Starting phenix.real_space_refine on Mon Mar 11 19:41:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbx_13308/03_2024/7pbx_13308_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbx_13308/03_2024/7pbx_13308.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbx_13308/03_2024/7pbx_13308.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbx_13308/03_2024/7pbx_13308.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbx_13308/03_2024/7pbx_13308_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbx_13308/03_2024/7pbx_13308_updated.pdb" } resolution = 3.43 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= 0.187 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 11991 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Ac GLU 129": "OE1" <-> "OE2" Residue "Ac GLU 156": "OE1" <-> "OE2" Residue "Ac GLU 186": "OE1" <-> "OE2" Residue "Ac GLU 191": "OE1" <-> "OE2" Residue "Ac GLU 255": "OE1" <-> "OE2" Residue "Ac GLU 257": "OE1" <-> "OE2" Residue "Ac GLU 303": "OE1" <-> "OE2" Residue "Ac GLU 304": "OE1" <-> "OE2" Residue "Ac GLU 391": "OE1" <-> "OE2" Residue "Ac GLU 518": "OE1" <-> "OE2" Residue "Ad GLU 156": "OE1" <-> "OE2" Residue "Ad GLU 172": "OE1" <-> "OE2" Residue "Ad GLU 178": "OE1" <-> "OE2" Residue "Ad GLU 191": "OE1" <-> "OE2" Residue "Ad GLU 214": "OE1" <-> "OE2" Residue "Ad PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ad GLU 232": "OE1" <-> "OE2" Residue "Ad GLU 238": "OE1" <-> "OE2" Residue "Ad GLU 252": "OE1" <-> "OE2" Residue "Ad GLU 255": "OE1" <-> "OE2" Residue "Ad GLU 303": "OE1" <-> "OE2" Residue "Ad GLU 315": "OE1" <-> "OE2" Residue "Ad GLU 338": "OE1" <-> "OE2" Residue "Ad GLU 355": "OE1" <-> "OE2" Residue "Ad GLU 367": "OE1" <-> "OE2" Residue "Ad GLU 386": "OE1" <-> "OE2" Residue "Ad GLU 388": "OE1" <-> "OE2" Residue "Ad GLU 397": "OE1" <-> "OE2" Residue "Ad GLU 434": "OE1" <-> "OE2" Residue "Ad GLU 484": "OE1" <-> "OE2" Residue "Af GLU 39": "OE1" <-> "OE2" Residue "Af GLU 50": "OE1" <-> "OE2" Residue "Af GLU 53": "OE1" <-> "OE2" Residue "Af GLU 82": "OE1" <-> "OE2" Residue "Ai GLU 129": "OE1" <-> "OE2" Residue "Ai GLU 156": "OE1" <-> "OE2" Residue "Ai GLU 186": "OE1" <-> "OE2" Residue "Ai GLU 191": "OE1" <-> "OE2" Residue "Ai GLU 255": "OE1" <-> "OE2" Residue "Ai GLU 257": "OE1" <-> "OE2" Residue "Ai GLU 303": "OE1" <-> "OE2" Residue "Ai GLU 304": "OE1" <-> "OE2" Residue "Ai GLU 391": "OE1" <-> "OE2" Residue "Ai GLU 518": "OE1" <-> "OE2" Residue "Aj GLU 156": "OE1" <-> "OE2" Residue "Aj GLU 172": "OE1" <-> "OE2" Residue "Aj GLU 178": "OE1" <-> "OE2" Residue "Aj GLU 191": "OE1" <-> "OE2" Residue "Aj GLU 214": "OE1" <-> "OE2" Residue "Aj PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Aj GLU 232": "OE1" <-> "OE2" Residue "Aj GLU 238": "OE1" <-> "OE2" Residue "Aj GLU 252": "OE1" <-> "OE2" Residue "Aj GLU 255": "OE1" <-> "OE2" Residue "Aj GLU 303": "OE1" <-> "OE2" Residue "Aj GLU 315": "OE1" <-> "OE2" Residue "Aj GLU 338": "OE1" <-> "OE2" Residue "Aj GLU 355": "OE1" <-> "OE2" Residue "Aj GLU 367": "OE1" <-> "OE2" Residue "Aj GLU 386": "OE1" <-> "OE2" Residue "Aj GLU 388": "OE1" <-> "OE2" Residue "Aj GLU 397": "OE1" <-> "OE2" Residue "Aj GLU 434": "OE1" <-> "OE2" Residue "Aj GLU 484": "OE1" <-> "OE2" Residue "Al GLU 39": "OE1" <-> "OE2" Residue "Al GLU 50": "OE1" <-> "OE2" Residue "Al GLU 53": "OE1" <-> "OE2" Residue "Al GLU 