Starting phenix.real_space_refine on Mon Mar 11 19:44:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbj_13293/03_2024/7pbj_13293_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbj_13293/03_2024/7pbj_13293.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbj_13293/03_2024/7pbj_13293.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbj_13293/03_2024/7pbj_13293.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbj_13293/03_2024/7pbj_13293_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbj_13293/03_2024/7pbj_13293_updated.pdb" } resolution = 3.4 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= 0.023 sd= 0.191 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: 6 Type Number sf(0) Gaussians P 28 5.49 5 Mg 14 5.21 5 S 294 5.16 5 C 36876 2.51 5 N 10269 2.21 5 O 12005 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Ad GLU 102": "OE1" <-> "OE2" Residue "Ad GLU 129": "OE1" <-> "OE2" Residue "Ad GLU 172": "OE1" <-> "OE2" Residue "Ad GLU 191": "OE1" <-> "OE2" Residue "Ad GLU 238": "OE1" <-> "OE2" Residue "Ad GLU 252": "OE1" <-> "OE2" Residue "Ad GLU 255": "OE1" <-> "OE2" Residue "Ad GLU 257": "OE1" <-> "OE2" Residue "Ad GLU 303": "OE1" <-> "OE2" Residue "Ad GLU 310": "OE1" <-> "OE2" Residue "Ad GLU 339": "OE1" <-> "OE2" Residue "Ad ARG 368": "NH1" <-> "NH2" Residue "Ad GLU 460": "OE1" <-> "OE2" Residue "Ad GLU 484": "OE1" <-> "OE2" Residue "Ad TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ad GLU 518": "OE1" <-> "OE2" Residue "Ae ARG 36": "NH1" <-> "NH2" Residue "Ae GLU 61": "OE1" <-> "OE2" Residue "Ae GLU 164": "OE1" <-> "OE2" Residue "Ae GLU 172": "OE1" <-> "OE2" Residue "Ae PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ae GLU 214": "OE1" <-> "OE2" Residue "Ae GLU 238": "OE1" <-> "OE2" Residue "Ae GLU 252": "OE1" <-> "OE2" Residue "Ae GLU 255": "OE1" <-> "OE2" Residue "Ae GLU 257": "OE1" <-> "OE2" Residue "Ae GLU 303": "OE1" <-> "OE2" Residue "Ae GLU 308": "OE1" <-> "OE2" Residue "Ae GLU 338": "OE1" <-> "OE2" Residue "Ae GLU 355": "OE1" <-> "OE2" Residue "Ae GLU 367": "OE1" <-> "OE2" Residue "Ae GLU 388": "OE1" <-> "OE2" Residue "Ae GLU 434": "OE1" <-> "OE2" Residue "Ae TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Af GLU 39": "OE1" <-> "OE2" Residue "Af GLU 50": "OE1" <-> "OE2" Residue "Af GLU 76": "OE1" <-> "OE2" Residue "Af GLU 96": "OE1" <-> "OE2" Residue "Ak GLU 102": "OE1" <-> "OE2" Residue "Ak GLU 129": "OE1" <-> "OE2" Residue "Ak GLU 172": "OE1" <-> "OE2" Residue "Ak GLU 191": "OE1" <-> "OE2" Residue "Ak GLU 238": "OE1" <-> "OE2" Residue "Ak GLU 252": "OE1" <-> "OE2" Residue "Ak GLU 255": "OE1" <-> "OE2" Residue "Ak GLU 257": "OE1" <-> "OE2" Residue "Ak GLU 303": "OE1" <-> "OE2" Residue "Ak GLU 310": "OE1" <-> "OE2" Residue "Ak GLU 339": "OE1" <-> "OE2" Residue "Ak ARG 368": "NH1" <-> "NH2" Residue "Ak GLU 460": "OE1" <-> "OE2" Residue "Ak GLU 484": "OE1" <-> "OE2" Residue "Ak TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ak GLU 518": "OE1" <-> "OE2" Residue "Al ARG 36": "NH1" <-> "NH2" Residue "Al GLU 61": "OE1" <-> "OE2" Residue "Al GLU 164": "OE1" <-> "OE2" Residue "Al GLU 172": "OE1" <-> "OE2" Residue "Al PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Al GLU 214": "OE1" <-> "OE2" Residue "Al GLU 238": "OE1" <-> "OE2" Residue "Al GLU 252": "OE1" <-> "OE2" Residue "Al GLU 255": "OE1" <-> "OE2" Residue "Al GLU 257": "OE1" <-> "OE2" Residue "Al GLU 303": "OE1" <-> "OE2" Residue "Al GLU 308": "OE1" <-> "OE2" Residue "Al GLU 338": "OE1" <-> "OE2" Residue "Al GLU 355": "OE1" <-> "OE2" Residue "Al GLU 367": "OE1" <-> "OE2" Residue "Al GLU 388": "OE1" <-> "OE2" Residue "Al GLU 434": "OE1" <-> "OE2" Residue "Al TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Am GLU 39": "OE1" <-> "OE2" Residue "Am GLU 50": "OE1" <-> "OE2" Residue "Am GLU 76": "OE1" <-> "OE2" Residue "Am GLU 96": "OE1" <-> "OE2" Residue "Ar GLU 102": "OE1" <-> "OE2" Residue "Ar GLU 129": "OE1" <-> "OE2" Residue "Ar GLU 172": "OE1" <-> "OE2" Residue "Ar GLU 191": "OE1" <-> "OE2" Residue "Ar GLU 238": "OE1" <-> "OE2" Residue "Ar GLU 252": "OE1" <-> "OE2" Residue "Ar GLU 255": "OE1" <-> "OE2" Residue "Ar GLU 257": "OE1" <-> "OE2" Residue "Ar GLU 303": "OE1" <-> "OE2" Residue "Ar GLU 310": "OE1" <-> "OE2" Residue "Ar GLU 339": "OE1" <-> "OE2" Residue "Ar ARG 368": "NH1" <-> "NH2" Residue "Ar GLU 460": "OE1" <-> "OE2" Residue "Ar GLU 484": "OE1" <-> "OE2" Residue "Ar TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ar GLU 518": "OE1" <-> "OE2" Residue "As ARG 36": "NH1" <-> "NH2" Residue "As GLU 61": "OE1" <-> "OE2" Residue "As GLU 164": "OE1" <-> "OE2" Residue "As GLU 172": "OE1" <-> "OE2" Residue "As PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "As GLU 214": "OE1" <-> "OE2" Residue "As GLU 238": "OE1" <-> "OE2" Residue "As GLU 252": "OE1" <-> "OE2" Residue "As GLU 255": "OE1" <-> "OE2" Residue "As GLU 257": "OE1" <-> "OE2" Residue "As GLU 303": "OE1" <-> "OE2" Residue "As GLU 308": "OE1" <-> "OE2" Residue "As GLU 338": "OE1" <-> "OE2" Residue "As GLU 355": "OE1" <-> "OE2" Residue "As GLU 367": "OE1" <-> "OE2" Residue "As GLU 388": "OE1" <-> "OE2" Residue "As GLU 434": "OE1" <-> "OE2" Residue "As TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "At GLU 39": "OE1" <-> "OE2" Residue "At GLU 50": "OE1" <-> "OE2" Residue "At GLU 76": "OE1" <-> "OE2" Residue "At GLU 96": "OE1" <-> "OE2" Residue "Ay GLU 102": "OE1" <-> "OE2" Residue "Ay GLU 129": "OE1" <-> "OE2" Residue "Ay GLU 172": "OE1" <-> "OE2" Residue "Ay GLU 191": "OE1" <-> "OE2" Residue "Ay GLU 238": "OE1" <-> "OE2" Residue "Ay GLU 252": "OE1" <-> "OE2" Residue "Ay GLU 255": "OE1" <-> "OE2" Residue "Ay GLU 257": "OE1" <-> "OE2" Residue "Ay GLU 303": "OE1" <-> "OE2" Residue "Ay GLU 310": "OE1" <-> "OE2" Residue "Ay GLU 339": "OE1" <-> "OE2" Residue "Ay ARG 368": "NH1" <-> "NH2" Residue "Ay GLU 460": "OE1" <-> "OE2" Residue "Ay GLU 484": "OE1" <-> "OE2" Residue "Ay TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ay GLU 518": "OE1" <-> "OE2" Residue "Az ARG 36": "NH1" <-> "NH2" Residue "Az GLU 61": "OE1" <-> "OE2" Residue "Az GLU 164": "OE1" <-> "OE2" Residue "Az GLU 172": "OE1" <-> "OE2" Residue "Az PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Az GLU 214": "OE1" <-> "OE2" Residue "Az GLU 238": "OE1" <-> "OE2" Residue "Az GLU 252": "OE1" <-> "OE2" Residue "Az GLU 255": "OE1" <-> "OE2" Residue "Az GLU 257": "OE1" <-> "OE2" Residue "Az GLU 303": "OE1" <-> "OE2" Residue "Az GLU 308": "OE1" <-> "OE2" Residue "Az GLU 338": "OE1" <-> "OE2" Residue "Az GLU 355": "OE1" <-> "OE2" Residue "Az GLU 367": "OE1" <-> "OE2" Residue "Az GLU 388": "OE1" <-> "OE2" Residue "Az GLU 434": "OE1" <-> "OE2" Residue "Az TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ba GLU 39": "OE1" <-> "OE2" Residue "Ba GLU 50": "OE1" <-> "OE2" Residue "Ba GLU 76": "OE1" <-> "OE2" Residue "Ba GLU 96": "OE1" <-> "OE2" Residue "Bf GLU 102": "OE1" <-> "OE2" Residue "Bf GLU 129": "OE1" <-> "OE2" Residue "Bf GLU 172": "OE1" <-> "OE2" Residue "Bf GLU 191": "OE1" <-> "OE2" Residue "Bf GLU 238": "OE1" <-> "OE2" Residue "Bf GLU 252": "OE1" <-> "OE2" Residue "Bf GLU 255": "OE1" <-> "OE2" Residue "Bf GLU 257": "OE1" <-> "OE2" Residue "Bf GLU 303": "OE1" <-> "OE2" Residue "Bf GLU 310": "OE1" <-> "OE2" Residue "Bf GLU 339": "OE1" <-> "OE2" Residue "Bf ARG 368": "NH1" <-> "NH2" Residue "Bf GLU 460": "OE1" <-> "OE2" Residue "Bf GLU 484": "OE1" <-> "OE2" Residue "Bf TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bf GLU 518": "OE1" <-> "OE2" Residue "Bg ARG 36": "NH1" <-> "NH2" Residue "Bg GLU 61": "OE1" <-> "OE2" Residue "Bg GLU 164": "OE1" <-> "OE2" Residue "Bg GLU 172": "OE1" <-> "OE2" Residue "Bg PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bg GLU 214": "OE1" <-> "OE2" Residue "Bg GLU 238": "OE1" <-> "OE2" Residue "Bg GLU 252": "OE1" <-> "OE2" Residue "Bg GLU 255": "OE1" <-> "OE2" Residue "Bg GLU 257": "OE1" <-> "OE2" Residue "Bg GLU 303": "OE1" <-> "OE2" Residue "Bg GLU 308": "OE1" <-> "OE2" Residue "Bg GLU 338": "OE1" <-> "OE2" Residue "Bg GLU 355": "OE1" <-> "OE2" Residue "Bg GLU 367": "OE1" <-> "OE2" Residue "Bg GLU 388": "OE1" <-> "OE2" Residue "Bg GLU 434": "OE1" <-> "OE2" Residue "Bg TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bh GLU 39": "OE1" <-> "OE2" Residue "Bh GLU 50": "OE1" <-> "OE2" Residue "Bh GLU 76": "OE1" <-> "OE2" Residue "Bh GLU 96": "OE1" <-> "OE2" Residue "Bm GLU 102": "OE1" <-> "OE2" Residue "Bm GLU 129": "OE1" <-> "OE2" Residue "Bm GLU 172": "OE1" <-> "OE2" Residue "Bm GLU 191": "OE1" <-> "OE2" Residue "Bm GLU 238": "OE1" <-> "OE2" Residue "Bm GLU 252": "OE1" <-> "OE2" Residue "Bm GLU 255": "OE1" <-> "OE2" Residue "Bm GLU 257": "OE1" <-> "OE2" Residue "Bm GLU 303": "OE1" <-> "OE2" Residue "Bm GLU 310": "OE1" <-> "OE2" Residue "Bm GLU 339": "OE1" <-> "OE2" Residue "Bm ARG 368": "NH1" <-> "NH2" Residue "Bm GLU 460": "OE1" <-> "OE2" Residue "Bm GLU 484": "OE1" <-> "OE2" Residue "Bm TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bm GLU 518": "OE1" <-> "OE2" Residue "Bn ARG 36": "NH1" <-> "NH2" Residue "Bn GLU 61": "OE1" <-> "OE2" Residue "Bn GLU 164": "OE1" <-> "OE2" Residue "Bn GLU 172": "OE1" <-> "OE2" Residue "Bn PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bn GLU 214": "OE1" <-> "OE2" Residue "Bn GLU 238": "OE1" <-> "OE2" Residue "Bn GLU 252": "OE1" <-> "OE2" Residue "Bn GLU 255": "OE1" <-> "OE2" Residue "Bn GLU 257": "OE1" <-> "OE2" Residue "Bn GLU 303": "OE1" <-> "OE2" Residue "Bn GLU 308": "OE1" <-> "OE2" Residue "Bn GLU 338": "OE1" <-> "OE2" Residue "Bn GLU 355": "OE1" <-> "OE2" Residue "Bn GLU 367": "OE1" <-> "OE2" Residue "Bn GLU 388": "OE1" <-> "OE2" Residue "Bn GLU 434": "OE1" <-> "OE2" Residue "Bn TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bo GLU 39": "OE1" <-> "OE2" Residue "Bo GLU 50": "OE1" <-> "OE2" Residue "Bo GLU 76": "OE1" <-> "OE2" Residue "Bo GLU 96": "OE1" <-> "OE2" Residue "Bt GLU 102": "OE1" <-> "OE2" Residue "Bt GLU 129": "OE1" <-> "OE2" Residue "Bt GLU 172": "OE1" <-> "OE2" Residue "Bt GLU 191": "OE1" <-> "OE2" Residue "Bt GLU 238": "OE1" <-> "OE2" Residue "Bt GLU 252": "OE1" <-> "OE2" Residue "Bt GLU 255": "OE1" <-> "OE2" Residue "Bt GLU 257": "OE1" <-> "OE2" Residue "Bt GLU 303": "OE1" <-> "OE2" Residue "Bt GLU 310": "OE1" <-> "OE2" Residue "Bt GLU 339": "OE1" <-> "OE2" Residue "Bt ARG 368": "NH1" <-> "NH2" Residue "Bt GLU 460": "OE1" <-> "OE2" Residue "Bt GLU 484": "OE1" <-> "OE2" Residue "Bt TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bt GLU 518": "OE1" <-> "OE2" Residue "Bu ARG 36": "NH1" <-> "NH2" Residue "Bu GLU 61": "OE1" <-> "OE2" Residue "Bu GLU 164": "OE1" <-> "OE2" Residue "Bu GLU 172": "OE1" <-> "OE2" Residue "Bu PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bu GLU 214": "OE1" <-> "OE2" Residue "Bu GLU 238": "OE1" <-> "OE2" Residue "Bu GLU 252": "OE1" <-> "OE2" Residue "Bu GLU 255": "OE1" <-> "OE2" Residue "Bu GLU 257": "OE1" <-> "OE2" Residue "Bu GLU 303": "OE1" <-> "OE2" Residue "Bu GLU 308": "OE1" <-> "OE2" Residue "Bu GLU 338": "OE1" <-> "OE2" Residue "Bu GLU 355": "OE1" <-> "OE2" Residue "Bu GLU 367": "OE1" <-> "OE2" Residue "Bu GLU 388": "OE1" <-> "OE2" Residue "Bu GLU 434": "OE1" <-> "OE2" Residue "Bu TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bv GLU 39": "OE1" <-> "OE2" Residue "Bv GLU 50": "OE1" <-> "OE2" Residue "Bv GLU 76": "OE1" <-> "OE2" Residue "Bv GLU 96": "OE1" <-> "OE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 59486 Number of models: 1 Model: "" Number of chains: 42 Chain: "Ad" Number of atoms: 3856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3856 Classifications: {'peptide': 524} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "Ae" Number of atoms: 3856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3856 Classifications: {'peptide': 524} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "Af" Number of atoms: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 728 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "Ak" Number of atoms: 3856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3856 Classifications: {'peptide': 524} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "Al" Number of atoms: 3856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3856 Classifications: {'peptide': 524} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "Am" Number of atoms: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 728 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "Ar" Number of atoms: 3856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3856 Classifications: {'peptide': 524} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "As" Number of atoms: 3856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3856 Classifications: {'peptide': 524} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "At" Number of atoms: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 728 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "Ay" Number of atoms: 3856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3856 Classifications: {'peptide': 524} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "Az" Number of atoms: 3856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3856 Classifications: {'peptide': 524} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "Ba" Number of atoms: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 728 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "Bf" Number of atoms: 3856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3856 Classifications: {'peptide': 524} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "Bg" Number of atoms: 3856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3856 Classifications: {'peptide': 524} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "Bh" Number of atoms: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 728 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "Bm" Number of atoms: 3856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3856 Classifications: {'peptide': 524} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "Bn" Number of atoms: 3856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3856 Classifications: {'peptide': 524} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "Bo" Number of atoms: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 728 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "Bt" Number of atoms: 3856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3856 Classifications: {'peptide': 524} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "Bu" Number of atoms: 3856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3856 Classifications: {'peptide': 524} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 509} Chain: "Bv" Number of atoms: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 728 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "Ad" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Ae" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Ak" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Al" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Ar" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "As" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Ay" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Az" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Bf" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Bg" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Bm" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Bn" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Bt" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Bu" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Ad" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "Ak" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "Ar" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "Ay" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "Bf" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "Bm" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "Bt" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 22.75, per 1000 atoms: 0.38 Number of scatterers: 59486 At special positions: 0 Unit cell: (158.301, 158.301, 218.079, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 294 16.00 P 28 15.00 Mg 14 11.99 O 12005 8.00 N 10269 7.00 C 36876 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 18.05 Conformation dependent library (CDL) restraints added in 8.1 seconds 15946 Ramachandran restraints generated. 7973 Oldfield, 0 Emsley, 7973 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14490 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 294 helices and 105 sheets defined 49.7% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.21 Creating SS restraints... Processing helix chain 'Ad' and resid 9 through 30 removed outlier: 3.704A pdb=" N VALAd 29 " --> pdb=" O ASPAd 25 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THRAd 30 " --> pdb=" O ALAAd 26 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 53 through 59 Processing helix chain 'Ad' and resid 65 through 84 Processing helix chain 'Ad' and resid 89 through 109 Processing helix chain 'Ad' and resid 113 through 134 Processing helix chain 'Ad' and resid 141 through 151 Processing helix chain 'Ad' and resid 156 through 168 Processing helix chain 'Ad' and resid 202 through 204 No H-bonds generated for 'chain 'Ad' and resid 202 through 204' Processing helix chain 'Ad' and resid 230 through 243 Proline residue: Ad 235 - end of helix Processing helix chain 'Ad' and resid 259 through 268 removed outlier: 3.880A pdb=" N VALAd 264 " --> pdb=" O ALAAd 260 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N METAd 267 " --> pdb=" O VALAd 263 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 283 through 295 Processing helix chain 'Ad' and resid 339 through 355 removed outlier: 3.712A pdb=" N GLUAd 354 " --> pdb=" O ARGAd 350 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 359 through 364 Processing helix chain 'Ad' and resid 367 through 374 Processing helix chain 'Ad' and resid 386 through 409 Processing helix chain 'Ad' and resid 417 through 425 Processing helix chain 'Ad' and resid 434 through 457 removed outlier: 3.653A pdb=" N GLUAd 448 " --> pdb=" O LEUAd 444 " (cutoff:3.500A) Proline residue: Ad 450 - end of helix Processing helix chain 'Ad' and resid 462 through 471 Processing helix chain 'Ad' and resid 488 through 491 No H-bonds generated for 'chain 'Ad' and resid 488 through 491' Processing helix chain 'Ad' and resid 497 through 516 Processing helix chain 'Ae' and resid 9 through 30 removed outlier: 3.518A pdb=" N VALAe 29 " --> pdb=" O ASPAe 25 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N THRAe 30 " --> pdb=" O ALAAe 26 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 53 through 59 Processing helix chain 'Ae' and resid 65 through 84 removed outlier: 3.596A pdb=" N GLYAe 70 " --> pdb=" O PHEAe 66 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLUAe 76 " --> pdb=" O GLNAe 72 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VALAe 77 " --> pdb=" O METAe 73 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALAAe 78 " --> pdb=" O VALAe 74 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 89 through 108 Processing helix chain 'Ae' and resid 113 through 134 Processing helix chain 'Ae' and resid 141 through 151 Processing helix chain 'Ae' and resid 156 through 169 Processing helix chain 'Ae' and resid 202 through 204 No H-bonds generated for 'chain 'Ae' and resid 202 through 204' Processing helix chain 'Ae' and resid 230 through 243 Proline residue: Ae 235 - end of helix Processing helix chain 'Ae' and resid 256 through 268 Processing helix chain 'Ae' and resid 282 through 296 Processing helix chain 'Ae' and resid 309 through 311 No H-bonds generated for 'chain 'Ae' and resid 309 through 311' Processing helix chain 'Ae' and resid 314 through 316 No H-bonds generated for 'chain 'Ae' and resid 314 through 316' Processing helix chain 'Ae' and resid 339 through 353 Processing helix chain 'Ae' and resid 359 through 372 removed outlier: 3.552A pdb=" N LYSAe 364 " --> pdb=" O TYRAe 360 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 386 through 409 Processing helix chain 'Ae' and resid 417 through 425 Processing helix chain 'Ae' and resid 434 through 458 removed outlier: 4.127A pdb=" N GLUAe 448 " --> pdb=" O LEUAe 444 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALAAe 449 " --> pdb=" O ARGAe 445 " (cutoff:3.500A) Proline residue: Ae 450 - end of helix Processing helix chain 'Ae' and resid 462 through 471 Processing helix chain 'Ae' and resid 488 through 491 No H-bonds generated for 'chain 'Ae' and resid 488 through 491' Processing helix chain 'Ae' and resid 497 through 516 Processing helix chain 'Af' and resid 22 through 24 No H-bonds generated