Starting phenix.real_space_refine on Mon Mar 25 10:02:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tb3_25791/03_2024/7tb3_25791.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tb3_25791/03_2024/7tb3_25791.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tb3_25791/03_2024/7tb3_25791.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tb3_25791/03_2024/7tb3_25791.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tb3_25791/03_2024/7tb3_25791.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tb3_25791/03_2024/7tb3_25791.pdb" } resolution = 2.57 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= 0.008 sd= 0.050 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 312 5.16 5 C 30168 2.51 5 N 8448 2.21 5 O 9072 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 54": "OE1" <-> "OE2" Residue "I TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 79": "OE1" <-> "OE2" Residue "J TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 49": "OE1" <-> "OE2" Residue "K GLU 79": "OE1" <-> "OE2" Residue "K TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 79": "OE1" <-> "OE2" Residue "W TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 48000 Number of models: 1 Model: "" Number of chains: 24 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 Time building chain proxies: 43.17, per 1000 atoms: 0.90 Number of scatterers: 48000 At special positions: 0 Unit cell: (164, 164, 164, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 312 16.00 O 9072 8.00 N 8448 7.00 C 30168 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=2.02 Simple disulfide: pdb=" SG CYS A 31 " - pdb=" SG CYS J 237 " distance=2.02 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS J 27 " distance=2.09 Simple disulfide: pdb=" SG CYS A 237 " - pdb=" SG CYS J 31 " distance=2.10 Simple disulfide: pdb=" SG CYS B 27 " - pdb=" SG CYS I 169 " distance=2.07 Simple disulfide: pdb=" SG CYS B 31 " - pdb=" SG CYS I 237 " distance=2.19 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS I 27 " distance=2.00 Simple disulfide: pdb=" SG CYS B 237 " - pdb=" SG CYS I 31 " distance=2.06 Simple disulfide: pdb=" SG CYS C 27 " - pdb=" SG CYS L 169 " distance=2.14 Simple disulfide: pdb=" SG CYS C 31 " - pdb=" SG CYS L 237 " distance=2.11 Simple disulfide: pdb=" SG CYS C 169 " - pdb=" SG CYS L 27 " distance=2.25 Simple disulfide: pdb=" SG CYS C 237 " - pdb=" SG CYS L 31 " distance=2.24 Simple disulfide: pdb=" SG CYS D 27 " - pdb=" SG CYS K 169 " distance=2.09 Simple disulfide: pdb=" SG CYS D 31 " - pdb=" SG CYS K 237 " distance=1.97 Simple disulfide: pdb=" SG CYS D 169 " - pdb=" SG CYS K 27 " distance=2.12 Simple disulfide: pdb=" SG CYS D 237 " - pdb=" SG CYS K 31 " distance=2.01 Simple disulfide: pdb=" SG CYS E 27 " - pdb=" SG CYS N 169 " distance=2.03 Simple disulfide: pdb=" SG CYS E 31 " - pdb=" SG CYS N 237 " distance=2.10 Simple disulfide: pdb=" SG CYS E 169 " - pdb=" SG CYS N 27 " distance=1.98 Simple disulfide: pdb=" SG CYS E 237 " - pdb=" SG CYS N 31 " distance=2.07 Simple disulfide: pdb=" SG CYS F 27 " - pdb=" SG CYS M 169 " distance=2.08 Simple disulfide: pdb=" SG CYS F 31 " - pdb=" SG CYS M 237 " distance=1.99 Simple disulfide: pdb=" SG CYS F 169 " - pdb=" SG CYS M 27 " distance=2.06 Simple disulfide: pdb=" SG CYS F 237 " - pdb=" SG CYS M 31 " distance=1.96 Simple disulfide: pdb=" SG CYS G 27 " - pdb=" SG CYS P 169 " distance=1.95 Simple disulfide: pdb=" SG CYS G 31 " - pdb=" SG CYS P 237 " distance=2.00 Simple disulfide: pdb=" SG CYS G 169 " - pdb=" SG CYS P 27 " distance=2.08 Simple disulfide: pdb=" SG CYS G 237 " - pdb=" SG CYS P 31 " distance=2.15 Simple disulfide: pdb=" SG CYS H 27 " - pdb=" SG CYS O 169 " distance=2.02 Simple disulfide: pdb=" SG CYS H 31 " - pdb=" SG CYS O 237 " distance=1.92 Simple disulfide: pdb=" SG CYS H 169 " - pdb=" SG CYS O 27 " distance=2.04 Simple disulfide: pdb=" SG CYS H 237 " - pdb=" SG CYS O 31 " distance=1.97 Simple disulfide: pdb=" SG CYS Q 27 " - pdb=" SG CYS X 169 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 31 " - pdb=" SG CYS X 237 " distance=2.05 Simple disulfide: pdb=" SG CYS Q 169 " - pdb=" SG CYS X 27 " distance=1.95 Simple disulfide: pdb=" SG CYS Q 237 " - pdb=" SG CYS X 31 " distance=1.99 Simple disulfide: pdb=" SG CYS R 27 " - pdb=" SG CYS W 169 " distance=1.96 Simple disulfide: pdb=" SG CYS R 31 " - pdb=" SG CYS W 237 " distance=1.92 Simple disulfide: pdb=" SG CYS R 169 " - pdb=" SG CYS W 27 " distance=1.96 Simple disulfide: pdb=" SG CYS R 237 " - pdb=" SG CYS W 31 " distance=1.96 Simple disulfide: pdb=" SG CYS S 27 " - pdb=" SG CYS V 169 " distance=1.97 Simple disulfide: pdb=" SG CYS S 31 " - pdb=" SG CYS V 237 " distance=1.99 Simple disulfide: pdb=" SG CYS S 169 " - pdb=" SG CYS V 27 " distance=2.00 Simple disulfide: pdb=" SG CYS S 237 " - pdb=" SG CYS V 31 " distance=2.01 Simple disulfide: pdb=" SG CYS T 27 " - pdb=" SG CYS U 169 " distance=1.96 Simple disulfide: pdb=" SG CYS T 31 " - pdb=" SG CYS U 237 " distance=2.07 Simple disulfide: pdb=" SG CYS T 169 " - pdb=" SG CYS U 27 " distance=1.91 Simple disulfide: pdb=" SG CYS T 237 " - pdb=" SG CYS U 31 " distance=1.90 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: 18.28 Conformation dependent library (CDL) restraints added in 16.6 seconds 11616 Ramachandran restraints generated. 5808 Oldfield, 0 Emsley, 5808 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11328 Finding SS restraints... Secondary structure from input PDB file: 216 helices and 0 sheets defined 76.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.73 Creating SS restraints... Processing helix chain 'A' and resid 9 through 25 removed outlier: 3.988A pdb=" N LYS A 19 " --> pdb=" O HIS A 15 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU A 20 " --> pdb=" O LEU A 16 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL A 21 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN A 22 " --> pdb=" O HIS A 18 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE A 25 " --> pdb=" O VAL A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 55 removed outlier: 3.677A pdb=" N GLU A 39 " --> pdb=" O ASP A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 74 Processing helix chain 'A' and resid 88 through 117 Processing helix chain 'A' and resid 123 through 151 Processing helix chain 'A' and resid 171 through 199 Processing helix chain 'A' and resid 201 through 211 Processing helix chain 'A' and resid 212 through 234 removed outlier: 3.917A pdb=" N LYS A 218 " --> pdb=" O SER A 214 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS A 232 " --> pdb=" O THR A 228 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 247 removed outlier: 3.711A pdb=" N GLU A 242 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR A 243 " --> pdb=" O GLY A 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 25 removed outlier: 3.987A pdb=" N LYS B 19 " --> pdb=" O HIS B 15 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU B 20 " --> pdb=" O LEU B 16 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL B 21 " --> pdb=" O VAL B 17 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN B 22 " --> pdb=" O HIS B 18 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE B 25 " --> pdb=" O VAL B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 55 removed outlier: 3.693A pdb=" N GLU B 39 " --> pdb=" O ASP B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 74 Processing helix chain 'B' and resid 88 through 117 Processing helix chain 'B' and resid 123 through 151 Processing helix chain 'B' and resid 171 through 199 Processing helix chain 'B' and resid 201 through 211 Processing helix chain 'B' and resid 212 through 234 removed outlier: 3.918A pdb=" N LYS B 218 " --> pdb=" O SER B 214 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS B 232 " --> pdb=" O THR B 228 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY B 234 " --> pdb=" O LEU B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 247 removed outlier: 3.711A pdb=" N GLU B 242 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR B 243 " --> pdb=" O GLY B 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 25 removed outlier: 3.988A pdb=" N LYS C 19 " --> pdb=" O HIS C 15 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU C 20 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL C 21 " --> pdb=" O VAL C 17 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN C 22 " --> pdb=" O HIS C 18 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N PHE C 25 " --> pdb=" O VAL C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 55 removed outlier: 3.598A pdb=" N GLU C 39 " --> pdb=" O ASP C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 74 Processing helix chain 'C' and resid 88 through 117 Processing helix chain 'C' and resid 123 through 151 Processing helix chain 'C' and resid 171 through 199 Processing helix chain 'C' and resid 201 through 211 Processing helix chain 'C' and resid 212 through 234 removed outlier: 3.918A pdb=" N LYS C 218 " --> pdb=" O SER C 214 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS C 232 " --> pdb=" O THR C 228 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY C 234 " --> pdb=" O LEU C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 247 removed outlier: 3.710A pdb=" N GLU C 242 " --> pdb=" O ALA C 238 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR C 243 " --> pdb=" O GLY C 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 25 removed outlier: 3.974A pdb=" N LYS D 19 " --> pdb=" O HIS D 15 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU D 20 " --> pdb=" O LEU D 16 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL D 21 " --> pdb=" O VAL D 17 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN D 22 " --> pdb=" O HIS D 18 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N PHE D 25 " --> pdb=" O VAL D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 55 removed outlier: 3.599A pdb=" N GLU D 39 " --> pdb=" O ASP D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 74 Processing helix chain 'D' and resid 88 through 117 Processing helix chain 'D' and resid 123 through 151 Processing helix chain 'D' and resid 171 through 199 Processing helix chain 'D' and resid 201 through 211 Processing helix chain 'D' and resid 212 through 234 removed outlier: 3.919A pdb=" N LYS D 218 " --> pdb=" O SER D 214 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS D 232 " --> pdb=" O THR D 228 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY D 234 " --> pdb=" O LEU D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 247 removed outlier: 3.711A pdb=" N GLU D 242 " --> pdb=" O ALA D 238 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR D 243 " --> pdb=" O GLY D 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 25 removed outlier: 4.002A pdb=" N LYS E 19 " --> pdb=" O HIS E 15 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU E 20 " --> pdb=" O LEU E 16 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL E 21 " --> pdb=" O VAL E 17 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN E 22 " --> pdb=" O HIS E 18 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE E 25 " --> pdb=" O VAL E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 55 removed outlier: 3.692A pdb=" N GLU E 39 " --> pdb=" O ASP E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 74 Processing helix chain 'E' and resid 88 through 117 Processing helix chain 'E' and resid 123 through 151 Processing helix chain 'E' and resid 171 through 199 Processing helix chain 'E' and resid 201 through 211 Processing helix chain 'E' and resid 212 through 234 removed outlier: 3.918A pdb=" N LYS E 218 " --> pdb=" O SER E 214 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS E 232 " --> pdb=" O THR E 228 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY E 234 " --> pdb=" O LEU E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 247 removed outlier: 3.711A pdb=" N GLU E 242 " --> pdb=" O ALA E 238 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR E 243 " --> pdb=" O GLY E 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 25 removed outlier: 3.997A pdb=" N LYS F 19 " --> pdb=" O HIS F 15 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU F 20 " --> pdb=" O LEU F 16 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL F 21 " --> pdb=" O VAL F 17 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN F 22 " --> pdb=" O HIS F 18 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE F 25 " --> pdb=" O VAL F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 55 removed outlier: 3.671A pdb=" N GLU F 39 " --> pdb=" O ASP F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 74 Processing helix chain 'F' and resid 88 through 117 Processing helix chain 'F' and resid 123 through 151 Processing helix chain 'F' and resid 171 through 199 Processing helix chain 'F' and resid 201 through 211 Processing helix chain 'F' and resid 212 through 234 removed outlier: 3.918A pdb=" N LYS F 218 " --> pdb=" O SER F 214 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS F 232 " --> pdb=" O THR F 228 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY F 234 " --> pdb=" O LEU F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 247 removed outlier: 3.710A pdb=" N GLU F 242 " --> pdb=" O ALA F 238 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR F 243 " --> pdb=" O GLY F 239 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 25 removed outlier: 3.987A pdb=" N LYS G 19 " --> pdb=" O HIS G 15 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU G 20 " --> pdb=" O LEU G 16 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL G 21 " --> pdb=" O VAL G 17 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN G 22 " --> pdb=" O HIS G 18 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE