Starting phenix.real_space_refine on Mon Mar 25 22:20:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tbh_25799/03_2024/7tbh_25799_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tbh_25799/03_2024/7tbh_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_25799/03_2024/7tbh_25799.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tbh_25799/03_2024/7tbh_25799.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tbh_25799/03_2024/7tbh_25799_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tbh_25799/03_2024/7tbh_25799_updated.pdb" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 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: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 47.48, per 1000 atoms: 0.92 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: 18.62 Conformation dependent library (CDL) restraints added in 16.2 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: 7.94 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: 16.94 Time building geometry restraints manager: 20.08 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: 2.880 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: 0.040 Extract box with map and model: 17.730 Check model and map are aligned: 3.640 Set scattering table: 0.000 Process input model: 153.550 Find NCS groups from input model: 3.640 Set up NCS constraints: 0.760 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:11.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 193.600 ------------------------------------------------------------------------------- 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 % Allowed : 3.88 % Favored : 95.69 % 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: 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP H 168 HIS 0.002 0.000 HIS T 193 PHE 0.002 0.000 PHE F 126 TYR 0.008 0.001 TYR F 71 ARG 0.002 0.000 ARG A 36 *********************** 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 : 6.087 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 REVERT: A 26 PRO cc_start: 0.8183 (Cg_endo) cc_final: 0.7964 (Cg_exo) REVERT: A 201 ASP cc_start: 0.7212 (t0) cc_final: 0.6957 (t0) REVERT: B 26 PRO cc_start: 0.8157 (Cg_endo) cc_final: 0.7956 (Cg_exo) REVERT: B 201 ASP cc_start: 0.7219 (t0) cc_final: 0.6963 (t0) REVERT: C 26 PRO cc_start: 0.8180 (Cg_endo) cc_final: 0.7962 (Cg_exo) REVERT: C 201 ASP cc_start: 0.7222 (t0) cc_final: 0.6970 (t0) REVERT: D 26 PRO cc_start: 0.8182 (Cg_endo) cc_final: 0.7964 (Cg_exo) REVERT: D 201 ASP cc_start: 0.7223 (t0) cc_final: 0.6976 (t0) REVERT: E 26 PRO cc_start: 0.8176 (Cg_endo) cc_final: 0.7956 (Cg_exo) REVERT: E 201 ASP cc_start: 0.7209 (t0) cc_final: 0.6950 (t0) REVERT: F 26 PRO cc_start: 0.8175 (Cg_endo) cc_final: 0.7968 (Cg_exo) REVERT: F 201 ASP cc_start: 0.7222 (t0) cc_final: 0.6973 (t0) REVERT: G 26 PRO cc_start: 0.8218 (Cg_endo) cc_final: 0.8007 (Cg_exo) REVERT: G 201 ASP cc_start: 0.7225 (t0) cc_final: 0.6977 (t0) REVERT: H 26 PRO cc_start: 0.8188 (Cg_endo) cc_final: 0.7972 (Cg_exo) REVERT: H 201 ASP cc_start: 0.7220 (t0) cc_final: 0.6973 (t0) REVERT: I 26 PRO cc_start: 0.8191 (Cg_endo) cc_final: 0.7983 (Cg_exo) REVERT: I 201 ASP cc_start: 0.7248 (t0) cc_final: 0.6999 (t0) REVERT: J 26 PRO cc_start: 0.8187 (Cg_endo) cc_final: 0.7984 (Cg_exo) REVERT: J 201 ASP cc_start: 0.7249 (t0) cc_final: 0.7002 (t0) REVERT: K 26 PRO cc_start: 0.8192 (Cg_endo) cc_final: 0.7981 (Cg_exo) REVERT: K 201 ASP cc_start: 0.7257 (t0) cc_final: 0.7009 (t0) REVERT: L 26 PRO cc_start: 0.8187 (Cg_endo) cc_final: 0.7982 (Cg_exo) REVERT: L 201 ASP cc_start: 0.7245 (t0) cc_final: 0.7000 (t0) REVERT: M 26 PRO cc_start: 0.8187 (Cg_endo) cc_final: 0.7984 (Cg_exo) REVERT: M 201 ASP cc_start: 0.7249 (t0) cc_final: 0.7005 (t0) REVERT: N 26 PRO cc_start: 0.8184 (Cg_endo) cc_final: 0.7977 (Cg_exo) REVERT: N 201 ASP cc_start: 0.7258 (t0) cc_final: 0.7012 (t0) REVERT: O 26 PRO cc_start: 0.8187 (Cg_endo) cc_final: 0.7976 (Cg_exo) REVERT: O 201 ASP cc_start: 0.7239 (t0) cc_final: 0.6990 (t0) REVERT: P 26 PRO cc_start: 0.8189 (Cg_endo) cc_final: 0.7984 (Cg_exo) REVERT: P 201 ASP cc_start: 0.7248 (t0) cc_final: 0.7000 (t0) REVERT: Q 26 PRO cc_start: 0.8214 (Cg_endo) cc_final: 0.8004 (Cg_exo) REVERT: Q 201 ASP cc_start: 0.7225 (t0) cc_final: 0.6977 (t0) REVERT: R 26 PRO cc_start: 0.8225 (Cg_endo) cc_final: 0.8015 (Cg_exo) REVERT: R 201 ASP cc_start: 0.7209 (t0) cc_final: 0.6962 (t0) REVERT: S 26 PRO cc_start: 0.8181 (Cg_endo) cc_final: 0.7963 (Cg_exo) REVERT: S 201 ASP cc_start: 0.7228 (t0) cc_final: 0.6981 (t0) REVERT: T 26 PRO cc_start: 0.8185 (Cg_endo) cc_final: 0.7975 (Cg_exo) REVERT: T 201 ASP cc_start: 0.7225 (t0) cc_final: 0.6978 (t0) REVERT: U 26 PRO cc_start: 0.8184 (Cg_endo) cc_final: 0.7977 (Cg_exo) REVERT: U 201 ASP cc_start: 0.7248 (t0) cc_final: 0.7000 (t0) REVERT: V 201 ASP cc_start: 0.7259 (t0) cc_final: 0.7013 (t0) REVERT: W 26 PRO cc_start: 0.8191 (Cg_endo) cc_final: 0.7981 (Cg_exo) REVERT: W 201 ASP cc_start: 0.7234 (t0) cc_final: 0.6987 (t0) REVERT: X 26 PRO cc_start: 0.8185 (Cg_endo) cc_final: 0.7979 (Cg_exo) REVERT: X 201 ASP cc_start: 0.7245 (t0) cc_final: 0.6998 (t0) outliers start: 24 outliers final: 0 residues processed: 1448 average time/residue: 1.5841 time to fit residues: 2867.5920 Evaluate side-chains 980 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 980 time to evaluate : 5.822 ------------------------------------------------------------------------------- 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: 0.0770 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: 1.9990 chunk 350 optimal weight: 0.9980 chunk 544 optimal weight: 0.3980 overall best weight: 1.0942 ------------------------------------------------------------------------------- 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: 0.7835 moved from start: 0.2791 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 : 0.606 6.689 71064 Z= 0.313 Chirality : 0.037 0.146 7488 Planarity : 0.004 0.022 9264 Dihedral : 4.156 36.553 7104 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.64 % Favored : 95.96 % Rotamer: Outliers : 2.30 % Allowed : 17.95 % Favored : 79.75 % 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: 1.79 (0.11), residues: 6144 helix: 2.27 (0.08), residues: 4776 sheet: None (None), residues: 0 loop : -3.02 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP F 168 HIS 0.009 0.001 HIS P 180 PHE 0.028 0.003 PHE C 207 TYR 0.018 0.002 TYR H 71 ARG 0.008 0.001 ARG O 118 *********************** 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 885 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 756 time to evaluate : 5.734 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 REVERT: A 22 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8546 (mp10) REVERT: A 218 LYS cc_start: 0.8854 (mttp) cc_final: 0.8360 (mttm) REVERT: B 22 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8555 (mp10) REVERT: B 218 LYS cc_start: 0.8854 (mttp) cc_final: 0.8362 (mttm) REVERT: C 22 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8557 (mp10) REVERT: C 218 LYS cc_start: 0.8856 (mttp) cc_final: 0.8366 (mttm) REVERT: D 22 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8552 (mp10) REVERT: D 218 LYS cc_start: 0.8853 (mttp) cc_final: 0.8361 (mttm) REVERT: E 22 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8542 (mp10) REVERT: E 218 LYS cc_start: 0.8857 (mttp) cc_final: 0.8363 (mttm) REVERT: F 22 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8547 (mp10) REVERT: F 218 LYS cc_start: 0.8847 (mttp) cc_final: 0.8358 (mttm) REVERT: G 22 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8556 (mp10) REVERT: G 218 LYS cc_start: 0.8850 (mttp) cc_final: 0.8361 (mttm) REVERT: H 22 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8555 (mp10) REVERT: H 218 LYS cc_start: 0.8850 (mttp) cc_final: 0.8361 (mttm) REVERT: I 22 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8558 (mp10) REVERT: I 218 LYS cc_start: 0.8848 (mttp) cc_final: 0.8356 (mttm) REVERT: J 22 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8550 (mp10) REVERT: J 218 LYS cc_start: 0.8848 (mttp) cc_final: 0.8356 (mttm) REVERT: K 22 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8554 (mp10) REVERT: K 218 LYS cc_start: 0.8849 (mttp) cc_final: 0.8353 (mttm) REVERT: L 22 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8555 (mp10) REVERT: L 218 LYS cc_start: 0.8852 (mttp) cc_final: 0.8357 (mttm) REVERT: M 12 LEU cc_start: 0.7353 (OUTLIER) cc_final: 0.6991 (pp) REVERT: M 22 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.8554 (mp10) REVERT: M 218 LYS cc_start: 0.8854 (mttp) cc_final: 0.8358 (mttm) REVERT: N 22 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8550 (mp10) REVERT: N 218 LYS cc_start: 0.8857 (mttp) cc_final: 0.8362 (mttm) REVERT: O 22 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8555 (mp10) REVERT: O 218 LYS cc_start: 0.8852 (mttp) cc_final: 0.8357 (mttm) REVERT: P 22 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8544 (mp10) REVERT: P 218 LYS cc_start: 0.8857 (mttp) cc_final: 0.8359 (mttm) REVERT: Q 22 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8556 (mp10) REVERT: Q 218 LYS cc_start: 0.8855 (mttp) cc_final: 0.8362 (mttm) REVERT: R 22 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8553 (mp10) REVERT: R 218 LYS cc_start: 0.8856 (mttp) cc_final: 0.8362 (mttm) REVERT: S 22 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8541 (mp10) REVERT: S 218 LYS cc_start: 0.8851 (mttp) cc_final: 0.8364 (mttm) REVERT: T 22 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8546 (mp10) REVERT: T 218 LYS cc_start: 0.8851 (mttp) cc_final: 0.8361 (mttm) REVERT: U 22 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8552 (mp10) REVERT: U 218 LYS cc_start: 0.8851 (mttp) cc_final: 0.8358 (mttm) REVERT: V 22 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8542 (mp10) REVERT: V 218 LYS cc_start: 0.8849 (mttp) cc_final: 0.8355 (mttm) REVERT: W 22 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8556 (mp10) REVERT: W 218 LYS cc_start: 0.8851 (mttp) cc_final: 0.8357 (mttm) REVERT: X 22 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8551 (mp10) REVERT: X 218 LYS cc_start: 0.8850 (mttp) cc_final: 0.8355 (mttm) outliers start: 129 outliers final: 42 residues processed: 837 average time/residue: 1.6286 time to fit residues: 1705.3371 Evaluate side-chains 775 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 708 time to evaluate : 5.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLN Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain C residue 22 GLN Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain E residue 22 GLN Chi-restraints excluded: chain E residue 114 CYS Chi-restraints excluded: chain F residue 22 GLN Chi-restraints excluded: chain F residue 114 CYS Chi-restraints excluded: chain G residue 22 GLN Chi-restraints excluded: chain G residue 114 CYS Chi-restraints excluded: chain H residue 22 GLN Chi-restraints excluded: chain H residue 114 CYS Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain I residue 22 GLN Chi-restraints excluded: chain I residue 114 CYS Chi-restraints excluded: chain I residue 139 GLU Chi-restraints excluded: chain J residue 22 GLN Chi-restraints excluded: chain J residue 114 CYS Chi-restraints excluded: chain J residue 139 GLU Chi-restraints excluded: chain K residue 22 GLN Chi-restraints excluded: chain K residue 114 CYS Chi-restraints excluded: chain K residue 139 GLU Chi-restraints excluded: chain L residue 22 GLN Chi-restraints excluded: chain L residue 114 CYS Chi-restraints excluded: chain L residue 139 GLU Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 22 GLN Chi-restraints excluded: chain M residue 114 CYS Chi-restraints excluded: chain M residue 139 GLU Chi-restraints excluded: chain N residue 22 GLN Chi-restraints excluded: chain N residue 114 CYS Chi-restraints excluded: chain N residue 139 GLU Chi-restraints excluded: chain O residue 22 GLN Chi-restraints excluded: chain O residue 114 CYS Chi-restraints excluded: chain P residue 22 GLN Chi-restraints excluded: chain P residue 114 CYS Chi-restraints excluded: chain P residue 139 GLU Chi-restraints excluded: chain Q residue 22 GLN Chi-restraints excluded: chain Q residue 114 CYS Chi-restraints excluded: chain Q residue 139 GLU Chi-restraints excluded: chain R residue 22 GLN Chi-restraints excluded: chain R residue 114 CYS Chi-restraints excluded: chain S residue 22 GLN Chi-restraints excluded: chain S residue 114 CYS Chi-restraints excluded: chain S residue 139 GLU Chi-restraints excluded: chain T residue 22 GLN Chi-restraints excluded: chain T residue 114 CYS Chi-restraints excluded: chain T residue 139 GLU Chi-restraints excluded: chain U residue 22 GLN Chi-restraints excluded: chain U residue 114 CYS Chi-restraints excluded: chain U residue 139 GLU Chi-restraints excluded: chain V residue 22 GLN Chi-restraints excluded: chain V residue 114 CYS Chi-restraints excluded: chain W residue 22 GLN Chi-restraints excluded: chain W residue 114 CYS Chi-restraints excluded: chain W residue 139 GLU Chi-restraints excluded: chain X residue 22 GLN Chi-restraints excluded: chain X residue 114 CYS Chi-restraints excluded: chain X residue 139 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 302 optimal weight: 1.9990 chunk 169 optimal weight: 0.9990 chunk 453 optimal weight: 4.9990 chunk 371 optimal weight: 7.9990 chunk 150 optimal weight: 9.9990 chunk 545 optimal weight: 1.9990 chunk 589 optimal weight: 10.0000 chunk 486 optimal weight: 8.9990 chunk 541 optimal weight: 6.9990 chunk 186 optimal weight: 5.9990 chunk 437 optimal weight: 50.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 D 98 GLN D 158 GLN E 98 GLN E 158 GLN F 98 GLN F 158 GLN G 98 GLN G 158 GLN H 98 GLN H 158 GLN I 98 GLN I 158 GLN J 98 GLN J 158 GLN K 98 GLN K 158 GLN L 98 GLN L 158 GLN M 98 GLN M 158 GLN N 98 GLN N 158 GLN O 98 GLN O 158 GLN P 98 GLN P 158 GLN Q 98 GLN Q 158 GLN R 98 GLN R 158 GLN S 98 GLN S 158 GLN T 98 GLN T 158 GLN U 98 GLN U 158 GLN V 98 GLN V 158 GLN W 98 GLN W 158 GLN X 98 GLN X 158 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.4961 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= 0.314 Angle : 0.701 15.797 71064 Z= 0.366 Chirality : 0.040 0.154 7488 Planarity : 0.005 0.038 9264 Dihedral : 4.716 43.012 7104 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.14 % Favored : 96.47 % Rotamer: Outliers : 3.26 % Allowed : 16.61 % Favored : 80.13 % 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: 1.81 (0.11), residues: 6144 helix: 2.21 (0.08), residues: 4776 sheet: None (None), residues: 0 loop : -2.67 (0.18), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.004 TRP A 168 HIS 0.009 0.001 HIS B 140 PHE 0.025 0.004 PHE W 207 TYR 0.016 0.002 TYR I 62 ARG 0.007 0.000 ARG H 154 *********************** 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 862 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 686 time to evaluate : 5.645 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: A 12 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.6984 (pp) REVERT: A 22 GLN cc_start: 0.8854 (tp-100) cc_final: 0.8566 (mp10) REVERT: A 52 MET cc_start: 0.2066 (tmm) cc_final: 0.1797 (tmt) REVERT: A 218 LYS cc_start: 0.8936 (mttp) cc_final: 0.8610 (mtpp) REVERT: B 12 LEU cc_start: 0.7278 (OUTLIER) cc_final: 0.6932 (pp) REVERT: B 52 MET cc_start: 0.1957 (tmm) cc_final: 0.1693 (tmt) REVERT: B 218 LYS cc_start: 0.8935 (mttp) cc_final: 0.8610 (mtpp) REVERT: C 12 LEU cc_start: 0.7305 (OUTLIER) cc_final: 0.6951 (pp) REVERT: C 52 MET cc_start: 0.1807 (tmm) cc_final: 0.1587 (tmt) REVERT: C 218 LYS cc_start: 0.8938 (mttp) cc_final: 0.8610 (mtpp) REVERT: D 12 LEU cc_start: 0.7302 (OUTLIER) cc_final: 0.6949 (pp) REVERT: D 52 MET cc_start: 0.1824 (tmm) cc_final: 0.1573 (tmt) REVERT: D 218 LYS cc_start: 0.8935 (mttp) cc_final: 0.8611 (mtpp) REVERT: E 12 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.6926 (pp) REVERT: E 52 MET cc_start: 0.1953 (tmm) cc_final: 0.1687 (tmt) REVERT: E 218 LYS cc_start: 0.8938 (mttp) cc_final: 0.8610 (mtpp) REVERT: F 12 LEU cc_start: 0.7262 (OUTLIER) cc_final: 0.6918 (pp) REVERT: F 22 GLN cc_start: 0.8824 (tp-100) cc_final: 0.8574 (mp10) REVERT: F 52 MET cc_start: 0.1788 (tmm) cc_final: 0.1515 (tmt) REVERT: F 218 LYS cc_start: 0.8930 (mttp) cc_final: 0.8612 (mtpp) REVERT: G 12 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.6964 (pp) REVERT: G 52 MET cc_start: 0.1813 (tmm) cc_final: 0.1593 (tmt) REVERT: G 218 LYS cc_start: 0.8932 (mttp) cc_final: 0.8610 (mtpp) REVERT: H 12 LEU cc_start: 0.7299 (OUTLIER) cc_final: 0.6945 (pp) REVERT: H 52 MET cc_start: 0.1835 (tmm) cc_final: 0.1544 (tmt) REVERT: H 218 LYS cc_start: 0.8935 (mttp) cc_final: 0.8612 (mtpp) REVERT: I 12 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.6955 (pp) REVERT: I 22 GLN cc_start: 0.8823 (tp-100) cc_final: 0.8568 (mp10) REVERT: I 52 MET cc_start: 0.1800 (tmm) cc_final: 0.1531 (tmt) REVERT: I 218 LYS cc_start: 0.8933 (mttp) cc_final: 0.8610 (mtpp) REVERT: J 12 LEU cc_start: 0.7259 (OUTLIER) cc_final: 0.6917 (pp) REVERT: J 22 GLN cc_start: 0.8821 (tp-100) cc_final: 0.8564 (mp10) REVERT: J 52 MET cc_start: 0.1765 (tmm) cc_final: 0.1532 (tmt) REVERT: J 218 LYS cc_start: 0.8933 (mttp) cc_final: 0.8611 (mtpp) REVERT: K 12 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.6989 (pp) REVERT: K 22 GLN cc_start: 0.8828 (tp-100) cc_final: 0.8568 (mp10) REVERT: K 52 MET cc_start: 0.1806 (tmm) cc_final: 0.1571 (tmt) REVERT: K 218 LYS cc_start: 0.8936 (mttp) cc_final: 0.8611 (mtpp) REVERT: L 12 LEU cc_start: 0.7276 (OUTLIER) cc_final: 0.6943 (pp) REVERT: L 22 GLN cc_start: 0.8828 (tp-100) cc_final: 0.8568 (mp10) REVERT: L 52 MET cc_start: 0.1825 (tmm) cc_final: 0.1584 (tmt) REVERT: L 218 LYS cc_start: 0.8939 (mttp) cc_final: 0.8613 (mtpp) REVERT: M 12 LEU cc_start: 0.7283 (OUTLIER) cc_final: 0.6928 (pp) REVERT: M 22 GLN cc_start: 0.8823 (tp-100) cc_final: 0.8565 (mp10) REVERT: M 52 MET cc_start: 0.1770 (tmm) cc_final: 0.1561 (tmt) REVERT: M 218 LYS cc_start: 0.8938 (mttp) cc_final: 0.8611 (mtpp) REVERT: N 12 LEU cc_start: 0.7307 (OUTLIER) cc_final: 0.6967 (pp) REVERT: N 22 GLN cc_start: 0.8833 (tp-100) cc_final: 0.8561 (mp10) REVERT: N 52 MET cc_start: 0.1829 (tmm) cc_final: 0.1608 (tmt) REVERT: N 218 LYS cc_start: 0.8940 (mttp) cc_final: 0.8610 (mtpp) REVERT: O 12 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.6947 (pp) REVERT: O 22 GLN cc_start: 0.8838 (tp-100) cc_final: 0.8579 (mp10) REVERT: O 52 MET cc_start: 0.1828 (tmm) cc_final: 0.1543 (tmt) REVERT: O 218 LYS cc_start: 0.8937 (mttp) cc_final: 0.8609 (mtpp) REVERT: P 12 LEU cc_start: 0.7263 (OUTLIER) cc_final: 0.6918 (pp) REVERT: P 52 MET cc_start: 0.1796 (tmm) cc_final: 0.1527 (tmt) REVERT: P 218 LYS cc_start: 0.8940 (mttp) cc_final: 0.8610 (mtpp) REVERT: Q 12 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.6950 (pp) REVERT: Q 52 MET cc_start: 0.1827 (tmm) cc_final: 0.1579 (tmt) REVERT: Q 218 LYS cc_start: 0.8937 (mttp) cc_final: 0.8608 (mtpp) REVERT: R 12 LEU cc_start: 0.7323 (OUTLIER) cc_final: 0.6984 (pp) REVERT: R 22 GLN cc_start: 0.8839 (tp-100) cc_final: 0.8563 (mp10) REVERT: R 52 MET cc_start: 0.1831 (tmm) cc_final: 0.1545 (tmt) REVERT: R 218 LYS cc_start: 0.8939 (mttp) cc_final: 0.8610 (mtpp) REVERT: S 12 LEU cc_start: 0.7308 (OUTLIER) cc_final: 0.6954 (pp) REVERT: S 52 MET cc_start: 0.1858 (tmm) cc_final: 0.1607 (tmt) REVERT: S 218 LYS cc_start: 0.8935 (mttp) cc_final: 0.8611 (mtpp) REVERT: T 12 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.6973 (pp) REVERT: T 22 GLN cc_start: 0.8831 (tp-100) cc_final: 0.8559 (mp10) REVERT: T 52 MET cc_start: 0.1847 (tmm) cc_final: 0.1595 (tmt) REVERT: T 218 LYS cc_start: 0.8935 (mttp) cc_final: 0.8608 (mtpp) REVERT: U 12 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.6957 (pp) REVERT: U 22 GLN cc_start: 0.8825 (tp-100) cc_final: 0.8568 (mp10) REVERT: U 52 MET cc_start: 0.1812 (tmm) cc_final: 0.1540 (tmt) REVERT: U 218 LYS cc_start: 0.8937 (mttp) cc_final: 0.8611 (mtpp) REVERT: V 12 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.6958 (pp) REVERT: V 22 GLN cc_start: 0.8830 (tp-100) cc_final: 0.8572 (mp10) REVERT: V 52 MET cc_start: 0.1808 (tmm) cc_final: 0.1539 (tmt) REVERT: V 218 LYS cc_start: 0.8936 (mttp) cc_final: 0.8612 (mtpp) REVERT: W 12 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.6966 (pp) REVERT: W 22 GLN cc_start: 0.8825 (tp-100) cc_final: 0.8567 (mp10) REVERT: W 52 MET cc_start: 0.1782 (tmm) cc_final: 0.1568 (tmt) REVERT: W 218 LYS cc_start: 0.8934 (mttp) cc_final: 0.8610 (mtpp) REVERT: X 12 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.6935 (pp) REVERT: X 22 GLN cc_start: 0.8819 (tp-100) cc_final: 0.8567 (mp10) REVERT: X 52 MET cc_start: 0.1766 (tmm) cc_final: 0.1498 (tmt) REVERT: X 218 LYS cc_start: 0.8936 (mttp) cc_final: 0.8610 (mtpp) outliers start: 176 outliers final: 52 residues processed: 838 average time/residue: 1.5242 time to fit residues: 1613.1026 Evaluate side-chains 562 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 486 time to evaluate : 6.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 194 LYS Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 214 SER Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 214 SER Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 194 LYS Chi-restraints excluded: chain K residue 214 SER Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 147 LEU Chi-restraints excluded: chain L residue 164 ASP Chi-restraints excluded: chain L residue 214 SER Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 194 LYS Chi-restraints excluded: chain M residue 214 SER Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 164 ASP Chi-restraints excluded: chain N residue 194 LYS Chi-restraints excluded: chain N residue 214 SER Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 214 SER Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain P residue 214 SER Chi-restraints excluded: chain Q residue 12 LEU Chi-restraints excluded: chain Q residue 147 LEU Chi-restraints excluded: chain Q residue 194 LYS Chi-restraints excluded: chain Q residue 214 SER Chi-restraints excluded: chain R residue 12 LEU Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 194 LYS Chi-restraints excluded: chain R residue 214 SER Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain S residue 164 ASP Chi-restraints excluded: chain S residue 194 LYS Chi-restraints excluded: chain S residue 214 SER Chi-restraints excluded: chain T residue 12 LEU Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain T residue 214 SER Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 214 SER Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 214 SER Chi-restraints excluded: chain W residue 12 LEU Chi-restraints excluded: chain W residue 194 LYS Chi-restraints excluded: chain W residue 214 SER Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 214 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 539 optimal weight: 7.9990 chunk 410 optimal weight: 20.0000 chunk 283 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 260 optimal weight: 7.9990 chunk 366 optimal weight: 8.9990 chunk 547 optimal weight: 0.9980 chunk 579 optimal weight: 30.0000 chunk 286 optimal weight: 4.9990 chunk 519 optimal weight: 8.9990 chunk 156 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN A 140 HIS B 86 ASN C 86 ASN D 86 ASN E 86 ASN ** E 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 22 GLN F 86 ASN F 100 ASN G 86 ASN G 100 ASN H 86 ASN ** H 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 140 HIS I 22 GLN I 86 ASN I 140 HIS J 86 ASN J 140 HIS K 86 ASN L 22 GLN L 86 ASN M 86 ASN M 100 ASN M 140 HIS N 22 GLN N 86 ASN N 100 ASN N 140 HIS O 22 GLN O 86 ASN P 86 ASN Q 86 ASN Q 140 HIS R 22 GLN R 86 ASN ** R 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 86 ASN S 100 ASN S 140 HIS T 22 GLN T 86 ASN T 140 HIS U 22 GLN U 86 ASN U 140 HIS V 22 GLN V 86 ASN W 22 GLN W 86 ASN ** W 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 140 HIS X 86 ASN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.5443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 52800 Z= 0.245 Angle : 0.598 8.116 71064 Z= 0.306 Chirality : 0.038 0.150 7488 Planarity : 0.005 0.059 9264 Dihedral : 4.728 52.161 7104 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.12 % Favored : 96.49 % Rotamer: Outliers : 2.99 % Allowed : 18.27 % Favored : 78.74 % 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: 2.20 (0.11), residues: 6144 helix: 2.46 (0.08), residues: 4800 sheet: None (None), residues: 0 loop : -2.52 (0.18), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 168 HIS 0.011 0.001 HIS A 140 PHE 0.025 0.003 PHE G 116 TYR 0.018 0.002 TYR T 212 ARG 0.005 0.001 ARG M 165 *********************** 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 679 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 511 time to evaluate : 5.786 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: A 12 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.6966 (pp) REVERT: A 52 MET cc_start: 0.2206 (tmm) cc_final: 0.1752 (tmt) REVERT: B 12 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.6959 (pp) REVERT: B 52 MET cc_start: 0.1991 (tmm) cc_final: 0.1566 (tmt) REVERT: C 12 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.6974 (pp) REVERT: C 52 MET cc_start: 0.2187 (tmm) cc_final: 0.1788 (tmt) REVERT: D 12 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.6974 (pp) REVERT: D 52 MET cc_start: 0.1987 (tmm) cc_final: 0.1560 (tmt) REVERT: E 12 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.6971 (pp) REVERT: E 52 MET cc_start: 0.1985 (tmm) cc_final: 0.1557 (tmt) REVERT: F 12 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.6887 (pp) REVERT: F 52 MET cc_start: 0.1982 (tmm) cc_final: 0.1603 (tmt) REVERT: G 12 LEU cc_start: 0.7305 (OUTLIER) cc_final: 0.6961 (pp) REVERT: G 52 MET cc_start: 0.2188 (tmm) cc_final: 0.1789 (tmt) REVERT: H 12 LEU cc_start: 0.7310 (OUTLIER) cc_final: 0.6969 (pp) REVERT: H 52 MET cc_start: 0.1976 (tmm) cc_final: 0.1605 (tmt) REVERT: I 12 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6898 (pp) REVERT: I 52 MET cc_start: 0.1993 (tmm) cc_final: 0.1624 (tmt) REVERT: J 12 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.6886 (pp) REVERT: J 52 MET cc_start: 0.1999 (tmm) cc_final: 0.1623 (tmt) REVERT: K 12 LEU cc_start: 0.7301 (OUTLIER) cc_final: 0.6947 (pp) REVERT: K 52 MET cc_start: 0.2035 (tmm) cc_final: 0.1608 (tmt) REVERT: L 12 LEU cc_start: 0.7295 (OUTLIER) cc_final: 0.6929 (pp) REVERT: L 52 MET cc_start: 0.2210 (tmm) cc_final: 0.1804 (tmt) REVERT: M 12 LEU cc_start: 0.7235 (OUTLIER) cc_final: 0.6875 (pp) REVERT: M 52 MET cc_start: 0.2004 (tmm) cc_final: 0.1625 (tmt) REVERT: N 12 LEU cc_start: 0.7288 (OUTLIER) cc_final: 0.6938 (pp) REVERT: N 52 MET cc_start: 0.2110 (tmm) cc_final: 0.1664 (tmt) REVERT: O 12 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.6911 (pp) REVERT: O 52 MET cc_start: 0.1982 (tmm) cc_final: 0.1608 (tmt) REVERT: P 12 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.6948 (pp) REVERT: P 52 MET cc_start: 0.1978 (tmm) cc_final: 0.1606 (tmt) REVERT: Q 12 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.6975 (pp) REVERT: Q 52 MET cc_start: 0.1985 (tmm) cc_final: 0.1614 (tmt) REVERT: R 12 LEU cc_start: 0.7302 (OUTLIER) cc_final: 0.6949 (pp) REVERT: R 52 MET cc_start: 0.1987 (tmm) cc_final: 0.1620 (tmt) REVERT: S 12 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.6968 (pp) REVERT: S 52 MET cc_start: 0.1998 (tmm) cc_final: 0.1572 (tmt) REVERT: T 12 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.6938 (pp) REVERT: T 52 MET cc_start: 0.2004 (tmm) cc_final: 0.1573 (tmt) REVERT: U 12 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.6907 (pp) REVERT: U 52 MET cc_start: 0.2003 (tmm) cc_final: 0.1633 (tmt) REVERT: V 12 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.6913 (pp) REVERT: V 52 MET cc_start: 0.1998 (tmm) cc_final: 0.1624 (tmt) REVERT: W 12 LEU cc_start: 0.7243 (OUTLIER) cc_final: 0.6889 (pp) REVERT: W 52 MET cc_start: 0.2020 (tmm) cc_final: 0.1636 (tmt) REVERT: X 12 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.6900 (pp) REVERT: X 52 MET cc_start: 0.2001 (tmm) cc_final: 0.1627 (tmt) outliers start: 168 outliers final: 45 residues processed: 632 average time/residue: 1.3214 time to fit residues: 1091.8449 Evaluate side-chains 538 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 469 time to evaluate : 5.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 194 LYS Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 214 SER Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 214 SER Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 194 LYS Chi-restraints excluded: chain K residue 214 SER Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 147 LEU Chi-restraints excluded: chain L residue 214 SER Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 194 LYS Chi-restraints excluded: chain M residue 214 SER Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 194 LYS Chi-restraints excluded: chain N residue 214 SER Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 214 SER Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain P residue 214 SER Chi-restraints excluded: chain Q residue 12 LEU Chi-restraints excluded: chain Q residue 147 LEU Chi-restraints excluded: chain Q residue 194 LYS Chi-restraints excluded: chain Q residue 214 SER Chi-restraints excluded: chain R residue 12 LEU Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 194 LYS Chi-restraints excluded: chain R residue 214 SER Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain S residue 194 LYS Chi-restraints excluded: chain S residue 214 SER Chi-restraints excluded: chain T residue 12 LEU Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain T residue 214 SER Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 214 SER Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 214 SER Chi-restraints excluded: chain W residue 12 LEU Chi-restraints excluded: chain W residue 194 LYS Chi-restraints excluded: chain W residue 214 SER Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 214 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 483 optimal weight: 20.0000 chunk 329 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 431 optimal weight: 3.9990 chunk 239 optimal weight: 5.9990 chunk 494 optimal weight: 3.9990 chunk 400 optimal weight: 6.9990 chunk 0 optimal weight: 60.0000 chunk 296 optimal weight: 2.9990 chunk 520 optimal weight: 2.9990 chunk 146 optimal weight: 50.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN ** E 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.6006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 52800 Z= 0.280 Angle : 0.643 9.525 71064 Z= 0.321 Chirality : 0.038 0.140 7488 Planarity : 0.004 0.038 9264 Dihedral : 4.867 54.367 7104 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.39 % Allowed : 2.70 % Favored : 96.91 % Rotamer: Outliers : 2.40 % Allowed : 17.09 % Favored : 80.50 % 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 (0.11), residues: 6144 helix: 2.37 (0.08), residues: 4920 sheet: None (None), residues: 0 loop : -1.34 (0.19), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 168 HIS 0.005 0.001 HIS F 18 PHE 0.023 0.003 PHE N 116 TYR 0.021 0.002 TYR J 212 ARG 0.004 0.001 ARG A 165 *********************** 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 644 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 509 time to evaluate : 5.852 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: A 12 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.6981 (pp) REVERT: A 52 MET cc_start: 0.2393 (tmm) cc_final: 0.1883 (tmt) REVERT: B 12 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.6964 (pp) REVERT: B 52 MET cc_start: 0.2391 (tmm) cc_final: 0.1890 (tmt) REVERT: C 12 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.6966 (pp) REVERT: C 52 MET cc_start: 0.2338 (tmm) cc_final: 0.1831 (tmt) REVERT: D 12 LEU cc_start: 0.7308 (OUTLIER) cc_final: 0.6963 (pp) REVERT: D 52 MET cc_start: 0.2357 (tmm) cc_final: 0.1856 (tmt) REVERT: E 12 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.6961 (pp) REVERT: E 52 MET cc_start: 0.2390 (tmm) cc_final: 0.1884 (tmt) REVERT: F 12 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.6957 (pp) REVERT: F 52 MET cc_start: 0.2284 (tmm) cc_final: 0.1802 (tmt) REVERT: G 12 LEU cc_start: 0.7301 (OUTLIER) cc_final: 0.6964 (pp) REVERT: G 52 MET cc_start: 0.2480 (tmm) cc_final: 0.1953 (tmt) REVERT: H 12 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.6973 (pp) REVERT: H 52 MET cc_start: 0.2377 (tmm) cc_final: 0.1862 (tmt) REVERT: I 12 LEU cc_start: 0.7323 (OUTLIER) cc_final: 0.6950 (pp) REVERT: I 52 MET cc_start: 0.2435 (tmm) cc_final: 0.1942 (tmt) REVERT: J 12 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.6943 (pp) REVERT: J 52 MET cc_start: 0.2379 (tmm) cc_final: 0.1868 (tmt) REVERT: K 12 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.6959 (pp) REVERT: K 52 MET cc_start: 0.2467 (tmm) cc_final: 0.1970 (tmt) REVERT: L 12 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.6959 (pp) REVERT: L 52 MET cc_start: 0.2357 (tmm) cc_final: 0.1851 (tmt) REVERT: M 12 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.6933 (pp) REVERT: M 52 MET cc_start: 0.2410 (tmm) cc_final: 0.1964 (tmt) REVERT: N 12 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.6961 (pp) REVERT: N 52 MET cc_start: 0.2409 (tmm) cc_final: 0.1898 (tmt) REVERT: O 12 LEU cc_start: 0.7340 (OUTLIER) cc_final: 0.6965 (pp) REVERT: O 52 MET cc_start: 0.2361 (tmm) cc_final: 0.1855 (tmt) REVERT: P 12 LEU cc_start: 0.7271 (OUTLIER) cc_final: 0.6943 (pp) REVERT: P 52 MET cc_start: 0.2388 (tmm) cc_final: 0.1892 (tmt) REVERT: Q 12 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.6965 (pp) REVERT: Q 52 MET cc_start: 0.2389 (tmm) cc_final: 0.1877 (tmt) REVERT: R 12 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.6962 (pp) REVERT: R 52 MET cc_start: 0.2284 (tmm) cc_final: 0.1810 (tmt) REVERT: S 12 LEU cc_start: 0.7315 (OUTLIER) cc_final: 0.6967 (pp) REVERT: S 52 MET cc_start: 0.2447 (tmm) cc_final: 0.1925 (tmt) REVERT: T 12 LEU cc_start: 0.7329 (OUTLIER) cc_final: 0.6952 (pp) REVERT: T 52 MET cc_start: 0.2390 (tmm) cc_final: 0.1879 (tmt) REVERT: U 12 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.6948 (pp) REVERT: U 52 MET cc_start: 0.2439 (tmm) cc_final: 0.1948 (tmt) REVERT: V 12 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.6954 (pp) REVERT: V 52 MET cc_start: 0.2336 (tmm) cc_final: 0.1863 (tmt) REVERT: W 12 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.6961 (pp) REVERT: W 52 MET cc_start: 0.2393 (tmm) cc_final: 0.1877 (tmt) REVERT: X 12 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.6952 (pp) REVERT: X 52 MET cc_start: 0.2382 (tmm) cc_final: 0.1876 (tmt) outliers start: 135 outliers final: 52 residues processed: 616 average time/residue: 1.2539 time to fit residues: 1022.2188 Evaluate side-chains 530 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 454 time to evaluate : 5.