for 'chain 'Af' and resid 22 through 24' Processing helix chain 'Ak' and resid 9 through 30 removed outlier: 3.704A pdb=" N VALAk 29 " --> pdb=" O ASPAk 25 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THRAk 30 " --> pdb=" O ALAAk 26 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 53 through 59 Processing helix chain 'Ak' and resid 65 through 84 Processing helix chain 'Ak' and resid 89 through 109 Processing helix chain 'Ak' and resid 113 through 134 Processing helix chain 'Ak' and resid 141 through 151 Processing helix chain 'Ak' and resid 156 through 168 Processing helix chain 'Ak' and resid 202 through 204 No H-bonds generated for 'chain 'Ak' and resid 202 through 204' Processing helix chain 'Ak' and resid 230 through 243 Proline residue: Ak 235 - end of helix Processing helix chain 'Ak' and resid 259 through 268 removed outlier: 3.880A pdb=" N VALAk 264 " --> pdb=" O ALAAk 260 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N METAk 267 " --> pdb=" O VALAk 263 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 283 through 295 Processing helix chain 'Ak' and resid 339 through 355 removed outlier: 3.712A pdb=" N GLUAk 354 " --> pdb=" O ARGAk 350 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 359 through 364 Processing helix chain 'Ak' and resid 367 through 374 Processing helix chain 'Ak' and resid 386 through 409 Processing helix chain 'Ak' and resid 417 through 425 Processing helix chain 'Ak' and resid 434 through 457 removed outlier: 3.653A pdb=" N GLUAk 448 " --> pdb=" O LEUAk 444 " (cutoff:3.500A) Proline residue: Ak 450 - end of helix Processing helix chain 'Ak' and resid 462 through 471 Processing helix chain 'Ak' and resid 488 through 491 No H-bonds generated for 'chain 'Ak' and resid 488 through 491' Processing helix chain 'Ak' and resid 497 through 516 Processing helix chain 'Al' and resid 9 through 30 removed outlier: 3.518A pdb=" N VALAl 29 " --> pdb=" O ASPAl 25 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N THRAl 30 " --> pdb=" O ALAAl 26 " (cutoff:3.500A) Processing helix chain 'Al' and resid 53 through 59 Processing helix chain 'Al' and resid 65 through 84 removed outlier: 3.596A pdb=" N GLYAl 70 " --> pdb=" O PHEAl 66 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLUAl 76 " --> pdb=" O GLNAl 72 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VALAl 77 " --> pdb=" O METAl 73 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALAAl 78 " --> pdb=" O VALAl 74 " (cutoff:3.500A) Processing helix chain 'Al' and resid 89 through 108 Processing helix chain 'Al' and resid 113 through 134 Processing helix chain 'Al' and resid 141 through 151 Processing helix chain 'Al' and resid 156 through 169 Processing helix chain 'Al' and resid 202 through 204 No H-bonds generated for 'chain 'Al' and resid 202 through 204' Processing helix chain 'Al' and resid 230 through 243 Proline residue: Al 235 - end of helix Processing helix chain 'Al' and resid 256 through 268 Processing helix chain 'Al' and resid 282 through 296 Processing helix chain 'Al' and resid 309 through 311 No H-bonds generated for 'chain 'Al' and resid 309 through 311' Processing helix chain 'Al' and resid 314 through 316 No H-bonds generated for 'chain 'Al' and resid 314 through 316' Processing helix chain 'Al' and resid 339 through 353 Processing helix chain 'Al' and resid 359 through 372 removed outlier: 3.551A pdb=" N LYSAl 364 " --> pdb=" O TYRAl 360 " (cutoff:3.500A) Processing helix chain 'Al' and resid 386 through 409 Processing helix chain 'Al' and resid 417 through 425 Processing helix chain 'Al' and resid 434 through 458 removed outlier: 4.126A pdb=" N GLUAl 448 " --> pdb=" O LEUAl 444 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALAAl 449 " --> pdb=" O ARGAl 445 " (cutoff:3.500A) Proline residue: Al 450 - end of helix Processing helix chain 'Al' and resid 462 through 471 Processing helix chain 'Al' and resid 488 through 491 No H-bonds generated for 'chain 'Al' and resid 488 through 491' Processing helix chain 'Al' and resid 497 through 516 Processing helix chain 'Am' and resid 22 through 24 No H-bonds generated for 'chain 'Am' and resid 22 through 24' Processing helix chain 'Ar' and resid 9 through 30 removed outlier: 3.704A pdb=" N VALAr 29 " --> pdb=" O ASPAr 25 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THRAr 30 " --> pdb=" O ALAAr 26 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 53 through 59 Processing helix chain 'Ar' and resid 65 through 84 Processing helix chain 'Ar' and resid 89 through 109 Processing helix chain 'Ar' and resid 113 through 134 Processing helix chain 'Ar' and resid 141 through 151 Processing helix chain 'Ar' and resid 156 through 168 Processing helix chain 'Ar' and resid 202 through 204 No H-bonds generated for 'chain 'Ar' and resid 202 through 204' Processing helix chain 'Ar' and resid 230 through 243 Proline residue: Ar 235 - end of helix Processing helix chain 'Ar' and resid 259 through 268 removed outlier: 3.880A pdb=" N VALAr 264 " --> pdb=" O ALAAr 260 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N METAr 267 " --> pdb=" O VALAr 263 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 283 through 295 Processing helix chain 'Ar' and resid 339 through 355 removed outlier: 3.713A pdb=" N GLUAr 354 " --> pdb=" O ARGAr 350 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 359 through 364 Processing helix chain 'Ar' and resid 367 through 374 Processing helix chain 'Ar' and resid 386 through 409 Processing helix chain 'Ar' and resid 417 through 425 Processing helix chain 'Ar' and resid 434 through 457 removed outlier: 3.653A pdb=" N GLUAr 448 " --> pdb=" O LEUAr 444 " (cutoff:3.500A) Proline residue: Ar 450 - end of helix Processing helix chain 'Ar' and resid 462 through 471 Processing helix chain 'Ar' and resid 488 through 491 No H-bonds generated for 'chain 'Ar' and resid 488 through 491' Processing helix chain 'Ar' and resid 497 through 516 Processing helix chain 'As' and resid 9 through 30 removed outlier: 3.518A pdb=" N VALAs 29 " --> pdb=" O ASPAs 25 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N THRAs 30 " --> pdb=" O ALAAs 26 " (cutoff:3.500A) Processing helix chain 'As' and resid 53 through 59 Processing helix chain 'As' and resid 65 through 84 removed outlier: 3.596A pdb=" N GLYAs 70 " --> pdb=" O PHEAs 66 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLUAs 76 " --> pdb=" O GLNAs 72 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VALAs 77 " --> pdb=" O METAs 73 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALAAs 78 " --> pdb=" O VALAs 74 " (cutoff:3.500A) Processing helix chain 'As' and resid 89 through 108 Processing helix chain 'As' and resid 113 through 134 Processing helix chain 'As' and resid 141 through 151 Processing helix chain 'As' and resid 156 through 169 Processing helix chain 'As' and resid 202 through 204 No H-bonds generated for 'chain 'As' and resid 202 through 204' Processing helix chain 'As' and resid 230 through 243 Proline residue: As 235 - end of helix Processing helix chain 'As' and resid 256 through 268 Processing helix chain 'As' and resid 282 through 296 Processing helix chain 'As' and resid 309 through 311 No H-bonds generated for 'chain 'As' and resid 309 through 311' Processing helix chain 'As' and resid 314 through 316 No H-bonds generated for 'chain 'As' and resid 314 through 316' Processing helix chain 'As' and resid 339 through 353 Processing helix chain 'As' and resid 359 through 372 removed outlier: 3.552A pdb=" N LYSAs 364 " --> pdb=" O TYRAs 360 " (cutoff:3.500A) Processing helix chain 'As' and resid 386 through 409 Processing helix chain 'As' and resid 417 through 425 Processing helix chain 'As' and resid 434 through 458 removed outlier: 4.127A pdb=" N GLUAs 448 " --> pdb=" O LEUAs 444 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALAAs 449 " --> pdb=" O ARGAs 445 " (cutoff:3.500A) Proline residue: As 450 - end of helix Processing helix chain 'As' and resid 462 through 471 Processing helix chain 'As' and resid 488 through 491 No H-bonds generated for 'chain 'As' and resid 488 through 491' Processing helix chain 'As' and resid 497 through 516 Processing helix chain 'At' and resid 22 through 24 No H-bonds generated for 'chain 'At' and resid 22 through 24' Processing helix chain 'Ay' and resid 9 through 30 removed outlier: 3.704A pdb=" N VALAy 29 " --> pdb=" O ASPAy 25 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THRAy 30 " --> pdb=" O ALAAy 26 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 53 through 59 Processing helix chain 'Ay' and resid 65 through 84 Processing helix chain 'Ay' and resid 89 through 109 Processing helix chain 'Ay' and resid 113 through 134 Processing helix chain 'Ay' and resid 141 through 151 Processing helix chain 'Ay' and resid 156 through 168 Processing helix chain 'Ay' and resid 202 through 204 No H-bonds generated for 'chain 'Ay' and resid 202 through 204' Processing helix chain 'Ay' and resid 230 through 243 Proline residue: Ay 235 - end of helix Processing helix chain 'Ay' and resid 259 through 268 removed outlier: 3.880A pdb=" N VALAy 264 " --> pdb=" O ALAAy 260 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N METAy 267 " --> pdb=" O VALAy 263 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 283 through 295 Processing helix chain 'Ay' and resid 339 through 355 removed outlier: 3.713A pdb=" N GLUAy 354 " --> pdb=" O ARGAy 350 " (cutoff:3.500A) Processing helix chain 'Ay' and resid 359 through 364 Processing helix chain 'Ay' and resid 367 through 374 Processing helix chain 'Ay' and resid 386 through 409 Processing helix chain 'Ay' and resid 417 through 425 Processing helix chain 'Ay' and resid 434 through 457 removed outlier: 3.654A pdb=" N GLUAy 448 " --> pdb=" O LEUAy 444 " (cutoff:3.500A) Proline residue: Ay 450 - end of helix Processing helix chain 'Ay' and resid 462 through 471 Processing helix chain 'Ay' and resid 488 through 491 No H-bonds generated for 'chain 'Ay' and resid 488 through 491' Processing helix chain 'Ay' and resid 497 through 516 Processing helix chain 'Az' and resid 9 through 30 removed outlier: 3.518A pdb=" N VALAz 29 " --> pdb=" O ASPAz 25 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N THRAz 30 " --> pdb=" O ALAAz 26 " (cutoff:3.500A) Processing helix chain 'Az' and resid 53 through 59 Processing helix chain 'Az' and resid 65 through 84 removed outlier: 3.597A pdb=" N GLYAz 70 " --> pdb=" O PHEAz 66 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLUAz 76 " --> pdb=" O GLNAz 72 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VALAz 77 " --> pdb=" O METAz 73 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALAAz 78 " --> pdb=" O VALAz 74 " (cutoff:3.500A) Processing helix chain 'Az' and resid 89 through 108 Processing helix chain 'Az' and resid 113 through 134 Processing helix chain 'Az' and resid 141 through 151 Processing helix chain 'Az' and resid 156 through 169 Processing helix chain 'Az' and resid 202 through 204 No H-bonds generated for 'chain 'Az' and resid 202 through 204' Processing helix chain 'Az' and resid 230 through 243 Proline residue: Az 235 - end of helix Processing helix chain 'Az' and resid 256 through 268 Processing helix chain 'Az' and resid 282 through 296 Processing helix chain 'Az' and resid 309 through 311 No H-bonds generated for 'chain 'Az' and resid 309 through 311' Processing helix chain 'Az' and resid 314 through 316 No H-bonds generated for 'chain 'Az' and resid 314 through 316' Processing helix chain 'Az' and resid 339 through 353 Processing helix chain 'Az' and resid 359 through 372 removed outlier: 3.552A pdb=" N LYSAz 364 " --> pdb=" O TYRAz 360 " (cutoff:3.500A) Processing helix chain 'Az' and resid 386 through 409 Processing helix chain 'Az' and resid 417 through 425 Processing helix chain 'Az' and resid 434 through 458 removed outlier: 4.127A pdb=" N GLUAz 448 " --> pdb=" O LEUAz 444 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALAAz 449 " --> pdb=" O ARGAz 445 " (cutoff:3.500A) Proline residue: Az 450 - end of helix Processing helix chain 'Az' and resid 462 through 471 Processing helix chain 'Az' and resid 488 through 491 No H-bonds generated for 'chain 'Az' and resid 488 through 491' Processing helix chain 'Az' and resid 497 through 516 Processing helix chain 'Ba' and resid 22 through 24 No H-bonds generated for 'chain 'Ba' and resid 22 through 24' Processing helix chain 'Bf' and resid 9 through 30 removed outlier: 3.703A pdb=" N VALBf 29 " --> pdb=" O ASPBf 25 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THRBf 30 " --> pdb=" O ALABf 26 " (cutoff:3.500A) Processing helix chain 'Bf' and resid 53 through 59 Processing helix chain 'Bf' and resid 65 through 84 Processing helix chain 'Bf' and resid 89 through 109 Processing helix chain 'Bf' and resid 113 through 134 Processing helix chain 'Bf' and resid 141 through 151 Processing helix chain 'Bf' and resid 156 through 168 Processing helix chain 'Bf' and resid 202 through 204 No H-bonds generated for 'chain 'Bf' and resid 202 through 204' Processing helix chain 'Bf' and resid 230 through 243 Proline residue: Bf 235 - end of helix Processing helix chain 'Bf' and resid 259 through 268 removed outlier: 3.879A pdb=" N VALBf 264 " --> pdb=" O ALABf 260 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N METBf 267 " --> pdb=" O VALBf 263 " (cutoff:3.500A) Processing helix chain 'Bf' and resid 283 through 295 Processing helix chain 'Bf' and resid 339 through 355 removed outlier: 3.712A pdb=" N GLUBf 354 " --> pdb=" O ARGBf 350 " (cutoff:3.500A) Processing helix chain 'Bf' and resid 359 through 364 Processing helix chain 'Bf' and resid 367 through 374 Processing helix chain 'Bf' and resid 386 through 409 Processing helix chain 'Bf' and resid 417 through 425 Processing helix chain 'Bf' and resid 434 through 457 removed outlier: 3.654A pdb=" N GLUBf 448 " --> pdb=" O LEUBf 444 " (cutoff:3.500A) Proline residue: Bf 450 - end of helix Processing helix chain 'Bf' and resid 462 through 471 Processing helix chain 'Bf' and resid 488 through 491 No H-bonds generated for 'chain 'Bf' and resid 488 through 491' Processing helix chain 'Bf' and resid 497 through 516 Processing helix chain 'Bg' and resid 9 through 30 removed outlier: 3.518A pdb=" N VALBg 29 " --> pdb=" O ASPBg 25 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N THRBg 30 " --> pdb=" O ALABg 26 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 53 through 59 Processing helix chain 'Bg' and resid 65 through 84 removed outlier: 3.596A pdb=" N GLYBg 70 " --> pdb=" O PHEBg 66 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLUBg 76 " --> pdb=" O GLNBg 72 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VALBg 77 " --> pdb=" O METBg 73 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALABg 78 " --> pdb=" O VALBg 74 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 89 through 108 Processing helix chain 'Bg' and resid 113 through 134 Processing helix chain 'Bg' and resid 141 through 151 Processing helix chain 'Bg' and resid 156 through 169 Processing helix chain 'Bg' and resid 202 through 204 No H-bonds generated for 'chain 'Bg' and resid 202 through 204' Processing helix chain 'Bg' and resid 230 through 243 Proline residue: Bg 235 - end of helix Processing helix chain 'Bg' and resid 256 through 268 Processing helix chain 'Bg' and resid 282 through 296 Processing helix chain 'Bg' and resid 309 through 311 No H-bonds generated for 'chain 'Bg' and resid 309 through 311' Processing helix chain 'Bg' and resid 314 through 316 No H-bonds generated for 'chain 'Bg' and resid 314 through 316' Processing helix chain 'Bg' and resid 339 through 353 Processing helix chain 'Bg' and resid 359 through 372 removed outlier: 3.552A pdb=" N LYSBg 364 " --> pdb=" O TYRBg 360 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 386 through 409 Processing helix chain 'Bg' and resid 417 through 425 Processing helix chain 'Bg' and resid 434 through 458 removed outlier: 4.126A pdb=" N GLUBg 448 " --> pdb=" O LEUBg 444 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALABg 449 " --> pdb=" O ARGBg 445 " (cutoff:3.500A) Proline residue: Bg 450 - end of helix Processing helix chain 'Bg' and resid 462 through 471 Processing helix chain 'Bg' and resid 488 through 491 No H-bonds generated for 'chain 'Bg' and resid 488 through 491' Processing helix chain 'Bg' and resid 497 through 516 Processing helix chain 'Bh' and resid 22 through 24 No H-bonds generated for 'chain 'Bh' and resid 22 through 24' Processing helix chain 'Bm' and resid 9 through 30 removed outlier: 3.705A pdb=" N VALBm 29 " --> pdb=" O ASPBm 25 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THRBm 30 " --> pdb=" O ALABm 26 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 53 through 59 Processing helix chain 'Bm' and resid 65 through 84 Processing helix chain 'Bm' and resid 89 through 109 Processing helix chain 'Bm' and resid 113 through 134 Processing helix chain 'Bm' and resid 141 through 151 Processing helix chain 'Bm' and resid 156 through 168 Processing helix chain 'Bm' and resid 202 through 204 No H-bonds generated for 'chain 'Bm' and resid 202 through 204' Processing helix chain 'Bm' and resid 230 through 243 Proline residue: Bm 235 - end of helix Processing helix chain 'Bm' and resid 259 through 268 removed outlier: 3.880A pdb=" N VALBm 264 " --> pdb=" O ALABm 260 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N METBm 267 " --> pdb=" O VALBm 263 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 283 through 295 Processing helix chain 'Bm' and resid 339 through 355 removed outlier: 3.712A pdb=" N GLUBm 354 " --> pdb=" O ARGBm 350 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 359 through 364 Processing helix chain 'Bm' and resid 367 through 374 Processing helix chain 'Bm' and resid 386 through 409 Processing helix chain 'Bm' and resid 417 through 425 Processing helix chain 'Bm' and resid 434 through 457 removed outlier: 3.653A pdb=" N GLUBm 448 " --> pdb=" O LEUBm 444 " (cutoff:3.500A) Proline residue: Bm 450 - end of helix Processing helix chain 'Bm' and resid 462 through 471 Processing helix chain 'Bm' and resid 488 through 491 No H-bonds generated for 'chain 'Bm' and resid 488 through 491' Processing helix chain 'Bm' and resid 497 through 516 Processing helix chain 'Bn' and resid 9 through 30 removed outlier: 3.518A pdb=" N VALBn 29 " --> pdb=" O ASPBn 25 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N THRBn 30 " --> pdb=" O ALABn 26 " (cutoff:3.500A) Processing helix chain 'Bn' and resid 53 through 59 Processing helix chain 'Bn' and resid 65 through 84 removed outlier: 3.596A pdb=" N GLYBn 70 " --> pdb=" O PHEBn 66 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLUBn 76 " --> pdb=" O GLNBn 72 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VALBn 77 " --> pdb=" O METBn 73 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALABn 78 " --> pdb=" O VALBn 74 " (cutoff:3.500A) Processing helix chain 'Bn' and resid 89 through 108 Processing helix chain 'Bn' and resid 113 through 134 Processing helix chain 'Bn' and resid 141 through 151 Processing helix chain 'Bn' and resid 156 through 169 Processing helix chain 'Bn' and resid 202 through 204 No H-bonds generated for 'chain 'Bn' and resid 202 through 204' Processing helix chain 'Bn' and resid 230 through 243 Proline residue: Bn 235 - end of helix Processing helix chain 'Bn' and resid 256 through 268 Processing helix chain 'Bn' and resid 282 through 296 Processing helix chain 'Bn' and resid 309 through 311 No H-bonds generated for 'chain 'Bn' and resid 309 through 311' Processing helix chain 'Bn' and resid 314 through 316 No H-bonds generated for 'chain 'Bn' and resid 314 through 316' Processing helix chain 'Bn' and resid 339 through 353 Processing helix chain 'Bn' and resid 359 through 372 removed outlier: 3.552A pdb=" N LYSBn 364 " --> pdb=" O TYRBn 360 " (cutoff:3.500A) Processing helix chain 'Bn' and resid 386 through 409 Processing helix chain 'Bn' and resid 417 through 425 Processing helix chain 'Bn' and resid 434 through 458 removed outlier: 4.126A pdb=" N GLUBn 448 " --> pdb=" O LEUBn 444 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALABn 449 " --> pdb=" O ARGBn 445 " (cutoff:3.500A) Proline residue: Bn 450 - end of helix Processing helix chain 'Bn' and resid 462 through 471 Processing helix chain 'Bn' and resid 488 through 491 No H-bonds generated for 'chain 'Bn' and resid 488 through 491' Processing helix chain 'Bn' and resid 497 through 516 Processing helix chain 'Bo' and resid 22 through 24 No H-bonds generated for 'chain 'Bo' and resid 22 through 24' Processing helix chain 'Bt' and resid 9 through 30 removed