G 25 " --> pdb=" O VAL G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 55 removed outlier: 3.599A pdb=" N GLU G 39 " --> pdb=" O ASP G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 74 Processing helix chain 'G' and resid 88 through 117 Processing helix chain 'G' and resid 123 through 151 Processing helix chain 'G' and resid 171 through 199 Processing helix chain 'G' and resid 201 through 211 Processing helix chain 'G' and resid 212 through 234 removed outlier: 3.918A pdb=" N LYS G 218 " --> pdb=" O SER G 214 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS G 232 " --> pdb=" O THR G 228 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLY G 234 " --> pdb=" O LEU G 230 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 247 removed outlier: 3.711A pdb=" N GLU G 242 " --> pdb=" O ALA G 238 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR G 243 " --> pdb=" O GLY G 239 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 25 removed outlier: 4.037A pdb=" N LYS H 19 " --> pdb=" O HIS H 15 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU H 20 " --> pdb=" O LEU H 16 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL H 21 " --> pdb=" O VAL H 17 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN H 22 " --> pdb=" O HIS H 18 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE H 25 " --> pdb=" O VAL H 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 55 removed outlier: 3.671A pdb=" N GLU H 39 " --> pdb=" O ASP H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 74 Processing helix chain 'H' and resid 88 through 117 Processing helix chain 'H' and resid 123 through 151 Processing helix chain 'H' and resid 171 through 199 Processing helix chain 'H' and resid 201 through 211 Processing helix chain 'H' and resid 212 through 234 removed outlier: 3.919A pdb=" N LYS H 218 " --> pdb=" O SER H 214 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS H 232 " --> pdb=" O THR H 228 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY H 234 " --> pdb=" O LEU H 230 " (cutoff:3.500A) Processing helix chain 'H' and resid 238 through 247 removed outlier: 3.710A pdb=" N GLU H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR H 243 " --> pdb=" O GLY H 239 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 25 removed outlier: 3.995A pdb=" N LYS I 19 " --> pdb=" O HIS I 15 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU I 20 " --> pdb=" O LEU I 16 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL I 21 " --> pdb=" O VAL I 17 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN I 22 " --> pdb=" O HIS I 18 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE I 25 " --> pdb=" O VAL I 21 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 55 removed outlier: 3.675A pdb=" N GLU I 39 " --> pdb=" O ASP I 35 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 74 Processing helix chain 'I' and resid 88 through 117 Processing helix chain 'I' and resid 123 through 151 Processing helix chain 'I' and resid 171 through 199 Processing helix chain 'I' and resid 201 through 211 Processing helix chain 'I' and resid 212 through 234 removed outlier: 3.918A pdb=" N LYS I 218 " --> pdb=" O SER I 214 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS I 232 " --> pdb=" O THR I 228 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY I 234 " --> pdb=" O LEU I 230 " (cutoff:3.500A) Processing helix chain 'I' and resid 238 through 247 removed outlier: 3.711A pdb=" N GLU I 242 " --> pdb=" O ALA I 238 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR I 243 " --> pdb=" O GLY I 239 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 25 removed outlier: 3.976A pdb=" N LYS J 19 " --> pdb=" O HIS J 15 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU J 20 " --> pdb=" O LEU J 16 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL J 21 " --> pdb=" O VAL J 17 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN J 22 " --> pdb=" O HIS J 18 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE J 25 " --> pdb=" O VAL J 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 35 through 55 removed outlier: 3.694A pdb=" N GLU J 39 " --> pdb=" O ASP J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 74 Processing helix chain 'J' and resid 88 through 117 Processing helix chain 'J' and resid 123 through 151 Processing helix chain 'J' and resid 171 through 199 Processing helix chain 'J' and resid 201 through 211 Processing helix chain 'J' and resid 212 through 234 removed outlier: 3.918A pdb=" N LYS J 218 " --> pdb=" O SER J 214 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS J 232 " --> pdb=" O THR J 228 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY J 234 " --> pdb=" O LEU J 230 " (cutoff:3.500A) Processing helix chain 'J' and resid 238 through 247 removed outlier: 3.710A pdb=" N GLU J 242 " --> pdb=" O ALA J 238 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR J 243 " --> pdb=" O GLY J 239 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 25 removed outlier: 4.010A pdb=" N LYS K 19 " --> pdb=" O HIS K 15 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU K 20 " --> pdb=" O LEU K 16 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL K 21 " --> pdb=" O VAL K 17 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN K 22 " --> pdb=" O HIS K 18 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE K 25 " --> pdb=" O VAL K 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 35 through 55 removed outlier: 3.550A pdb=" N GLU K 39 " --> pdb=" O ASP K 35 " (cutoff:3.500A) Processing helix chain 'K' and resid 59 through 74 Processing helix chain 'K' and resid 88 through 117 Processing helix chain 'K' and resid 123 through 151 Processing helix chain 'K' and resid 171 through 199 Processing helix chain 'K' and resid 201 through 211 Processing helix chain 'K' and resid 212 through 234 removed outlier: 3.918A pdb=" N LYS K 218 " --> pdb=" O SER K 214 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS K 232 " --> pdb=" O THR K 228 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY K 234 " --> pdb=" O LEU K 230 " (cutoff:3.500A) Processing helix chain 'K' and resid 238 through 247 removed outlier: 3.711A pdb=" N GLU K 242 " --> pdb=" O ALA K 238 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR K 243 " --> pdb=" O GLY K 239 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 25 removed outlier: 3.984A pdb=" N LYS L 19 " --> pdb=" O HIS L 15 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU L 20 " --> pdb=" O LEU L 16 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL L 21 " --> pdb=" O VAL L 17 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN L 22 " --> pdb=" O HIS L 18 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE L 25 " --> pdb=" O VAL L 21 " (cutoff:3.500A) Processing helix chain 'L' and resid 35 through 55 removed outlier: 3.662A pdb=" N GLU L 39 " --> pdb=" O ASP L 35 " (cutoff:3.500A) Processing helix chain 'L' and resid 59 through 74 Processing helix chain 'L' and resid 88 through 117 Processing helix chain 'L' and resid 123 through 151 Processing helix chain 'L' and resid 171 through 199 Processing helix chain 'L' and resid 201 through 211 Processing helix chain 'L' and resid 212 through 234 removed outlier: 3.918A pdb=" N LYS L 218 " --> pdb=" O SER L 214 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS L 232 " --> pdb=" O THR L 228 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY L 234 " --> pdb=" O LEU L 230 " (cutoff:3.500A) Processing helix chain 'L' and resid 238 through 247 removed outlier: 3.711A pdb=" N GLU L 242 " --> pdb=" O ALA L 238 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR L 243 " --> pdb=" O GLY L 239 " (cutoff:3.500A) Processing helix chain 'M' and resid 10 through 25 removed outlier: 3.987A pdb=" N LYS M 19 " --> pdb=" O HIS M 15 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU M 20 " --> pdb=" O LEU M 16 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL M 21 " --> pdb=" O VAL M 17 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN M 22 " --> pdb=" O HIS M 18 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE M 25 " --> pdb=" O VAL M 21 " (cutoff:3.500A) Processing helix chain 'M' and resid 35 through 55 removed outlier: 3.696A pdb=" N GLU M 39 " --> pdb=" O ASP M 35 " (cutoff:3.500A) Processing helix chain 'M' and resid 59 through 74 Processing helix chain 'M' and resid 88 through 117 Processing helix chain 'M' and resid 123 through 151 Processing helix chain 'M' and resid 171 through 199 Processing helix chain 'M' and resid 201 through 211 Processing helix chain 'M' and resid 212 through 234 removed outlier: 3.918A pdb=" N LYS M 218 " --> pdb=" O SER M 214 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS M 232 " --> pdb=" O THR M 228 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY M 234 " --> pdb=" O LEU M 230 " (cutoff:3.500A) Processing helix chain 'M' and resid 238 through 247 removed outlier: 3.710A pdb=" N GLU M 242 " --> pdb=" O ALA M 238 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR M 243 " --> pdb=" O GLY M 239 " (cutoff:3.500A) Processing helix chain 'N' and resid 10 through 25 removed outlier: 4.021A pdb=" N LYS N 19 " --> pdb=" O HIS N 15 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU N 20 " --> pdb=" O LEU N 16 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL N 21 " --> pdb=" O VAL N 17 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN N 22 " --> pdb=" O HIS N 18 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE N 25 " --> pdb=" O VAL N 21 " (cutoff:3.500A) Processing helix chain 'N' and resid 35 through 55 removed outlier: 3.698A pdb=" N GLU N 39 " --> pdb=" O ASP N 35 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 74 Processing helix chain 'N' and resid 88 through 117 Processing helix chain 'N' and resid 123 through 151 Processing helix chain 'N' and resid 171 through 199 Processing helix chain 'N' and resid 201 through 211 Processing helix chain 'N' and resid 212 through 234 removed outlier: 3.918A pdb=" N LYS N 218 " --> pdb=" O SER N 214 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS N 232 " --> pdb=" O THR N 228 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY N 234 " --> pdb=" O LEU N 230 " (cutoff:3.500A) Processing helix chain 'N' and resid 238 through 247 removed outlier: 3.711A pdb=" N GLU N 242 " --> pdb=" O ALA N 238 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR N 243 " --> pdb=" O GLY N 239 " (cutoff:3.500A) Processing helix chain 'O' and resid 10 through 25 removed outlier: 3.984A pdb=" N LYS O 19 " --> pdb=" O HIS O 15 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU O 20 " --> pdb=" O LEU O 16 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL O 21 " --> pdb=" O VAL O 17 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN O 22 " --> pdb=" O HIS O 18 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE O 25 " --> pdb=" O VAL O 21 " (cutoff:3.500A) Processing helix chain 'O' and resid 35 through 55 removed outlier: 3.671A pdb=" N GLU O 39 " --> pdb=" O ASP O 35 " (cutoff:3.500A) Processing helix chain 'O' and resid 59 through 74 Processing helix chain 'O' and resid 88 through 117 Processing helix chain 'O' and resid 123 through 151 Processing helix chain 'O' and resid 171 through 199 Processing helix chain 'O' and resid 201 through 211 Processing helix chain 'O' and resid 212 through 234 removed outlier: 3.918A pdb=" N LYS O 218 " --> pdb=" O SER O 214 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS O 232 " --> pdb=" O THR O 228 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY O 234 " --> pdb=" O LEU O 230 " (cutoff:3.500A) Processing helix chain 'O' and resid 238 through 247 removed outlier: 3.710A pdb=" N GLU O 242 " --> pdb=" O ALA O 238 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR O 243 " --> pdb=" O GLY O 239 " (cutoff:3.500A) Processing helix chain 'P' and resid 10 through 25 removed outlier: 3.980A pdb=" N LYS P 19 " --> pdb=" O HIS P 15 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU P 20 " --> pdb=" O LEU P 16 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL P 21 " --> pdb=" O VAL P 17 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN P 22 " --> pdb=" O HIS P 18 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE P 25 " --> pdb=" O VAL P 21 " (cutoff:3.500A) Processing helix chain 'P' and resid 35 through 55 removed outlier: 3.696A pdb=" N GLU P 39 " --> pdb=" O ASP P 35 " (cutoff:3.500A) Processing helix chain 'P' and resid 59 through 74 Processing helix chain 'P' and resid 88 through 117 Processing helix chain 'P' and resid 123 through 151 Processing helix chain 'P' and resid 171 through 199 Processing helix chain 'P' and resid 201 through 211 Processing helix chain 'P' and resid 212 through 234 removed outlier: 3.918A pdb=" N LYS P 218 " --> pdb=" O SER P 214 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS P 232 " --> pdb=" O THR P 228 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY P 234 " --> pdb=" O LEU P 230 " (cutoff:3.500A) Processing helix chain 'P' and resid 238 through 247 removed outlier: 3.710A pdb=" N GLU P 242 " --> pdb=" O ALA P 238 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR P 243 " --> pdb=" O GLY P 239 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 25 removed outlier: 3.988A pdb=" N LYS Q 19 " --> pdb=" O HIS Q 15 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU Q 20 " --> pdb=" O LEU Q 16 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL Q 21 " --> pdb=" O VAL Q 17 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN Q 22 " --> pdb=" O HIS Q 18 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE Q 25 " --> pdb=" O VAL Q 21 " (cutoff:3.500A) Processing