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain I residue 214 SER Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain J residue 208 ILE Chi-restraints excluded: chain J residue 214 SER Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 214 SER Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 147 LEU Chi-restraints excluded: chain L residue 214 SER Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 208 ILE Chi-restraints excluded: chain M residue 214 SER Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 147 LEU Chi-restraints excluded: chain N residue 214 SER Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 147 LEU Chi-restraints excluded: chain O residue 208 ILE Chi-restraints excluded: chain O residue 214 SER Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain P residue 147 LEU Chi-restraints excluded: chain P residue 208 ILE Chi-restraints excluded: chain P residue 214 SER Chi-restraints excluded: chain Q residue 12 LEU Chi-restraints excluded: chain Q residue 147 LEU Chi-restraints excluded: chain Q residue 214 SER Chi-restraints excluded: chain R residue 12 LEU Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 214 SER Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain S residue 214 SER Chi-restraints excluded: chain T residue 12 LEU Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 147 LEU Chi-restraints excluded: chain U residue 214 SER Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 147 LEU Chi-restraints excluded: chain V residue 214 SER Chi-restraints excluded: chain W residue 12 LEU Chi-restraints excluded: chain W residue 147 LEU Chi-restraints excluded: chain W residue 208 ILE Chi-restraints excluded: chain W residue 214 SER Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 147 LEU Chi-restraints excluded: chain X residue 214 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 195 optimal weight: 20.0000 chunk 522 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 chunk 340 optimal weight: 50.0000 chunk 143 optimal weight: 6.9990 chunk 580 optimal weight: 20.0000 chunk 481 optimal weight: 30.0000 chunk 268 optimal weight: 50.0000 chunk 48 optimal weight: 60.0000 chunk 192 optimal weight: 50.0000 chunk 304 optimal weight: 0.8980 overall best weight: 6.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 98 GLN L 98 GLN P 98 GLN X 98 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.6816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.088 52800 Z= 0.552 Angle : 0.744 8.016 71064 Z= 0.373 Chirality : 0.044 0.302 7488 Planarity : 0.005 0.045 9264 Dihedral : 4.899 43.858 7104 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.91 % Favored : 95.70 % Rotamer: Outliers : 2.51 % Allowed : 16.08 % Favored : 81.41 % 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: 2.52 (0.11), residues: 6144 helix: 2.66 (0.08), residues: 4584 sheet: None (None), residues: 0 loop : -1.55 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP Q 168 HIS 0.007 0.002 HIS D 203 PHE 0.031 0.004 PHE O 116 TYR 0.024 0.002 TYR O 212 ARG 0.006 0.001 ARG D 154 *********************** 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 590 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 449 time to evaluate : 5.741 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: A 12 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.7015 (pp) REVERT: A 214 SER cc_start: 0.9410 (OUTLIER) cc_final: 0.9196 (p) REVERT: B 12 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.7098 (pp) REVERT: C 12 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.7118 (pp) REVERT: D 12 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.7096 (pp) REVERT: E 12 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.7096 (pp) REVERT: F 12 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.7046 (pp) REVERT: G 12 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.7115 (pp) REVERT: H 12 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.7112 (pp) REVERT: H 52 MET cc_start: 0.2705 (OUTLIER) cc_final: 0.2504 (tmm) REVERT: I 12 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.7036 (pp) REVERT: J 12 LEU cc_start: 0.7353 (OUTLIER) cc_final: 0.7045 (pp) REVERT: K 12 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.7051 (pp) REVERT: L 12 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.7046 (pp) REVERT: L 214 SER cc_start: 0.9408 (OUTLIER) cc_final: 0.9197 (p) REVERT: M 12 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.7034 (pp) REVERT: N 12 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.7032 (pp) REVERT: O 12 LEU cc_start: 0.7362 (OUTLIER) cc_final: 0.7048 (pp) REVERT: P 12 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7086 (pp) REVERT: Q 12 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.7117 (pp) REVERT: R 12 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.7023 (pp) REVERT: S 12 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.7101 (pp) REVERT: T 12 LEU cc_start: 0.7354 (OUTLIER) cc_final: 0.7038 (pp) REVERT: U 12 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.7035 (pp) REVERT: V 12 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.7041 (pp) REVERT: W 12 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.7046 (pp) REVERT: X 12 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.7040 (pp) outliers start: 141 outliers final: 83 residues processed: 521 average time/residue: 1.1901 time to fit residues: 830.6849 Evaluate side-chains 536 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 426 time to evaluate : 5.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 208 ILE Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 52 MET Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain I residue 214 SER Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain J residue 208 ILE Chi-restraints excluded: chain J residue 214 SER Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 208 ILE Chi-restraints excluded: chain K residue 214 SER Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 147 LEU Chi-restraints excluded: chain L residue 208 ILE Chi-restraints excluded: chain L residue 214 SER Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 208 ILE Chi-restraints excluded: chain M residue 214 SER Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 147 LEU Chi-restraints excluded: chain N residue 208 ILE Chi-restraints excluded: chain N residue 214 SER Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 147 LEU Chi-restraints excluded: chain O residue 208 ILE Chi-restraints excluded: chain O residue 214 SER Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain P residue 147 LEU Chi-restraints excluded: chain P residue 208 ILE Chi-restraints excluded: chain P residue 214 SER Chi-restraints excluded: chain Q residue 12 LEU Chi-restraints excluded: chain Q residue 147 LEU Chi-restraints excluded: chain Q residue 208 ILE Chi-restraints excluded: chain Q residue 214 SER Chi-restraints excluded: chain R residue 12 LEU Chi-restraints excluded: chain R residue 21 VAL Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 208 ILE Chi-restraints excluded: chain R residue 214 SER Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain S residue 208 ILE Chi-restraints excluded: chain S residue 214 SER Chi-restraints excluded: chain T residue 12 LEU Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain T residue 208 ILE Chi-restraints excluded: chain T residue 214 SER Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 21 VAL Chi-restraints excluded: chain U residue 147 LEU Chi-restraints excluded: chain U residue 208 ILE Chi-restraints excluded: chain U residue 214 SER Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 21 VAL Chi-restraints excluded: chain V residue 147 LEU Chi-restraints excluded: chain V residue 208 ILE Chi-restraints excluded: chain V residue 214 SER Chi-restraints excluded: chain W residue 12 LEU Chi-restraints excluded: chain W residue 21 VAL Chi-restraints excluded: chain W residue 147 LEU Chi-restraints excluded: chain W residue 208 ILE Chi-restraints excluded: chain W residue 214 SER Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 147 LEU Chi-restraints excluded: chain X residue 208 ILE Chi-restraints excluded: chain X residue 214 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 559 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 330 optimal weight: 0.7980 chunk 423 optimal weight: 5.9990 chunk 328 optimal weight: 2.9990 chunk 488 optimal weight: 1.9990 chunk 324 optimal weight: 0.8980 chunk 578 optimal weight: 30.0000 chunk 361 optimal weight: 20.0000 chunk 352 optimal weight: 2.9990 chunk 266 optimal weight: 40.