outlier: 3.705A pdb=" N VALBt 29 " --> pdb=" O ASPBt 25 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THRBt 30 " --> pdb=" O ALABt 26 " (cutoff:3.500A) Processing helix chain 'Bt' and resid 53 through 59 Processing helix chain 'Bt' and resid 65 through 84 Processing helix chain 'Bt' and resid 89 through 109 Processing helix chain 'Bt' and resid 113 through 134 Processing helix chain 'Bt' and resid 141 through 151 Processing helix chain 'Bt' and resid 156 through 168 Processing helix chain 'Bt' and resid 202 through 204 No H-bonds generated for 'chain 'Bt' and resid 202 through 204' Processing helix chain 'Bt' and resid 230 through 243 Proline residue: Bt 235 - end of helix Processing helix chain 'Bt' and resid 259 through 268 removed outlier: 3.880A pdb=" N VALBt 264 " --> pdb=" O ALABt 260 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N METBt 267 " --> pdb=" O VALBt 263 " (cutoff:3.500A) Processing helix chain 'Bt' and resid 283 through 295 Processing helix chain 'Bt' and resid 339 through 355 removed outlier: 3.712A pdb=" N GLUBt 354 " --> pdb=" O ARGBt 350 " (cutoff:3.500A) Processing helix chain 'Bt' and resid 359 through 364 Processing helix chain 'Bt' and resid 367 through 374 Processing helix chain 'Bt' and resid 386 through 409 Processing helix chain 'Bt' and resid 417 through 425 Processing helix chain 'Bt' and resid 434 through 457 removed outlier: 3.654A pdb=" N GLUBt 448 " --> pdb=" O LEUBt 444 " (cutoff:3.500A) Proline residue: Bt 450 - end of helix Processing helix chain 'Bt' and resid 462 through 471 Processing helix chain 'Bt' and resid 488 through 491 No H-bonds generated for 'chain 'Bt' and resid 488 through 491' Processing helix chain 'Bt' and resid 497 through 516 Processing helix chain 'Bu' and resid 9 through 30 removed outlier: 3.518A pdb=" N VALBu 29 " --> pdb=" O ASPBu 25 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N THRBu 30 " --> pdb=" O ALABu 26 " (cutoff:3.500A) Processing helix chain 'Bu' and resid 53 through 59 Processing helix chain 'Bu' and resid 65 through 84 removed outlier: 3.596A pdb=" N GLYBu 70 " --> pdb=" O PHEBu 66 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLUBu 76 " --> pdb=" O GLNBu 72 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VALBu 77 " --> pdb=" O METBu 73 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALABu 78 " --> pdb=" O VALBu 74 " (cutoff:3.500A) Processing helix chain 'Bu' and resid 89 through 108 Processing helix chain 'Bu' and resid 113 through 134 Processing helix chain 'Bu' and resid 141 through 151 Processing helix chain 'Bu' and resid 156 through 169 Processing helix chain 'Bu' and resid 202 through 204 No H-bonds generated for 'chain 'Bu' and resid 202 through 204' Processing helix chain 'Bu' and resid 230 through 243 Proline residue: Bu 235 - end of helix Processing helix chain 'Bu' and resid 256 through 268 Processing helix chain 'Bu' and resid 282 through 296 Processing helix chain 'Bu' and resid 309 through 311 No H-bonds generated for 'chain 'Bu' and resid 309 through 311' Processing helix chain 'Bu' and resid 314 through 316 No H-bonds generated for 'chain 'Bu' and resid 314 through 316' Processing helix chain 'Bu' and resid 339 through 353 Processing helix chain 'Bu' and resid 359 through 372 removed outlier: 3.552A pdb=" N LYSBu 364 " --> pdb=" O TYRBu 360 " (cutoff:3.500A) Processing helix chain 'Bu' and resid 386 through 409 Processing helix chain 'Bu' and resid 417 through 425 Processing helix chain 'Bu' and resid 434 through 458 removed outlier: 4.126A pdb=" N GLUBu 448 " --> pdb=" O LEUBu 444 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALABu 449 " --> pdb=" O ARGBu 445 " (cutoff:3.500A) Proline residue: Bu 450 - end of helix Processing helix chain 'Bu' and resid 462 through 471 Processing helix chain 'Bu' and resid 488 through 491 No H-bonds generated for 'chain 'Bu' and resid 488 through 491' Processing helix chain 'Bu' and resid 497 through 516 Processing helix chain 'Bv' and resid 22 through 24 No H-bonds generated for 'chain 'Bv' and resid 22 through 24' Processing sheet with id= A, first strand: chain 'Ad' and resid 4 through 8 Processing sheet with id= B, first strand: chain 'Ad' and resid 38 through 40 Processing sheet with id= C, first strand: chain 'Ad' and resid 175 through 180 removed outlier: 6.764A pdb=" N ALAAd 377 " --> pdb=" O THRAd 176 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N GLUAd 178 " --> pdb=" O ALAAd 377 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ILEAd 379 " --> pdb=" O GLUAd 178 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N GLYAd 180 " --> pdb=" O ILEAd 379 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N VALAd 381 " --> pdb=" O GLYAd 180 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'Ad' and resid 213 through 216 Processing sheet with id= E, first strand: chain 'Ad' and resid 219 through 222 removed outlier: 6.924A pdb=" N ALAAd 274 " --> pdb=" O ILEAd 249 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ALAAd 251 " --> pdb=" O ALAAd 274 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N VALAd 276 " --> pdb=" O ALAAd 251 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'Ad' and resid 411 through 413 Processing sheet with id= G, first strand: chain 'Ad' and resid 476 through 479 Processing sheet with id= H, first strand: chain 'Ae' and resid 4 through 8 Processing sheet with id= I, first strand: chain 'Ae' and resid 38 through 40 Processing sheet with id= J, first strand: chain 'Ae' and resid 174 through 179 Processing sheet with id= K, first strand: chain 'Ae' and resid 193 through 195 Processing sheet with id= L, first strand: chain 'Ae' and resid 219 through 222 removed outlier: 3.761A pdb=" N ALAAe 251 " --> pdb=" O VALAe 276 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'Ae' and resid 411 through 413 Processing sheet with id= N, first strand: chain 'Ae' and resid 476 through 479 Processing sheet with id= O, first strand: chain 'Af' and resid 74 through 78 removed outlier: 8.720A pdb=" N GLUAf 82 " --> pdb=" O ARGAf 14 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ARGAf 14 " --> pdb=" O GLUAf 82 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N LYSAf 13 " --> pdb=" O VALAf 40 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N VALAf 40 " --> pdb=" O LYSAf 13 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'Ak' and resid 4 through 8 Processing sheet with id= Q, first strand: chain 'Ak' and resid 38 through 40 Processing sheet with id= R, first strand: chain 'Ak' and resid 175 through 180 removed outlier: 6.763A pdb=" N ALAAk 377 " --> pdb=" O THRAk 176 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N GLUAk 178 " --> pdb=" O ALAAk 377 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ILEAk 379 " --> pdb=" O GLUAk 178 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N GLYAk 180 " --> pdb=" O ILEAk 379 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N VALAk 381 " --> pdb=" O GLYAk 180 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'Ak' and resid 213 through 216 Processing sheet with id= T, first strand: chain 'Ak' and resid 219 through 222 removed outlier: 6.925A pdb=" N ALAAk 274 " --> pdb=" O ILEAk 249 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ALAAk 251 " --> pdb=" O ALAAk 274 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N VALAk 276 " --> pdb=" O ALAAk 251 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'Ak' and resid 411 through 413 Processing sheet with id= V, first strand: chain 'Ak' and resid 476 through 479 Processing sheet with id= W, first strand: chain 'Al' and resid 4 through 8 Processing sheet with id= X, first strand: chain 'Al' and resid 38 through 40 Processing sheet with id= Y, first strand: chain 'Al' and resid 174 through 179 Processing sheet with id= Z, first strand: chain 'Al' and resid 193 through 195 Processing sheet with id= AA, first strand: chain 'Al' and resid 219 through 222 removed outlier: 3.761A pdb=" N ALAAl 251 " --> pdb=" O VALAl 276 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'Al' and resid 411 through 413 Processing sheet with id= AC, first strand: chain 'Al' and resid 476 through 479 Processing sheet with id= AD, first strand: chain 'Am' and resid 74 through 78 removed outlier: 8.720A pdb=" N GLUAm 82 " --> pdb=" O ARGAm 14 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ARGAm 14 " --> pdb=" O GLUAm 82 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N LYSAm 13 " --> pdb=" O VALAm 40 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N VALAm 40 " --> pdb=" O LYSAm 13 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'Ar' and resid 4 through 8 Processing sheet with id= AF, first strand: chain 'Ar' and resid 38 through 40 Processing sheet with id= AG, first strand: chain 'Ar' and resid 175 through 180 removed outlier: 6.765A pdb=" N ALAAr 377 " --> pdb=" O THRAr 176 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N GLUAr 178 " --> pdb=" O ALAAr 377 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ILEAr 379 " --> pdb=" O GLUAr 178 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N GLYAr 180 " --> pdb=" O ILEAr 379 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N VALAr 381 " --> pdb=" O GLYAr 180 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'Ar' and resid 213 through 216 Processing sheet with id= AI, first strand: chain 'Ar' and resid 219 through 222 removed outlier: 6.925A pdb=" N ALAAr 274 " --> pdb=" O ILEAr 249 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ALAAr 251 " --> pdb=" O ALAAr 274 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N VALAr 276 " --> pdb=" O ALAAr 251 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'Ar' and resid 411 through 413 Processing sheet with id= AK, first strand: chain 'Ar' and resid 476 through 479 Processing sheet with id= AL, first strand: chain 'As' and resid 4 through 8 Processing sheet with id= AM, first strand: chain 'As' and resid 38 through 40 Processing sheet with id= AN, first strand: chain 'As' and resid 174 through 179 Processing sheet with id= AO, first strand: chain 'As' and resid 193 through 195 Processing sheet with id= AP, first strand: chain 'As' and resid 219 through 222 removed outlier: 3.761A pdb=" N ALAAs 251 " --> pdb=" O VALAs 276 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'As' and resid 411 through 413 Processing sheet with id= AR, first strand: chain 'As' and resid 476 through 479 Processing sheet with id= AS, first strand: chain 'At' and resid 74 through 78 removed outlier: 8.720A pdb=" N GLUAt 82 " --> pdb=" O ARGAt 14 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ARGAt 14 " --> pdb=" O GLUAt 82 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N LYSAt 13 " --> pdb=" O VALAt 40 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N VALAt 40 " --> pdb=" O LYSAt 13 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'Ay' and resid 4 through 8 Processing sheet with id= AU, first strand: chain 'Ay' and resid 38 through 40 Processing sheet with id= AV, first strand: chain 'Ay' and resid 175 through 180 removed outlier: 6.764A pdb=" N ALAAy 377 " --> pdb=" O THRAy 176 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N GLUAy 178 " --> pdb=" O ALAAy 377 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ILEAy 379 " --> pdb=" O GLUAy 178 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N GLYAy 180 " --> pdb=" O ILEAy 379 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N VALAy 381 " --> pdb=" O GLYAy 180 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'Ay' and resid 213 through 216 Processing sheet with id= AX, first strand: chain 'Ay' and resid 219 through 222 removed outlier: 6.924A pdb=" N ALAAy 274 " --> pdb=" O ILEAy 249 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ALAAy 251 " --> pdb=" O ALAAy 274 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N VALAy 276 " --> pdb=" O ALAAy 251 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'Ay' and resid 411 through 413 Processing sheet with id= AZ, first strand: chain 'Ay' and resid 476 through 479 Processing sheet with id= BA, first strand: chain 'Az' and resid 4 through 8 Processing sheet with id= BB, first strand: chain 'Az' and resid 38 through 40 Processing sheet with id= BC, first strand: chain 'Az' and resid 174 through 179 Processing sheet with id= BD, first strand: chain 'Az' and resid 193 through 195 Processing sheet with id= BE, first strand: chain 'Az' and resid 219 through 222 removed outlier: 3.761A pdb=" N ALAAz 251 " --> pdb=" O VALAz 276 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'Az' and resid 411 through 413 Processing sheet with id= BG, first strand: chain 'Az' and resid 476 through 479 Processing sheet with id= BH, first strand: chain 'Ba' and resid 74 through 78 removed outlier: 8.720A pdb=" N GLUBa 82 " --> pdb=" O ARGBa 14 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N ARGBa 14 " --> pdb=" O GLUBa 82 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N LYSBa 13 " --> pdb=" O VALBa 40 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N VALBa 40 " --> pdb=" O LYSBa 13 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'Bf' and resid 4 through 8 Processing sheet with id= BJ, first strand: chain 'Bf' and resid 38 through 40 Processing sheet with id= BK, first strand: chain 'Bf' and resid 175 through 180 removed outlier: 6.765A pdb=" N ALABf 377 " --> pdb=" O THRBf 176 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N GLUBf 178 " --> pdb=" O ALABf 377 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ILEBf 379 " --> pdb=" O GLUBf 178 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N GLYBf 180 " --> pdb=" O ILEBf 379 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N VALBf 381 " --> pdb=" O GLYBf 180 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'Bf' and resid 213 through 216 Processing sheet with id= BM, first strand: chain 'Bf' and resid 219 through 222 removed outlier: 6.924A pdb=" N ALABf 274 " --> pdb=" O ILEBf 249 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ALABf 251 " --> pdb=" O ALABf 274 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N VALBf 276 " --> pdb=" O ALABf 251 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'Bf' and resid 411 through 413 Processing sheet with id= BO, first strand: chain 'Bf' and resid 476 through 479 Processing sheet with id= BP, first strand: chain 'Bg' and resid 4 through 8 Processing sheet with id= BQ, first strand: chain 'Bg' and resid 38 through 40 Processing sheet with id= BR, first strand: chain 'Bg' and resid 174 through 179 Processing sheet with id= BS, first strand: chain 'Bg' and resid 193 through 195 Processing sheet with id= BT, first strand: chain 'Bg' and resid 219 through 222 removed outlier: 3.760A pdb=" N ALABg 251 " --> pdb=" O VALBg 276 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'Bg' and resid 411 through 413 Processing sheet with id= BV, first strand: chain 'Bg' and resid 476 through 479 Processing sheet with id= BW, first strand: chain 'Bh' and resid 74 through 78 removed outlier: 8.720A pdb=" N GLUBh 82 " --> pdb=" O ARGBh 14 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ARGBh 14 " --> pdb=" O GLUBh 82 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N LYSBh 13 " --> pdb=" O VALBh 40 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N VALBh 40 " --> pdb=" O LYSBh 13 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'Bm' and resid 4 through 8 Processing sheet with id= BY, first strand: chain 'Bm' and resid 38 through 40 Processing sheet with id= BZ, first strand: chain 'Bm' and resid 175 through 180 removed outlier: 6.765A pdb=" N ALABm 377 " --> pdb=" O THRBm 176 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N GLUBm 178 " --> pdb=" O ALABm 377 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ILEBm 379 " --> pdb=" O GLUBm 178 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N GLYBm 180 " --> pdb=" O ILEBm 379 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N VALBm 381 " --> pdb=" O GLYBm 180 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'Bm' and resid 213 through 216 Processing sheet with id= CB, first strand: chain 'Bm' and resid 219 through 222 removed outlier: 6.923A pdb=" N ALABm 274 " --> pdb=" O ILEBm 249 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ALABm 251 " --> pdb=" O ALABm 274 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N VALBm 276 " --> pdb=" O ALABm 251 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'Bm' and resid 411 through 413 Processing sheet with id= CD, first strand: chain 'Bm' and resid 476 through 479 Processing sheet with id= CE, first strand: chain 'Bn' and resid 4 through 8 Processing sheet with id= CF, first strand: chain 'Bn' and resid 38 through 40 Processing sheet with id= CG, first strand: chain 'Bn' and resid 174 through 179 Processing sheet with id= CH, first strand: chain 'Bn' and resid 193 through 195 Processing sheet with id= CI, first strand: chain 'Bn' and resid 219 through 222 removed outlier: 3.760A pdb=" N ALABn 251 " --> pdb=" O VALBn 276 " (cutoff:3.500A) Processing sheet with id= CJ, first strand: chain 'Bn' and resid 411 through 413 Processing sheet with id= CK, first strand: chain 'Bn' and resid 476 through 479 Processing sheet with id= CL, first strand: chain 'Bo' and resid 74 through 78 removed outlier: 8.720A pdb=" N GLUBo 82 " --> pdb=" O ARGBo 14 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ARGBo 14 " --> pdb=" O GLUBo 82 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N LYSBo 13 " --> pdb=" O VALBo 40 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N VALBo 40 " --> pdb=" O LYSBo 13 " (cutoff:3.500A) Processing sheet with id= CM, first strand: chain 'Bt' and resid 4 through 8 Processing sheet with id= CN, first strand: chain 'Bt' and resid 38 through 40 Processing sheet with id= CO, first strand: chain 'Bt' and resid 175 through 180 removed outlier: 6.764A pdb=" N ALABt 377 " --> pdb=" O THRBt 176 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N GLUBt 178 " --> pdb=" O ALABt 377 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ILEBt 379 " --> pdb=" O GLUBt 178 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N GLYBt 180 " --> pdb=" O ILEBt 379 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N VALBt 381 " --> pdb=" O GLYBt 180 " (cutoff:3.500A) Processing sheet with id= CP, first strand: chain 'Bt' and resid 213 through 216 Processing sheet with id= CQ, first strand: chain 'Bt' and resid 219 through 222 removed outlier: 6.924A pdb=" N ALABt 274 " --> pdb=" O ILEBt 249 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ALABt 251 " --> pdb=" O ALABt 274 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N VALBt 276 " --> pdb=" O ALABt 251 " (cutoff:3.500A) Processing sheet with id= CR, first strand: chain 'Bt' and resid 411 through 413 Processing sheet with id= CS, first strand: chain 'Bt' and resid 476 through 479 Processing sheet with id= CT, first strand: chain 'Bu' and resid 4 through 8 Processing sheet with id= CU, first strand: chain 'Bu' and resid 38 through 40 Processing sheet with id= CV, first strand: chain 'Bu' and resid 174 through 179 Processing sheet with id= CW, first strand: chain 'Bu' and resid 193 through 195 Processing sheet with id= CX, first strand: chain 'Bu' and resid 219 through 222 removed outlier: 3.761A pdb=" N ALABu 251 " --> pdb=" O VALBu 276 " (cutoff:3.500A) Processing sheet with id= CY, first strand: chain 'Bu' and resid 411 through 413 Processing sheet with id= CZ, first strand: chain 'Bu' and resid 476 through 479 Processing sheet with id= DA, first strand: chain 'Bv' and resid 74 through 78 removed outlier: 8.720A pdb=" N GLUBv 82 " --> pdb=" O ARGBv 14 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ARGBv 14 " --> pdb=" O GLUBv 82 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N LYSBv 13 " --> pdb=" O VALBv 40 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N VALBv 40 " --> pdb=" O LYSBv 13 " (cutoff:3.500A) 3276 hydrogen bonds defined for protein. 9471 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: 22.85 Time building geometry restraints manager: 19.