helix chain 'Q' and resid 35 through 55 removed outlier: 3.669A pdb=" N GLU Q 39 " --> pdb=" O ASP Q 35 " (cutoff:3.500A) Processing helix chain 'Q' and resid 59 through 74 Processing helix chain 'Q' and resid 88 through 117 Processing helix chain 'Q' and resid 123 through 151 Processing helix chain 'Q' and resid 171 through 199 Processing helix chain 'Q' and resid 201 through 211 Processing helix chain 'Q' and resid 212 through 234 removed outlier: 3.918A pdb=" N LYS Q 218 " --> pdb=" O SER Q 214 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS Q 232 " --> pdb=" O THR Q 228 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY Q 234 " --> pdb=" O LEU Q 230 " (cutoff:3.500A) Processing helix chain 'Q' and resid 238 through 247 removed outlier: 3.710A pdb=" N GLU Q 242 " --> pdb=" O ALA Q 238 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR Q 243 " --> pdb=" O GLY Q 239 " (cutoff:3.500A) Processing helix chain 'R' and resid 10 through 25 removed outlier: 4.016A pdb=" N LYS R 19 " --> pdb=" O HIS R 15 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU R 20 " --> pdb=" O LEU R 16 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL R 21 " --> pdb=" O VAL R 17 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN R 22 " --> pdb=" O HIS R 18 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N PHE R 25 " --> pdb=" O VAL R 21 " (cutoff:3.500A) Processing helix chain 'R' and resid 35 through 55 removed outlier: 3.689A pdb=" N GLU R 39 " --> pdb=" O ASP R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 74 Processing helix chain 'R' and resid 88 through 117 Processing helix chain 'R' and resid 123 through 151 Processing helix chain 'R' and resid 171 through 199 Processing helix chain 'R' and resid 201 through 211 Processing helix chain 'R' and resid 212 through 234 removed outlier: 3.918A pdb=" N LYS R 218 " --> pdb=" O SER R 214 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS R 232 " --> pdb=" O THR R 228 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY R 234 " --> pdb=" O LEU R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 238 through 247 removed outlier: 3.711A pdb=" N GLU R 242 " --> pdb=" O ALA R 238 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR R 243 " --> pdb=" O GLY R 239 " (cutoff:3.500A) Processing helix chain 'S' and resid 10 through 25 removed outlier: 3.996A pdb=" N LYS S 19 " --> pdb=" O HIS S 15 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU S 20 " --> pdb=" O LEU S 16 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL S 21 " --> pdb=" O VAL S 17 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN S 22 " --> pdb=" O HIS S 18 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE S 25 " --> pdb=" O VAL S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 35 through 55 removed outlier: 3.668A pdb=" N GLU S 39 " --> pdb=" O ASP S 35 " (cutoff:3.500A) Processing helix chain 'S' and resid 59 through 74 Processing helix chain 'S' and resid 88 through 117 Processing helix chain 'S' and resid 123 through 151 Processing helix chain 'S' and resid 171 through 199 Processing helix chain 'S' and resid 201 through 211 Processing helix chain 'S' and resid 212 through 234 removed outlier: 3.918A pdb=" N LYS S 218 " --> pdb=" O SER S 214 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS S 232 " --> pdb=" O THR S 228 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY S 234 " --> pdb=" O LEU S 230 " (cutoff:3.500A) Processing helix chain 'S' and resid 238 through 247 removed outlier: 3.710A pdb=" N GLU S 242 " --> pdb=" O ALA S 238 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR S 243 " --> pdb=" O GLY S 239 " (cutoff:3.500A) Processing helix chain 'T' and resid 10 through 25 removed outlier: 4.021A pdb=" N LYS T 19 " --> pdb=" O HIS T 15 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU T 20 " --> pdb=" O LEU T 16 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL T 21 " --> pdb=" O VAL T 17 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN T 22 " --> pdb=" O HIS T 18 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE T 25 " --> pdb=" O VAL T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 35 through 55 removed outlier: 3.692A pdb=" N GLU T 39 " --> pdb=" O ASP T 35 " (cutoff:3.500A) Processing helix chain 'T' and resid 59 through 74 Processing helix chain 'T' and resid 88 through 117 Processing helix chain 'T' and resid 123 through 151 Processing helix chain 'T' and resid 171 through 199 Processing helix chain 'T' and resid 201 through 211 Processing helix chain 'T' and resid 212 through 234 removed outlier: 3.918A pdb=" N LYS T 218 " --> pdb=" O SER T 214 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS T 232 " --> pdb=" O THR T 228 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY T 234 " --> pdb=" O LEU T 230 " (cutoff:3.500A) Processing helix chain 'T' and resid 238 through 247 removed outlier: 3.710A pdb=" N GLU T 242 " --> pdb=" O ALA T 238 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR T 243 " --> pdb=" O GLY T 239 " (cutoff:3.500A) Processing helix chain 'U' and resid 10 through 25 removed outlier: 3.999A pdb=" N LYS U 19 " --> pdb=" O HIS U 15 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU U 20 " --> pdb=" O LEU U 16 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL U 21 " --> pdb=" O VAL U 17 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN U 22 " --> pdb=" O HIS U 18 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N PHE U 25 " --> pdb=" O VAL U 21 " (cutoff:3.500A) Processing helix chain 'U' and resid 35 through 55 removed outlier: 3.598A pdb=" N GLU U 39 " --> pdb=" O ASP U 35 " (cutoff:3.500A) Processing helix chain 'U' and resid 59 through 74 Processing helix chain 'U' and resid 88 through 117 Processing helix chain 'U' and resid 123 through 151 Processing helix chain 'U' and resid 171 through 199 Processing helix chain 'U' and resid 201 through 211 Processing helix chain 'U' and resid 212 through 234 removed outlier: 3.918A pdb=" N LYS U 218 " --> pdb=" O SER U 214 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS U 232 " --> pdb=" O THR U 228 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY U 234 " --> pdb=" O LEU U 230 " (cutoff:3.500A) Processing helix chain 'U' and resid 238 through 247 removed outlier: 3.710A pdb=" N GLU U 242 " --> pdb=" O ALA U 238 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR U 243 " --> pdb=" O GLY U 239 " (cutoff:3.500A) Processing helix chain 'V' and resid 10 through 25 removed outlier: 3.969A pdb=" N LYS V 19 " --> pdb=" O HIS V 15 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU V 20 " --> pdb=" O LEU V 16 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL V 21 " --> pdb=" O VAL V 17 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN V 22 " --> pdb=" O HIS V 18 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE V 25 " --> pdb=" O VAL V 21 " (cutoff:3.500A) Processing helix chain 'V' and resid 35 through 55 removed outlier: 3.690A pdb=" N GLU V 39 " --> pdb=" O ASP V 35 " (cutoff:3.500A) Processing helix chain 'V' and resid 59 through 74 Processing helix chain 'V' and resid 88 through 117 Processing helix chain 'V' and resid 123 through 151 Processing helix chain 'V' and resid 171 through 199 Processing helix chain 'V' and resid 201 through 211 Processing helix chain 'V' and resid 212 through 234 removed outlier: 3.918A pdb=" N LYS V 218 " --> pdb=" O SER V 214 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS V 232 " --> pdb=" O THR V 228 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY V 234 " --> pdb=" O LEU V 230 " (cutoff:3.500A) Processing helix chain 'V' and resid 238 through 247 removed outlier: 3.711A pdb=" N GLU V 242 " --> pdb=" O ALA V 238 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR V 243 " --> pdb=" O GLY V 239 " (cutoff:3.500A) Processing helix chain 'W' and resid 10 through 25 removed outlier: 3.982A pdb=" N LYS W 19 " --> pdb=" O HIS W 15 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU W 20 " --> pdb=" O LEU W 16 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL W 21 " --> pdb=" O VAL W 17 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN W 22 " --> pdb=" O HIS W 18 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE W 25 " --> pdb=" O VAL W 21 " (cutoff:3.500A) Processing helix chain 'W' and resid 35 through 55 removed outlier: 3.597A pdb=" N GLU W 39 " --> pdb=" O ASP W 35 " (cutoff:3.500A) Processing helix chain 'W' and resid 59 through 74 Processing helix chain 'W' and resid 88 through 117 Processing helix chain 'W' and resid 123 through 151 Processing helix chain 'W' and resid 171 through 199 Processing helix chain 'W' and resid 201 through 211 Processing helix chain 'W' and resid 212 through 234 removed outlier: 3.919A pdb=" N LYS W 218 " --> pdb=" O SER W 214 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS W 232 " --> pdb=" O THR W 228 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY W 234 " --> pdb=" O LEU W 230 " (cutoff:3.500A) Processing helix chain 'W' and resid 238 through 247 removed outlier: 3.711A pdb=" N GLU W 242 " --> pdb=" O ALA W 238 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR W 243 " --> pdb=" O GLY W 239 " (cutoff:3.500A) Processing helix chain 'X' and resid 10 through 25 removed outlier: 3.963A pdb=" N LYS X 19 " --> pdb=" O HIS X 15 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU X 20 " --> pdb=" O LEU X 16 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL X 21 " --> pdb=" O VAL X 17 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN X 22 " --> pdb=" O HIS X 18 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE X 25 " --> pdb=" O VAL X 21 " (cutoff:3.500A) Processing helix chain 'X' and resid 35 through 55 removed outlier: 3.678A pdb=" N GLU X 39 " --> pdb=" O ASP X 35 " (cutoff:3.500A) Processing helix chain 'X' and resid 59 through 74 Processing helix chain 'X' and resid 88 through 117 Processing helix chain 'X' and resid 123 through 151 Processing helix chain 'X' and resid 171 through 199 Processing helix chain 'X' and resid 201 through 211 Processing helix chain 'X' and resid 212 through 234 removed outlier: 3.918A pdb=" N LYS X 218 " --> pdb=" O SER X 214 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS X 232 " --> pdb=" O THR X 228 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY X 234 " --> pdb=" O LEU X 230 " (cutoff:3.500A) Processing helix chain 'X' and resid 238 through 247 removed outlier: 3.711A pdb=" N GLU X 242 " --> pdb=" O ALA X 238 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR X 243 " --> pdb=" O GLY X 239 " (cutoff:3.500A) 3313 hydrogen bonds defined for protein. 9915 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.79 Time building geometry restraints manager: 19.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 16176 1.34 - 1.46: 10603 1.46 - 1.58: 21725 1.58 - 1.69: 0 1.69 - 1.81: 480 Bond restraints: 48984 Sorted by residual: bond pdb=" CA GLU A 76 " pdb=" C GLU A 76 " ideal model delta sigma weight residual 1.517 1.532 -0.014 6.30e-03 2.52e+04 5.22e+00 bond pdb=" CA GLU M 76 " pdb=" C GLU M 76 " ideal model delta sigma weight residual 1.517 1.532 -0.014 6.30e-03 2.52e+04 5.22e+00 bond pdb=" CA GLU I 76 " pdb=" C GLU I 76 " ideal model delta sigma weight residual 1.517 1.531 -0.014 6.30e-03 2.52e+04 4.88e+00 bond pdb=" CA GLU L 76 " pdb=" C GLU L 76 " ideal model delta sigma weight residual 1.517 1.531 -0.014 6.30e-03 2.52e+04 4.87e+00 bond pdb=" CA GLU P 76 " pdb=" C GLU P 76 " ideal model delta sigma weight residual 1.517 1.531 -0.014 6.30e-03 2.52e+04 4.86e+00 ... (remaining 48979 not shown) Histogram of bond angle deviations from ideal: 100.80 - 107.44: 1397 107.44 - 114.07: 27158 114.07 - 120.71: 23405 120.71 - 127.34: 13521 127.34 - 133.98: 423 Bond angle restraints: 65904 Sorted by residual: angle pdb=" N LYS R 232 " pdb=" CA LYS R 232 " pdb=" C LYS R 232 " ideal model delta sigma weight residual 114.62 110.96 3.66 1.14e+00 7.69e-01 1.03e+01 angle pdb=" N LYS I 232 " pdb=" CA LYS I 232 " pdb=" C LYS I 232 " ideal model delta sigma weight residual 114.62 110.96 3.66 1.14e+00 7.69e-01 1.03e+01 angle pdb=" N LYS N 232 " pdb=" CA LYS N 232 " pdb=" C LYS N 232 " ideal model delta sigma weight residual 114.62 110.97 3.65 1.14e+00 7.69e-01 1.03e+01 angle pdb=" N LYS E 232 " pdb=" CA LYS E 232 " pdb=" C LYS E 232 " ideal model delta sigma weight residual 114.62 110.97 3.65 1.14e+00 7.69e-01 1.03e+01 angle pdb=" N LYS M 232 " pdb=" CA LYS M 232 " pdb=" C LYS M 232 " ideal model delta sigma weight residual 114.62 110.97 3.65 1.14e+00 7.69e-01 1.03e+01 ... (remaining 65899 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 29122 17.92 - 35.83: 942 35.83 - 53.75: 151 53.75 - 71.67: 53 71.67 - 89.59: 44 Dihedral angle restraints: 30312 sinusoidal: 12792 harmonic: 17520 Sorted by residual: dihedral pdb=" CB GLU G 49 " pdb=" CG GLU G 49 " pdb=" CD GLU G 49 " pdb=" OE1 GLU G 49 " ideal model delta sinusoidal sigma weight residual 0.00 86.44 -86.44 1 3.00e+01 1.11e-03 1.00e+01 dihedral pdb=" CB GLU C 79 " pdb=" CG GLU C 79 " pdb=" CD GLU C 79 " pdb=" OE1 GLU C 79 " ideal model delta sinusoidal sigma weight residual 0.00 -85.32 85.32 1 3.00e+01 1.11e-03 9.80e+00 dihedral pdb=" CB GLU J 79 " pdb=" CG GLU J 79 " pdb=" CD GLU J 79 " pdb=" OE1 GLU J 79 " ideal model delta sinusoidal sigma weight residual 0.00 -84.91 84.91 1 3.00e+01 1.11e-03 9.72e+00 ... (remaining 30309 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 4999 0.028 - 0.057: 1454 0.057 - 0.085: 386 0.085 - 0.114: 73 0.114 - 0.142: 24 Chirality restraints: 6936 Sorted by residual: chirality pdb=" CG LEU O 77 " pdb=" CB LEU O 77 " pdb=" CD1 LEU O 77 " pdb=" CD2 LEU O 77 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 5.04e-01 chirality pdb=" CG LEU Q 77 " pdb=" CB LEU Q 77 " pdb=" CD1 LEU Q 77 " pdb=" CD2 LEU Q 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 H 77 " pdb=" CB LEU H 77 " pdb=" CD1 LEU H 77 " pdb=" CD2 LEU H 77 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 4.97e-01 ... (remaining 6933 not shown) Planarity restraints: 8616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE G 70 " 0.004 2.00e-02 2.50e+03 8.74e-03 7.64e-01 pdb=" C ILE G 70 " -0.015 2.00e-02 2.50e+03 pdb=" O ILE G 70 " 0.006 2.00e-02 2.50e+03 pdb=" N TYR G 71 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU F 49 " -0.004 2.00e-02 2.50e+03 8.44e-03 7.12e-01 pdb=" C GLU F 49 " 0.015 2.00e-02 2.50e+03 pdb=" O GLU F 49 " -0.005 2.00e-02 2.50e+03 pdb=" N GLY F 50 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU K 49 " -0.004 2.00e-02 2.50e+03 8.42e-03 7.10e-01 pdb=" C GLU K 49 " 0.015 2.00e-02 2.50e+03 pdb=" O GLU K 49 " -0.005 2.00e-02 2.50e+03 pdb=" N GLY K 50 " -0.005 2.00e-02 2.50e+03 ... (remaining 8613 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 5593 2.75 - 3.29: 48106 3.29 - 3.82: 82314 3.82 - 4.36: 88539 4.36 - 4.90: 156758 Nonbonded interactions: 381310 Sorted by model distance: nonbonded pdb=" OG1 THR H 249 " pdb=" OH TYR L 243 " model vdw 2.212 2.440 nonbonded pdb=" OG1 THR L 249 " pdb=" OH TYR P 243 " model vdw 2.220 2.440 nonbonded pdb=" OH TYR K 243 " pdb=" OG1 THR Q 249 " model vdw 2.246 2.440 nonbonded pdb=" OH TYR C 243 " pdb=" OG1 THR S 249 " model vdw 2.253 2.440 nonbonded pdb=" OH TYR J 243 " pdb=" OG1 THR N 249 " model vdw 2.258 2.440 ... (remaining 381305 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)) } 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: 0.010 Normalize map: mean=0, sd=1: 3.