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 C 216 GLN D 98 GLN D 193 HIS D 216 GLN E 193 HIS E 216 GLN F 98 GLN ** F 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 216 GLN G 98 GLN G 193 HIS G 216 GLN H 98 GLN H 193 HIS H 216 GLN I 98 GLN I 193 HIS I 216 GLN J 98 GLN J 193 HIS J 216 GLN J 248 HIS K 98 GLN ** K 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 216 GLN K 248 HIS L 193 HIS M 98 GLN M 193 HIS M 216 GLN N 98 GLN ** N 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 216 GLN O 98 GLN O 193 HIS O 216 GLN P 193 HIS P 216 GLN Q 98 GLN ** Q 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 216 GLN R 98 GLN R 193 HIS R 216 GLN S 98 GLN ** S 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 216 GLN T 98 GLN T 193 HIS U 98 GLN U 193 HIS U 216 GLN V 98 GLN V 193 HIS V 216 GLN W 98 GLN W 193 HIS W 216 GLN X 193 HIS X 216 GLN Total number of N/Q/H flips: 61 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.6755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 52800 Z= 0.196 Angle : 0.595 6.738 71064 Z= 0.300 Chirality : 0.037 0.141 7488 Planarity : 0.004 0.029 9264 Dihedral : 4.820 49.876 7104 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.39 % Allowed : 2.71 % Favored : 96.90 % Rotamer: Outliers : 1.50 % Allowed : 16.93 % Favored : 81.57 % 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: 2.85 (0.11), residues: 6144 helix: 2.77 (0.08), residues: 4776 sheet: None (None), residues: 0 loop : -1.55 (0.18), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP S 168 HIS 0.003 0.001 HIS W 203 PHE 0.021 0.002 PHE O 116 TYR 0.019 0.001 TYR W 212 ARG 0.005 0.000 ARG V 231 *********************** 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 543 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 459 time to evaluate : 5.823 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: A 12 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.6997 (pp) REVERT: B 12 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.7054 (pp) REVERT: C 12 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.7060 (pp) REVERT: D 12 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.7053 (pp) REVERT: E 12 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.7053 (pp) REVERT: F 12 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.7044 (pp) REVERT: G 12 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.7059 (pp) REVERT: H 12 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.7054 (pp) REVERT: I 12 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.7033 (pp) REVERT: J 12 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.6978 (pp) REVERT: K 12 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.7042 (pp) REVERT: K 194 LYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8790 (ttmm) REVERT: L 12 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.7048 (pp) REVERT: M 12 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.6971 (pp) REVERT: N 12 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.7037 (pp) REVERT: O 12 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.7017 (pp) REVERT: P 12 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.7052 (pp) REVERT: Q 12 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.7054 (pp) REVERT: R 12 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.7045 (pp) REVERT: S 12 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7061 (pp) REVERT: T 12 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.7026 (pp) REVERT: U 12 LEU cc_start: 0.7368 (OUTLIER) cc_final: 0.7037 (pp) REVERT: V 12 LEU cc_start: 0.7334 (OUTLIER) cc_final: 0.6970 (pp) REVERT: W 12 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.6980 (pp) REVERT: X 12 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.7040 (pp) outliers start: 84 outliers final: 55 residues processed: 509 average time/residue: 1.2983 time to fit residues: 870.9427 Evaluate side-chains 511 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 431 time to evaluate : 5.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 208 ILE Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain J residue 208 ILE Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 194 LYS Chi-restraints excluded: chain K residue 208 ILE Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 147 LEU Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 208 ILE Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 147 LEU Chi-restraints excluded: chain N residue 208 ILE Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 147 LEU Chi-restraints excluded: chain O residue 208 ILE Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain P residue 147 LEU Chi-restraints excluded: chain P residue 208 ILE Chi-restraints excluded: chain Q residue 12 LEU Chi-restraints excluded: chain Q residue 147 LEU Chi-restraints excluded: chain Q residue 208 ILE Chi-restraints excluded: chain R residue 12 LEU Chi-restraints excluded: chain R residue 21 VAL Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 208 ILE Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain S residue 208 ILE Chi-restraints excluded: chain T residue 12 LEU Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain T residue 208 ILE Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 21 VAL Chi-restraints excluded: chain U residue 147 LEU Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 21 VAL Chi-restraints excluded: chain V residue 147 LEU Chi-restraints excluded: chain W residue 12 LEU Chi-restraints excluded: chain W residue 21 VAL Chi-restraints excluded: chain W residue 147 LEU Chi-restraints excluded: chain W residue 208 ILE Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 147 LEU Chi-restraints excluded: chain X residue 208 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 357 optimal weight: 0.9990 chunk 230 optimal weight: 0.9990 chunk 345 optimal weight: 5.9990 chunk 174 optimal weight: 0.6980 chunk 113 optimal weight: 8.9990 chunk 112 optimal weight: 0.8980 chunk 367 optimal weight: 0.6980 chunk 393 optimal weight: 3.9990 chunk 285 optimal weight: 0.7980 chunk 53 optimal weight: 30.0000 chunk 454 optimal weight: 8.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 193 HIS K 98 GLN K 193 HIS N 193 HIS Q 193 HIS S 193 HIS T 216 GLN V 98 GLN X 98 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.6705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 52800 Z= 0.168 Angle : 0.580 7.625 71064 Z= 0.293 Chirality : 0.036 0.136 7488 Planarity : 0.004 0.028 9264 Dihedral : 4.764 51.123 7104 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.02 % Favored : 96.86 % Rotamer: Outliers : 1.99 % Allowed : 17.24 % Favored : 80.77 % 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: 4800 sheet: None (None), residues: 0 loop : -1.59 (0.18), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP S 168 HIS 0.002 0.000 HIS J 203 PHE 0.016 0.002 PHE N 116 TYR 0.016 0.001 TYR P 212 ARG 0.004 0.000 ARG K 231 *********************** 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 597 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 485 time to evaluate : 5.659 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: A 12 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.7024 (pp) REVERT: B 12 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.7016 (pp) REVERT: C 12 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.7017 (pp) REVERT: D 12 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.7014 (pp) REVERT: E 12 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.7014 (pp) REVERT: F 12 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.7032 (pp) REVERT: F 194 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8766 (tppp) REVERT: G 12 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.7013 (pp) REVERT: H 12 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.7008 (pp) REVERT: I 12 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.7022 (pp) REVERT: J 12 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.7079 (pp) REVERT: K 12 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.7031 (pp) REVERT: K 194 LYS cc_start: 0.9107 (OUTLIER) cc_final: 0.8763 (tppp) REVERT: L 12 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.7022 (pp) REVERT: M 12 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.7025 (pp) REVERT: M 194 LYS cc_start: 0.9106 (OUTLIER) cc_final: 0.8764 (tppp) REVERT: N 12 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7019 (pp) REVERT: N 194 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8782 (ttmm) REVERT: O 12 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.7072 (pp) REVERT: P 12 LEU cc_start: 0.7329 (OUTLIER) cc_final: 0.7004 (pp) REVERT: Q 12 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.7015 (pp) REVERT: Q 194 LYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8764 (tppp) REVERT: R 12 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.7018 (pp) REVERT: R 194 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8763 (tppp) REVERT: S 12 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.7019 (pp) REVERT: S 194 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8765 (tppp) REVERT: T 12 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.7006 (pp) REVERT: U 12 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.7008 (pp) REVERT: V 12 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.7022 (pp) REVERT: W 12 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.7025 (pp) REVERT: W 194 LYS cc_start: 0.9106 (OUTLIER) cc_final: 0.8764 (tppp) REVERT: X 12 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.7059 (pp) outliers start: 112 outliers final: 50 residues processed: 569 average time/residue: 1.2373 time to fit residues: 928.6509 Evaluate side-chains 541 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 459 time to evaluate : 5.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 194 LYS Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain J residue 208 ILE Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 194 LYS Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 147 LEU Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 194 LYS Chi-restraints excluded: chain M residue 208 ILE Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 147 LEU Chi-restraints excluded: chain N residue 194 LYS Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 147 LEU Chi-restraints excluded: chain O residue 208 ILE Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain P residue 147 LEU Chi-restraints excluded: chain P residue 208 ILE Chi-restraints excluded: chain Q residue 12 LEU Chi-restraints excluded: chain Q residue 147 LEU Chi-restraints excluded: chain Q residue 194 LYS Chi-restraints excluded: chain Q residue 208 ILE Chi-restraints excluded: chain R residue 12 LEU Chi-restraints excluded: chain R residue 21 VAL Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 194 LYS Chi-restraints excluded: chain R residue 208 ILE Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain S residue 194 LYS Chi-restraints excluded: chain S residue 208 ILE Chi-restraints excluded: chain T residue 12 LEU Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 21 VAL Chi-restraints excluded: chain U residue 147 LEU Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 21 VAL Chi-restraints excluded: chain V residue 147 LEU Chi-restraints excluded: chain W residue 12 LEU Chi-restraints excluded: chain W residue 21 VAL Chi-restraints excluded: chain W residue 147 LEU Chi-restraints excluded: chain W residue 194 LYS Chi-restraints excluded: chain W residue 208 ILE Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 147 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 526 optimal weight: 4.9990 chunk 554 optimal weight: 7.9990 chunk 505 optimal weight: 7.9990 chunk 538 optimal weight: 3.9990 chunk 553 optimal weight: 6.9990 chunk 324 optimal weight: 8.9990 chunk 234 optimal weight: 4.9990 chunk 423 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 chunk 486 optimal weight: 8.9990 chunk 509 optimal weight: 30.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 98 GLN V 98 GLN X 98 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.6923 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= 0.355 Angle : 0.657 6.846 71064 Z= 0.330 Chirality : 0.042 0.254 7488 Planarity : 0.004 0.030 9264 Dihedral : 4.761 47.787 7104 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.39 % Allowed : 2.75 % Favored : 96.86 % Rotamer: Outliers : 1.60 % Allowed : 17.63 % Favored : 80.77 % 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: 2.79 (0.11), residues: 6144 helix: 2.60 (0.08), residues: 4848 sheet: None (None), residues: 0 loop : -1.25 (0.19), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP F 168 HIS 0.004 0.001 HIS O 203 PHE 0.025 0.003 PHE O 116 TYR 0.019 0.002 TYR P 212 ARG 0.004 0.001 ARG A 165 *********************** 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 557 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 467 time to evaluate : 5.486 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: A 12 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.7007 (pp) REVERT: B 12 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.7066 (pp) REVERT: C 12 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.7062 (pp) REVERT: D 12 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.7061 (pp) REVERT: E 12 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.7060 (pp) REVERT: F 12 LEU cc_start: 0.7310 (OUTLIER) cc_final: 0.6986 (pp) REVERT: F 194 LYS cc_start: 0.9125 (OUTLIER) cc_final: 0.8787 (tppp) REVERT: G 12 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.7061 (pp) REVERT: H 12 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.7073 (pp) REVERT: I 12 LEU cc_start: 0.7301 (OUTLIER) cc_final: 0.6976 (pp) REVERT: J 12 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.6993 (pp) REVERT: K 12 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.6989 (pp) REVERT: K 194 LYS cc_start: 0.9137 (OUTLIER) cc_final: 0.8820 (tppp) REVERT: L 12 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.6992 (pp) REVERT: M 12 LEU cc_start: 0.7307 (OUTLIER) cc_final: 0.6975 (pp) REVERT: M 194 LYS cc_start: 0.9135 (OUTLIER) cc_final: 0.8822 (tppp) REVERT: N 12 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.6987 (pp) REVERT: N 194 LYS cc_start: 0.9133 (OUTLIER) cc_final: 0.8818 (tppp) REVERT: O 12 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.6989 (pp) REVERT: P 12 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.7060 (pp) REVERT: Q 12 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.7062 (pp) REVERT: Q 194 LYS cc_start: 0.9133 (OUTLIER) cc_final: 0.8820 (tppp) REVERT: R 12 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.6989 (pp) REVERT: R 194 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8818 (tppp) REVERT: S 12 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.7065 (pp) REVERT: S 194 LYS cc_start: 0.9117 (OUTLIER) cc_final: 0.8783 (tppp) REVERT: T 12 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.6977 (pp) REVERT: U 12 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.6976 (pp) REVERT: V 12 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.6983 (pp) REVERT: W 12 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.6999 (pp) REVERT: W 194 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8818 (tppp) REVERT: X 12 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.6998 (pp) outliers start: 90 outliers final: 56 residues processed: 526 average time/residue: 1.3018 time to fit residues: 895.7530 Evaluate side-chains 532 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 444 time to evaluate : 5.