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.39: 21770 1.39 - 1.60: 37534 1.60 - 1.80: 311 1.80 - 2.01: 284 2.01 - 2.22: 7 Bond restraints: 59906 Sorted by residual: bond pdb=" C PROAy 525 " pdb=" O PROAy 525 " ideal model delta sigma weight residual 1.231 2.215 -0.984 2.00e-02 2.50e+03 2.42e+03 bond pdb=" C PROBt 525 " pdb=" O PROBt 525 " ideal model delta sigma weight residual 1.231 2.215 -0.984 2.00e-02 2.50e+03 2.42e+03 bond pdb=" C PROAd 525 " pdb=" O PROAd 525 " ideal model delta sigma weight residual 1.231 2.215 -0.984 2.00e-02 2.50e+03 2.42e+03 bond pdb=" C PROBm 525 " pdb=" O PROBm 525 " ideal model delta sigma weight residual 1.231 2.215 -0.984 2.00e-02 2.50e+03 2.42e+03 bond pdb=" C PROAk 525 " pdb=" O PROAk 525 " ideal model delta sigma weight residual 1.231 2.215 -0.984 2.00e-02 2.50e+03 2.42e+03 ... (remaining 59901 not shown) Histogram of bond angle deviations from ideal: 50.29 - 72.36: 7 72.36 - 94.44: 7 94.44 - 116.52: 39977 116.52 - 138.59: 40957 138.59 - 160.67: 7 Bond angle restraints: 80955 Sorted by residual: angle pdb=" O PROAk 525 " pdb=" C PROAk 525 " pdb=" OXT PROAk 525 " ideal model delta sigma weight residual 118.00 50.29 67.71 3.00e+00 1.11e-01 5.09e+02 angle pdb=" O PROAy 525 " pdb=" C PROAy 525 " pdb=" OXT PROAy 525 " ideal model delta sigma weight residual 118.00 50.31 67.69 3.00e+00 1.11e-01 5.09e+02 angle pdb=" O PROAd 525 " pdb=" C PROAd 525 " pdb=" OXT PROAd 525 " ideal model delta sigma weight residual 118.00 50.32 67.68 3.00e+00 1.11e-01 5.09e+02 angle pdb=" O PROBm 525 " pdb=" C PROBm 525 " pdb=" OXT PROBm 525 " ideal model delta sigma weight residual 118.00 50.34 67.66 3.00e+00 1.11e-01 5.09e+02 angle pdb=" O PROAr 525 " pdb=" C PROAr 525 " pdb=" OXT PROAr 525 " ideal model delta sigma weight residual 118.00 50.34 67.66 3.00e+00 1.11e-01 5.09e+02 ... (remaining 80950 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.92: 34874 32.92 - 65.84: 1967 65.84 - 98.76: 259 98.76 - 131.68: 14 131.68 - 164.60: 7 Dihedral angle restraints: 37121 sinusoidal: 14532 harmonic: 22589 Sorted by residual: dihedral pdb=" C VALBo 95 " pdb=" N VALBo 95 " pdb=" CA VALBo 95 " pdb=" CB VALBo 95 " ideal model delta harmonic sigma weight residual -122.00 -140.06 18.06 0 2.50e+00 1.60e-01 5.22e+01 dihedral pdb=" C VALBa 95 " pdb=" N VALBa 95 " pdb=" CA VALBa 95 " pdb=" CB VALBa 95 " ideal model delta harmonic sigma weight residual -122.00 -140.03 18.03 0 2.50e+00 1.60e-01 5.20e+01 dihedral pdb=" C VALAf 95 " pdb=" N VALAf 95 " pdb=" CA VALAf 95 " pdb=" CB VALAf 95 " ideal model delta harmonic sigma weight residual -122.00 -139.97 17.97 0 2.50e+00 1.60e-01 5.17e+01 ... (remaining 37118 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 7286 0.140 - 0.281: 2243 0.281 - 0.421: 257 0.421 - 0.561: 28 0.561 - 0.701: 14 Chirality restraints: 9828 Sorted by residual: chirality pdb=" CA VALBo 95 " pdb=" N VALBo 95 " pdb=" C VALBo 95 " pdb=" CB VALBo 95 " both_signs ideal model delta sigma weight residual False 2.44 1.74 0.70 2.00e-01 2.50e+01 1.23e+01 chirality pdb=" CA VALBa 95 " pdb=" N VALBa 95 " pdb=" C VALBa 95 " pdb=" CB VALBa 95 " both_signs ideal model delta sigma weight residual False 2.44 1.74 0.70 2.00e-01 2.50e+01 1.23e+01 chirality pdb=" CA VALBh 95 " pdb=" N VALBh 95 " pdb=" C VALBh 95 " pdb=" CB VALBh 95 " both_signs ideal model delta sigma weight residual False 2.44 1.74 0.70 2.00e-01 2.50e+01 1.22e+01 ... (remaining 9825 not shown) Planarity restraints: 10542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VALAk 136 " 0.028 2.00e-02 2.50e+03 5.50e-02 3.02e+01 pdb=" C VALAk 136 " -0.095 2.00e-02 2.50e+03 pdb=" O VALAk 136 " 0.035 2.00e-02 2.50e+03 pdb=" N PROAk 137 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VALBm 136 " -0.028 2.00e-02 2.50e+03 5.50e-02 3.02e+01 pdb=" C VALBm 136 " 0.095 2.00e-02 2.50e+03 pdb=" O VALBm 136 " -0.035 2.00e-02 2.50e+03 pdb=" N PROBm 137 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VALBf 136 " -0.028 2.00e-02 2.50e+03 5.49e-02 3.02e+01 pdb=" C VALBf 136 " 0.095 2.00e-02 2.50e+03 pdb=" O VALBf 136 " -0.035 2.00e-02 2.50e+03 pdb=" N PROBf 137 " -0.032 2.00e-02 2.50e+03 ... (remaining 10539 not shown) Histogram of nonbonded interaction distances: 0.65 - 1.50: 133 1.50 - 2.35: 395 2.35 - 3.20: 55538 3.20 - 4.05: 167372 4.05 - 4.90: 285698 Warning: very small nonbonded interaction distances. Nonbonded interactions: 509136 Sorted by model distance: nonbonded pdb=" CB ALAAd 46 " pdb=" OE2 GLUAk 76 " model vdw 0.650 3.460 nonbonded pdb=" CB ALABf 46 " pdb=" OE2 GLUBm 76 " model vdw 0.687 3.460 nonbonded pdb=" OE2 GLUBf 76 " pdb=" CB ALABt 46 " model vdw 0.689 3.460 nonbonded pdb=" OE2 GLUAr 76 " pdb=" CB ALABm 46 " model vdw 0.694 3.460 nonbonded pdb=" CB ALAAk 46 " pdb=" OE2 GLUAy 76 " model vdw 0.708 3.460 ... (remaining 509131 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 'Ad' selection = chain 'Ae' selection = chain 'Ak' selection = chain 'Al' selection = chain 'Ar' selection = chain 'As' selection = chain 'Ay' selection = chain 'Az' selection = chain 'Bf' selection = chain 'Bg' selection = chain 'Bm' selection = chain 'Bn' selection = chain 'Bt' selection = chain 'Bu' } ncs_group { reference = chain 'Af' selection = chain 'Am' selection = chain 'At' selection = chain 'Ba' selection = chain 'Bh' selection = chain 'Bo' selection = chain 'Bv' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 12.960 Check model and map are aligned: 0.660 Set scattering table: 0.430 Process input model: 124.300 Find NCS groups from input model: 3.990 Set up NCS constraints: 0.570 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:2.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 148.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6529 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 : 0.018 0.984 59906 Z= 1.213 Angle : 2.204 67.712 80955 Z= 1.540 Chirality : 0.131 0.701 9828 Planarity : 0.011 0.169 10542 Dihedral : 19.503 164.600 22631 Min Nonbonded Distance : 0.650 Molprobity Statistics. All-atom Clashscore : 29.74 Ramachandran Plot: Outliers : 0.64 % Allowed : 2.50 % Favored : 96.86 % Rotamer: Outliers : 11.71 % Allowed : 14.64 % Favored : 73.65 % Cbeta Deviations : 1.93 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.69 (0.09), residues: 7973 helix: 2.34 (0.07), residues: 4060 sheet: 0.50 (0.14), residues: 1008 loop : -0.41 (0.10), residues: 2905 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.004 HISBh 7 PHE 0.049 0.008 PHEAm 67 TYR 0.037 0.006 TYRBg 199 ARG 0.023 0.002 ARGBv 4 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15946 Ramachandran restraints generated. 7973 Oldfield, 0 Emsley, 7973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15946 Ramachandran restraints generated. 7973 Oldfield, 0 Emsley, 7973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1236 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 728 poor density : 508 time to evaluate : 5.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ae 488 MET cc_start: 0.8277 (mmp) cc_final: 0.8042 (mmm) REVERT: Al 51 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8474 (tttp) REVERT: Al 389 MET cc_start: 0.7292 (tpp) cc_final: 0.6895 (tpp) REVERT: As 51 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8488 (tttp) REVERT: Bg 104 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8872 (mp) REVERT: Bm 518 GLU cc_start: 0.6504 (OUTLIER) cc_final: 0.6224 (tp30) REVERT: Bn 51 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8577 (tttp) REVERT: Bt 73 MET cc_start: 0.7762 (mtp) cc_final: 0.7516 (mtm) REVERT: Bu 51 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8642 (tttp) outliers start: 728 outliers final: 203 residues processed: 1186 average time/residue: 0.6141 time to fit residues: 1204.8241 Evaluate side-chains 589 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 380 time to evaluate : 5.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ad residue 54 VAL Chi-restraints excluded: chain Ad residue 186 GLU Chi-restraints excluded: chain Ad residue 191 GLU Chi-restraints excluded: chain Ad residue 203 TYR Chi-restraints excluded: chain Ad residue 210 THR Chi-restraints excluded: chain Ad residue 225 LYS Chi-restraints excluded: chain Ad residue 233 MET Chi-restraints excluded: chain Ad residue 236 VAL Chi-restraints excluded: chain Ad residue 240 VAL Chi-restraints excluded: chain Ad residue 245 LYS Chi-restraints excluded: chain Ad residue 250 ILE Chi-restraints excluded: chain Ad residue 259 LEU Chi-restraints excluded: chain Ad residue 268 ARG Chi-restraints excluded: chain Ad residue 292 ILE Chi-restraints excluded: chain Ad residue 299 THR Chi-restraints excluded: chain Ad residue 300 VAL Chi-restraints excluded: chain Ad residue 304 GLU Chi-restraints excluded: chain Ad residue 308 GLU Chi-restraints excluded: chain Ad residue 321 LYS Chi-restraints excluded: chain Ad residue 336 VAL Chi-restraints excluded: chain Ad residue 351 GLN Chi-restraints excluded: chain Ad residue 354 GLU Chi-restraints excluded: chain Ad residue 355 GLU Chi-restraints excluded: chain Ad residue 357 THR Chi-restraints excluded: chain Ad residue 521 VAL Chi-restraints excluded: chain Ae residue 284 ARG Chi-restraints excluded: chain Ae residue 429 LEU Chi-restraints excluded: chain Ak residue 54 VAL Chi-restraints excluded: chain Ak residue 186 GLU Chi-restraints excluded: chain Ak residue 191 GLU Chi-restraints excluded: chain Ak residue 203 TYR Chi-restraints excluded: chain Ak residue 210 THR Chi-restraints excluded: chain Ak residue 225 LYS Chi-restraints excluded: chain Ak residue 236 VAL Chi-restraints excluded: chain Ak residue 240 VAL Chi-restraints excluded: chain Ak residue 245 LYS Chi-restraints excluded: chain Ak residue 250 ILE Chi-restraints excluded: chain Ak residue 259 LEU Chi-restraints excluded: chain Ak residue 268 ARG Chi-restraints excluded: chain Ak residue 292 ILE Chi-restraints excluded: chain Ak residue 299 THR Chi-restraints excluded: chain Ak residue 300 VAL Chi-restraints excluded: chain Ak residue 304 GLU Chi-restraints excluded: chain Ak residue 308 GLU Chi-restraints excluded: chain Ak residue 321 LYS Chi-restraints excluded: chain Ak residue 336 VAL Chi-restraints excluded: chain Ak residue 351 GLN Chi-restraints excluded: chain Ak residue 354 GLU Chi-restraints excluded: chain Ak residue 355 GLU Chi-restraints excluded: chain Ak residue 357 THR Chi-restraints excluded: chain Ak residue 521 VAL Chi-restraints excluded: chain Al residue 51 LYS Chi-restraints excluded: chain Al residue 63 GLU Chi-restraints excluded: chain Al residue 284 ARG Chi-restraints excluded: chain Al residue 429 LEU Chi-restraints excluded: chain Ar residue 54 VAL Chi-restraints excluded: chain Ar residue 187 LEU Chi-restraints excluded: chain Ar residue 191 GLU Chi-restraints excluded: chain Ar residue 194 GLN Chi-restraints excluded: chain Ar residue 203 TYR Chi-restraints excluded: chain Ar residue 210 THR Chi-restraints excluded: chain Ar residue 225 LYS Chi-restraints excluded: chain Ar residue 236 VAL Chi-restraints excluded: chain Ar residue 240 VAL Chi-restraints excluded: chain Ar residue 245 LYS Chi-restraints excluded: chain Ar residue 250 ILE Chi-restraints excluded: chain Ar residue 259 LEU Chi-restraints excluded: chain Ar residue 268 ARG Chi-restraints excluded: chain Ar residue 292 ILE Chi-restraints excluded: chain Ar residue 299 THR Chi-restraints excluded: chain Ar residue 300 VAL Chi-restraints excluded: chain Ar residue 304 GLU Chi-restraints excluded: chain Ar residue 308 GLU Chi-restraints excluded: chain Ar residue 321 LYS Chi-restraints excluded: chain Ar residue 336 VAL Chi-restraints excluded: chain Ar residue 351 GLN Chi-restraints excluded: chain Ar residue 354 GLU Chi-restraints excluded: chain Ar residue 355 GLU Chi-restraints excluded: chain Ar residue 357 THR Chi-restraints excluded: chain Ar residue 521 VAL Chi-restraints excluded: chain As residue 51 LYS Chi-restraints excluded: chain As residue 63 GLU Chi-restraints excluded: chain As residue 128 VAL Chi-restraints excluded: chain As residue 284 ARG Chi-restraints excluded: chain As residue 429 LEU Chi-restraints excluded: chain At residue 2 ASN Chi-restraints excluded: chain Ay residue 54 VAL Chi-restraints excluded: chain Ay residue 186 GLU Chi-restraints excluded: chain Ay residue 187 LEU Chi-restraints excluded: chain Ay residue 191 GLU Chi-restraints excluded: chain Ay residue 203 TYR Chi-restraints excluded: chain Ay residue 210 THR Chi-restraints excluded: chain Ay residue 225 LYS Chi-restraints excluded: chain Ay residue 233 MET Chi-restraints excluded: chain Ay residue 236 VAL Chi-restraints excluded: chain Ay residue 240 VAL Chi-restraints excluded: chain Ay residue 245 LYS Chi-restraints excluded: chain Ay residue 250 ILE Chi-restraints excluded: chain Ay residue 259 LEU Chi-restraints excluded: chain Ay residue 268 ARG Chi-restraints excluded: chain Ay residue 277 LYS Chi-restraints excluded: chain Ay residue 292 ILE Chi-restraints excluded: chain Ay residue 299 THR Chi-restraints excluded: chain Ay residue 300 VAL Chi-restraints excluded: chain Ay residue 304 GLU Chi-restraints excluded: chain Ay residue 308 GLU Chi-restraints excluded: chain Ay residue 321 LYS Chi-restraints excluded: chain Ay residue 336 VAL Chi-restraints excluded: chain Ay residue 351 GLN Chi-restraints excluded: chain Ay residue 354 GLU Chi-restraints excluded: chain Ay residue 355 GLU Chi-restraints excluded: chain Ay residue 357 THR Chi-restraints excluded: chain Ay residue 365 LEU Chi-restraints excluded: chain Ay residue 521 VAL Chi-restraints excluded: chain Az residue 63 GLU Chi-restraints excluded: chain Az residue 284 ARG Chi-restraints excluded: chain Az residue 429 LEU Chi-restraints excluded: chain Bf residue 54 VAL Chi-restraints excluded: chain Bf residue 186 GLU Chi-restraints excluded: chain Bf residue 191 GLU Chi-restraints excluded: chain Bf residue 194 GLN Chi-restraints excluded: chain Bf residue 203 TYR Chi-restraints excluded: chain Bf residue 210 THR Chi-restraints excluded: chain Bf residue 225 LYS Chi-restraints excluded: chain Bf residue 233 MET Chi-restraints excluded: chain Bf residue 236 VAL Chi-restraints excluded: chain Bf residue 240 VAL Chi-restraints excluded: chain Bf residue 245 LYS Chi-restraints excluded: chain Bf residue 250 ILE Chi-restraints excluded: chain Bf residue 259 LEU Chi-restraints excluded: chain Bf residue 268 ARG Chi-restraints excluded: chain Bf residue 292 ILE Chi-restraints excluded: chain Bf residue 299 THR Chi-restraints excluded: chain Bf residue 300 VAL Chi-restraints excluded: chain Bf residue 304 GLU Chi-restraints excluded: chain Bf residue 308 GLU Chi-restraints excluded: chain Bf residue 321 LYS Chi-restraints excluded: chain Bf residue 336 VAL Chi-restraints excluded: chain Bf residue 351 GLN Chi-restraints excluded: chain Bf residue 354 GLU Chi-restraints excluded: chain Bf residue 355 GLU Chi-restraints excluded: chain Bf residue 357 THR Chi-restraints excluded: chain Bf residue 365 LEU Chi-restraints excluded: chain Bf residue 521 VAL Chi-restraints excluded: chain Bg residue 63 GLU Chi-restraints excluded: chain Bg residue 104 LEU Chi-restraints excluded: chain Bg residue 284 ARG Chi-restraints excluded: chain Bg residue 429 LEU Chi-restraints excluded: chain Bh residue 2 ASN Chi-restraints excluded: chain Bm residue 186 GLU Chi-restraints excluded: chain Bm residue 187 LEU Chi-restraints excluded: chain Bm residue 191 GLU Chi-restraints excluded: chain Bm residue 203 TYR Chi-restraints excluded: chain Bm residue 210 THR Chi-restraints excluded: chain Bm residue 225 LYS Chi-restraints excluded: chain Bm residue 233 MET Chi-restraints excluded: chain Bm residue 236 VAL Chi-restraints excluded: chain Bm residue 240 VAL Chi-restraints excluded: chain Bm residue 245 LYS Chi-restraints excluded: chain Bm residue 250 ILE Chi-restraints excluded: chain Bm residue 259 LEU Chi-restraints excluded: chain Bm residue 268 ARG Chi-restraints excluded: chain Bm residue 277 LYS Chi-restraints excluded: chain Bm residue 292 ILE Chi-restraints excluded: chain Bm residue 299 THR Chi-restraints excluded: chain Bm residue 300 VAL Chi-restraints excluded: chain Bm residue 304 GLU Chi-restraints excluded: chain Bm residue 308 GLU Chi-restraints excluded: chain Bm residue 321 LYS Chi-restraints excluded: chain Bm residue 336 VAL Chi-restraints excluded: chain Bm residue 351 GLN Chi-restraints excluded: chain Bm residue 354 GLU Chi-restraints excluded: chain Bm residue 355 GLU Chi-restraints excluded: chain Bm residue 357 THR Chi-restraints excluded: chain Bm residue 518 GLU Chi-restraints excluded: chain Bm residue 521 VAL Chi-restraints excluded: chain Bn residue 51 LYS Chi-restraints excluded: chain Bn residue 63 GLU Chi-restraints excluded: chain Bn residue 284 ARG Chi-restraints excluded: chain Bn residue 429 LEU Chi-restraints excluded: chain Bt residue 54 VAL Chi-restraints excluded: chain Bt residue 186 GLU Chi-restraints excluded: chain Bt residue 191 GLU Chi-restraints excluded: chain Bt residue 203 TYR Chi-restraints excluded: chain Bt residue 210 THR Chi-restraints excluded: chain Bt residue 225 LYS Chi-restraints excluded: chain Bt residue 233 MET Chi-restraints excluded: chain Bt residue 236 VAL Chi-restraints excluded: chain Bt residue 240 VAL Chi-restraints excluded: chain Bt residue 245 LYS Chi-restraints excluded: chain Bt residue 250 ILE Chi-restraints excluded: chain Bt residue 259 LEU Chi-restraints excluded: chain Bt residue 268 ARG Chi-restraints excluded: chain Bt residue 292 ILE Chi-restraints excluded: chain Bt residue 299 THR Chi-restraints excluded: chain Bt residue 300 VAL Chi-restraints excluded: chain Bt residue 304 GLU Chi-restraints excluded: chain Bt residue 308 GLU Chi-restraints excluded: chain Bt residue 321 LYS Chi-restraints excluded: chain Bt residue 336 VAL Chi-restraints excluded: chain Bt residue 351 GLN Chi-restraints excluded: chain Bt residue 354 GLU Chi-restraints excluded: chain Bt residue 355 GLU Chi-restraints excluded: chain Bt residue 357 THR Chi-restraints excluded: chain Bt residue 521 VAL Chi-restraints excluded: chain Bu residue 51 LYS Chi-restraints excluded: chain Bu residue 128 VAL Chi-restraints excluded: chain Bu residue 284 ARG Chi-restraints excluded: chain Bu residue 429 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 667 optimal weight: 0.9980 chunk 599 optimal weight: 10.0000 chunk 332 optimal weight: 3.9990 chunk 204 optimal weight: 3.9990 chunk 404 optimal weight: 5.9990 chunk 320 optimal weight: 0.9990 chunk 619 optimal weight: 0.9980 chunk 239 optimal weight: 1.9990 chunk 376 optimal weight: 5.9990 chunk 461 optimal weight: 0.9990 chunk 718 optimal weight: 6.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ad 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 453 GLN Ae 21 ASN ** Ae 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 146 GLN Ae 366 GLN Ae 453 GLN ** Ae 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 112 ASN ** Ak 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 453 GLN Al 21 ASN ** Al 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 146 GLN Al 366 GLN ** Al 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ar 453 GLN As 21 ASN ** As 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** As 146 GLN As 366 GLN As 453 GLN At 2 ASN Ay 112 ASN ** Ay 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ay 453 GLN Az 21 ASN ** Az 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Az 146 GLN Az 366 GLN ** Az 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bf 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bf 453 GLN Bg 21 ASN ** Bg 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 146 GLN Bg 366 GLN Bg 453 GLN Bh 2 ASN Bm 112 ASN ** Bm 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bm 453 GLN Bn 21 ASN ** Bn 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bn 146 GLN Bn 366 GLN Bn 453 GLN ** Bt 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bt 453 GLN Bu 21 ASN ** Bu 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bu 146 GLN Bu 366 GLN ** Bu 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6606 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 59906 Z= 0.283 Angle : 0.781 12.715 80955 Z= 0.402 Chirality : 0.046 0.213 9828 Planarity : 0.005 0.042 10542 Dihedral : 13.063 154.485 9114 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.07 % Favored : 97.58 % Rotamer: Outliers : 4.15 % Allowed : 18.84 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 1.42 (0.09), residues: 7973 helix: 2.11 (0.07), residues: 4116 sheet: 0.55 (0.16), residues: 945 loop : -0.62 (0.10), residues: 2912 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HISBo 7 PHE 0.020 0.002 PHEAd 66 TYR 0.014 0.002 TYRAl 199 ARG 0.011 0.001 ARGAf 14 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15946 Ramachandran restraints generated. 7973 Oldfield, 0 Emsley, 7973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15946 Ramachandran restraints generated. 7973 Oldfield, 0 Emsley, 7973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 258 poor density : 382 time to evaluate : 5.