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 14.280 Check model and map are aligned: 0.660 Set scattering table: 0.410 Process input model: 144.410 Find NCS groups from input model: 3.770 Set up NCS constraints: 0.310 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:11.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 179.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 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 : 0.002 0.019 48984 Z= 0.100 Angle : 0.414 6.147 65904 Z= 0.254 Chirality : 0.031 0.142 6936 Planarity : 0.002 0.021 8616 Dihedral : 9.420 89.586 18840 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.41 % Allowed : 9.46 % Favored : 90.13 % Rotamer: Outliers : 1.06 % Allowed : 4.07 % Favored : 94.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.76 (0.11), residues: 5808 helix: 1.73 (0.08), residues: 4440 sheet: None (None), residues: 0 loop : -3.90 (0.13), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP R 168 HIS 0.002 0.000 HIS K 193 PHE 0.003 0.000 PHE Q 25 TYR 0.004 0.000 TYR O 62 ARG 0.001 0.000 ARG K 59 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11616 Ramachandran restraints generated. 5808 Oldfield, 0 Emsley, 5808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11616 Ramachandran restraints generated. 5808 Oldfield, 0 Emsley, 5808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1680 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 1625 time to evaluate : 5.436 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: A 129 TYR cc_start: 0.8135 (t80) cc_final: 0.7630 (t80) REVERT: B 22 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7441 (mp10) REVERT: B 129 TYR cc_start: 0.8077 (t80) cc_final: 0.7705 (t80) REVERT: C 22 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7475 (mp10) REVERT: C 129 TYR cc_start: 0.8085 (t80) cc_final: 0.7375 (t80) REVERT: D 22 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7420 (mp10) REVERT: D 129 TYR cc_start: 0.8024 (t80) cc_final: 0.7293 (t80) REVERT: E 22 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7534 (mp10) REVERT: E 129 TYR cc_start: 0.8067 (t80) cc_final: 0.7359 (t80) REVERT: F 10 GLN cc_start: 0.4098 (OUTLIER) cc_final: 0.2464 (mt0) REVERT: F 22 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7541 (mp10) REVERT: F 129 TYR cc_start: 0.8084 (t80) cc_final: 0.7414 (t80) REVERT: G 22 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7495 (mp10) REVERT: G 129 TYR cc_start: 0.8096 (t80) cc_final: 0.7484 (t80) REVERT: H 22 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7335 (mp10) REVERT: H 129 TYR cc_start: 0.8010 (t80) cc_final: 0.7342 (t80) REVERT: I 22 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7590 (mp10) REVERT: I 49 GLU cc_start: 0.5417 (OUTLIER) cc_final: 0.5127 (tp30) REVERT: I 129 TYR cc_start: 0.8125 (t80) cc_final: 0.7392 (t80) REVERT: J 49 GLU cc_start: 0.5538 (OUTLIER) cc_final: 0.5338 (tp30) REVERT: J 129 TYR cc_start: 0.8037 (t80) cc_final: 0.7576 (t80) REVERT: K 10 GLN cc_start: 0.3430 (OUTLIER) cc_final: 0.1896 (mp10) REVERT: K 22 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7384 (mp10) REVERT: K 129 TYR cc_start: 0.8069 (t80) cc_final: 0.7523 (t80) REVERT: L 22 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7576 (mp10) REVERT: M 129 TYR cc_start: 0.8060 (t80) cc_final: 0.7206 (t80) REVERT: N 22 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7509 (mp10) REVERT: N 129 TYR cc_start: 0.8010 (t80) cc_final: 0.7392 (t80) REVERT: O 129 TYR cc_start: 0.8030 (t80) cc_final: 0.7260 (t80) REVERT: P 11 ASP cc_start: 0.7415 (OUTLIER) cc_final: 0.6928 (p0) REVERT: P 49 GLU cc_start: 0.5535 (OUTLIER) cc_final: 0.5270 (tp30) REVERT: P 129 TYR cc_start: 0.8040 (t80) cc_final: 0.7260 (t80) REVERT: Q 22 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7622 (mp10) REVERT: Q 129 TYR cc_start: 0.8073 (t80) cc_final: 0.7370 (t80) REVERT: R 22 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7502 (mp10) REVERT: R 129 TYR cc_start: 0.8079 (t80) cc_final: 0.7427 (t80) REVERT: S 22 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7578 (mp10) REVERT: S 49 GLU cc_start: 0.5210 (OUTLIER) cc_final: 0.4969 (tp30) REVERT: S 129 TYR cc_start: 0.8028 (t80) cc_final: 0.7430 (t80) REVERT: T 22 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7427 (mp10) REVERT: T 129 TYR cc_start: 0.8062 (t80) cc_final: 0.7662 (t80) REVERT: U 22 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7573 (mp10) REVERT: U 129 TYR cc_start: 0.8146 (t80) cc_final: 0.7714 (t80) REVERT: V 22 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7469 (mp10) REVERT: V 129 TYR cc_start: 0.8017 (t80) cc_final: 0.7226 (t80) REVERT: W 129 TYR cc_start: 0.8030 (t80) cc_final: 0.7455 (t80) REVERT: X 22 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7597 (mp10) REVERT: X 129 TYR cc_start: 0.8015 (t80) cc_final: 0.7397 (t80) outliers start: 55 outliers final: 10 residues processed: 1679 average time/residue: 1.5575 time to fit residues: 3225.6780 Evaluate side-chains 925 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 890 time to evaluate : 5.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain C residue 22 GLN Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain E residue 22 GLN Chi-restraints excluded: chain F residue 10 GLN Chi-restraints excluded: chain F residue 22 GLN Chi-restraints excluded: chain G residue 22 GLN Chi-restraints excluded: chain G residue 54 GLU Chi-restraints excluded: chain H residue 22 GLN Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain I residue 22 GLN Chi-restraints excluded: chain I residue 49 GLU Chi-restraints excluded: chain J residue 49 GLU Chi-restraints excluded: chain J residue 54 GLU Chi-restraints excluded: chain K residue 10 GLN Chi-restraints excluded: chain K residue 22 GLN Chi-restraints excluded: chain K residue 38 MET Chi-restraints excluded: chain L residue 22 GLN Chi-restraints excluded: chain L residue 164 ASP Chi-restraints excluded: chain N residue 22 GLN Chi-restraints excluded: chain P residue 11 ASP Chi-restraints excluded: chain P residue 49 GLU Chi-restraints excluded: chain P residue 54 GLU Chi-restraints excluded: chain Q residue 22 GLN Chi-restraints excluded: chain Q residue 54 GLU Chi-restraints excluded: chain R residue 22 GLN Chi-restraints excluded: chain R residue 54 GLU Chi-restraints excluded: chain S residue 22 GLN Chi-restraints excluded: chain S residue 49 GLU Chi-restraints excluded: chain T residue 22 GLN Chi-restraints excluded: chain U residue 22 GLN Chi-restraints excluded: chain V residue 22 GLN Chi-restraints excluded: chain X residue 22 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 486 optimal weight: 9.9990 chunk 436 optimal weight: 30.0000 chunk 242 optimal weight: 8.9990 chunk 149 optimal weight: 10.0000 chunk 294 optimal weight: 0.0770 chunk 233 optimal weight: 0.7980 chunk 451 optimal weight: 1.9990 chunk 174 optimal weight: 7.9990 chunk 274 optimal weight: 0.9990 chunk 336 optimal weight: 50.0000 chunk 523 optimal weight: 0.5980 overall best weight: 0.8942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN A 74 GLN A 98 GLN A 100 ASN A 125 ASN A 150 GLN A 248 HIS B 74 GLN B 82 GLN ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 150 GLN B 248 HIS ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN ** C 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN C 150 GLN C 248 HIS ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN D 100 ASN D 125 ASN D 150 GLN D 248 HIS E 82 GLN ** E 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN ** E 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 ASN E 150 GLN E 248 HIS ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 88 HIS F 98 GLN F 125 ASN F 150 GLN F 173 ASN F 248 HIS G 82 GLN ** G 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 GLN G 100 ASN G 150 GLN G 248 HIS H 74 GLN H 82 GLN H 98 GLN H 125 ASN H 150 GLN H 248 HIS I 74 GLN ** I 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 88 HIS I 98 GLN ** I 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 125 ASN I 150 GLN I 248 HIS ** J 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 GLN J 100 ASN J 125 ASN J 150 GLN J 248 HIS K 10 GLN K 82 GLN ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 HIS K 98 GLN K 100 ASN K 125 ASN K 150 GLN K 248 HIS L 82 GLN ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 98 GLN L 125 ASN L 150 GLN L 248 HIS M 22 GLN M 74 GLN M 82 GLN ** M 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 98 GLN M 100 ASN M 125 ASN M 150 GLN M 248 HIS N 98 GLN ** N 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 248 HIS O 82 GLN ** O 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 98 GLN ** O 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 125 ASN O 150 GLN O 248 HIS P 98 GLN P 100 ASN P 125 ASN P 150 GLN P 248 HIS ** Q 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 98 GLN Q 100 ASN Q 125 ASN Q 148 GLN Q 150 GLN Q 248 HIS R 82 GLN ** R 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 98 GLN R 100 ASN R 150 GLN R 248 HIS S 74 GLN S 82 GLN S 98 GLN S 100 ASN S 248 HIS T 98 GLN T 100 ASN T 150 GLN T 248 HIS U 98 GLN U 125 ASN U 150 GLN U 248 HIS V 82 GLN ** V 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 98 GLN V 100 ASN V 125 ASN V 150 GLN V 248 HIS W 82 GLN ** W 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 88 HIS W 98 GLN W 100 ASN W 125 ASN W 150 GLN W 248 HIS X 98 GLN X 100 ASN X 248 HIS Total number of N/Q/H flips: 128 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 48984 Z= 0.202 Angle : 0.636 10.285 65904 Z= 0.322 Chirality : 0.039 0.176 6936 Planarity : 0.005 0.064 8616 Dihedral : 5.632 99.459 6607 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.15 % Allowed : 18.97 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.92 (0.12), residues: 5808 helix: 2.42 (0.08), residues: 4488 sheet: None (None), residues: 0 loop : -3.10 (0.14), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 168 HIS 0.004 0.001 HIS L 203 PHE 0.025 0.003 PHE H 207 TYR 0.019 0.002 TYR F 115 ARG 0.005 0.000 ARG S 165 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11616 Ramachandran restraints generated. 5808 Oldfield, 0 Emsley, 5808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11616 Ramachandran restraints generated. 5808 Oldfield, 0 Emsley, 5808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1048 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 936 time to evaluate : 5.424 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 52 MET cc_start: 0.1744 (tmm) cc_final: -0.0142 (pmt) REVERT: A 200 ASN cc_start: 0.7918 (m-40) cc_final: 0.7715 (m-40) REVERT: B 22 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7451 (mp10) REVERT: B 52 MET cc_start: 0.1657 (tmm) cc_final: -0.0146 (pmt) REVERT: C 22 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7422 (mp10) REVERT: D 22 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.7345 (mp10) REVERT: E 22 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7504 (mp10) REVERT: E 52 MET cc_start: 0.1756 (tmm) cc_final: -0.0110 (pmt) REVERT: F 10 GLN cc_start: 0.3842 (OUTLIER) cc_final: 0.2307 (mt0) REVERT: F 22 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7459 (mp10) REVERT: G 22 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7457 (mp10) REVERT: G 52 MET cc_start: 0.1446 (tmm) cc_final: -0.0430 (pmt) REVERT: H 22 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.7393 (mp10) REVERT: I 22 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7446 (mp10) REVERT: I 52 MET cc_start: 0.1727 (tmm) cc_final: -0.0133 (pmt) REVERT: K 22 GLN cc_start: 0.7729 (OUTLIER) cc_final: 0.7359 (mp10) REVERT: K 52 MET cc_start: 0.1556 (tmm) cc_final: 0.0007 (ppp) REVERT: L 22 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7497 (mp10) REVERT: N 22 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7478 (mp10) REVERT: N 200 ASN cc_start: 0.7874 (m-40) cc_final: 0.7653 (m-40) REVERT: P 11 ASP cc_start: 0.7387 (OUTLIER) cc_final: 0.6920 (p0) REVERT: Q 22 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7475 (mp10) REVERT: R 22 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7447 (mp10) REVERT: R 52 MET cc_start: 0.1448 (tmm) cc_final: -0.0259 (pmt) REVERT: S 22 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7466 (mp10) REVERT: T 22 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.7539 (mp10) REVERT: T 200 ASN cc_start: 0.7873 (m-40) cc_final: 0.7666 (m-40) REVERT: U 22 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7513 (mp10) REVERT: U 52 MET cc_start: 0.1598 (tmm) cc_final: -0.0312 (pmt) REVERT: V 22 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.7430 (mp10) REVERT: W 52 MET cc_start: 0.0553 (tmm) cc_final: -0.1098 (OUTLIER) REVERT: W 216 GLN cc_start: 0.7776 (tp40) cc_final: 0.7521 (tp40) REVERT: X 22 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7499 (mp10) REVERT: X 52 MET cc_start: 0.1523 (tmm) cc_final: -0.0234 (pmm) outliers start: 112 outliers final: 11 residues processed: 1016 average time/residue: 1.4471 time to fit residues: 1845.5648 Evaluate side-chains 773 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 743 time to evaluate : 5.