7488 Planarity : 0.004 0.027 9264 Dihedral : 4.594 44.732 7104 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.39 % Allowed : 2.16 % Favored : 97.45 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.84 (0.11), residues: 6144 helix: 2.75 (0.08), residues: 4776 sheet: None (None), residues: 0 loop : -1.49 (0.18), residues: 1368 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12288 Ramachandran restraints generated. 6144 Oldfield, 0 Emsley, 6144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 447 time to evaluate : 4.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 24 residues processed: 485 average time/residue: 1.1939 time to fit residues: 742.4919 Evaluate side-chains 444 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 420 time to evaluate : 4.295 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 24 residues processed: 0 time to fit residues: 5.9477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 291 optimal weight: 30.0000 chunk 378 optimal weight: 6.9990 chunk 507 optimal weight: 8.9990 chunk 145 optimal weight: 10.0000 chunk 438 optimal weight: 9.9990 chunk 70 optimal weight: 0.0770 chunk 132 optimal weight: 1.9990 chunk 476 optimal weight: 8.9990 chunk 199 optimal weight: 6.9990 chunk 489 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 overall best weight: 2.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 98 GLN ** I 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 GLN ** J 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 98 GLN ** N 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.126290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.078621 restraints weight = 263210.452| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 4.33 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3214 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 72 | |-----------------------------------------------------------------------------| r_final: 0.3218 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.6860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 52800 Z= 0.235 Angle : 0.594 9.206 71064 Z= 0.301 Chirality : 0.037 0.161 7488 Planarity : 0.004 0.026 9264 Dihedral : 4.585 44.093 7104 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.39 % Allowed : 1.91 % Favored : 97.70 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.87 (0.11), residues: 6144 helix: 2.76 (0.08), residues: 4776 sheet: None (None), residues: 0 loop : -1.43 (0.18), residues: 1368 =============================================================================== Job complete usr+sys time: 17047.27 seconds wall clock time: 298 minutes 32.09 seconds (17912.09 seconds total)