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ae 491 MET cc_start: 0.8429 (mtp) cc_final: 0.8120 (mtm) REVERT: Ak 491 MET cc_start: 0.7419 (mtp) cc_final: 0.7217 (mtm) REVERT: As 284 ARG cc_start: 0.2527 (OUTLIER) cc_final: 0.1928 (ptm160) REVERT: Ay 514 MET cc_start: 0.8086 (mmt) cc_final: 0.7784 (mmm) REVERT: Ay 520 MET cc_start: 0.8408 (mtm) cc_final: 0.8146 (mtt) REVERT: Bg 73 MET cc_start: 0.6557 (mtm) cc_final: 0.6290 (mtm) REVERT: Bm 254 VAL cc_start: 0.2193 (OUTLIER) cc_final: 0.1869 (p) REVERT: Bt 73 MET cc_start: 0.7754 (mtp) cc_final: 0.7481 (mtm) outliers start: 258 outliers final: 125 residues processed: 608 average time/residue: 0.6143 time to fit residues: 627.4167 Evaluate side-chains 461 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 334 time to evaluate : 5.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ad residue 203 TYR Chi-restraints excluded: chain Ad residue 210 THR Chi-restraints excluded: chain Ad residue 220 ILE Chi-restraints excluded: chain Ad residue 236 VAL Chi-restraints excluded: chain Ad residue 245 LYS Chi-restraints excluded: chain Ad residue 252 GLU Chi-restraints excluded: chain Ad residue 254 VAL Chi-restraints excluded: chain Ad residue 261 THR Chi-restraints excluded: chain Ad residue 268 ARG Chi-restraints excluded: chain Ad residue 300 VAL Chi-restraints excluded: chain Ad residue 304 GLU Chi-restraints excluded: chain Ad residue 351 GLN Chi-restraints excluded: chain Ad residue 355 GLU Chi-restraints excluded: chain Ae residue 178 GLU Chi-restraints excluded: chain Ae residue 284 ARG Chi-restraints excluded: chain Ae residue 360 TYR Chi-restraints excluded: chain Af residue 71 TYR Chi-restraints excluded: chain Af residue 95 VAL Chi-restraints excluded: chain Ak residue 191 GLU Chi-restraints excluded: chain Ak residue 203 TYR Chi-restraints excluded: chain Ak residue 210 THR Chi-restraints excluded: chain Ak residue 220 ILE Chi-restraints excluded: chain Ak residue 236 VAL Chi-restraints excluded: chain Ak residue 245 LYS Chi-restraints excluded: chain Ak residue 254 VAL Chi-restraints excluded: chain Ak residue 259 LEU Chi-restraints excluded: chain Ak residue 268 ARG Chi-restraints excluded: chain Ak residue 300 VAL Chi-restraints excluded: chain Ak residue 304 GLU Chi-restraints excluded: chain Ak residue 351 GLN Chi-restraints excluded: chain Ak residue 354 GLU Chi-restraints excluded: chain Ak residue 355 GLU Chi-restraints excluded: chain Al residue 284 ARG Chi-restraints excluded: chain Al residue 360 TYR Chi-restraints excluded: chain Am residue 71 TYR Chi-restraints excluded: chain Am residue 95 VAL Chi-restraints excluded: chain Ar residue 184 GLN Chi-restraints excluded: chain Ar residue 187 LEU Chi-restraints excluded: chain Ar residue 191 GLU Chi-restraints excluded: chain Ar residue 203 TYR Chi-restraints excluded: chain Ar residue 210 THR Chi-restraints excluded: chain Ar residue 220 ILE Chi-restraints excluded: chain Ar residue 236 VAL Chi-restraints excluded: chain Ar residue 245 LYS Chi-restraints excluded: chain Ar residue 252 GLU Chi-restraints excluded: chain Ar residue 259 LEU Chi-restraints excluded: chain Ar residue 261 THR Chi-restraints excluded: chain Ar residue 268 ARG Chi-restraints excluded: chain Ar residue 300 VAL Chi-restraints excluded: chain Ar residue 302 SER Chi-restraints excluded: chain Ar residue 304 GLU Chi-restraints excluded: chain Ar residue 351 GLN Chi-restraints excluded: chain Ar residue 354 GLU Chi-restraints excluded: chain Ar residue 355 GLU Chi-restraints excluded: chain As residue 284 ARG Chi-restraints excluded: chain As residue 360 TYR Chi-restraints excluded: chain At residue 71 TYR Chi-restraints excluded: chain Ay residue 203 TYR Chi-restraints excluded: chain Ay residue 210 THR Chi-restraints excluded: chain Ay residue 220 ILE Chi-restraints excluded: chain Ay residue 236 VAL Chi-restraints excluded: chain Ay residue 245 LYS Chi-restraints excluded: chain Ay residue 252 GLU Chi-restraints excluded: chain Ay residue 254 VAL Chi-restraints excluded: chain Ay residue 268 ARG Chi-restraints excluded: chain Ay residue 300 VAL Chi-restraints excluded: chain Ay residue 304 GLU Chi-restraints excluded: chain Ay residue 351 GLN Chi-restraints excluded: chain Ay residue 355 GLU Chi-restraints excluded: chain Ay residue 365 LEU Chi-restraints excluded: chain Az residue 191 GLU Chi-restraints excluded: chain Az residue 284 ARG Chi-restraints excluded: chain Az residue 360 TYR Chi-restraints excluded: chain Ba residue 64 ILE Chi-restraints excluded: chain Ba residue 71 TYR Chi-restraints excluded: chain Ba residue 94 ILE Chi-restraints excluded: chain Ba residue 95 VAL Chi-restraints excluded: chain Bf residue 11 ASP Chi-restraints excluded: chain Bf residue 191 GLU Chi-restraints excluded: chain Bf residue 203 TYR Chi-restraints excluded: chain Bf residue 210 THR Chi-restraints excluded: chain Bf residue 236 VAL Chi-restraints excluded: chain Bf residue 245 LYS Chi-restraints excluded: chain Bf residue 252 GLU Chi-restraints excluded: chain Bf residue 254 VAL Chi-restraints excluded: chain Bf residue 259 LEU Chi-restraints excluded: chain Bf residue 268 ARG Chi-restraints excluded: chain Bf residue 300 VAL Chi-restraints excluded: chain Bf residue 304 GLU Chi-restraints excluded: chain Bf residue 351 GLN Chi-restraints excluded: chain Bf residue 355 GLU Chi-restraints excluded: chain Bf residue 365 LEU Chi-restraints excluded: chain Bg residue 284 ARG Chi-restraints excluded: chain Bg residue 360 TYR Chi-restraints excluded: chain Bg residue 379 ILE Chi-restraints excluded: chain Bh residue 71 TYR Chi-restraints excluded: chain Bm residue 184 GLN Chi-restraints excluded: chain Bm residue 203 TYR Chi-restraints excluded: chain Bm residue 210 THR Chi-restraints excluded: chain Bm residue 220 ILE Chi-restraints excluded: chain Bm residue 236 VAL Chi-restraints excluded: chain Bm residue 245 LYS Chi-restraints excluded: chain Bm residue 252 GLU Chi-restraints excluded: chain Bm residue 254 VAL Chi-restraints excluded: chain Bm residue 300 VAL Chi-restraints excluded: chain Bm residue 302 SER Chi-restraints excluded: chain Bm residue 304 GLU Chi-restraints excluded: chain Bm residue 351 GLN Chi-restraints excluded: chain Bm residue 355 GLU Chi-restraints excluded: chain Bn residue 284 ARG Chi-restraints excluded: chain Bn residue 360 TYR Chi-restraints excluded: chain Bo residue 71 TYR Chi-restraints excluded: chain Bt residue 203 TYR Chi-restraints excluded: chain Bt residue 210 THR Chi-restraints excluded: chain Bt residue 220 ILE Chi-restraints excluded: chain Bt residue 236 VAL Chi-restraints excluded: chain Bt residue 245 LYS Chi-restraints excluded: chain Bt residue 252 GLU Chi-restraints excluded: chain Bt residue 254 VAL Chi-restraints excluded: chain Bt residue 268 ARG Chi-restraints excluded: chain Bt residue 300 VAL Chi-restraints excluded: chain Bt residue 304 GLU Chi-restraints excluded: chain Bt residue 351 GLN Chi-restraints excluded: chain Bt residue 355 GLU Chi-restraints excluded: chain Bu residue 360 TYR Chi-restraints excluded: chain Bv residue 64 ILE Chi-restraints excluded: chain Bv residue 71 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 399 optimal weight: 0.6980 chunk 222 optimal weight: 20.0000 chunk 597 optimal weight: 30.0000 chunk 489 optimal weight: 10.0000 chunk 198 optimal weight: 8.9990 chunk 719 optimal weight: 0.9990 chunk 777 optimal weight: 3.9990 chunk 640 optimal weight: 10.0000 chunk 713 optimal weight: 3.9990 chunk 245 optimal weight: 50.0000 chunk 577 optimal weight: 10.0000 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ad 37 ASN ** Ad 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 319 GLN ** Ae 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 112 ASN Ak 37 ASN ** Ak 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 319 GLN ** Al 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ar 37 ASN ** Ar 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** As 112 ASN Ay 37 ASN ** Ay 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ay 319 GLN ** Az 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Az 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bf 37 ASN ** Bf 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bf 319 GLN Bg 37 ASN ** Bg 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bm 37 ASN ** Bm 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bm 319 GLN ** Bn 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bt 37 ASN ** Bt 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bt 319 GLN ** Bu 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bu 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6726 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 59906 Z= 0.372 Angle : 0.705 9.733 80955 Z= 0.364 Chirality : 0.046 0.254 9828 Planarity : 0.004 0.080 10542 Dihedral : 10.961 149.071 8818 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.93 % Favored : 96.83 % Rotamer: Outliers : 3.39 % Allowed : 19.64 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.99 (0.09), residues: 7973 helix: 1.63 (0.08), residues: 4151 sheet: 0.58 (0.16), residues: 924 loop : -0.71 (0.10), residues: 2898 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HISAz 401 PHE 0.014 0.002 PHEAd 66 TYR 0.010 0.002 TYRAl 199 ARG 0.005 0.001 ARGBm 268 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15946 Ramachandran restraints generated. 7973 Oldfield, 0 Emsley, 7973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15946 Ramachandran restraints generated. 7973 Oldfield, 0 Emsley, 7973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 338 time to evaluate : 5.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ay 520 MET cc_start: 0.8468 (mtm) cc_final: 0.8253 (mtm) REVERT: Bg 73 MET cc_start: 0.6628 (mtm) cc_final: 0.6326 (mtm) outliers start: 211 outliers final: 126 residues processed: 516 average time/residue: 0.5535 time to fit residues: 487.6841 Evaluate side-chains 455 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 329 time to evaluate : 5.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ad residue 150 ILE Chi-restraints excluded: chain Ad residue 203 TYR Chi-restraints excluded: chain Ad residue 210 THR Chi-restraints excluded: chain Ad residue 236 VAL Chi-restraints excluded: chain Ad residue 245 LYS Chi-restraints excluded: chain Ad residue 252 GLU Chi-restraints excluded: chain Ad residue 254 VAL Chi-restraints excluded: chain Ad residue 261 THR Chi-restraints excluded: chain Ad residue 304 GLU Chi-restraints excluded: chain Ad residue 351 GLN Chi-restraints excluded: chain Ad residue 355 GLU Chi-restraints excluded: chain Ad residue 517 THR Chi-restraints excluded: chain Ae residue 281 PHE Chi-restraints excluded: chain Ae residue 284 ARG Chi-restraints excluded: chain Ae residue 360 TYR Chi-restraints excluded: chain Af residue 71 TYR Chi-restraints excluded: chain Af residue 95 VAL Chi-restraints excluded: chain Ak residue 11 ASP Chi-restraints excluded: chain Ak residue 203 TYR Chi-restraints excluded: chain Ak residue 210 THR Chi-restraints excluded: chain Ak residue 236 VAL Chi-restraints excluded: chain Ak residue 245 LYS Chi-restraints excluded: chain Ak residue 252 GLU Chi-restraints excluded: chain Ak residue 254 VAL Chi-restraints excluded: chain Ak residue 259 LEU Chi-restraints excluded: chain Ak residue 304 GLU Chi-restraints excluded: chain Ak residue 351 GLN Chi-restraints excluded: chain Ak residue 355 GLU Chi-restraints excluded: chain Ak residue 366 GLN Chi-restraints excluded: chain Al residue 284 ARG Chi-restraints excluded: chain Al residue 360 TYR Chi-restraints excluded: chain Al residue 518 GLU Chi-restraints excluded: chain Am residue 30 SER Chi-restraints excluded: chain Am residue 60 LYS Chi-restraints excluded: chain Am residue 71 TYR Chi-restraints excluded: chain Ar residue 184 GLN Chi-restraints excluded: chain Ar residue 191 GLU Chi-restraints excluded: chain Ar residue 203 TYR Chi-restraints excluded: chain Ar residue 210 THR Chi-restraints excluded: chain Ar residue 220 ILE Chi-restraints excluded: chain Ar residue 236 VAL Chi-restraints excluded: chain Ar residue 245 LYS Chi-restraints excluded: chain Ar residue 252 GLU Chi-restraints excluded: chain Ar residue 254 VAL Chi-restraints excluded: chain Ar residue 259 LEU Chi-restraints excluded: chain Ar residue 261 THR Chi-restraints excluded: chain Ar residue 304 GLU Chi-restraints excluded: chain Ar residue 351 GLN Chi-restraints excluded: chain Ar residue 355 GLU Chi-restraints excluded: chain As residue 104 LEU Chi-restraints excluded: chain As residue 281 PHE Chi-restraints excluded: chain As residue 284 ARG Chi-restraints excluded: chain As residue 360 TYR Chi-restraints excluded: chain At residue 30 SER Chi-restraints excluded: chain At residue 71 TYR Chi-restraints excluded: chain At residue 79 ASP Chi-restraints excluded: chain At residue 95 VAL Chi-restraints excluded: chain Ay residue 203 TYR Chi-restraints excluded: chain Ay residue 210 THR Chi-restraints excluded: chain Ay residue 236 VAL Chi-restraints excluded: chain Ay residue 245 LYS Chi-restraints excluded: chain Ay residue 252 GLU Chi-restraints excluded: chain Ay residue 304 GLU Chi-restraints excluded: chain Ay residue 351 GLN Chi-restraints excluded: chain Ay residue 355 GLU Chi-restraints excluded: chain Ay residue 517 THR Chi-restraints excluded: chain Az residue 281 PHE Chi-restraints excluded: chain Az residue 284 ARG Chi-restraints excluded: chain Az residue 360 TYR Chi-restraints excluded: chain Ba residue 64 ILE Chi-restraints excluded: chain Ba residue 71 TYR Chi-restraints excluded: chain Ba residue 79 ASP Chi-restraints excluded: chain Ba residue 94 ILE Chi-restraints excluded: chain Ba residue 95 VAL Chi-restraints excluded: chain Bf residue 11 ASP Chi-restraints excluded: chain Bf residue 203 TYR Chi-restraints excluded: chain Bf residue 210 THR Chi-restraints excluded: chain Bf residue 236 VAL Chi-restraints excluded: chain Bf residue 245 LYS Chi-restraints excluded: chain Bf residue 252 GLU Chi-restraints excluded: chain Bf residue 254 VAL Chi-restraints excluded: chain Bf residue 259 LEU Chi-restraints excluded: chain Bf residue 304 GLU Chi-restraints excluded: chain Bf residue 351 GLN Chi-restraints excluded: chain Bf residue 355 GLU Chi-restraints excluded: chain Bf residue 366 GLN Chi-restraints excluded: chain Bg residue 114 MET Chi-restraints excluded: chain Bg residue 281 PHE Chi-restraints excluded: chain Bg residue 284 ARG Chi-restraints excluded: chain Bg residue 307 MET Chi-restraints excluded: chain Bg residue 360 TYR Chi-restraints excluded: chain Bg residue 509 SER Chi-restraints excluded: chain Bh residue 71 TYR Chi-restraints excluded: chain Bh residue 95 VAL Chi-restraints excluded: chain Bm residue 203 TYR Chi-restraints excluded: chain Bm residue 210 THR Chi-restraints excluded: chain Bm residue 236 VAL Chi-restraints excluded: chain Bm residue 245 LYS Chi-restraints excluded: chain Bm residue 252 GLU Chi-restraints excluded: chain Bm residue 261 THR Chi-restraints excluded: chain Bm residue 304 GLU Chi-restraints excluded: chain Bm residue 351 GLN Chi-restraints excluded: chain Bm residue 355 GLU Chi-restraints excluded: chain Bn residue 284 ARG Chi-restraints excluded: chain Bn residue 360 TYR Chi-restraints excluded: chain Bo residue 71 TYR Chi-restraints excluded: chain Bo residue 80 ASN Chi-restraints excluded: chain Bo residue 95 VAL Chi-restraints excluded: chain Bt residue 63 GLU Chi-restraints excluded: chain Bt residue 203 TYR Chi-restraints excluded: chain Bt residue 210 THR Chi-restraints excluded: chain Bt residue 236 VAL Chi-restraints excluded: chain Bt residue 245 LYS Chi-restraints excluded: chain Bt residue 252 GLU Chi-restraints excluded: chain Bt residue 254 VAL Chi-restraints excluded: chain Bt residue 304 GLU Chi-restraints excluded: chain Bt residue 351 GLN Chi-restraints excluded: chain Bt residue 355 GLU Chi-restraints excluded: chain Bu residue 281 PHE Chi-restraints excluded: chain Bu residue 360 TYR Chi-restraints excluded: chain Bu residue 367 GLU Chi-restraints excluded: chain Bu residue 442 VAL Chi-restraints excluded: chain Bv residue 64 ILE Chi-restraints excluded: chain Bv residue 71 TYR Chi-restraints excluded: chain Bv residue 79 ASP Chi-restraints excluded: chain Bv residue 95 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 710 optimal weight: 5.9990 chunk 541 optimal weight: 9.9990 chunk 373 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 343 optimal weight: 10.0000 chunk 483 optimal weight: 50.0000 chunk 722 optimal weight: 0.1980 chunk 764 optimal weight: 0.7980 chunk 377 optimal weight: 0.4980 chunk 684 optimal weight: 0.9980 chunk 206 optimal weight: 8.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ad 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 453 GLN ** Ar 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Az 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Az 453 GLN ** Bf 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 37 ASN ** Bg 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bm 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bn 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bo 68 ASN ** Bt 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bu 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bu 453 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 59906 Z= 0.203 Angle : 0.614 9.761 80955 Z= 0.313 Chirality : 0.043 0.220 9828 Planarity : 0.003 0.043 10542 Dihedral : 9.880 124.305 8769 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.70 % Favored : 97.18 % Rotamer: Outliers : 3.30 % Allowed : 19.45 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.27 (0.09), residues: 7973 helix: 1.83 (0.08), residues: 4193 sheet: 0.71 (0.17), residues: 903 loop : -0.56 (0.11), residues: 2877 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HISAt 7 PHE 0.011 0.002 PHEBm 44 TYR 0.009 0.001 TYRBu 199 ARG 0.010 0.000 ARGAz 231 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15946 Ramachandran restraints generated. 7973 Oldfield, 0 Emsley, 7973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15946 Ramachandran restraints generated. 7973 Oldfield, 0 Emsley, 7973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 335 time to evaluate : 5.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Al 284 ARG cc_start: 0.2839 (OUTLIER) cc_final: 0.2066 (ptm160) REVERT: Ay 389 MET cc_start: 0.4605 (mmt) cc_final: 0.4401 (mmm) REVERT: Ay 520 MET cc_start: 0.8357 (mtm) cc_final: 0.8088 (mtt) REVERT: Bg 73 MET cc_start: 0.6581 (mtm) cc_final: 0.6189 (mtm) REVERT: Bm 514 MET cc_start: 0.8228 (mmt) cc_final: 0.8018 (mmm) REVERT: Bt 514 MET cc_start: 0.8292 (mmt) cc_final: 0.7922 (mmm) outliers start: 205 outliers final: 123 residues processed: 512 average time/residue: 0.5411 time to fit residues: 476.3685 Evaluate side-chains 451 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 327 time to evaluate : 5.