82": "OE1" <-> "OE2" Residue "Ao GLU 129": "OE1" <-> "OE2" Residue "Ao GLU 156": "OE1" <-> "OE2" Residue "Ao GLU 186": "OE1" <-> "OE2" Residue "Ao GLU 191": "OE1" <-> "OE2" Residue "Ao GLU 255": "OE1" <-> "OE2" Residue "Ao GLU 257": "OE1" <-> "OE2" Residue "Ao GLU 303": "OE1" <-> "OE2" Residue "Ao GLU 304": "OE1" <-> "OE2" Residue "Ao GLU 391": "OE1" <-> "OE2" Residue "Ao GLU 518": "OE1" <-> "OE2" Residue "Ap GLU 156": "OE1" <-> "OE2" Residue "Ap GLU 172": "OE1" <-> "OE2" Residue "Ap GLU 178": "OE1" <-> "OE2" Residue "Ap GLU 191": "OE1" <-> "OE2" Residue "Ap GLU 214": "OE1" <-> "OE2" Residue "Ap PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ap GLU 232": "OE1" <-> "OE2" Residue "Ap GLU 238": "OE1" <-> "OE2" Residue "Ap GLU 252": "OE1" <-> "OE2" Residue "Ap GLU 255": "OE1" <-> "OE2" Residue "Ap GLU 303": "OE1" <-> "OE2" Residue "Ap GLU 315": "OE1" <-> "OE2" Residue "Ap GLU 338": "OE1" <-> "OE2" Residue "Ap GLU 355": "OE1" <-> "OE2" Residue "Ap GLU 367": "OE1" <-> "OE2" Residue "Ap GLU 386": "OE1" <-> "OE2" Residue "Ap GLU 388": "OE1" <-> "OE2" Residue "Ap GLU 397": "OE1" <-> "OE2" Residue "Ap GLU 434": "OE1" <-> "OE2" Residue "Ap GLU 484": "OE1" <-> "OE2" Residue "Ar GLU 39": "OE1" <-> "OE2" Residue "Ar GLU 50": "OE1" <-> "OE2" Residue "Ar GLU 53": "OE1" <-> "OE2" Residue "Ar GLU 82": "OE1" <-> "OE2" Residue "Au GLU 129": "OE1" <-> "OE2" Residue "Au GLU 156": "OE1" <-> "OE2" Residue "Au GLU 186": "OE1" <-> "OE2" Residue "Au GLU 191": "OE1" <-> "OE2" Residue "Au GLU 255": "OE1" <-> "OE2" Residue "Au GLU 257": "OE1" <-> "OE2" Residue "Au GLU 303": "OE1" <-> "OE2" Residue "Au GLU 304": "OE1" <-> "OE2" Residue "Au GLU 391": "OE1" <-> "OE2" Residue "Au GLU 518": "OE1" <-> "OE2" Residue "Av GLU 156": "OE1" <-> "OE2" Residue "Av GLU 172": "OE1" <-> "OE2" Residue "Av GLU 178": "OE1" <-> "OE2" Residue "Av GLU 191": "OE1" <-> "OE2" Residue "Av GLU 214": "OE1" <-> "OE2" Residue "Av PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Av GLU 232": "OE1" <-> "OE2" Residue "Av GLU 238": "OE1" <-> "OE2" Residue "Av GLU 252": "OE1" <-> "OE2" Residue "Av GLU 255": "OE1" <-> "OE2" Residue "Av GLU 303": "OE1" <-> "OE2" Residue "Av GLU 315": "OE1" <-> "OE2" Residue "Av GLU 338": "OE1" <-> "OE2" Residue "Av GLU 355": "OE1" <-> "OE2" Residue "Av GLU 367": "OE1" <-> "OE2" Residue "Av GLU 386": "OE1" <-> "OE2" Residue "Av GLU 388": "OE1" <-> "OE2" Residue "Av GLU 397": "OE1" <-> "OE2" Residue "Av GLU 434": "OE1" <-> "OE2" Residue "Av GLU 484": "OE1" <-> "OE2" Residue "Ax GLU 39": "OE1" <-> "OE2" Residue "Ax GLU 50": "OE1" <-> "OE2" Residue "Ax GLU 53": "OE1" <-> "OE2" Residue "Ax GLU 82": "OE1" <-> "OE2" Residue "Ba GLU 129": "OE1" <-> "OE2" Residue "Ba GLU 156": "OE1" <-> "OE2" Residue "Ba GLU 186": "OE1" <-> "OE2" Residue "Ba GLU 191": "OE1" <-> "OE2" Residue "Ba GLU 255": "OE1" <-> "OE2" Residue "Ba GLU 257": "OE1" <-> "OE2" Residue "Ba GLU 303": "OE1" <-> "OE2" Residue "Ba GLU 304": "OE1" <-> "OE2" Residue "Ba GLU 391": "OE1" <-> "OE2" Residue "Ba GLU 518": "OE1" <-> "OE2" Residue "Bb GLU 156": "OE1" <-> "OE2" Residue "Bb GLU 172": "OE1" <-> "OE2" Residue "Bb GLU 178": "OE1" <-> "OE2" Residue "Bb GLU 191": "OE1" <-> "OE2" Residue "Bb GLU 214": "OE1" <-> "OE2" Residue "Bb PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bb GLU 232": "OE1" <-> "OE2" Residue "Bb GLU 238": "OE1" <-> "OE2" Residue "Bb GLU 252": "OE1" <-> "OE2" Residue "Bb GLU 255": "OE1" <-> "OE2" Residue "Bb GLU 303": "OE1" <-> "OE2" Residue "Bb GLU 315": "OE1" <-> "OE2" Residue "Bb GLU 338": "OE1" <-> "OE2" Residue "Bb GLU 355": "OE1" <-> "OE2" Residue "Bb GLU 367": "OE1" <-> "OE2" Residue "Bb GLU 386": "OE1" <-> "OE2" Residue "Bb GLU 388": "OE1" <-> "OE2" Residue "Bb GLU 397": "OE1" <-> "OE2" Residue "Bb GLU 434": "OE1" <-> "OE2" Residue "Bb GLU 484": "OE1" <-> "OE2" Residue "Bd GLU 39": "OE1" <-> "OE2" Residue "Bd GLU 50": "OE1" <-> "OE2" Residue "Bd GLU 53": "OE1" <-> "OE2" Residue "Bd GLU 82": "OE1" <-> "OE2" Residue "Bg GLU 129": "OE1" <-> "OE2" Residue "Bg GLU 156": "OE1" <-> "OE2" Residue "Bg GLU 186": "OE1" <-> "OE2" Residue "Bg GLU 191": "OE1" <-> "OE2" Residue "Bg GLU 255": "OE1" <-> "OE2" Residue "Bg GLU 257": "OE1" <-> "OE2" Residue "Bg GLU 303": "OE1" <-> "OE2" Residue "Bg GLU 304": "OE1" <-> "OE2" Residue "Bg GLU 391": "OE1" <-> "OE2" Residue "Bg GLU 518": "OE1" <-> "OE2" Residue "Bh GLU 156": "OE1" <-> "OE2" Residue "Bh GLU 172": "OE1" <-> "OE2" Residue "Bh GLU 178": "OE1" <-> "OE2" Residue "Bh GLU 191": "OE1" <-> "OE2" Residue "Bh GLU 214": "OE1" <-> "OE2" Residue "Bh PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bh GLU 232": "OE1" <-> "OE2" Residue "Bh GLU 238": "OE1" <-> "OE2" Residue "Bh GLU 252": "OE1" <-> "OE2" Residue "Bh GLU 255": "OE1" <-> "OE2" Residue "Bh GLU 303": "OE1" <-> "OE2" Residue "Bh GLU 315": "OE1" <-> "OE2" Residue "Bh GLU 338": "OE1" <-> "OE2" Residue "Bh GLU 355": "OE1" <-> "OE2" Residue "Bh GLU 367": "OE1" <-> "OE2" Residue "Bh GLU 386": "OE1" <-> "OE2" Residue "Bh GLU 388": "OE1" <-> "OE2" Residue "Bh GLU 397": "OE1" <-> "OE2" Residue "Bh GLU 434": "OE1" <-> "OE2" Residue "Bh GLU 484": "OE1" <-> "OE2" Residue "Bj GLU 39": "OE1" <-> "OE2" Residue "Bj GLU 50": "OE1" <-> "OE2" Residue "Bj GLU 53": "OE1" <-> "OE2" Residue "Bj GLU 82": "OE1" <-> "OE2" Residue "Bm GLU 129": "OE1" <-> "OE2" Residue "Bm GLU 156": "OE1" <-> "OE2" Residue "Bm GLU 186": "OE1" <-> "OE2" Residue "Bm GLU 191": "OE1" <-> "OE2" Residue "Bm GLU 255": "OE1" <-> "OE2" Residue "Bm GLU 257": "OE1" <-> "OE2" Residue "Bm GLU 303": "OE1" <-> "OE2" Residue "Bm GLU 304": "OE1" <-> "OE2" Residue "Bm GLU 391": "OE1" <-> "OE2" Residue "Bm GLU 518": "OE1" <-> "OE2" Residue "Bn GLU 156": "OE1" <-> "OE2" Residue "Bn GLU 172": "OE1" <-> "OE2" Residue "Bn GLU 178": "OE1" <-> "OE2" Residue "Bn GLU 191": "OE1" <-> "OE2" Residue "Bn GLU 214": "OE1" <-> "OE2" Residue "Bn PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bn GLU 232": "OE1" <-> "OE2" Residue "Bn GLU 238": "OE1" <-> "OE2" Residue "Bn GLU 252": "OE1" <-> "OE2" Residue "Bn GLU 255": "OE1" <-> "OE2" Residue "Bn GLU 303": "OE1" <-> "OE2" Residue "Bn GLU 315": "OE1" <-> "OE2" Residue "Bn GLU 338": "OE1" <-> "OE2" Residue "Bn GLU 355": "OE1" <-> "OE2" Residue "Bn GLU 367": "OE1" <-> "OE2" Residue "Bn GLU 386": "OE1" <-> "OE2" Residue "Bn GLU 388": "OE1" <-> "OE2" Residue "Bn GLU 397": "OE1" <-> "OE2" Residue "Bn GLU 434": "OE1" <-> "OE2" Residue "Bn GLU 484": "OE1" <-> "OE2" Residue "Bp GLU 39": "OE1" <-> "OE2" Residue "Bp GLU 50": "OE1" <-> "OE2" Residue "Bp GLU 53": "OE1" <-> "OE2" Residue "Bp GLU 82": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 59472 Number of models: 1 Model: "" Number of chains: 35 Chain: "Ac" 