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain C residue 22 GLN Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain E residue 22 GLN Chi-restraints excluded: chain F residue 10 GLN Chi-restraints excluded: chain F residue 22 GLN Chi-restraints excluded: chain G residue 22 GLN Chi-restraints excluded: chain G residue 54 GLU Chi-restraints excluded: chain H residue 22 GLN Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain I residue 22 GLN Chi-restraints excluded: chain I residue 54 GLU Chi-restraints excluded: chain J residue 54 GLU Chi-restraints excluded: chain K residue 22 GLN Chi-restraints excluded: chain L residue 22 GLN Chi-restraints excluded: chain N residue 22 GLN Chi-restraints excluded: chain P residue 11 ASP Chi-restraints excluded: chain P residue 54 GLU Chi-restraints excluded: chain Q residue 22 GLN Chi-restraints excluded: chain Q residue 54 GLU Chi-restraints excluded: chain R residue 22 GLN Chi-restraints excluded: chain R residue 54 GLU Chi-restraints excluded: chain S residue 22 GLN Chi-restraints excluded: chain S residue 197 THR Chi-restraints excluded: chain T residue 22 GLN Chi-restraints excluded: chain U residue 22 GLN Chi-restraints excluded: chain V residue 22 GLN Chi-restraints excluded: chain X residue 22 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 290 optimal weight: 20.0000 chunk 162 optimal weight: 4.9990 chunk 435 optimal weight: 20.0000 chunk 356 optimal weight: 0.9980 chunk 144 optimal weight: 50.0000 chunk 524 optimal weight: 6.9990 chunk 566 optimal weight: 0.0870 chunk 466 optimal weight: 2.9990 chunk 519 optimal weight: 6.9990 chunk 178 optimal weight: 2.9990 chunk 420 optimal weight: 0.7980 overall best weight: 1.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 GLN ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 GLN B 187 GLN ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 GLN ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 HIS D 148 GLN ** E 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 GLN F 10 GLN ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 148 GLN ** G 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 GLN ** H 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 GLN H 187 GLN ** I 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 GLN ** J 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 88 HIS J 148 GLN ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 148 GLN ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 148 GLN M 187 GLN ** N 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 148 GLN ** O 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 148 GLN ** Q 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 187 GLN ** R 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 148 GLN R 187 GLN S 148 GLN ** T 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 125 ASN T 148 GLN ** U 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 148 GLN ** V 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 148 GLN W 187 GLN X 148 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.5400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 48984 Z= 0.232 Angle : 0.622 8.399 65904 Z= 0.320 Chirality : 0.043 0.185 6936 Planarity : 0.005 0.061 8616 Dihedral : 5.313 58.872 6587 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.19 % Allowed : 18.43 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.30 (0.12), residues: 5808 helix: 2.59 (0.08), residues: 4488 sheet: None (None), residues: 0 loop : -2.55 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 168 HIS 0.005 0.001 HIS B 203 PHE 0.024 0.002 PHE W 207 TYR 0.062 0.002 TYR L 62 ARG 0.011 0.001 ARG K 37 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11616 Ramachandran restraints generated. 5808 Oldfield, 0 Emsley, 5808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11616 Ramachandran restraints generated. 5808 Oldfield, 0 Emsley, 5808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 611 time to evaluate : 6.021 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: B 22 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7332 (mp10) REVERT: B 215 GLU cc_start: 0.6315 (pp20) cc_final: 0.6113 (tm-30) REVERT: C 22 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7387 (mp10) REVERT: C 52 MET cc_start: 0.0945 (tmt) cc_final: -0.0753 (pmm) REVERT: D 22 GLN cc_start: 0.7646 (OUTLIER) cc_final: 0.7214 (mp10) REVERT: D 38 MET cc_start: 0.7667 (mpp) cc_final: 0.6694 (ttt) REVERT: E 22 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.7345 (mp10) REVERT: F 22 GLN cc_start: 0.7681 (OUTLIER) cc_final: 0.7278 (mp10) REVERT: G 22 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7304 (mp10) REVERT: H 22 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.7178 (mp10) REVERT: I 22 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7378 (mp10) REVERT: K 22 GLN cc_start: 0.7658 (OUTLIER) cc_final: 0.7218 (mp10) REVERT: K 215 GLU cc_start: 0.6373 (pp20) cc_final: 0.6158 (tm-30) REVERT: L 22 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.7343 (mp10) REVERT: N 22 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7391 (mp10) REVERT: P 11 ASP cc_start: 0.7408 (OUTLIER) cc_final: 0.6904 (p0) REVERT: Q 22 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7346 (mp10) REVERT: R 22 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7371 (mp10) REVERT: S 22 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7433 (mp10) REVERT: T 22 GLN cc_start: 0.7683 (OUTLIER) cc_final: 0.7308 (mp10) REVERT: T 52 MET cc_start: 0.1286 (tmm) cc_final: -0.0617 (pmm) REVERT: U 22 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.7452 (mp10) REVERT: V 22 GLN cc_start: 0.7767 (OUTLIER) cc_final: 0.7324 (mp10) REVERT: X 22 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7391 (mp10) outliers start: 166 outliers final: 75 residues processed: 751 average time/residue: 1.7477 time to fit residues: 1598.4233 Evaluate side-chains 584 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 490 time to evaluate : 5.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain C residue 22 GLN Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain E residue 22 GLN Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain F residue 22 GLN Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain G residue 22 GLN Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 208 ILE Chi-restraints excluded: chain H residue 22 GLN Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain I residue 22 GLN Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 208 ILE Chi-restraints excluded: chain K residue 22 GLN Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 195 LEU Chi-restraints excluded: chain K residue 208 ILE Chi-restraints excluded: chain L residue 22 GLN Chi-restraints excluded: chain L residue 147 LEU Chi-restraints excluded: chain L residue 199 LYS Chi-restraints excluded: chain L residue 208 ILE Chi-restraints excluded: chain L residue 242 GLU Chi-restraints excluded: chain M residue 172 LEU Chi-restraints excluded: chain M residue 197 THR Chi-restraints excluded: chain M residue 208 ILE Chi-restraints excluded: chain N residue 22 GLN Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 147 LEU Chi-restraints excluded: chain N residue 172 LEU Chi-restraints excluded: chain N residue 197 THR Chi-restraints excluded: chain O residue 147 LEU Chi-restraints excluded: chain O residue 172 LEU Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain P residue 11 ASP Chi-restraints excluded: chain P residue 54 GLU Chi-restraints excluded: chain P residue 147 LEU Chi-restraints excluded: chain P residue 172 LEU Chi-restraints excluded: chain P residue 197 THR Chi-restraints excluded: chain P residue 208 ILE Chi-restraints excluded: chain Q residue 22 GLN Chi-restraints excluded: chain Q residue 147 LEU Chi-restraints excluded: chain Q residue 172 LEU Chi-restraints excluded: chain Q residue 197 THR Chi-restraints excluded: chain Q residue 208 ILE Chi-restraints excluded: chain R residue 22 GLN Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 197 THR Chi-restraints excluded: chain S residue 22 GLN Chi-restraints excluded: chain S residue 121 VAL Chi-restraints excluded: chain S residue 172 LEU Chi-restraints excluded: chain T residue 22 GLN Chi-restraints excluded: chain T residue 121 VAL Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain T residue 197 THR Chi-restraints excluded: chain T residue 208 ILE Chi-restraints excluded: chain U residue 22 GLN Chi-restraints excluded: chain U residue 147 LEU Chi-restraints excluded: chain V residue 22 GLN Chi-restraints excluded: chain V residue 147 LEU Chi-restraints excluded: chain V residue 172 LEU Chi-restraints excluded: chain V residue 197 THR Chi-restraints excluded: chain W residue 147 LEU Chi-restraints excluded: chain W residue 197 THR Chi-restraints excluded: chain X residue 22 GLN Chi-restraints excluded: chain X residue 121 VAL Chi-restraints excluded: chain X residue 147 LEU Chi-restraints excluded: chain X residue 172 LEU Chi-restraints excluded: chain X residue 208 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 517 optimal weight: 2.9990 chunk 393 optimal weight: 6.9990 chunk 271 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 250 optimal weight: 3.9990 chunk 351 optimal weight: 2.9990 chunk 525 optimal weight: 7.9990 chunk 556 optimal weight: 4.9990 chunk 274 optimal weight: 2.9990 chunk 498 optimal weight: 0.8980 chunk 150 optimal weight: 7.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 187 GLN C 82 GLN ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 187 GLN ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 187 GLN I 82 GLN ** I 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 187 GLN J 82 GLN ** J 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 187 GLN ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 187 GLN ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 148 GLN ** M 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 187 GLN ** O 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 148 GLN ** P 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 187 GLN ** R 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 187 GLN T 187 GLN ** U 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 98 GLN ** V 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 148 GLN ** W 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 82 GLN ** X 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 187 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.6218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 48984 Z= 0.276 Angle : 0.623 9.173 65904 Z= 0.314 Chirality : 0.042 0.209 6936 Planarity : 0.004 0.055 8616 Dihedral : 5.126 59.707 6566 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.09 % Allowed : 20.81 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.38 (0.12), residues: 5808 helix: 2.64 (0.08), residues: 4488 sheet: None (None), residues: 0 loop : -2.45 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 168 HIS 0.005 0.001 HIS B 140 PHE 0.018 0.002 PHE I 116 TYR 0.018 0.001 TYR D 212 ARG 0.005 0.001 ARG F 118 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11616 Ramachandran restraints generated. 5808 Oldfield, 0 Emsley, 5808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11616 Ramachandran restraints generated. 5808 Oldfield, 0 Emsley, 5808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 475 time to evaluate : 5.