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ad residue 203 TYR Chi-restraints excluded: chain Ad residue 236 VAL Chi-restraints excluded: chain Ad residue 245 LYS Chi-restraints excluded: chain Ad residue 254 VAL Chi-restraints excluded: chain Ad residue 261 THR Chi-restraints excluded: chain Ad residue 304 GLU Chi-restraints excluded: chain Ad residue 351 GLN Chi-restraints excluded: chain Ad residue 355 GLU Chi-restraints excluded: chain Ad residue 366 GLN Chi-restraints excluded: chain Ad residue 483 GLU Chi-restraints excluded: chain Ae residue 281 PHE Chi-restraints excluded: chain Ae residue 284 ARG Chi-restraints excluded: chain Ae residue 360 TYR Chi-restraints excluded: chain Af residue 71 TYR Chi-restraints excluded: chain Ak residue 11 ASP Chi-restraints excluded: chain Ak residue 203 TYR Chi-restraints excluded: chain Ak residue 245 LYS Chi-restraints excluded: chain Ak residue 252 GLU Chi-restraints excluded: chain Ak residue 254 VAL Chi-restraints excluded: chain Ak residue 259 LEU Chi-restraints excluded: chain Ak residue 261 THR Chi-restraints excluded: chain Ak residue 304 GLU Chi-restraints excluded: chain Ak residue 351 GLN Chi-restraints excluded: chain Ak residue 355 GLU Chi-restraints excluded: chain Ak residue 366 GLN Chi-restraints excluded: chain Al residue 284 ARG Chi-restraints excluded: chain Al residue 360 TYR Chi-restraints excluded: chain Al residue 518 GLU Chi-restraints excluded: chain Am residue 25 ILE Chi-restraints excluded: chain Am residue 71 TYR Chi-restraints excluded: chain Am residue 95 VAL Chi-restraints excluded: chain Ar residue 150 ILE Chi-restraints excluded: chain Ar residue 184 GLN Chi-restraints excluded: chain Ar residue 203 TYR Chi-restraints excluded: chain Ar residue 245 LYS Chi-restraints excluded: chain Ar residue 252 GLU Chi-restraints excluded: chain Ar residue 254 VAL Chi-restraints excluded: chain Ar residue 259 LEU Chi-restraints excluded: chain Ar residue 261 THR Chi-restraints excluded: chain Ar residue 302 SER Chi-restraints excluded: chain Ar residue 304 GLU Chi-restraints excluded: chain Ar residue 351 GLN Chi-restraints excluded: chain Ar residue 355 GLU Chi-restraints excluded: chain Ar residue 366 GLN Chi-restraints excluded: chain As residue 281 PHE Chi-restraints excluded: chain As residue 284 ARG Chi-restraints excluded: chain As residue 360 TYR Chi-restraints excluded: chain As residue 420 ILE Chi-restraints excluded: chain As residue 518 GLU Chi-restraints excluded: chain At residue 58 ASP Chi-restraints excluded: chain At residue 71 TYR Chi-restraints excluded: chain At residue 95 VAL Chi-restraints excluded: chain Ay residue 150 ILE Chi-restraints excluded: chain Ay residue 203 TYR Chi-restraints excluded: chain Ay residue 236 VAL Chi-restraints excluded: chain Ay residue 245 LYS Chi-restraints excluded: chain Ay residue 252 GLU Chi-restraints excluded: chain Ay residue 254 VAL Chi-restraints excluded: chain Ay residue 304 GLU Chi-restraints excluded: chain Ay residue 351 GLN Chi-restraints excluded: chain Ay residue 355 GLU Chi-restraints excluded: chain Az residue 281 PHE Chi-restraints excluded: chain Az residue 284 ARG Chi-restraints excluded: chain Az residue 360 TYR Chi-restraints excluded: chain Ba residue 60 LYS Chi-restraints excluded: chain Ba residue 71 TYR Chi-restraints excluded: chain Ba residue 79 ASP Chi-restraints excluded: chain Ba residue 94 ILE Chi-restraints excluded: chain Bf residue 191 GLU Chi-restraints excluded: chain Bf residue 203 TYR Chi-restraints excluded: chain Bf residue 236 VAL Chi-restraints excluded: chain Bf residue 245 LYS Chi-restraints excluded: chain Bf residue 252 GLU Chi-restraints excluded: chain Bf residue 254 VAL Chi-restraints excluded: chain Bf residue 259 LEU Chi-restraints excluded: chain Bf residue 261 THR Chi-restraints excluded: chain Bf residue 304 GLU Chi-restraints excluded: chain Bf residue 319 GLN Chi-restraints excluded: chain Bf residue 351 GLN Chi-restraints excluded: chain Bf residue 355 GLU Chi-restraints excluded: chain Bf residue 365 LEU Chi-restraints excluded: chain Bf residue 366 GLN Chi-restraints excluded: chain Bg residue 281 PHE Chi-restraints excluded: chain Bg residue 284 ARG Chi-restraints excluded: chain Bg residue 360 TYR Chi-restraints excluded: chain Bh residue 58 ASP Chi-restraints excluded: chain Bh residue 71 TYR Chi-restraints excluded: chain Bh residue 95 VAL Chi-restraints excluded: chain Bm residue 150 ILE Chi-restraints excluded: chain Bm residue 203 TYR Chi-restraints excluded: chain Bm residue 236 VAL Chi-restraints excluded: chain Bm residue 245 LYS Chi-restraints excluded: chain Bm residue 252 GLU Chi-restraints excluded: chain Bm residue 261 THR Chi-restraints excluded: chain Bm residue 302 SER Chi-restraints excluded: chain Bm residue 304 GLU Chi-restraints excluded: chain Bm residue 351 GLN Chi-restraints excluded: chain Bm residue 355 GLU Chi-restraints excluded: chain Bm residue 366 GLN Chi-restraints excluded: chain Bn residue 104 LEU Chi-restraints excluded: chain Bn residue 281 PHE Chi-restraints excluded: chain Bn residue 284 ARG Chi-restraints excluded: chain Bn residue 360 TYR Chi-restraints excluded: chain Bo residue 30 SER Chi-restraints excluded: chain Bo residue 58 ASP Chi-restraints excluded: chain Bo residue 71 TYR Chi-restraints excluded: chain Bo residue 79 ASP Chi-restraints excluded: chain Bo residue 80 ASN Chi-restraints excluded: chain Bo residue 95 VAL Chi-restraints excluded: chain Bt residue 11 ASP Chi-restraints excluded: chain Bt residue 150 ILE Chi-restraints excluded: chain Bt residue 203 TYR Chi-restraints excluded: chain Bt residue 236 VAL Chi-restraints excluded: chain Bt residue 245 LYS Chi-restraints excluded: chain Bt residue 252 GLU Chi-restraints excluded: chain Bt residue 304 GLU Chi-restraints excluded: chain Bt residue 351 GLN Chi-restraints excluded: chain Bt residue 355 GLU Chi-restraints excluded: chain Bu residue 281 PHE Chi-restraints excluded: chain Bu residue 360 TYR Chi-restraints excluded: chain Bu residue 367 GLU Chi-restraints excluded: chain Bv residue 64 ILE Chi-restraints excluded: chain Bv residue 71 TYR Chi-restraints excluded: chain Bv residue 95 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 636 optimal weight: 9.9990 chunk 434 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 569 optimal weight: 0.9990 chunk 315 optimal weight: 9.9990 chunk 652 optimal weight: 9.9990 chunk 528 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 390 optimal weight: 4.9990 chunk 686 optimal weight: 9.9990 chunk 192 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ad 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 37 ASN ** Ae 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 453 GLN ** Ak 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 453 GLN ** Ar 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** As 37 ASN ** As 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Az 37 ASN ** Az 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Az 453 GLN ** Bf 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 37 ASN Bg 72 GLN ** Bg 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bm 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bm 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bn 37 ASN ** Bn 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bt 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bu 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bu 453 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 59906 Z= 0.398 Angle : 0.681 13.064 80955 Z= 0.347 Chirality : 0.046 0.260 9828 Planarity : 0.004 0.046 10542 Dihedral : 9.489 132.573 8757 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.25 % Favored : 96.65 % Rotamer: Outliers : 3.46 % Allowed : 19.98 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.77 (0.09), residues: 7973 helix: 1.46 (0.08), residues: 4130 sheet: 0.48 (0.16), residues: 938 loop : -0.83 (0.10), residues: 2905 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HISAt 7 PHE 0.014 0.002 PHEBm 44 TYR 0.011 0.002 TYRBu 199 ARG 0.005 0.001 ARGAy 368 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15946 Ramachandran restraints generated. 7973 Oldfield, 0 Emsley, 7973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15946 Ramachandran restraints generated. 7973 Oldfield, 0 Emsley, 7973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 331 time to evaluate : 5.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ae 193 MET cc_start: 0.6650 (tpt) cc_final: 0.6434 (tpt) REVERT: Al 284 ARG cc_start: 0.3032 (OUTLIER) cc_final: 0.2203 (ptm160) REVERT: Bg 73 MET cc_start: 0.6547 (mtm) cc_final: 0.6291 (mtm) REVERT: Bn 514 MET cc_start: 0.7777 (mtp) cc_final: 0.7488 (mtp) REVERT: Bt 16 MET cc_start: 0.7491 (mtm) cc_final: 0.7229 (mtm) outliers start: 215 outliers final: 144 residues processed: 513 average time/residue: 0.5556 time to fit residues: 488.5331 Evaluate side-chains 468 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 323 time to evaluate : 5.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ad residue 49 ILE Chi-restraints excluded: chain Ad residue 91 THR Chi-restraints excluded: chain Ad residue 150 ILE Chi-restraints excluded: chain Ad residue 203 TYR Chi-restraints excluded: chain Ad residue 245 LYS Chi-restraints excluded: chain Ad residue 252 GLU Chi-restraints excluded: chain Ad residue 254 VAL Chi-restraints excluded: chain Ad residue 304 GLU Chi-restraints excluded: chain Ad residue 351 GLN Chi-restraints excluded: chain Ad residue 355 GLU Chi-restraints excluded: chain Ad residue 420 ILE Chi-restraints excluded: chain Ad residue 483 GLU Chi-restraints excluded: chain Ae residue 281 PHE Chi-restraints excluded: chain Ae residue 284 ARG Chi-restraints excluded: chain Ae residue 360 TYR Chi-restraints excluded: chain Af residue 30 SER Chi-restraints excluded: chain Af residue 71 TYR Chi-restraints excluded: chain Af residue 95 VAL Chi-restraints excluded: chain Ak residue 11 ASP Chi-restraints excluded: chain Ak residue 54 VAL Chi-restraints excluded: chain Ak residue 91 THR Chi-restraints excluded: chain Ak residue 150 ILE Chi-restraints excluded: chain Ak residue 203 TYR Chi-restraints excluded: chain Ak residue 245 LYS Chi-restraints excluded: chain Ak residue 252 GLU Chi-restraints excluded: chain Ak residue 254 VAL Chi-restraints excluded: chain Ak residue 259 LEU Chi-restraints excluded: chain Ak residue 261 THR Chi-restraints excluded: chain Ak residue 304 GLU Chi-restraints excluded: chain Ak residue 351 GLN Chi-restraints excluded: chain Ak residue 355 GLU Chi-restraints excluded: chain Ak residue 420 ILE Chi-restraints excluded: chain Al residue 114 MET Chi-restraints excluded: chain Al residue 284 ARG Chi-restraints excluded: chain Al residue 360 TYR Chi-restraints excluded: chain Al residue 518 GLU Chi-restraints excluded: chain Am residue 25 ILE Chi-restraints excluded: chain Am residue 60 LYS Chi-restraints excluded: chain Am residue 71 TYR Chi-restraints excluded: chain Am residue 79 ASP Chi-restraints excluded: chain Am residue 95 VAL Chi-restraints excluded: chain Ar residue 91 THR Chi-restraints excluded: chain Ar residue 150 ILE Chi-restraints excluded: chain Ar residue 203 TYR Chi-restraints excluded: chain Ar residue 245 LYS Chi-restraints excluded: chain Ar residue 252 GLU Chi-restraints excluded: chain Ar residue 259 LEU Chi-restraints excluded: chain Ar residue 261 THR Chi-restraints excluded: chain Ar residue 302 SER Chi-restraints excluded: chain Ar residue 304 GLU Chi-restraints excluded: chain Ar residue 351 GLN Chi-restraints excluded: chain Ar residue 355 GLU Chi-restraints excluded: chain Ar residue 365 LEU Chi-restraints excluded: chain Ar residue 420 ILE Chi-restraints excluded: chain As residue 281 PHE Chi-restraints excluded: chain As residue 284 ARG Chi-restraints excluded: chain As residue 360 TYR Chi-restraints excluded: chain As residue 420 ILE Chi-restraints excluded: chain As residue 509 SER Chi-restraints excluded: chain As residue 518 GLU Chi-restraints excluded: chain At residue 25 ILE Chi-restraints excluded: chain At residue 58 ASP Chi-restraints excluded: chain At residue 71 TYR Chi-restraints excluded: chain Ay residue 23 LEU Chi-restraints excluded: chain Ay residue 91 THR Chi-restraints excluded: chain Ay residue 150 ILE Chi-restraints excluded: chain Ay residue 203 TYR Chi-restraints excluded: chain Ay residue 245 LYS Chi-restraints excluded: chain Ay residue 252 GLU Chi-restraints excluded: chain Ay residue 304 GLU Chi-restraints excluded: chain Ay residue 351 GLN Chi-restraints excluded: chain Ay residue 355 GLU Chi-restraints excluded: chain Ay residue 420 ILE Chi-restraints excluded: chain Ay residue 483 GLU Chi-restraints excluded: chain Ay residue 517 THR Chi-restraints excluded: chain Az residue 44 PHE Chi-restraints excluded: chain Az residue 281 PHE Chi-restraints excluded: chain Az residue 284 ARG Chi-restraints excluded: chain Az residue 360 TYR Chi-restraints excluded: chain Ba residue 60 LYS Chi-restraints excluded: chain Ba residue 71 TYR Chi-restraints excluded: chain Ba residue 79 ASP Chi-restraints excluded: chain Ba residue 94 ILE Chi-restraints excluded: chain Bf residue 23 LEU Chi-restraints excluded: chain Bf residue 91 THR Chi-restraints excluded: chain Bf residue 150 ILE Chi-restraints excluded: chain Bf residue 203 TYR Chi-restraints excluded: chain Bf residue 245 LYS Chi-restraints excluded: chain Bf residue 252 GLU Chi-restraints excluded: chain Bf residue 254 VAL Chi-restraints excluded: chain Bf residue 259 LEU Chi-restraints excluded: chain Bf residue 304 GLU Chi-restraints excluded: chain Bf residue 319 GLN Chi-restraints excluded: chain Bf residue 351 GLN Chi-restraints excluded: chain Bf residue 355 GLU Chi-restraints excluded: chain Bf residue 365 LEU Chi-restraints excluded: chain Bf residue 420 ILE Chi-restraints excluded: chain Bg residue 114 MET Chi-restraints excluded: chain Bg residue 281 PHE Chi-restraints excluded: chain Bg residue 284 ARG Chi-restraints excluded: chain Bg residue 360 TYR Chi-restraints excluded: chain Bh residue 58 ASP Chi-restraints excluded: chain Bh residue 64 ILE Chi-restraints excluded: chain Bh residue 71 TYR Chi-restraints excluded: chain Bh residue 95 VAL Chi-restraints excluded: chain Bm residue 23 LEU Chi-restraints excluded: chain Bm residue 91 THR Chi-restraints excluded: chain Bm residue 104 LEU Chi-restraints excluded: chain Bm residue 150 ILE Chi-restraints excluded: chain Bm residue 203 TYR Chi-restraints excluded: chain Bm residue 245 LYS Chi-restraints excluded: chain Bm residue 304 GLU Chi-restraints excluded: chain Bm residue 351 GLN Chi-restraints excluded: chain Bm residue 355 GLU Chi-restraints excluded: chain Bm residue 366 GLN Chi-restraints excluded: chain Bm residue 420 ILE Chi-restraints excluded: chain Bm residue 517 THR Chi-restraints excluded: chain Bn residue 104 LEU Chi-restraints excluded: chain Bn residue 281 PHE Chi-restraints excluded: chain Bn residue 284 ARG Chi-restraints excluded: chain Bn residue 360 TYR Chi-restraints excluded: chain Bo residue 25 ILE Chi-restraints excluded: chain Bo residue 58 ASP Chi-restraints excluded: chain Bo residue 71 TYR Chi-restraints excluded: chain Bo residue 79 ASP Chi-restraints excluded: chain Bo residue 80 ASN Chi-restraints excluded: chain Bo residue 95 VAL Chi-restraints excluded: chain Bt residue 11 ASP Chi-restraints excluded: chain Bt residue 54 VAL Chi-restraints excluded: chain Bt residue 63 GLU Chi-restraints excluded: chain Bt residue 150 ILE Chi-restraints excluded: chain Bt residue 203 TYR Chi-restraints excluded: chain Bt residue 245 LYS Chi-restraints excluded: chain Bt residue 304 GLU Chi-restraints excluded: chain Bt residue 351 GLN Chi-restraints excluded: chain Bt residue 355 GLU Chi-restraints excluded: chain Bt residue 420 ILE Chi-restraints excluded: chain Bt residue 517 THR Chi-restraints excluded: chain Bu residue 44 PHE Chi-restraints excluded: chain Bu residue 281 PHE Chi-restraints excluded: chain Bu residue 360 TYR Chi-restraints excluded: chain Bv residue 58 ASP Chi-restraints excluded: chain Bv residue 71 TYR Chi-restraints excluded: chain Bv residue 79 ASP Chi-restraints excluded: chain Bv residue 95 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 257 optimal weight: 10.0000 chunk 688 optimal weight: 0.9990 chunk 151 optimal weight: 8.9990 chunk 448 optimal weight: 7.9990 chunk 188 optimal weight: 0.8980 chunk 765 optimal weight: 9.9990 chunk 635 optimal weight: 0.8980 chunk 354 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 253 optimal weight: 40.0000 chunk 401 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ad 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 72 GLN ** Ae 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 453 GLN ** Ak 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 453 GLN ** Ar 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** As 37 ASN ** As 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Az 37 ASN ** Az 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Az 453 GLN ** Bf 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bg 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bm 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bm 475 ASN Bn 37 ASN ** Bn 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bt 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bu 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bu 453 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 59906 Z= 0.226 Angle : 0.620 18.363 80955 Z= 0.310 Chirality : 0.043 0.436 9828 Planarity : 0.003 0.044 10542 Dihedral : 9.156 134.943 8752 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.01 % Favored : 96.90 % Rotamer: Outliers : 2.69 % Allowed : 21.07 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.09), residues: 7973 helix: 1.63 (0.08), residues: 4158 sheet: 0.54 (0.16), residues: 1001 loop : -0.83 (0.11), residues: 2814 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HISAr 401 PHE 0.011 0.001 PHEBg 44 TYR 0.009 0.001 TYRBu 199 ARG 0.005 0.000 ARGAy 368 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15946 Ramachandran restraints generated. 7973 Oldfield, 0 Emsley, 7973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15946 Ramachandran restraints generated. 7973 Oldfield, 0 Emsley, 7973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 333 time to evaluate : 5.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ae 193 MET cc_start: 0.6531 (tpt) cc_final: 0.6313 (tpt) REVERT: Ak 514 MET cc_start: 0.8298 (tpp) cc_final: 0.7973 (mmm) REVERT: Am 1 MET cc_start: 0.3616 (tpp) cc_final: 0.2860 (tpt) REVERT: Bg 73 MET cc_start: 0.6454 (mtm) cc_final: 0.6213 (mtm) REVERT: Bm 514 MET cc_start: 0.8277 (mmt) cc_final: 0.8048 (mmm) REVERT: Bt 16 MET cc_start: 0.7459 (mtm) cc_final: 0.7147 (mtm) REVERT: Bt 73 MET cc_start: 0.7418 (mtm) cc_final: 0.7118 (mtm) outliers start: 167 outliers final: 126 residues processed: 474 average time/residue: 0.5476 time to fit residues: 443.3745 Evaluate side-chains 449 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 323 time to evaluate : 5.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ad residue 49 ILE Chi-restraints excluded: chain Ad residue 150 ILE Chi-restraints excluded: chain Ad residue 203 TYR Chi-restraints excluded: chain Ad residue 245 LYS Chi-restraints excluded: chain Ad residue 252 GLU Chi-restraints excluded: chain Ad residue 254 VAL Chi-restraints excluded: chain Ad residue 304 GLU Chi-restraints excluded: chain Ad residue 351 GLN Chi-restraints excluded: chain Ad residue 355 GLU Chi-restraints excluded: chain Ad residue 420 ILE Chi-restraints excluded: chain Ad residue 483 GLU Chi-restraints excluded: chain Ae residue 210 THR Chi-restraints excluded: chain Ae residue 281 PHE Chi-restraints excluded: chain Ae residue 284 ARG Chi-restraints excluded: chain Ae residue 360 TYR Chi-restraints excluded: chain Af residue 25 ILE Chi-restraints excluded: chain Af residue 30 SER Chi-restraints excluded: chain Af residue 71 TYR Chi-restraints excluded: chain Af residue 95 VAL Chi-restraints excluded: chain Ak residue 11 ASP Chi-restraints excluded: chain Ak residue 150 ILE Chi-restraints excluded: chain Ak residue 203 TYR Chi-restraints excluded: chain Ak residue 245 LYS Chi-restraints excluded: chain Ak residue 252 GLU Chi-restraints excluded: chain Ak residue 259 LEU Chi-restraints excluded: chain Ak residue 261 THR Chi-restraints excluded: chain Ak residue 304 GLU Chi-restraints excluded: chain Ak residue 351 GLN Chi-restraints excluded: chain Ak residue 355 GLU Chi-restraints excluded: chain Ak residue 420 ILE Chi-restraints excluded: chain Al residue 281 PHE Chi-restraints excluded: chain Al residue 284 ARG Chi-restraints excluded: chain Al residue 360 TYR Chi-restraints excluded: chain Al residue 387 VAL Chi-restraints excluded: chain Al residue 518 GLU Chi-restraints excluded: chain Am residue 60 LYS Chi-restraints excluded: chain Am residue 71 TYR Chi-restraints excluded: chain Ar residue 150 ILE Chi-restraints excluded: chain Ar residue 203 TYR Chi-restraints excluded: chain Ar residue 245 LYS Chi-restraints excluded: chain Ar residue 252 GLU Chi-restraints excluded: chain Ar residue 254 VAL Chi-restraints excluded: chain Ar residue 261 THR Chi-restraints excluded: chain Ar residue 302 SER Chi-restraints excluded: chain Ar residue 304 GLU Chi-restraints excluded: chain Ar residue 351 GLN Chi-restraints excluded: chain Ar residue 355 GLU Chi-restraints excluded: chain Ar residue 365 LEU Chi-restraints excluded: chain As residue 104 LEU Chi-restraints excluded: chain As residue 281 PHE Chi-restraints excluded: chain As residue 284 ARG Chi-restraints excluded: chain As residue 360 TYR Chi-restraints excluded: chain As residue 420 ILE Chi-restraints excluded: chain As residue 518 GLU Chi-restraints excluded: chain At residue 25 ILE Chi-restraints excluded: chain At residue 58 ASP Chi-restraints excluded: chain At residue 71 TYR Chi-restraints excluded: chain At residue 95 VAL Chi-restraints excluded: chain Ay residue 150 ILE Chi-restraints excluded: chain Ay residue 203 TYR Chi-restraints excluded: chain Ay residue 245 LYS Chi-restraints excluded: chain Ay residue 252 GLU Chi-restraints excluded: chain Ay residue 304 GLU Chi-restraints excluded: chain Ay residue 351 GLN Chi-restraints excluded: chain Ay residue 355 GLU Chi-restraints excluded: chain Az residue 281 PHE Chi-restraints