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: "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: "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: {'CIS': 1, 'PTRANS': 2, 'TRANS': 93} Chain: "Ai" 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: "Aj" 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: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 728 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 93} Chain: "Ao" 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: "Ap" 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: "Ar" Number of atoms: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 728 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 93} Chain: "Au" 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: "Av" 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: "Ax" Number of atoms: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 728 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 93} Chain: "Ba" 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: "Bb" 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: "Bd" Number of atoms: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 728 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 93} 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: 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: "Bj" Number of atoms: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 728 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 93} 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: "Bp" Number of atoms: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 728 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 93} Chain: "Ac" 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: 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: "Ai" 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: "Aj" 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: "Ao" 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: "Ap" 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: "Au" 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: "Av" 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: "Ba" 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: "Bb" 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: "Bh" 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} Time building chain proxies: 22.13, per 1000 atoms: 0.37 Number of scatterers: 59472 At special positions: 0 Unit cell: (157.194, 158.301, 214.758, 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 11991 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: 17.91 Conformation dependent library (CDL) restraints added in 9.2 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: 287 helices and 105 sheets defined 50.4% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.11 Creating SS restraints... Processing helix chain 'Ac' and resid 9 through 30 removed outlier: 4.212A pdb=" N THRAc 30 " --> pdb=" O ALAAc 26 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 53 through 59 Processing helix chain 'Ac' and resid 65 through 84 Processing helix chain 'Ac' and resid 89 through 109 Processing helix chain 'Ac' and resid 113 through 134 Processing helix chain 'Ac' and resid 141 through 151 removed outlier: 3.759A pdb=" N GLNAc 146 " --> pdb=" O LYSAc 142 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 