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.7285 (mp10) REVERT: C 22 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.7333 (mp10) REVERT: D 22 GLN cc_start: 0.7637 (OUTLIER) cc_final: 0.7228 (mp10) REVERT: D 38 MET cc_start: 0.7693 (mpp) cc_final: 0.6692 (tpt) REVERT: E 22 GLN cc_start: 0.7848 (OUTLIER) cc_final: 0.7336 (mp10) REVERT: E 52 MET cc_start: 0.1064 (tmt) cc_final: -0.0708 (pmm) REVERT: F 22 GLN cc_start: 0.7659 (OUTLIER) cc_final: 0.7246 (mp10) REVERT: F 38 MET cc_start: 0.8306 (mpp) cc_final: 0.6959 (tpt) REVERT: F 52 MET cc_start: 0.1575 (tmm) cc_final: -0.0086 (OUTLIER) REVERT: G 22 GLN cc_start: 0.7783 (OUTLIER) cc_final: 0.7244 (mp10) REVERT: H 22 GLN cc_start: 0.7579 (OUTLIER) cc_final: 0.7084 (mp10) REVERT: H 199 LYS cc_start: 0.9252 (OUTLIER) cc_final: 0.9016 (mptp) REVERT: I 22 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.7344 (mp10) REVERT: I 52 MET cc_start: 0.0932 (tmt) cc_final: -0.0823 (pmm) REVERT: J 52 MET cc_start: 0.0964 (tmt) cc_final: -0.0857 (pmm) REVERT: K 22 GLN cc_start: 0.7590 (OUTLIER) cc_final: 0.7134 (mp10) REVERT: K 38 MET cc_start: 0.7939 (mpp) cc_final: 0.6756 (tpt) REVERT: L 22 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.7243 (mp10) REVERT: L 38 MET cc_start: 0.7613 (mpp) cc_final: 0.6356 (tpt) REVERT: L 52 MET cc_start: 0.0748 (ppp) cc_final: -0.0762 (pmt) REVERT: P 11 ASP cc_start: 0.7383 (OUTLIER) cc_final: 0.6945 (p0) REVERT: Q 22 GLN cc_start: 0.7726 (OUTLIER) cc_final: 0.7251 (mp10) REVERT: Q 52 MET cc_start: 0.0841 (tmt) cc_final: -0.0864 (pmm) REVERT: R 22 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.7237 (mp10) REVERT: R 52 MET cc_start: 0.0796 (tmt) cc_final: -0.0889 (pmm) REVERT: S 22 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7267 (mp10) REVERT: U 22 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7392 (mp10) REVERT: V 22 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.7148 (mp10) REVERT: W 52 MET cc_start: 0.0564 (tmm) cc_final: -0.1185 (ppp) REVERT: W 199 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.8992 (mptp) REVERT: X 22 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.7290 (mp10) outliers start: 109 outliers final: 51 residues processed: 581 average time/residue: 1.6051 time to fit residues: 1158.9383 Evaluate side-chains 474 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 405 time to evaluate : 5.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain C residue 22 GLN Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain E residue 22 GLN Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 199 LYS Chi-restraints excluded: chain F residue 22 GLN Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain G residue 22 GLN Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain H residue 22 GLN Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain H residue 199 LYS Chi-restraints excluded: chain I residue 22 GLN Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain J residue 197 THR Chi-restraints excluded: chain K residue 22 GLN Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 197 THR Chi-restraints excluded: chain L residue 22 GLN Chi-restraints excluded: chain L residue 147 LEU Chi-restraints excluded: chain L residue 199 LYS Chi-restraints excluded: chain L residue 242 GLU Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 197 THR Chi-restraints excluded: chain N residue 197 THR Chi-restraints excluded: chain O residue 147 LEU Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain P residue 11 ASP Chi-restraints excluded: chain P residue 54 GLU Chi-restraints excluded: chain P residue 147 LEU Chi-restraints excluded: chain P residue 197 THR Chi-restraints excluded: chain P residue 199 LYS Chi-restraints excluded: chain Q residue 22 GLN Chi-restraints excluded: chain Q residue 147 LEU Chi-restraints excluded: chain Q residue 197 THR Chi-restraints excluded: chain R residue 22 GLN Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 197 THR Chi-restraints excluded: chain S residue 22 GLN Chi-restraints excluded: chain S residue 197 THR Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain T residue 197 THR Chi-restraints excluded: chain U residue 22 GLN Chi-restraints excluded: chain U residue 147 LEU Chi-restraints excluded: chain U residue 197 THR Chi-restraints excluded: chain V residue 22 GLN Chi-restraints excluded: chain V residue 147 LEU Chi-restraints excluded: chain V residue 197 THR Chi-restraints excluded: chain W residue 147 LEU Chi-restraints excluded: chain W residue 199 LYS Chi-restraints excluded: chain X residue 22 GLN Chi-restraints excluded: chain X residue 197 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 463 optimal weight: 6.9990 chunk 316 optimal weight: 20.0000 chunk 8 optimal weight: 2.9990 chunk 414 optimal weight: 4.9990 chunk 229 optimal weight: 5.9990 chunk 475 optimal weight: 3.9990 chunk 384 optimal weight: 50.0000 chunk 0 optimal weight: 50.0000 chunk 284 optimal weight: 0.9990 chunk 499 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN B 140 HIS ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 187 GLN ** E 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 GLN ** G 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 88 HIS G 98 GLN G 187 GLN H 98 GLN ** I 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 140 HIS L 86 ASN ** M 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 98 GLN ** N 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 98 GLN ** O 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 98 GLN P 98 GLN ** Q 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 98 GLN ** R 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 88 HIS R 98 GLN ** S 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 98 GLN ** T 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 98 GLN ** U 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 98 GLN ** W 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 98 GLN X 98 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.6876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 48984 Z= 0.382 Angle : 0.666 9.263 65904 Z= 0.334 Chirality : 0.044 0.196 6936 Planarity : 0.004 0.051 8616 Dihedral : 5.183 59.813 6560 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.27 % Allowed : 20.47 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.25 (0.12), residues: 5808 helix: 2.46 (0.08), residues: 4536 sheet: None (None), residues: 0 loop : -2.37 (0.16), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP U 168 HIS 0.010 0.002 HIS L 88 PHE 0.025 0.003 PHE L 116 TYR 0.022 0.002 TYR J 212 ARG 0.009 0.001 ARG Q 37 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11616 Ramachandran restraints generated. 5808 Oldfield, 0 Emsley, 5808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11616 Ramachandran restraints generated. 5808 Oldfield, 0 Emsley, 5808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 463 time to evaluate : 5.682 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: B 22 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.7220 (mp10) REVERT: C 22 GLN cc_start: 0.7739 (OUTLIER) cc_final: 0.7231 (mp10) REVERT: C 154 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7605 (mmp-170) REVERT: D 22 GLN cc_start: 0.7509 (OUTLIER) cc_final: 0.7100 (mp10) REVERT: D 38 MET cc_start: 0.7539 (mpp) cc_final: 0.6655 (tpt) REVERT: D 52 MET cc_start: 0.1216 (tmt) cc_final: -0.0626 (pmm) REVERT: E 22 GLN cc_start: 0.7793 (OUTLIER) cc_final: 0.7310 (mp10) REVERT: F 22 GLN cc_start: 0.7574 (OUTLIER) cc_final: 0.7162 (mp10) REVERT: F 38 MET cc_start: 0.8327 (mpp) cc_final: 0.6997 (tpt) REVERT: G 52 MET cc_start: 0.0837 (tmm) cc_final: -0.1242 (ptp) REVERT: H 38 MET cc_start: 0.7993 (mpp) cc_final: 0.6698 (tpt) REVERT: H 199 LYS cc_start: 0.9285 (OUTLIER) cc_final: 0.9080 (mptp) REVERT: H 216 GLN cc_start: 0.8897 (tp40) cc_final: 0.8668 (mm-40) REVERT: I 22 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7311 (mp10) REVERT: K 38 MET cc_start: 0.7935 (mpp) cc_final: 0.6756 (tpt) REVERT: L 22 GLN cc_start: 0.7613 (OUTLIER) cc_final: 0.7165 (mp10) REVERT: L 52 MET cc_start: 0.1390 (ppp) cc_final: -0.0154 (pmt) REVERT: P 11 ASP cc_start: 0.7327 (OUTLIER) cc_final: 0.6986 (p0) REVERT: S 22 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.7191 (mp10) REVERT: S 52 MET cc_start: 0.0796 (tmm) cc_final: -0.1082 (pmm) REVERT: S 199 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8839 (mttm) REVERT: T 22 GLN cc_start: 0.7609 (OUTLIER) cc_final: 0.7189 (mp10) REVERT: U 52 MET cc_start: 0.1457 (tmm) cc_final: -0.0556 (pmt) REVERT: W 199 LYS cc_start: 0.9265 (OUTLIER) cc_final: 0.9059 (mptp) REVERT: X 52 MET cc_start: 0.1023 (tmm) cc_final: -0.0795 (pmm) outliers start: 118 outliers final: 68 residues processed: 580 average time/residue: 1.5738 time to fit residues: 1134.3276 Evaluate side-chains 495 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 413 time to evaluate : 5.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain C residue 22 GLN Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain E residue 22 GLN Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain F residue 22 GLN Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 199 LYS Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain H residue 199 LYS Chi-restraints excluded: chain I residue 22 GLN Chi-restraints excluded: chain I residue 147 LEU Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain J residue 147 LEU Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 197 THR Chi-restraints excluded: chain L residue 22 GLN Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 147 LEU Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 199 LYS Chi-restraints excluded: chain L residue 242 GLU Chi-restraints excluded: chain M residue 120 ASP Chi-restraints excluded: chain M residue 197 THR Chi-restraints excluded: chain M residue 222 GLU Chi-restraints excluded: chain N residue 120 ASP Chi-restraints excluded: chain N residue 147 LEU Chi-restraints excluded: chain N residue 197 THR Chi-restraints excluded: chain O residue 147 LEU Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain O residue 222 GLU Chi-restraints excluded: chain P residue 11 ASP Chi-restraints excluded: chain P residue 54 GLU Chi-restraints excluded: chain P residue 147 LEU Chi-restraints excluded: chain P residue 197 THR Chi-restraints excluded: chain P residue 222 GLU Chi-restraints excluded: chain Q residue 22 GLN Chi-restraints excluded: chain Q residue 147 LEU Chi-restraints excluded: chain Q residue 197 THR Chi-restraints excluded: chain Q residue 199 LYS Chi-restraints excluded: chain R residue 120 ASP Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 197 THR Chi-restraints excluded: chain S residue 22 GLN Chi-restraints excluded: chain S residue 120 ASP Chi-restraints excluded: chain S residue 197 THR Chi-restraints excluded: chain S residue 199 LYS Chi-restraints excluded: chain T residue 22 GLN Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain T residue 197 THR Chi-restraints excluded: chain U residue 120 ASP Chi-restraints excluded: chain U residue 147 LEU Chi-restraints excluded: chain U residue 197 THR Chi-restraints excluded: chain V residue 147 LEU Chi-restraints excluded: chain V residue 197 THR Chi-restraints excluded: chain V residue 222 GLU Chi-restraints excluded: chain W residue 147 LEU Chi-restraints excluded: chain W residue 197 THR Chi-restraints excluded: chain W residue 199 LYS Chi-restraints excluded: chain X residue 120 ASP Chi-restraints excluded: chain X residue 147 LEU Chi-restraints excluded: chain X residue 197 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 187 optimal weight: 0.5980 chunk 501 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 326 optimal weight: 4.9990 chunk 137 optimal weight: 0.9980 chunk 557 optimal weight: 7.9990 chunk 462 optimal weight: 20.0000 chunk 258 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 chunk 292 optimal weight: 0.0470 overall best weight: 0.9282 ------------------------------------------------------------------------------- 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 C 86 ASN C 140 HIS D 86 ASN ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 HIS F 86 ASN ** G 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 86 ASN ** I 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 88 HIS ** J 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 GLN K 86 ASN ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 98 GLN ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 88 HIS ** O 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 86 ASN ** Q 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 140 HIS T 86 ASN T 88 HIS U 86 ASN ** U 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 88 HIS V 140 HIS ** W 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 82 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.6769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 48984 Z= 0.172 Angle : 0.563 8.627 65904 Z= 0.280 Chirality : 0.038 0.156 6936 Planarity : 0.003 0.049 8616 Dihedral : 4.413 59.462 6539 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.23 % Allowed : 20.64 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.77 (0.12), residues: 5808 helix: 2.86 (0.08), residues: 4536 sheet: None (None), residues: 0 loop : -2.30 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP S 168 HIS 0.009 0.001 HIS L 88 PHE 0.011 0.002 PHE S 207 TYR 0.013 0.001 TYR H 212 ARG 0.003 0.000 ARG S 231 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11616 Ramachandran restraints generated. 5808 Oldfield, 0 Emsley, 5808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11616 Ramachandran restraints generated. 5808 Oldfield, 0 Emsley, 5808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 436 time to evaluate : 6.094 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 38 MET cc_start: 0.8435 (mpm) cc_final: 0.7051 (tpt) REVERT: B 22 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.7223 (mp10) REVERT: C 22 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.7233 (mp10) REVERT: D 38 MET cc_start: 0.7560 (mpp) cc_final: 0.6682 (tpt) REVERT: E 22 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.7314 (mp10) REVERT: E 52 MET cc_start: 0.0930 (tmt) cc_final: -0.0980 (pmm) REVERT: F 22 GLN cc_start: 0.7530 (OUTLIER) cc_final: 0.7137 (mp10) REVERT: F 38 MET cc_start: 0.8351 (mpp) cc_final: 0.7021 (tpt) REVERT: F 52 MET cc_start: 0.1546 (tmm) cc_final: -0.0156 (pmm) REVERT: H 38 MET cc_start: 0.7969 (mpp) cc_final: 0.6714 (tpt) REVERT: I 22 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.7310 (mp10) REVERT: I 52 MET cc_start: 0.0917 (tmt) cc_final: -0.1002 (pmm) REVERT: K 38 MET cc_start: 0.7970 (mpp) cc_final: 0.6807 (tpt) REVERT: L 22 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.7270 (mp10) REVERT: L 38 MET cc_start: 0.7575 (mpp) cc_final: 0.6476 (tpt) REVERT: L 52 MET cc_start: 0.1168 (ppp) cc_final: -0.0280 (pmt) REVERT: P 11 ASP cc_start: 0.7395 (OUTLIER) cc_final: 0.7057 (p0) REVERT: Q 52 MET cc_start: 0.1375 (tmm) cc_final: -0.0561 (pmm) REVERT: R 52 MET cc_start: 0.0981 (tmm) cc_final: -0.0844 (pmm) REVERT: S 22 GLN cc_start: 0.7748 (OUTLIER) cc_final: 0.7170 (mp10) REVERT: T 22 GLN cc_start: 0.7614 (OUTLIER) cc_final: 0.7176 (mp10) REVERT: T 52 MET cc_start: 0.0660 (tmm) cc_final: -0.1268 (pmm) REVERT: W 38 MET cc_start: 0.8451 (mpp) cc_final: 0.7083 (tpt) REVERT: W 216 GLN cc_start: 0.8783 (tp40) cc_final: 0.8572 (mm-40) REVERT: X 52 MET cc_start: 0.0908 (tmm) cc_final: -0.1025 (pmm) outliers start: 64 outliers final: 30 residues processed: 499 average time/residue: 1.5864 time to fit residues: 983.1296 Evaluate side-chains 439 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 400 time to evaluate : 5.