excluded: chain Az residue 284 ARG Chi-restraints excluded: chain Az residue 360 TYR Chi-restraints excluded: chain Az residue 387 VAL Chi-restraints excluded: chain Ba residue 25 ILE Chi-restraints excluded: chain Ba residue 60 LYS Chi-restraints excluded: chain Ba residue 71 TYR Chi-restraints excluded: chain Ba residue 79 ASP Chi-restraints excluded: chain Ba residue 94 ILE Chi-restraints excluded: chain Ba residue 95 VAL Chi-restraints excluded: chain Bf residue 14 VAL Chi-restraints excluded: chain Bf residue 150 ILE Chi-restraints excluded: chain Bf residue 203 TYR Chi-restraints excluded: chain Bf residue 245 LYS Chi-restraints excluded: chain Bf residue 252 GLU Chi-restraints excluded: chain Bf residue 254 VAL Chi-restraints excluded: chain Bf residue 259 LEU Chi-restraints excluded: chain Bf residue 261 THR Chi-restraints excluded: chain Bf residue 304 GLU Chi-restraints excluded: chain Bf residue 319 GLN Chi-restraints excluded: chain Bf residue 351 GLN Chi-restraints excluded: chain Bf residue 355 GLU Chi-restraints excluded: chain Bf residue 365 LEU Chi-restraints excluded: chain Bg residue 281 PHE Chi-restraints excluded: chain Bg residue 284 ARG Chi-restraints excluded: chain Bg residue 360 TYR Chi-restraints excluded: chain Bg residue 387 VAL Chi-restraints excluded: chain Bh residue 58 ASP Chi-restraints excluded: chain Bh residue 71 TYR Chi-restraints excluded: chain Bh residue 95 VAL Chi-restraints excluded: chain Bm residue 14 VAL Chi-restraints excluded: chain Bm residue 150 ILE Chi-restraints excluded: chain Bm residue 203 TYR Chi-restraints excluded: chain Bm residue 245 LYS Chi-restraints excluded: chain Bm residue 304 GLU Chi-restraints excluded: chain Bm residue 351 GLN Chi-restraints excluded: chain Bm residue 355 GLU Chi-restraints excluded: chain Bm residue 366 GLN Chi-restraints excluded: chain Bn residue 104 LEU Chi-restraints excluded: chain Bn residue 213 VAL Chi-restraints excluded: chain Bn residue 281 PHE Chi-restraints excluded: chain Bn residue 284 ARG Chi-restraints excluded: chain Bn residue 360 TYR Chi-restraints excluded: chain Bo residue 25 ILE Chi-restraints excluded: chain Bo residue 30 SER Chi-restraints excluded: chain Bo residue 58 ASP Chi-restraints excluded: chain Bo residue 71 TYR Chi-restraints excluded: chain Bo residue 95 VAL Chi-restraints excluded: chain Bt residue 11 ASP Chi-restraints excluded: chain Bt residue 150 ILE Chi-restraints excluded: chain Bt residue 203 TYR Chi-restraints excluded: chain Bt residue 245 LYS Chi-restraints excluded: chain Bt residue 304 GLU Chi-restraints excluded: chain Bt residue 351 GLN Chi-restraints excluded: chain Bt residue 355 GLU Chi-restraints excluded: chain Bt residue 420 ILE Chi-restraints excluded: chain Bu residue 281 PHE Chi-restraints excluded: chain Bu residue 360 TYR Chi-restraints excluded: chain Bu residue 387 VAL Chi-restraints excluded: chain Bv residue 71 TYR Chi-restraints excluded: chain Bv residue 95 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 737 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 chunk 436 optimal weight: 0.9990 chunk 558 optimal weight: 9.9990 chunk 433 optimal weight: 4.9990 chunk 644 optimal weight: 0.2980 chunk 427 optimal weight: 3.9990 chunk 762 optimal weight: 8.9990 chunk 477 optimal weight: 40.0000 chunk 464 optimal weight: 5.9990 chunk 351 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ad 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 475 ASN Ad 487 ASN ** Ae 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 453 GLN ** Ak 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 72 GLN ** Al 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 68 ASN ** Ar 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** At 68 ASN ** Ay 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Az 37 ASN ** Az 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bf 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bg 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bm 72 GLN ** Bm 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bn 37 ASN ** Bn 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bt 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bu 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bu 453 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 59906 Z= 0.193 Angle : 0.601 17.136 80955 Z= 0.300 Chirality : 0.042 0.365 9828 Planarity : 0.003 0.039 10542 Dihedral : 8.956 138.636 8750 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.32 % Favored : 96.61 % Rotamer: Outliers : 2.56 % Allowed : 21.12 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.09), residues: 7973 helix: 1.77 (0.08), residues: 4179 sheet: 0.58 (0.16), residues: 1001 loop : -0.82 (0.11), residues: 2793 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HISAk 401 PHE 0.011 0.001 PHEBg 44 TYR 0.009 0.001 TYRAd 360 ARG 0.012 0.000 ARGAr 368 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15946 Ramachandran restraints generated. 7973 Oldfield, 0 Emsley, 7973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15946 Ramachandran restraints generated. 7973 Oldfield, 0 Emsley, 7973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 341 time to evaluate : 5.198 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: Ad 389 MET cc_start: 0.4743 (mmt) cc_final: 0.4483 (tpt) REVERT: At 1 MET cc_start: 0.3114 (tpp) cc_final: 0.2283 (tpp) REVERT: Az 284 ARG cc_start: 0.2541 (OUTLIER) cc_final: 0.1868 (ptm160) REVERT: Bg 73 MET cc_start: 0.6404 (mtm) cc_final: 0.6177 (mtm) REVERT: Bg 284 ARG cc_start: 0.2586 (OUTLIER) cc_final: 0.1854 (ptm160) REVERT: Bh 1 MET cc_start: 0.2697 (tpp) cc_final: 0.2164 (tpt) REVERT: Bm 514 MET cc_start: 0.8278 (mmt) cc_final: 0.8047 (mmm) REVERT: Bt 73 MET cc_start: 0.7294 (mtm) cc_final: 0.7014 (mtm) REVERT: Bt 514 MET cc_start: 0.8142 (mmt) cc_final: 0.7750 (mmm) REVERT: Bv 1 MET cc_start: 0.2532 (tpp) cc_final: 0.1059 (tmm) outliers start: 159 outliers final: 124 residues processed: 469 average time/residue: 0.5532 time to fit residues: 446.3927 Evaluate side-chains 449 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 323 time to evaluate : 5.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ad residue 49 ILE Chi-restraints excluded: chain Ad residue 150 ILE Chi-restraints excluded: chain Ad residue 203 TYR Chi-restraints excluded: chain Ad residue 210 THR Chi-restraints excluded: chain Ad residue 245 LYS Chi-restraints excluded: chain Ad residue 252 GLU Chi-restraints excluded: chain Ad residue 254 VAL Chi-restraints excluded: chain Ad residue 261 THR Chi-restraints excluded: chain Ad residue 304 GLU Chi-restraints excluded: chain Ad residue 351 GLN Chi-restraints excluded: chain Ad residue 355 GLU Chi-restraints excluded: chain Ad residue 420 ILE Chi-restraints excluded: chain Ad residue 483 GLU Chi-restraints excluded: chain Ae residue 176 THR Chi-restraints excluded: chain Ae residue 210 THR Chi-restraints excluded: chain Ae residue 281 PHE Chi-restraints excluded: chain Ae residue 284 ARG Chi-restraints excluded: chain Ae residue 360 TYR Chi-restraints excluded: chain Af residue 25 ILE Chi-restraints excluded: chain Af residue 30 SER Chi-restraints excluded: chain Af residue 71 TYR Chi-restraints excluded: chain Ak residue 11 ASP Chi-restraints excluded: chain Ak residue 150 ILE Chi-restraints excluded: chain Ak residue 203 TYR Chi-restraints excluded: chain Ak residue 245 LYS Chi-restraints excluded: chain Ak residue 252 GLU Chi-restraints excluded: chain Ak residue 259 LEU Chi-restraints excluded: chain Ak residue 261 THR Chi-restraints excluded: chain Ak residue 304 GLU Chi-restraints excluded: chain Ak residue 355 GLU Chi-restraints excluded: chain Al residue 281 PHE Chi-restraints excluded: chain Al residue 284 ARG Chi-restraints excluded: chain Al residue 360 TYR Chi-restraints excluded: chain Al residue 387 VAL Chi-restraints excluded: chain Al residue 518 GLU Chi-restraints excluded: chain Am residue 71 TYR Chi-restraints excluded: chain Ar residue 91 THR Chi-restraints excluded: chain Ar residue 150 ILE Chi-restraints excluded: chain Ar residue 203 TYR Chi-restraints excluded: chain Ar residue 261 THR Chi-restraints excluded: chain Ar residue 302 SER Chi-restraints excluded: chain Ar residue 304 GLU Chi-restraints excluded: chain Ar residue 351 GLN Chi-restraints excluded: chain Ar residue 355 GLU Chi-restraints excluded: chain Ar residue 365 LEU Chi-restraints excluded: chain Ar residue 420 ILE Chi-restraints excluded: chain As residue 281 PHE Chi-restraints excluded: chain As residue 284 ARG Chi-restraints excluded: chain As residue 360 TYR Chi-restraints excluded: chain As residue 420 ILE Chi-restraints excluded: chain At residue 58 ASP Chi-restraints excluded: chain At residue 71 TYR Chi-restraints excluded: chain At residue 95 VAL Chi-restraints excluded: chain Ay residue 150 ILE Chi-restraints excluded: chain Ay residue 203 TYR Chi-restraints excluded: chain Ay residue 245 LYS Chi-restraints excluded: chain Ay residue 304 GLU Chi-restraints excluded: chain Ay residue 351 GLN Chi-restraints excluded: chain Ay residue 355 GLU Chi-restraints excluded: chain Ay residue 420 ILE Chi-restraints excluded: chain Ay residue 483 GLU Chi-restraints excluded: chain Az residue 44 PHE Chi-restraints excluded: chain Az residue 176 THR Chi-restraints excluded: chain Az residue 281 PHE Chi-restraints excluded: chain Az residue 284 ARG Chi-restraints excluded: chain Az residue 360 TYR Chi-restraints excluded: chain Az residue 387 VAL Chi-restraints excluded: chain Ba residue 25 ILE Chi-restraints excluded: chain Ba residue 30 SER Chi-restraints excluded: chain Ba residue 60 LYS Chi-restraints excluded: chain Ba residue 71 TYR Chi-restraints excluded: chain Ba residue 79 ASP Chi-restraints excluded: chain Ba residue 94 ILE Chi-restraints excluded: chain Ba residue 95 VAL Chi-restraints excluded: chain Bf residue 11 ASP Chi-restraints excluded: chain Bf residue 150 ILE Chi-restraints excluded: chain Bf residue 203 TYR Chi-restraints excluded: chain Bf residue 245 LYS Chi-restraints excluded: chain Bf residue 252 GLU Chi-restraints excluded: chain Bf residue 254 VAL Chi-restraints excluded: chain Bf residue 259 LEU Chi-restraints excluded: chain Bf residue 261 THR Chi-restraints excluded: chain Bf residue 304 GLU Chi-restraints excluded: chain Bf residue 355 GLU Chi-restraints excluded: chain Bf residue 420 ILE Chi-restraints excluded: chain Bg residue 213 VAL Chi-restraints excluded: chain Bg residue 281 PHE Chi-restraints excluded: chain Bg residue 284 ARG Chi-restraints excluded: chain Bg residue 360 TYR Chi-restraints excluded: chain Bg residue 387 VAL Chi-restraints excluded: chain Bh residue 58 ASP Chi-restraints excluded: chain Bh residue 71 TYR Chi-restraints excluded: chain Bh residue 95 VAL Chi-restraints excluded: chain Bm residue 14 VAL Chi-restraints excluded: chain Bm residue 150 ILE Chi-restraints excluded: chain Bm residue 203 TYR Chi-restraints excluded: chain Bm residue 245 LYS Chi-restraints excluded: chain Bm residue 302 SER Chi-restraints excluded: chain Bm residue 304 GLU Chi-restraints excluded: chain Bm residue 351 GLN Chi-restraints excluded: chain Bm residue 355 GLU Chi-restraints excluded: chain Bm residue 366 GLN Chi-restraints excluded: chain Bm residue 420 ILE Chi-restraints excluded: chain Bn residue 104 LEU Chi-restraints excluded: chain Bn residue 176 THR Chi-restraints excluded: chain Bn residue 213 VAL Chi-restraints excluded: chain Bn residue 281 PHE Chi-restraints excluded: chain Bn residue 284 ARG Chi-restraints excluded: chain Bn residue 360 TYR Chi-restraints excluded: chain Bn residue 387 VAL Chi-restraints excluded: chain Bo residue 58 ASP Chi-restraints excluded: chain Bo residue 71 TYR Chi-restraints excluded: chain Bo residue 95 VAL Chi-restraints excluded: chain Bt residue 11 ASP Chi-restraints excluded: chain Bt residue 150 ILE Chi-restraints excluded: chain Bt residue 203 TYR Chi-restraints excluded: chain Bt residue 245 LYS Chi-restraints excluded: chain Bt residue 304 GLU Chi-restraints excluded: chain Bt residue 355 GLU Chi-restraints excluded: chain Bu residue 281 PHE Chi-restraints excluded: chain Bu residue 360 TYR Chi-restraints excluded: chain Bu residue 387 VAL Chi-restraints excluded: chain Bu residue 442 VAL Chi-restraints excluded: chain Bv residue 58 ASP Chi-restraints excluded: chain Bv residue 71 TYR Chi-restraints excluded: chain Bv residue 95 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 471 optimal weight: 9.9990 chunk 304 optimal weight: 2.9990 chunk 455 optimal weight: 7.9990 chunk 229 optimal weight: 7.9990 chunk 149 optimal weight: 0.8980 chunk 147 optimal weight: 5.9990 chunk 484 optimal weight: 6.9990 chunk 519 optimal weight: 6.9990 chunk 376 optimal weight: 20.0000 chunk 71 optimal weight: 9.9990 chunk 599 optimal weight: 5.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ad 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 453 GLN ** Ar 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Az 37 ASN Az 82 ASN Az 453 GLN ** Bf 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 37 ASN ** Bg 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bm 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bn 37 ASN ** Bn 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bn 475 ASN ** Bt 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bu 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 59906 Z= 0.413 Angle : 0.682 16.403 80955 Z= 0.344 Chirality : 0.045 0.338 9828 Planarity : 0.004 0.041 10542 Dihedral : 8.917 142.803 8737 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.39 % Favored : 96.53 % Rotamer: Outliers : 2.61 % Allowed : 21.46 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.09), residues: 7973 helix: 1.38 (0.08), residues: 4193 sheet: 0.23 (0.15), residues: 1085 loop : -0.90 (0.11), residues: 2695 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HISAe 401 PHE 0.012 0.002 PHEAl 44 TYR 0.012 0.002 TYRBn 199 ARG 0.009 0.001 ARGBm 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15946 Ramachandran restraints generated. 7973 Oldfield, 0 Emsley, 7973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15946 Ramachandran restraints generated. 7973 Oldfield, 0 Emsley, 7973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 319 time to evaluate : 5.148 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: Ad 389 MET cc_start: 0.5091 (mmt) cc_final: 0.4721 (tpt) REVERT: Ae 491 MET cc_start: 0.7884 (mtm) cc_final: 0.7671 (mtm) REVERT: Al 284 ARG cc_start: 0.3044 (OUTLIER) cc_final: 0.2294 (ptm160) REVERT: Az 284 ARG cc_start: 0.2671 (OUTLIER) cc_final: 0.1887 (ptm160) REVERT: Bg 73 MET cc_start: 0.6551 (mtm) cc_final: 0.6319 (mtm) REVERT: Bg 284 ARG cc_start: 0.2655 (OUTLIER) cc_final: 0.1974 (ptm160) outliers start: 162 outliers final: 137 residues processed: 451 average time/residue: 0.5347 time to fit residues: 417.2362 Evaluate side-chains 458 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 318 time to evaluate : 5.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ad residue 49 ILE Chi-restraints excluded: chain Ad residue 150 ILE Chi-restraints excluded: chain Ad residue 203 TYR Chi-restraints excluded: chain Ad residue 245 LYS Chi-restraints excluded: chain Ad residue 254 VAL Chi-restraints excluded: chain Ad residue 304 GLU Chi-restraints excluded: chain Ad residue 351 GLN Chi-restraints excluded: chain Ad residue 355 GLU Chi-restraints excluded: chain Ad residue 420 ILE Chi-restraints excluded: chain Ad residue 483 GLU Chi-restraints excluded: chain Ae residue 176 THR Chi-restraints excluded: chain Ae residue 210 THR Chi-restraints excluded: chain Ae residue 281 PHE Chi-restraints excluded: chain Ae residue 284 ARG Chi-restraints excluded: chain Ae residue 360 TYR Chi-restraints excluded: chain Af residue 25 ILE Chi-restraints excluded: chain Af residue 30 SER Chi-restraints excluded: chain Af residue 71 TYR Chi-restraints excluded: chain Af residue 95 VAL Chi-restraints excluded: chain Ak residue 11 ASP Chi-restraints excluded: chain Ak residue 91 THR Chi-restraints excluded: chain Ak residue 150 ILE Chi-restraints excluded: chain Ak residue 203 TYR Chi-restraints excluded: chain Ak residue 245 LYS Chi-restraints excluded: chain Ak residue 252 GLU Chi-restraints excluded: chain Ak residue 259 LEU Chi-restraints excluded: chain Ak residue 261 THR Chi-restraints excluded: chain Ak residue 304 GLU Chi-restraints excluded: chain Ak residue 351 GLN Chi-restraints excluded: chain Ak residue 355 GLU Chi-restraints excluded: chain Ak residue 420 ILE Chi-restraints excluded: chain Al residue 114 MET Chi-restraints excluded: chain Al residue 281 PHE Chi-restraints excluded: chain Al residue 284 ARG Chi-restraints excluded: chain Al residue 360 TYR Chi-restraints excluded: chain Al residue 387 VAL Chi-restraints excluded: chain Al residue 442 VAL Chi-restraints excluded: chain Al residue 518 GLU Chi-restraints excluded: chain Am residue 60 LYS Chi-restraints excluded: chain Am residue 71 TYR Chi-restraints excluded: chain Am residue 95 VAL Chi-restraints excluded: chain Ar residue 91 THR Chi-restraints excluded: chain Ar residue 150 ILE Chi-restraints excluded: chain Ar residue 203 TYR Chi-restraints excluded: chain Ar residue 261 THR Chi-restraints excluded: chain Ar residue 302 SER Chi-restraints excluded: chain Ar residue 304 GLU Chi-restraints excluded: chain Ar residue 355 GLU Chi-restraints excluded: chain Ar residue 365 LEU Chi-restraints excluded: chain Ar residue 420 ILE Chi-restraints excluded: chain As residue 104 LEU Chi-restraints excluded: chain As residue 284 ARG Chi-restraints excluded: chain As residue 301 ILE Chi-restraints excluded: chain As residue 360 TYR Chi-restraints excluded: chain As residue 420 ILE Chi-restraints excluded: chain As residue 518 GLU Chi-restraints excluded: chain At residue 58 ASP Chi-restraints excluded: chain At residue 71 TYR Chi-restraints excluded: chain At residue 95 VAL Chi-restraints excluded: chain Ay residue 150 ILE Chi-restraints excluded: chain Ay residue 203 TYR Chi-restraints excluded: chain Ay residue 245 LYS Chi-restraints excluded: chain Ay residue 252 GLU Chi-restraints excluded: chain Ay residue 304 GLU Chi-restraints excluded: chain Ay residue 355 GLU Chi-restraints excluded: chain Ay residue 420 ILE Chi-restraints excluded: chain Ay residue 483 GLU Chi-restraints excluded: chain Az residue 44 PHE Chi-restraints excluded: chain Az residue 176 THR Chi-restraints excluded: chain Az residue 213 VAL Chi-restraints excluded: chain Az residue 281 PHE Chi-restraints excluded: chain Az residue 284 ARG Chi-restraints excluded: chain Az residue 360 TYR Chi-restraints excluded: chain Ba residue 25 ILE Chi-restraints excluded: chain Ba residue 30 SER Chi-restraints excluded: chain Ba residue 60 LYS Chi-restraints excluded: chain Ba residue 71 TYR Chi-restraints excluded: chain Ba residue 79 ASP Chi-restraints excluded: chain Ba residue 95 VAL Chi-restraints excluded: chain Bf residue 11 ASP Chi-restraints excluded: chain Bf residue 150 ILE Chi-restraints excluded: chain Bf residue 203 TYR Chi-restraints excluded: chain Bf residue 245 LYS Chi-restraints excluded: chain Bf residue 252 GLU Chi-restraints excluded: chain Bf residue 254 VAL Chi-restraints excluded: chain Bf residue 259 LEU Chi-restraints excluded: chain Bf residue 261 THR Chi-restraints excluded: chain Bf residue 304 GLU Chi-restraints excluded: chain Bf residue 351 GLN Chi-restraints excluded: chain Bf residue 355 GLU Chi-restraints excluded: chain Bf residue 420 ILE Chi-restraints excluded: chain Bg residue 114 MET Chi-restraints excluded: chain Bg residue 213 VAL Chi-restraints excluded: chain Bg residue 281 PHE Chi-restraints excluded: chain Bg residue 284 ARG Chi-restraints excluded: chain Bg residue 360 TYR Chi-restraints excluded: chain Bg residue 387 VAL Chi-restraints excluded: chain Bg residue 509 SER Chi-restraints excluded: chain Bh residue 58 ASP Chi-restraints excluded: chain Bh residue 71 TYR Chi-restraints excluded: chain Bh residue 95 VAL Chi-restraints excluded: chain Bm residue 14 VAL Chi-restraints excluded: chain Bm residue 91 THR Chi-restraints excluded: chain Bm residue 104 LEU Chi-restraints excluded: chain Bm residue 150 ILE Chi-restraints excluded: chain Bm residue 203 TYR Chi-restraints excluded: chain Bm residue 245 LYS Chi-restraints excluded: chain Bm residue 302 SER Chi-restraints excluded: chain Bm residue 304 GLU Chi-restraints excluded: chain Bm residue 355 GLU Chi-restraints excluded: chain Bm residue 366 GLN Chi-restraints excluded: chain Bm residue 420 ILE Chi-restraints excluded: chain Bn residue 104 LEU Chi-restraints