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 194 LYS Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 232 LYS Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain J residue 208 ILE Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 194 LYS Chi-restraints excluded: chain K residue 208 ILE Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 147 LEU Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 194 LYS Chi-restraints excluded: chain M residue 208 ILE Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 147 LEU Chi-restraints excluded: chain N residue 194 LYS Chi-restraints excluded: chain N residue 208 ILE Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 147 LEU Chi-restraints excluded: chain O residue 208 ILE Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain P residue 147 LEU Chi-restraints excluded: chain P residue 208 ILE Chi-restraints excluded: chain Q residue 12 LEU Chi-restraints excluded: chain Q residue 147 LEU Chi-restraints excluded: chain Q residue 194 LYS Chi-restraints excluded: chain Q residue 208 ILE Chi-restraints excluded: chain R residue 12 LEU Chi-restraints excluded: chain R residue 21 VAL Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 194 LYS Chi-restraints excluded: chain R residue 208 ILE Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain S residue 194 LYS Chi-restraints excluded: chain S residue 208 ILE Chi-restraints excluded: chain T residue 12 LEU Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 21 VAL Chi-restraints excluded: chain U residue 147 LEU Chi-restraints excluded: chain U residue 208 ILE Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 21 VAL Chi-restraints excluded: chain V residue 147 LEU Chi-restraints excluded: chain V residue 208 ILE Chi-restraints excluded: chain W residue 12 LEU Chi-restraints excluded: chain W residue 21 VAL Chi-restraints excluded: chain W residue 147 LEU Chi-restraints excluded: chain W residue 194 LYS Chi-restraints excluded: chain W residue 208 ILE Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 147 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 537 optimal weight: 0.9990 chunk 353 optimal weight: 1.9990 chunk 569 optimal weight: 0.8980 chunk 347 optimal weight: 3.9990 chunk 270 optimal weight: 1.9990 chunk 396 optimal weight: 0.6980 chunk 597 optimal weight: 1.9990 chunk 550 optimal weight: 7.9990 chunk 475 optimal weight: 0.9990 chunk 49 optimal weight: 10.0000 chunk 367 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.6878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 52800 Z= 0.176 Angle : 0.609 8.256 71064 Z= 0.309 Chirality : 0.039 0.225 7488 Planarity : 0.004 0.029 9264 Dihedral : 4.756 48.515 7104 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.57 % Allowed : 17.81 % Favored : 80.63 % 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: 2.79 (0.11), residues: 6144 helix: 2.59 (0.08), residues: 4824 sheet: None (None), residues: 0 loop : -1.12 (0.19), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP N 168 HIS 0.002 0.000 HIS J 203 PHE 0.020 0.002 PHE X 116 TYR 0.018 0.001 TYR P 212 ARG 0.005 0.000 ARG A 165 ********************** 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 569 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 481 time to evaluate : 5.261 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: A 12 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.7003 (pp) REVERT: B 12 LEU cc_start: 0.7417 (OUTLIER) cc_final: 0.7080 (pp) REVERT: C 12 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.7081 (pp) REVERT: D 12 LEU cc_start: 0.7417 (OUTLIER) cc_final: 0.7080 (pp) REVERT: E 12 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7079 (pp) REVERT: F 12 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.7001 (pp) REVERT: G 12 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.7079 (pp) REVERT: H 12 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7076 (pp) REVERT: I 12 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.6991 (pp) REVERT: J 12 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.7003 (pp) REVERT: K 12 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.6994 (pp) REVERT: K 194 LYS cc_start: 0.9120 (OUTLIER) cc_final: 0.8779 (tppp) REVERT: L 12 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.6998 (pp) REVERT: M 12 LEU cc_start: 0.7334 (OUTLIER) cc_final: 0.6981 (pp) REVERT: N 12 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.6976 (pp) REVERT: N 194 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8770 (tppp) REVERT: O 12 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.6997 (pp) REVERT: P 12 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.7078 (pp) REVERT: Q 12 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.7080 (pp) REVERT: Q 194 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8773 (tppp) REVERT: R 12 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.7009 (pp) REVERT: R 145 MET cc_start: 0.8410 (mtp) cc_final: 0.7832 (mtp) REVERT: R 194 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8772 (tppp) REVERT: S 12 LEU cc_start: 0.7420 (OUTLIER) cc_final: 0.7082 (pp) REVERT: T 12 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.6967 (pp) REVERT: U 12 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.6986 (pp) REVERT: V 12 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.6989 (pp) REVERT: W 12 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.6985 (pp) REVERT: W 194 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8774 (tppp) REVERT: X 12 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.6990 (pp) outliers start: 88 outliers final: 55 residues processed: 538 average time/residue: 1.2016 time to fit residues: 850.5546 Evaluate side-chains 542 residues out of total 5568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 458 time to evaluate : 4.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 232 LYS Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 208 ILE Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 194 LYS Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 147 LEU Chi-restraints excluded: chain M residue 12 LEU Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain N residue 147 LEU Chi-restraints excluded: chain N residue 194 LYS Chi-restraints excluded: chain O residue 12 LEU Chi-restraints excluded: chain O residue 21 VAL Chi-restraints excluded: chain O residue 147 LEU Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 147 LEU Chi-restraints excluded: chain Q residue 12 LEU Chi-restraints excluded: chain Q residue 21 VAL Chi-restraints excluded: chain Q residue 147 LEU Chi-restraints excluded: chain Q residue 194 LYS Chi-restraints excluded: chain R residue 12 LEU Chi-restraints excluded: chain R residue 21 VAL Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 194 LYS Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain S residue 21 VAL Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain T residue 12 LEU Chi-restraints excluded: chain T residue 21 VAL Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain T residue 208 ILE Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 21 VAL Chi-restraints excluded: chain U residue 147 LEU Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 21 VAL Chi-restraints excluded: chain V residue 147 LEU Chi-restraints excluded: chain V residue 232 LYS Chi-restraints excluded: chain W residue 12 LEU Chi-restraints excluded: chain W residue 21 VAL Chi-restraints excluded: chain W residue 147 LEU Chi-restraints excluded: chain W residue 194 LYS Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 147 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 291 optimal weight: 8.9990 chunk 378 optimal weight: 3.9990 chunk 507 optimal weight: 10.0000 chunk 145 optimal weight: 7.9990 chunk 438 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 476 optimal weight: 4.9990 chunk 199 optimal weight: 1.9990 chunk 489 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.125853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.075866 restraints weight = 264857.616| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 4.70 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3128 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3128 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.6965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 52800 Z= 0.256 Angle : 0.618 9.373 71064 Z= 0.313 Chirality : 0.039 0.194 7488 Planarity : 0.004 0.036 9264 Dihedral : 4.682 46.352 7104 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.62 % Allowed : 17.50 % Favored : 80.88 % 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: 2.69 (0.08), residues: 4776 sheet: None (None), residues: 0 loop : -1.20 (0.19), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP T 168 HIS 0.003 0.001 HIS W 203 PHE 0.021 0.003 PHE N 116 TYR 0.018 0.001 TYR P 212 ARG 0.004 0.000 ARG A 165 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20000.98 seconds wall clock time: 353 minutes 17.84 seconds (21197.84 seconds total)