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain C residue 22 GLN Chi-restraints excluded: chain C residue 86 ASN Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain D residue 22 GLN Chi-restraints excluded: chain D residue 86 ASN Chi-restraints excluded: chain E residue 22 GLN Chi-restraints excluded: chain E residue 199 LYS Chi-restraints excluded: chain F residue 22 GLN Chi-restraints excluded: chain F residue 86 ASN Chi-restraints excluded: chain F residue 199 LYS Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 86 ASN Chi-restraints excluded: chain I residue 22 GLN Chi-restraints excluded: chain K residue 86 ASN Chi-restraints excluded: chain K residue 199 LYS Chi-restraints excluded: chain L residue 22 GLN Chi-restraints excluded: chain L residue 147 LEU Chi-restraints excluded: chain L residue 199 LYS Chi-restraints excluded: chain L residue 242 GLU Chi-restraints excluded: chain M residue 222 GLU Chi-restraints excluded: chain O residue 147 LEU Chi-restraints excluded: chain O residue 222 GLU Chi-restraints excluded: chain P residue 11 ASP Chi-restraints excluded: chain P residue 54 GLU Chi-restraints excluded: chain P residue 86 ASN Chi-restraints excluded: chain P residue 199 LYS Chi-restraints excluded: chain Q residue 22 GLN Chi-restraints excluded: chain Q residue 199 LYS Chi-restraints excluded: chain S residue 22 GLN Chi-restraints excluded: chain T residue 22 GLN Chi-restraints excluded: chain T residue 86 ASN Chi-restraints excluded: chain U residue 86 ASN Chi-restraints excluded: chain U residue 147 LEU Chi-restraints excluded: chain V residue 222 GLU Chi-restraints excluded: chain X residue 199 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 537 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 317 optimal weight: 8.9990 chunk 406 optimal weight: 0.8980 chunk 315 optimal weight: 9.9990 chunk 469 optimal weight: 5.9990 chunk 311 optimal weight: 5.9990 chunk 555 optimal weight: 20.0000 chunk 347 optimal weight: 4.9990 chunk 338 optimal weight: 30.0000 chunk 256 optimal weight: 1.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN A 98 GLN B 86 ASN C 86 ASN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 86 ASN ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 86 ASN ** G 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 86 ASN H 88 HIS ** I 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 98 GLN I 140 HIS ** J 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 86 ASN L 86 ASN ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 88 HIS N 86 ASN N 140 HIS ** O 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 86 ASN P 140 HIS ** Q 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 140 HIS S 86 ASN T 86 ASN U 86 ASN ** U 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 88 HIS X 86 ASN X 140 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.7018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 48984 Z= 0.428 Angle : 0.667 10.222 65904 Z= 0.331 Chirality : 0.045 0.182 6936 Planarity : 0.004 0.047 8616 Dihedral : 4.622 59.492 6539 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.94 % Allowed : 19.76 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.43 (0.12), residues: 5808 helix: 2.65 (0.08), residues: 4512 sheet: None (None), residues: 0 loop : -2.42 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP U 168 HIS 0.012 0.002 HIS K 88 PHE 0.024 0.003 PHE F 116 TYR 0.024 0.002 TYR A 212 ARG 0.007 0.001 ARG F 118 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11616 Ramachandran restraints generated. 5808 Oldfield, 0 Emsley, 5808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11616 Ramachandran restraints generated. 5808 Oldfield, 0 Emsley, 5808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 406 time to evaluate : 5.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.1282 (tmm) cc_final: -0.0816 (pmt) REVERT: B 22 GLN cc_start: 0.7658 (OUTLIER) cc_final: 0.7171 (mp10) REVERT: C 22 GLN cc_start: 0.7701 (OUTLIER) cc_final: 0.7143 (mp10) REVERT: E 52 MET cc_start: 0.0934 (tmt) cc_final: -0.0992 (pmm) REVERT: F 38 MET cc_start: 0.8413 (mpp) cc_final: 0.7178 (tpt) REVERT: F 52 MET cc_start: 0.1381 (tmm) cc_final: -0.0347 (pmt) REVERT: I 22 GLN cc_start: 0.7743 (OUTLIER) cc_final: 0.7252 (mp10) REVERT: I 52 MET cc_start: 0.0874 (tmt) cc_final: -0.1010 (pmm) REVERT: K 38 MET cc_start: 0.7894 (mpp) cc_final: 0.6738 (tpt) REVERT: L 22 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.7180 (mp10) REVERT: L 38 MET cc_start: 0.7596 (mpp) cc_final: 0.6445 (tpt) REVERT: L 52 MET cc_start: 0.1423 (ppp) cc_final: -0.0137 (pmt) REVERT: L 117 ASP cc_start: 0.7904 (t70) cc_final: 0.7682 (t0) REVERT: M 52 MET cc_start: 0.1417 (tmm) cc_final: -0.0618 (pmm) REVERT: P 11 ASP cc_start: 0.7401 (OUTLIER) cc_final: 0.7136 (p0) REVERT: Q 52 MET cc_start: 0.1442 (tmm) cc_final: -0.0526 (pmm) REVERT: R 38 MET cc_start: 0.8398 (mpp) cc_final: 0.6837 (tpt) REVERT: R 52 MET cc_start: 0.0981 (tmm) cc_final: -0.0946 (pmm) REVERT: W 38 MET cc_start: 0.8488 (mpp) cc_final: 0.7114 (tpt) REVERT: W 52 MET cc_start: 0.0409 (tmm) cc_final: -0.1478 (pmm) REVERT: X 52 MET cc_start: 0.1030 (tmm) cc_final: -0.0903 (pmm) outliers start: 101 outliers final: 60 residues processed: 504 average time/residue: 1.4757 time to fit residues: 939.5767 Evaluate side-chains 474 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 409 time to evaluate : 5.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 86 ASN Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain C residue 22 GLN Chi-restraints excluded: chain C residue 86 ASN Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain D residue 86 ASN Chi-restraints excluded: chain E residue 22 GLN Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 199 LYS Chi-restraints excluded: chain F residue 86 ASN Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 199 LYS Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 86 ASN Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain I residue 22 GLN Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain J residue 197 THR Chi-restraints excluded: chain K residue 86 ASN Chi-restraints excluded: chain K residue 197 THR Chi-restraints excluded: chain K residue 199 LYS Chi-restraints excluded: chain L residue 22 GLN Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 147 LEU Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 199 LYS Chi-restraints excluded: chain L residue 242 GLU Chi-restraints excluded: chain M residue 197 THR Chi-restraints excluded: chain M residue 222 GLU Chi-restraints excluded: chain N residue 86 ASN Chi-restraints excluded: chain N residue 147 LEU Chi-restraints excluded: chain N residue 197 THR Chi-restraints excluded: chain O residue 147 LEU Chi-restraints excluded: chain O residue 197 THR Chi-restraints excluded: chain O residue 222 GLU Chi-restraints excluded: chain P residue 11 ASP Chi-restraints excluded: chain P residue 54 GLU Chi-restraints excluded: chain P residue 86 ASN Chi-restraints excluded: chain P residue 197 THR Chi-restraints excluded: chain P residue 199 LYS Chi-restraints excluded: chain P residue 222 GLU Chi-restraints excluded: chain Q residue 197 THR Chi-restraints excluded: chain Q residue 199 LYS Chi-restraints excluded: chain R residue 197 THR Chi-restraints excluded: chain S residue 197 THR Chi-restraints excluded: chain S residue 199 LYS Chi-restraints excluded: chain T residue 86 ASN Chi-restraints excluded: chain T residue 197 THR Chi-restraints excluded: chain U residue 86 ASN Chi-restraints excluded: chain U residue 147 LEU Chi-restraints excluded: chain U residue 197 THR Chi-restraints excluded: chain U residue 208 ILE Chi-restraints excluded: chain V residue 197 THR Chi-restraints excluded: chain V residue 222 GLU Chi-restraints excluded: chain W residue 197 THR Chi-restraints excluded: chain X residue 86 ASN Chi-restraints excluded: chain X residue 147 LEU Chi-restraints excluded: chain X residue 199 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 343 optimal weight: 0.1980 chunk 221 optimal weight: 30.0000 chunk 331 optimal weight: 0.3980 chunk 167 optimal weight: 0.5980 chunk 109 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 352 optimal weight: 0.9980 chunk 378 optimal weight: 0.8980 chunk 274 optimal weight: 0.9980 chunk 51 optimal weight: 10.0000 chunk 436 optimal weight: 7.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 HIS ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 ASN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN D 86 ASN ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN D 140 HIS E 86 ASN ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 86 ASN ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 HIS ** G 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 140 HIS H 86 ASN H 140 HIS H 187 GLN I 86 ASN J 86 ASN ** J 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 140 HIS K 86 ASN ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 86 ASN ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 140 HIS M 86 ASN M 140 HIS O 86 ASN O 140 HIS ** P 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 86 ASN Q 140 HIS R 86 ASN ** S 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 140 HIS ** U 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 140 HIS ** V 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 140 HIS ** X 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.6915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 48984 Z= 0.150 Angle : 0.554 11.178 65904 Z= 0.274 Chirality : 0.038 0.154 6936 Planarity : 0.003 0.045 8616 Dihedral : 4.048 59.236 6527 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.96 % Allowed : 20.85 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.98 (0.12), residues: 5808 helix: 3.12 (0.08), residues: 4488 sheet: None (None), residues: 0 loop : -2.50 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP O 168 HIS 0.009 0.001 HIS B 88 PHE 0.011 0.001 PHE X 207 TYR 0.013 0.001 TYR F 115 ARG 0.003 0.000 ARG K 84 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11616 Ramachandran restraints generated. 5808 Oldfield, 0 Emsley, 5808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11616 Ramachandran restraints generated. 5808 Oldfield, 0 Emsley, 5808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 429 time to evaluate : 5.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.1326 (tmm) cc_final: -0.0722 (pmm) REVERT: B 22 GLN cc_start: 0.7648 (OUTLIER) cc_final: 0.7172 (mp10) REVERT: C 22 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.7173 (mp10) REVERT: D 38 MET cc_start: 0.8394 (mpm) cc_final: 0.7227 (tpt) REVERT: E 22 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.7234 (mp10) REVERT: E 52 MET cc_start: 0.0857 (tmt) cc_final: -0.1030 (pmm) REVERT: F 38 MET cc_start: 0.8412 (mpp) cc_final: 0.7163 (tpt) REVERT: G 52 MET cc_start: 0.0647 (tmm) cc_final: -0.1307 (pmm) REVERT: H 38 MET cc_start: 0.8422 (mpm) cc_final: 0.7164 (tpt) REVERT: I 22 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.7228 (mp10) REVERT: K 38 MET cc_start: 0.7920 (mpp) cc_final: 0.6866 (tpt) REVERT: L 22 GLN cc_start: 0.7530 (OUTLIER) cc_final: 0.7156 (mp10) REVERT: L 38 MET cc_start: 0.7564 (mpp) cc_final: 0.6538 (tpt) REVERT: L 52 MET cc_start: 0.1443 (ppp) cc_final: -0.0044 (pmt) REVERT: M 52 MET cc_start: 0.1383 (tmm) cc_final: -0.0650 (pmm) REVERT: O 38 MET cc_start: 0.7887 (mpp) cc_final: 0.6645 (tpt) REVERT: P 11 ASP cc_start: 0.7319 (OUTLIER) cc_final: 0.7075 (p0) REVERT: Q 52 MET cc_start: 0.1457 (tmm) cc_final: -0.0471 (pmm) REVERT: R 38 MET cc_start: 0.8386 (mpp) cc_final: 0.6810 (tpt) REVERT: R 52 MET cc_start: 0.0906 (tmm) cc_final: -0.0981 (pmm) REVERT: S 52 MET cc_start: 0.0554 (tmm) cc_final: -0.1409 (pmm) REVERT: T 22 GLN cc_start: 0.7573 (OUTLIER) cc_final: 0.7169 (mp10) REVERT: U 52 MET cc_start: 0.1005 (tmm) cc_final: -0.0898 (pmm) REVERT: W 38 MET cc_start: 0.8448 (mpp) cc_final: 0.7114 (tpt) REVERT: W 52 MET cc_start: 0.0358 (tmm) cc_final: -0.1502 (pmm) REVERT: X 52 MET cc_start: 0.0980 (tmm) cc_final: -0.0903 (pmm) outliers start: 50 outliers final: 28 residues processed: 479 average time/residue: 1.5719 time to fit residues: 939.9207 Evaluate side-chains 441 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 406 time to evaluate : 5.