excluded: chain Bn residue 176 THR Chi-restraints excluded: chain Bn residue 213 VAL Chi-restraints excluded: chain Bn residue 281 PHE Chi-restraints excluded: chain Bn residue 284 ARG Chi-restraints excluded: chain Bn residue 360 TYR Chi-restraints excluded: chain Bo residue 30 SER Chi-restraints excluded: chain Bo residue 58 ASP Chi-restraints excluded: chain Bo residue 60 LYS Chi-restraints excluded: chain Bo residue 71 TYR Chi-restraints excluded: chain Bo residue 80 ASN Chi-restraints excluded: chain Bo residue 95 VAL Chi-restraints excluded: chain Bt residue 11 ASP Chi-restraints excluded: chain Bt residue 23 LEU Chi-restraints excluded: chain Bt residue 150 ILE Chi-restraints excluded: chain Bt residue 203 TYR Chi-restraints excluded: chain Bt residue 245 LYS Chi-restraints excluded: chain Bt residue 302 SER Chi-restraints excluded: chain Bt residue 304 GLU Chi-restraints excluded: chain Bt residue 351 GLN Chi-restraints excluded: chain Bt residue 355 GLU Chi-restraints excluded: chain Bt residue 420 ILE Chi-restraints excluded: chain Bu residue 176 THR Chi-restraints excluded: chain Bu residue 360 TYR Chi-restraints excluded: chain Bu residue 387 VAL Chi-restraints excluded: chain Bu residue 442 VAL Chi-restraints excluded: chain Bv residue 71 TYR Chi-restraints excluded: chain Bv residue 95 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 693 optimal weight: 9.9990 chunk 730 optimal weight: 0.0980 chunk 666 optimal weight: 0.7980 chunk 710 optimal weight: 8.9990 chunk 427 optimal weight: 3.9990 chunk 309 optimal weight: 0.0670 chunk 557 optimal weight: 2.9990 chunk 218 optimal weight: 3.9990 chunk 641 optimal weight: 1.9990 chunk 671 optimal weight: 0.9980 chunk 707 optimal weight: 20.0000 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ad 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 290 GLN Ae 453 GLN ** Ak 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 290 GLN Al 453 GLN ** Ar 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Az 37 ASN Az 453 GLN Bf 72 GLN ** Bf 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bf 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 37 ASN ** Bg 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bm 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bm 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bn 37 ASN ** Bn 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bn 290 GLN ** Bt 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bu 72 GLN ** Bu 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bu 290 GLN Bu 453 GLN Bv 68 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 59906 Z= 0.168 Angle : 0.599 16.307 80955 Z= 0.299 Chirality : 0.042 0.296 9828 Planarity : 0.003 0.039 10542 Dihedral : 8.604 140.220 8728 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.44 % Favored : 96.50 % Rotamer: Outliers : 2.01 % Allowed : 22.20 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.09), residues: 7973 helix: 1.82 (0.08), residues: 4123 sheet: 0.58 (0.15), residues: 1064 loop : -0.88 (0.11), residues: 2786 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HISAz 401 PHE 0.011 0.001 PHEBu 281 TYR 0.008 0.001 TYRBu 476 ARG 0.009 0.000 ARGBm 285 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15946 Ramachandran restraints generated. 7973 Oldfield, 0 Emsley, 7973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15946 Ramachandran restraints generated. 7973 Oldfield, 0 Emsley, 7973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 330 time to evaluate : 5.235 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: Ad 389 MET cc_start: 0.5011 (mmt) cc_final: 0.4674 (tpt) REVERT: Al 284 ARG cc_start: 0.3008 (OUTLIER) cc_final: 0.2231 (ptm160) REVERT: Az 73 MET cc_start: 0.6631 (mtm) cc_final: 0.6408 (mtm) REVERT: Az 284 ARG cc_start: 0.2474 (OUTLIER) cc_final: 0.1783 (ptm160) REVERT: Bg 73 MET cc_start: 0.6373 (mtm) cc_final: 0.6152 (mtm) REVERT: Bm 514 MET cc_start: 0.8247 (mmt) cc_final: 0.7989 (mmm) REVERT: Bt 73 MET cc_start: 0.7138 (mtm) cc_final: 0.6839 (mtm) REVERT: Bv 1 MET cc_start: 0.3155 (tpp) cc_final: 0.2307 (tmm) outliers start: 125 outliers final: 110 residues processed: 430 average time/residue: 0.5563 time to fit residues: 407.8293 Evaluate side-chains 432 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 320 time to evaluate : 5.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ad residue 49 ILE Chi-restraints excluded: chain Ad residue 203 TYR Chi-restraints excluded: chain Ad residue 245 LYS Chi-restraints excluded: chain Ad residue 261 THR Chi-restraints excluded: chain Ad residue 304 GLU Chi-restraints excluded: chain Ad residue 355 GLU Chi-restraints excluded: chain Ad residue 420 ILE Chi-restraints excluded: chain Ae residue 210 THR Chi-restraints excluded: chain Ae residue 281 PHE Chi-restraints excluded: chain Ae residue 284 ARG Chi-restraints excluded: chain Af residue 25 ILE Chi-restraints excluded: chain Af residue 30 SER Chi-restraints excluded: chain Af residue 71 TYR Chi-restraints excluded: chain Af residue 95 VAL Chi-restraints excluded: chain Ak residue 11 ASP Chi-restraints excluded: chain Ak residue 150 ILE Chi-restraints excluded: chain Ak residue 203 TYR Chi-restraints excluded: chain Ak residue 245 LYS Chi-restraints excluded: chain Ak residue 252 GLU Chi-restraints excluded: chain Ak residue 259 LEU Chi-restraints excluded: chain Ak residue 304 GLU Chi-restraints excluded: chain Ak residue 355 GLU Chi-restraints excluded: chain Ak residue 420 ILE Chi-restraints excluded: chain Al residue 281 PHE Chi-restraints excluded: chain Al residue 284 ARG Chi-restraints excluded: chain Al residue 360 TYR Chi-restraints excluded: chain Al residue 387 VAL Chi-restraints excluded: chain Am residue 71 TYR Chi-restraints excluded: chain Am residue 95 VAL Chi-restraints excluded: chain Ar residue 150 ILE Chi-restraints excluded: chain Ar residue 203 TYR Chi-restraints excluded: chain Ar residue 261 THR Chi-restraints excluded: chain Ar residue 302 SER Chi-restraints excluded: chain Ar residue 304 GLU Chi-restraints excluded: chain Ar residue 355 GLU Chi-restraints excluded: chain Ar residue 420 ILE Chi-restraints excluded: chain As residue 104 LEU Chi-restraints excluded: chain As residue 284 ARG Chi-restraints excluded: chain As residue 420 ILE Chi-restraints excluded: chain At residue 58 ASP Chi-restraints excluded: chain At residue 71 TYR Chi-restraints excluded: chain At residue 95 VAL Chi-restraints excluded: chain Ay residue 150 ILE Chi-restraints excluded: chain Ay residue 203 TYR Chi-restraints excluded: chain Ay residue 245 LYS Chi-restraints excluded: chain Ay residue 252 GLU Chi-restraints excluded: chain Ay residue 271 VAL Chi-restraints excluded: chain Ay residue 304 GLU Chi-restraints excluded: chain Ay residue 355 GLU Chi-restraints excluded: chain Ay residue 420 ILE Chi-restraints excluded: chain Az residue 44 PHE Chi-restraints excluded: chain Az residue 176 THR Chi-restraints excluded: chain Az residue 281 PHE Chi-restraints excluded: chain Az residue 284 ARG Chi-restraints excluded: chain Az residue 360 TYR Chi-restraints excluded: chain Ba residue 25 ILE Chi-restraints excluded: chain Ba residue 30 SER Chi-restraints excluded: chain Ba residue 71 TYR Chi-restraints excluded: chain Ba residue 79 ASP Chi-restraints excluded: chain Ba residue 95 VAL Chi-restraints excluded: chain Bf residue 11 ASP Chi-restraints excluded: chain Bf residue 91 THR Chi-restraints excluded: chain Bf residue 150 ILE Chi-restraints excluded: chain Bf residue 203 TYR Chi-restraints excluded: chain Bf residue 245 LYS Chi-restraints excluded: chain Bf residue 252 GLU Chi-restraints excluded: chain Bf residue 259 LEU Chi-restraints excluded: chain Bf residue 261 THR Chi-restraints excluded: chain Bf residue 300 VAL Chi-restraints excluded: chain Bf residue 304 GLU Chi-restraints excluded: chain Bf residue 355 GLU Chi-restraints excluded: chain Bf residue 420 ILE Chi-restraints excluded: chain Bg residue 213 VAL Chi-restraints excluded: chain Bg residue 281 PHE Chi-restraints excluded: chain Bg residue 284 ARG Chi-restraints excluded: chain Bg residue 360 TYR Chi-restraints excluded: chain Bg residue 387 VAL Chi-restraints excluded: chain Bh residue 58 ASP Chi-restraints excluded: chain Bh residue 71 TYR Chi-restraints excluded: chain Bh residue 95 VAL Chi-restraints excluded: chain Bm residue 150 ILE Chi-restraints excluded: chain Bm residue 203 TYR Chi-restraints excluded: chain Bm residue 245 LYS Chi-restraints excluded: chain Bm residue 302 SER Chi-restraints excluded: chain Bm residue 304 GLU Chi-restraints excluded: chain Bm residue 355 GLU Chi-restraints excluded: chain Bm residue 366 GLN Chi-restraints excluded: chain Bm residue 420 ILE Chi-restraints excluded: chain Bn residue 104 LEU Chi-restraints excluded: chain Bn residue 176 THR Chi-restraints excluded: chain Bn residue 213 VAL Chi-restraints excluded: chain Bn residue 281 PHE Chi-restraints excluded: chain Bn residue 284 ARG Chi-restraints excluded: chain Bo residue 25 ILE Chi-restraints excluded: chain Bo residue 58 ASP Chi-restraints excluded: chain Bo residue 71 TYR Chi-restraints excluded: chain Bo residue 95 VAL Chi-restraints excluded: chain Bt residue 11 ASP Chi-restraints excluded: chain Bt residue 150 ILE Chi-restraints excluded: chain Bt residue 203 TYR Chi-restraints excluded: chain Bt residue 245 LYS Chi-restraints excluded: chain Bt residue 302 SER Chi-restraints excluded: chain Bt residue 304 GLU Chi-restraints excluded: chain Bt residue 351 GLN Chi-restraints excluded: chain Bt residue 355 GLU Chi-restraints excluded: chain Bt residue 420 ILE Chi-restraints excluded: chain Bu residue 360 TYR Chi-restraints excluded: chain Bu residue 387 VAL Chi-restraints excluded: chain Bu residue 442 VAL Chi-restraints excluded: chain Bv residue 68 ASN Chi-restraints excluded: chain Bv residue 71 TYR Chi-restraints excluded: chain Bv residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 466 optimal weight: 2.9990 chunk 751 optimal weight: 5.9990 chunk 458 optimal weight: 6.9990 chunk 356 optimal weight: 20.0000 chunk 522 optimal weight: 7.9990 chunk 788 optimal weight: 5.9990 chunk 725 optimal weight: 7.9990 chunk 627 optimal weight: 0.7980 chunk 65 optimal weight: 0.0870 chunk 484 optimal weight: 40.0000 chunk 384 optimal weight: 0.1980 overall best weight: 2.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ad 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 453 GLN ** Ak 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 453 GLN Am 68 ASN ** Ar 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** As 290 GLN ** Ay 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Az 37 ASN Az 453 GLN ** Bf 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 37 ASN ** Bg 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 290 GLN ** Bm 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bn 37 ASN ** Bn 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bt 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bt 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bu 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bu 453 GLN Bv 68 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 59906 Z= 0.234 Angle : 0.624 16.622 80955 Z= 0.309 Chirality : 0.042 0.315 9828 Planarity : 0.003 0.036 10542 Dihedral : 8.533 141.637 8725 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.31 % Favored : 96.63 % Rotamer: Outliers : 1.95 % Allowed : 22.35 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.09), residues: 7973 helix: 1.78 (0.08), residues: 4130 sheet: 0.60 (0.16), residues: 1064 loop : -0.86 (0.11), residues: 2779 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HISAk 401 PHE 0.014 0.001 PHEBv 67 TYR 0.009 0.001 TYRBg 199 ARG 0.008 0.000 ARGBt 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15946 Ramachandran restraints generated. 7973 Oldfield, 0 Emsley, 7973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15946 Ramachandran restraints generated. 7973 Oldfield, 0 Emsley, 7973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 321 time to evaluate : 5.221 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: Ad 389 MET cc_start: 0.5063 (mmt) cc_final: 0.4733 (tpt) REVERT: Az 284 ARG cc_start: 0.2495 (OUTLIER) cc_final: 0.1758 (ptm160) REVERT: Bf 16 MET cc_start: 0.7503 (mtm) cc_final: 0.7245 (mtm) REVERT: Bg 73 MET cc_start: 0.6458 (mtm) cc_final: 0.6229 (mtm) REVERT: Bh 1 MET cc_start: 0.3132 (tpp) cc_final: 0.2170 (tmm) REVERT: Bm 514 MET cc_start: 0.8280 (mmt) cc_final: 0.8044 (mmm) REVERT: Bt 73 MET cc_start: 0.7159 (mtm) cc_final: 0.6931 (mtm) REVERT: Bv 1 MET cc_start: 0.2924 (tpp) cc_final: 0.2086 (tmm) outliers start: 121 outliers final: 112 residues processed: 421 average time/residue: 0.5587 time to fit residues: 405.7305 Evaluate side-chains 433 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 320 time to evaluate : 5.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ad residue 49 ILE Chi-restraints excluded: chain Ad residue 203 TYR Chi-restraints excluded: chain Ad residue 245 LYS Chi-restraints excluded: chain Ad residue 261 THR Chi-restraints excluded: chain Ad residue 304 GLU Chi-restraints excluded: chain Ad residue 355 GLU Chi-restraints excluded: chain Ad residue 420 ILE Chi-restraints excluded: chain Ae residue 176 THR Chi-restraints excluded: chain Ae residue 210 THR Chi-restraints excluded: chain Ae residue 281 PHE Chi-restraints excluded: chain Ae residue 284 ARG Chi-restraints excluded: chain Af residue 25 ILE Chi-restraints excluded: chain Af residue 30 SER Chi-restraints excluded: chain Af residue 71 TYR Chi-restraints excluded: chain Af residue 95 VAL Chi-restraints excluded: chain Ak residue 11 ASP Chi-restraints excluded: chain Ak residue 150 ILE Chi-restraints excluded: chain Ak residue 203 TYR Chi-restraints excluded: chain Ak residue 245 LYS Chi-restraints excluded: chain Ak residue 252 GLU Chi-restraints excluded: chain Ak residue 259 LEU Chi-restraints excluded: chain Ak residue 304 GLU Chi-restraints excluded: chain Ak residue 355 GLU Chi-restraints excluded: chain Ak residue 420 ILE Chi-restraints excluded: chain Al residue 284 ARG Chi-restraints excluded: chain Al residue 360 TYR Chi-restraints excluded: chain Al residue 387 VAL Chi-restraints excluded: chain Al residue 442 VAL Chi-restraints excluded: chain Am residue 68 ASN Chi-restraints excluded: chain Am residue 71 TYR Chi-restraints excluded: chain Am residue 95 VAL Chi-restraints excluded: chain Ar residue 91 THR Chi-restraints excluded: chain Ar residue 150 ILE Chi-restraints excluded: chain Ar residue 203 TYR Chi-restraints excluded: chain Ar residue 261 THR Chi-restraints excluded: chain Ar residue 302 SER Chi-restraints excluded: chain Ar residue 304 GLU Chi-restraints excluded: chain Ar residue 355 GLU Chi-restraints excluded: chain Ar residue 366 GLN Chi-restraints excluded: chain Ar residue 420 ILE Chi-restraints excluded: chain As residue 104 LEU Chi-restraints excluded: chain As residue 284 ARG Chi-restraints excluded: chain As residue 420 ILE Chi-restraints excluded: chain At residue 58 ASP Chi-restraints excluded: chain At residue 71 TYR Chi-restraints excluded: chain At residue 95 VAL Chi-restraints excluded: chain Ay residue 150 ILE Chi-restraints excluded: chain Ay residue 203 TYR Chi-restraints excluded: chain Ay residue 245 LYS Chi-restraints excluded: chain Ay residue 252 GLU Chi-restraints excluded: chain Ay residue 271 VAL Chi-restraints excluded: chain Ay residue 304 GLU Chi-restraints excluded: chain Ay residue 355 GLU Chi-restraints excluded: chain Ay residue 366 GLN Chi-restraints excluded: chain Ay residue 420 ILE Chi-restraints excluded: chain Az residue 44 PHE Chi-restraints excluded: chain Az residue 176 THR Chi-restraints excluded: chain Az residue 281 PHE Chi-restraints excluded: chain Az residue 284 ARG Chi-restraints excluded: chain Az residue 360 TYR Chi-restraints excluded: chain Ba residue 25 ILE Chi-restraints excluded: chain Ba residue 30 SER Chi-restraints excluded: chain Ba residue 60 LYS Chi-restraints excluded: chain Ba residue 71 TYR Chi-restraints excluded: chain Ba residue 79 ASP Chi-restraints excluded: chain Ba residue 95 VAL Chi-restraints excluded: chain Bf residue 11 ASP Chi-restraints excluded: chain Bf residue 91 THR Chi-restraints excluded: chain Bf residue 150 ILE Chi-restraints excluded: chain Bf residue 203 TYR Chi-restraints excluded: chain Bf residue 245 LYS Chi-restraints excluded: chain Bf residue 252 GLU Chi-restraints excluded: chain Bf residue 259 LEU Chi-restraints excluded: chain Bf residue 261 THR Chi-restraints excluded: chain Bf residue 271 VAL Chi-restraints excluded: chain Bf residue 300 VAL Chi-restraints excluded: chain Bf residue 304 GLU Chi-restraints excluded: chain Bf residue 355 GLU Chi-restraints excluded: chain Bf residue 420 ILE Chi-restraints excluded: chain Bg residue 213 VAL Chi-restraints excluded: chain Bg residue 281 PHE Chi-restraints excluded: chain Bg residue 284 ARG Chi-restraints excluded: chain Bg residue 360 TYR Chi-restraints excluded: chain Bg residue 387 VAL Chi-restraints excluded: chain Bh residue 58 ASP Chi-restraints excluded: chain Bh residue 71 TYR Chi-restraints excluded: chain Bh residue 95 VAL Chi-restraints excluded: chain Bm residue 150 ILE Chi-restraints excluded: chain Bm residue 203 TYR Chi-restraints excluded: chain Bm residue 245 LYS Chi-restraints excluded: chain Bm residue 302 SER Chi-restraints excluded: chain Bm residue 304 GLU Chi-restraints excluded: chain Bm residue 366 GLN Chi-restraints excluded: chain Bm residue 420 ILE Chi-restraints excluded: chain Bn residue 104 LEU Chi-restraints excluded: chain Bn residue 176 THR Chi-restraints excluded: chain Bn residue 213 VAL Chi-restraints excluded: chain Bn residue 281 PHE Chi-restraints excluded: chain Bn residue 284 ARG Chi-restraints excluded: chain Bo residue 58 ASP Chi-restraints excluded: chain Bo residue 71 TYR Chi-restraints excluded: chain Bo residue 95 VAL Chi-restraints excluded: chain Bt residue 11 ASP Chi-restraints excluded: chain Bt residue 150 ILE Chi-restraints excluded: chain Bt residue 203 TYR Chi-restraints excluded: chain Bt residue 245 LYS Chi-restraints excluded: chain Bt residue 302 SER Chi-restraints excluded: chain Bt residue 304 GLU Chi-restraints excluded: chain Bt residue 420 ILE Chi-restraints excluded: chain Bu residue 387 VAL Chi-restraints excluded: chain Bu residue 442 VAL Chi-restraints excluded: chain Bv residue 71 TYR Chi-restraints excluded: chain Bv residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 498 optimal weight: 0.7980 chunk 668 optimal weight: 0.4980 chunk 192 optimal weight: 20.0000 chunk 578 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 174 optimal weight: 1.9990 chunk 628 optimal weight: 2.9990 chunk 263 optimal weight: 6.9990 chunk 645 optimal weight: 8.9990 chunk 79 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ad 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 453 GLN ** Ak 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ak 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ar 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ay 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Az 37 ASN ** Bf 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 37 ASN ** Bg 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bm 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bn 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bt 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bt 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bu 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bv 68 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.068979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.048711 restraints weight = 262905.657| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 3.02 r_work: 0.2934 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.228 59906 Z= 0.264 Angle : 0.677 59.199 80955 Z= 0.352 Chirality : 0.043 1.016 9828 Planarity : 0.003 0.058 10542 Dihedral : 8.519 141.614 8719 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.31 % Favored : 96.63 % Rotamer: Outliers : 1.88 % Allowed : 22.46 % Favored : 75.66 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 1.08 (0.09), residues: 7973 helix: 1.78 (0.08), residues: 4130 sheet: 0.60 (0.16), residues: 1064 loop : -0.86 (0.11), residues: 2779 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HISAk 401 PHE 0.012 0.001 PHEBu 281 TYR 0.008 0.001 TYRBg 199 ARG 0.009 0.000 ARGAy 368 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10650.57 seconds wall clock time: 190 minutes 19.52 seconds (11419.52 seconds total)