156 through 168 removed outlier: 3.644A pdb=" N LEUAc 161 " --> pdb=" O THRAc 157 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 230 through 243 Proline residue: Ac 235 - end of helix removed outlier: 3.703A pdb=" N ALAAc 243 " --> pdb=" O ALAAc 239 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 256 through 267 removed outlier: 4.706A pdb=" N THRAc 261 " --> pdb=" O GLUAc 257 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N VALAc 264 " --> pdb=" O ALAAc 260 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASNAc 265 " --> pdb=" O THRAc 261 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 282 through 296 Processing helix chain 'Ac' and resid 339 through 354 removed outlier: 4.326A pdb=" N ARGAc 345 " --> pdb=" O ALAAc 341 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VALAc 346 " --> pdb=" O ILEAc 342 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ALAAc 347 " --> pdb=" O GLNAc 343 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLNAc 348 " --> pdb=" O GLYAc 344 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILEAc 353 " --> pdb=" O ILEAc 349 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLUAc 354 " --> pdb=" O ARGAc 350 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 359 through 374 removed outlier: 3.758A pdb=" N ALAAc 370 " --> pdb=" O GLNAc 366 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 386 through 409 removed outlier: 3.681A pdb=" N ALAAc 394 " --> pdb=" O LYSAc 390 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ARGAc 395 " --> pdb=" O GLUAc 391 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 417 through 428 removed outlier: 5.232A pdb=" N ASPAc 428 " --> pdb=" O SERAc 424 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 434 through 458 removed outlier: 3.688A pdb=" N GLUAc 448 " --> pdb=" O LEUAc 444 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALAAc 449 " --> pdb=" O ARGAc 445 " (cutoff:3.500A) Proline residue: Ac 450 - end of helix Processing helix chain 'Ac' and resid 462 through 471 Processing helix chain 'Ac' and resid 488 through 491 No H-bonds generated for 'chain 'Ac' and resid 488 through 491' Processing helix chain 'Ac' and resid 497 through 515 Processing helix chain 'Ad' and resid 9 through 30 removed outlier: 4.138A 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 removed outlier: 3.620A pdb=" N GLYAd 70 " --> pdb=" O PHEAd 66 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLUAd 76 " --> pdb=" O GLNAd 72 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VALAd 77 " --> pdb=" O METAd 73 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALAAd 78 " --> pdb=" O VALAd 74 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 89 through 108 Processing helix chain 'Ad' and resid 113 through 134 Processing helix chain 'Ad' and resid 141 through 152 Processing helix chain 'Ad' and resid 156 through 169 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 256 through 266 removed outlier: 4.072A pdb=" N THRAd 261 " --> pdb=" O GLUAd 257 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 282 through 296 removed outlier: 3.509A pdb=" N ASPAd 291 " --> pdb=" O ALAAd 287 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 309 through 311 No H-bonds generated for 'chain 'Ad' and resid 309 through 311' Processing helix chain 'Ad' and resid 339 through 