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain C residue 22 GLN Chi-restraints excluded: chain C residue 86 ASN Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain D residue 86 ASN Chi-restraints excluded: chain E residue 22 GLN Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain E residue 199 LYS Chi-restraints excluded: chain F residue 86 ASN Chi-restraints excluded: chain F residue 199 LYS Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 86 ASN Chi-restraints excluded: chain I residue 22 GLN Chi-restraints excluded: chain I residue 86 ASN Chi-restraints excluded: chain J residue 86 ASN Chi-restraints excluded: chain K residue 86 ASN Chi-restraints excluded: chain L residue 22 GLN Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 199 LYS Chi-restraints excluded: chain L residue 242 GLU Chi-restraints excluded: chain M residue 86 ASN Chi-restraints excluded: chain O residue 86 ASN Chi-restraints excluded: chain O residue 222 GLU Chi-restraints excluded: chain P residue 11 ASP Chi-restraints excluded: chain P residue 54 GLU Chi-restraints excluded: chain P residue 199 LYS Chi-restraints excluded: chain P residue 222 GLU Chi-restraints excluded: chain Q residue 86 ASN Chi-restraints excluded: chain R residue 86 ASN Chi-restraints excluded: chain S residue 199 LYS Chi-restraints excluded: chain T residue 22 GLN Chi-restraints excluded: chain U residue 147 LEU Chi-restraints excluded: chain V residue 222 GLU Chi-restraints excluded: chain X residue 199 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 505 optimal weight: 0.8980 chunk 531 optimal weight: 40.0000 chunk 485 optimal weight: 30.0000 chunk 517 optimal weight: 2.9990 chunk 311 optimal weight: 6.9990 chunk 225 optimal weight: 5.9990 chunk 406 optimal weight: 0.6980 chunk 158 optimal weight: 6.9990 chunk 467 optimal weight: 6.9990 chunk 489 optimal weight: 2.9990 chunk 515 optimal weight: 5.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 ASN ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 ASN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 86 ASN ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 ASN ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 86 ASN ** G 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 86 ASN J 86 ASN ** J 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 86 ASN ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 86 ASN M 86 ASN N 86 ASN O 86 ASN P 86 ASN ** P 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 86 ASN R 86 ASN ** V 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 187 GLN X 86 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.7015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 48984 Z= 0.311 Angle : 0.629 10.725 65904 Z= 0.307 Chirality : 0.042 0.167 6936 Planarity : 0.004 0.047 8616 Dihedral : 4.151 58.971 6527 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.92 % Allowed : 20.99 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.81 (0.12), residues: 5808 helix: 2.94 (0.08), residues: 4512 sheet: None (None), residues: 0 loop : -2.40 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 168 HIS 0.013 0.001 HIS E 88 PHE 0.019 0.002 PHE F 116 TYR 0.020 0.001 TYR D 212 ARG 0.005 0.000 ARG F 118 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11616 Ramachandran restraints generated. 5808 Oldfield, 0 Emsley, 5808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11616 Ramachandran restraints generated. 5808 Oldfield, 0 Emsley, 5808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 410 time to evaluate : 6.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.1500 (tmm) cc_final: -0.0610 (pmm) REVERT: B 22 GLN cc_start: 0.7659 (OUTLIER) cc_final: 0.7175 (mp10) REVERT: C 22 GLN cc_start: 0.7716 (OUTLIER) cc_final: 0.7155 (mp10) REVERT: E 22 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.7201 (mp10) REVERT: F 38 MET cc_start: 0.8419 (mpp) cc_final: 0.7143 (tpt) REVERT: F 52 MET cc_start: 0.1822 (tmm) cc_final: -0.0171 (pmm) REVERT: G 52 MET cc_start: 0.0732 (tmm) cc_final: -0.1253 (pmm) REVERT: H 52 MET cc_start: 0.0235 (tmm) cc_final: -0.0014 (tmt) REVERT: I 22 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.7196 (mp10) REVERT: I 52 MET cc_start: 0.0816 (tmt) cc_final: -0.1112 (pmm) REVERT: K 38 MET cc_start: 0.7945 (mpp) cc_final: 0.6851 (tpt) REVERT: L 22 GLN cc_start: 0.7517 (OUTLIER) cc_final: 0.7137 (mp10) REVERT: L 38 MET cc_start: 0.7588 (mpp) cc_final: 0.6553 (tpt) REVERT: M 52 MET cc_start: 0.1463 (tmm) cc_final: -0.0593 (pmm) REVERT: O 38 MET cc_start: 0.7954 (mpp) cc_final: 0.6634 (tpt) REVERT: Q 52 MET cc_start: 0.1469 (tmm) cc_final: -0.0487 (pmm) REVERT: R 38 MET cc_start: 0.8397 (mpp) cc_final: 0.6826 (tpt) REVERT: R 52 MET cc_start: 0.0973 (tmm) cc_final: -0.0932 (pmm) REVERT: S 38 MET cc_start: 0.8444 (mpp) cc_final: 0.6872 (tpt) REVERT: S 52 MET cc_start: 0.0669 (tmm) cc_final: -0.1318 (pmm) REVERT: T 52 MET cc_start: 0.0500 (tmm) cc_final: -0.1477 (pmm) REVERT: U 52 MET cc_start: 0.1034 (tmm) cc_final: -0.1001 (pmm) REVERT: V 52 MET cc_start: 0.0416 (tmm) cc_final: -0.1552 (pmm) REVERT: W 38 MET cc_start: 0.8451 (mpp) cc_final: 0.7119 (tpt) REVERT: W 52 MET cc_start: 0.0318 (tmm) cc_final: -0.1574 (pmm) outliers start: 48 outliers final: 33 residues processed: 456 average time/residue: 1.5678 time to fit residues: 897.0728 Evaluate side-chains 446 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 408 time to evaluate : 5.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 86 ASN Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain C residue 22 GLN Chi-restraints excluded: chain C residue 86 ASN Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain D residue 86 ASN Chi-restraints excluded: chain E residue 22 GLN Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain E residue 199 LYS Chi-restraints excluded: chain F residue 86 ASN Chi-restraints excluded: chain F residue 199 LYS Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain I residue 22 GLN Chi-restraints excluded: chain I residue 86 ASN Chi-restraints excluded: chain J residue 86 ASN Chi-restraints excluded: chain K residue 86 ASN Chi-restraints excluded: chain K residue 199 LYS Chi-restraints excluded: chain L residue 22 GLN Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 199 LYS Chi-restraints excluded: chain L residue 242 GLU Chi-restraints excluded: chain M residue 86 ASN Chi-restraints excluded: chain N residue 86 ASN Chi-restraints excluded: chain O residue 86 ASN Chi-restraints excluded: chain O residue 222 GLU Chi-restraints excluded: chain P residue 54 GLU Chi-restraints excluded: chain P residue 86 ASN Chi-restraints excluded: chain P residue 199 LYS Chi-restraints excluded: chain P residue 222 GLU Chi-restraints excluded: chain Q residue 86 ASN Chi-restraints excluded: chain R residue 86 ASN Chi-restraints excluded: chain S residue 199 LYS Chi-restraints excluded: chain U residue 147 LEU Chi-restraints excluded: chain U residue 208 ILE Chi-restraints excluded: chain V residue 222 GLU Chi-restraints excluded: chain X residue 86 ASN Chi-restraints excluded: chain X residue 199 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 339 optimal weight: 3.9990 chunk 547 optimal weight: 2.9990 chunk 333 optimal weight: 5.9990 chunk 259 optimal weight: 0.7980 chunk 380 optimal weight: 1.9990 chunk 573 optimal weight: 0.6980 chunk 528 optimal weight: 50.0000 chunk 456 optimal weight: 50.0000 chunk 47 optimal weight: 2.9990 chunk 352 optimal weight: 3.9990 chunk 280 optimal weight: 0.7980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 ASN ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 86 ASN ** J 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 86 ASN ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 86 ASN O 86 ASN ** O 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 86 ASN ** Q 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 ASN S 86 ASN ** S 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 158 GLN W 187 GLN ** X 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.7014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 48984 Z= 0.205 Angle : 0.581 10.580 65904 Z= 0.286 Chirality : 0.039 0.155 6936 Planarity : 0.003 0.045 8616 Dihedral : 4.078 58.648 6525 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.88 % Allowed : 21.16 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.97 (0.12), residues: 5808 helix: 3.04 (0.08), residues: 4512 sheet: None (None), residues: 0 loop : -2.29 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP M 168 HIS 0.010 0.001 HIS B 88 PHE 0.013 0.002 PHE L 116 TYR 0.016 0.001 TYR L 212 ARG 0.005 0.000 ARG R 84 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11616 Ramachandran restraints generated. 5808 Oldfield, 0 Emsley, 5808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11616 Ramachandran restraints generated. 5808 Oldfield, 0 Emsley, 5808 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 420 time to evaluate : 5.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.1491 (tmm) cc_final: -0.0611 (pmm) REVERT: B 22 GLN cc_start: 0.7667 (OUTLIER) cc_final: 0.7178 (mp10) REVERT: C 22 GLN cc_start: 0.7714 (OUTLIER) cc_final: 0.7153 (mp10) REVERT: E 22 GLN cc_start: 0.7693 (OUTLIER) cc_final: 0.7197 (mp10) REVERT: E 52 MET cc_start: 0.0920 (tmt) cc_final: -0.1031 (pmm) REVERT: F 38 MET cc_start: 0.8433 (mpp) cc_final: 0.7196 (tpt) REVERT: F 52 MET cc_start: 0.1801 (tmm) cc_final: -0.0160 (pmm) REVERT: G 52 MET cc_start: 0.0657 (tmm) cc_final: -0.1291 (pmm) REVERT: H 52 MET cc_start: 0.0226 (tmm) cc_final: -0.0005 (tmt) REVERT: I 22 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.7194 (mp10) REVERT: I 52 MET cc_start: 0.0813 (tmt) cc_final: -0.1119 (pmm) REVERT: K 38 MET cc_start: 0.7938 (mpp) cc_final: 0.6890 (tpt) REVERT: L 22 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.7133 (mp10) REVERT: L 38 MET cc_start: 0.7574 (mpp) cc_final: 0.6550 (tpt) REVERT: L 52 MET cc_start: 0.0817 (tmt) cc_final: -0.0985 (pmm) REVERT: M 52 MET cc_start: 0.1450 (tmm) cc_final: -0.0596 (pmm) REVERT: O 38 MET cc_start: 0.7930 (mpp) cc_final: 0.6653 (tpt) REVERT: Q 52 MET cc_start: 0.1447 (tmm) cc_final: -0.0455 (pmm) REVERT: R 38 MET cc_start: 0.8401 (mpp) cc_final: 0.6866 (tpt) REVERT: R 52 MET cc_start: 0.0964 (tmm) cc_final: -0.0933 (pmm) REVERT: S 38 MET cc_start: 0.8441 (mpp) cc_final: 0.6874 (tpt) REVERT: S 52 MET cc_start: 0.0650 (tmm) cc_final: -0.1326 (pmm) REVERT: T 52 MET cc_start: 0.0540 (tmm) cc_final: -0.1449 (pmm) REVERT: U 52 MET cc_start: 0.1007 (tmm) cc_final: -0.1017 (pmm) REVERT: V 38 MET cc_start: 0.8394 (mpp) cc_final: 0.6883 (tpt) REVERT: V 52 MET cc_start: 0.0366 (tmm) cc_final: 0.0147 (tmt) REVERT: W 38 MET cc_start: 0.8440 (mpp) cc_final: 0.7091 (tpt) REVERT: W 52 MET cc_start: 0.0307 (tmm) cc_final: -0.1571 (pmm) outliers start: 46 outliers final: 27 residues processed: 456 average time/residue: 1.5123 time to fit residues: 863.3350 Evaluate side-chains 445 residues out of total 5160 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 413 time to evaluate : 5.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 86 ASN Chi-restraints excluded: chain B residue 199 LYS Chi-restraints excluded: chain C residue 22 GLN Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain E residue 22 GLN Chi-restraints excluded: chain E residue 199 LYS Chi-restraints excluded: chain F residue 199 LYS Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain I residue 22 GLN Chi-restraints excluded: chain I residue 86 ASN Chi-restraints excluded: chain J residue 195 LEU Chi-restraints excluded: chain K residue 199 LYS Chi-restraints excluded: chain L residue 22 GLN Chi-restraints excluded: chain L residue 86 ASN Chi-restraints excluded: chain L residue 199 LYS Chi-restraints excluded: chain L residue 242 GLU Chi-restraints excluded: chain M residue 86 ASN Chi-restraints excluded: chain M residue 222 GLU Chi-restraints excluded: chain O residue 86 ASN Chi-restraints excluded: chain O residue 222 GLU Chi-restraints excluded: chain P residue 54 GLU Chi-restraints excluded: chain P residue 199 LYS Chi-restraints excluded: chain P residue 222 GLU Chi-restraints excluded: chain Q residue 86 ASN Chi-restraints excluded: chain R residue 86 ASN Chi-restraints excluded: chain S residue 86 ASN Chi-restraints excluded: chain S residue 199 LYS Chi-restraints excluded: chain U residue 147 LEU Chi-restraints excluded: chain V residue 222 GLU Chi-restraints excluded: chain X residue 199 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 362 optimal weight: 6.9990 chunk 486 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 421 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 126 optimal weight: 30.0000 chunk 457 optimal weight: 7.9990 chunk 191 optimal weight: 3.9990 chunk 469 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 86 ASN ** J 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 86 ASN ** O 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 86 ASN ** P 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 187 GLN ** X 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.157142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.098726 restraints weight = 157849.781| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 3.66 r_work: 0.3025 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3040 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3040 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.7028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 48984 Z= 0.231 Angle : 0.598 11.574 65904 Z= 0.292 Chirality : 0.040 0.178 6936 Planarity : 0.003 0.044 8616 Dihedral : 4.077 58.512 6525 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.96 % Allowed : 21.49 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.01 (0.12), residues: 5808 helix: 3.05 (0.08), residues: 4512 sheet: None (None), residues: 0 loop : -2.18 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP Q 168 HIS 0.006 0.001 HIS D 88 PHE 0.014 0.002 PHE L 116 TYR 0.018 0.001 TYR G 243 ARG 0.004 0.000 ARG F 118 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20001.32 seconds wall clock time: 354 minutes 29.63 seconds (21269.63 seconds total)