354 Processing helix chain 'Ad' and resid 359 through 372 Processing helix chain 'Ad' and resid 386 through 409 Processing helix chain 'Ad' and resid 417 through 426 Processing helix chain 'Ad' and resid 434 through 458 removed outlier: 3.728A pdb=" N GLUAd 448 " --> pdb=" O LEUAd 444 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALAAd 449 " --> pdb=" O ARGAd 445 " (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 515 Processing helix chain 'Af' and resid 22 through 24 No H-bonds generated for 'chain 'Af' and resid 22 through 24' Processing helix chain 'Af' and resid 49 through 51 No H-bonds generated for 'chain 'Af' and resid 49 through 51' Processing helix chain 'Af' and resid 88 through 90 No H-bonds generated for 'chain 'Af' and resid 88 through 90' Processing helix chain 'Ai' and resid 9 through 30 removed outlier: 4.212A pdb=" N THRAi 30 " --> pdb=" O ALAAi 26 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 53 through 59 Processing helix chain 'Ai' and resid 65 through 84 Processing helix chain 'Ai' and resid 89 through 109 Processing helix chain 'Ai' and resid 113 through 134 Processing helix chain 'Ai' and resid 141 through 151 removed outlier: 3.760A pdb=" N GLNAi 146 " --> pdb=" O LYSAi 142 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 156 through 168 removed outlier: 3.643A pdb=" N LEUAi 161 " --> pdb=" O THRAi 157 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 230 through 243 Proline residue: Ai 235 - end of helix removed outlier: 3.703A pdb=" N ALAAi 243 " --> pdb=" O ALAAi 239 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 256 through 267 removed outlier: 4.706A pdb=" N THRAi 261 " --> pdb=" O GLUAi 257 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N VALAi 264 " --> pdb=" O ALAAi 260 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASNAi 265 " --> pdb=" O THRAi 261 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 282 through 296 Processing helix chain 'Ai' and resid 339 through 354 removed outlier: 4.327A pdb=" N ARGAi 345 " --> pdb=" O ALAAi 341 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VALAi 346 " --> pdb=" O ILEAi 342 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ALAAi 347 " --> pdb=" O GLNAi 343 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLNAi 348 " --> pdb=" O GLYAi 344 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILEAi 353 " --> pdb=" O ILEAi 349 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLUAi 354 " --> pdb=" O ARGAi 350 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 359 through 374 removed outlier: 3.758A pdb=" N ALAAi 370 " --> pdb=" O GLNAi 366 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 386 through 409 removed outlier: 3.681A pdb=" N ALAAi 394 " --> pdb=" O LYSAi 390 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ARGAi 395 " --> pdb=" O GLUAi 391 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 417 through 428 removed outlier: 5.232A pdb=" N ASPAi 428 " --> pdb=" O SERAi 424 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 434 through 458 removed outlier: 3.688A pdb=" N GLUAi 448 " --> pdb=" O LEUAi 444 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALAAi 449 " --> pdb=" O ARGAi 445 " (cutoff:3.500A) Proline residue: Ai 450 - end of helix Processing helix chain 'Ai' and resid 462 through 471 Processing helix chain 'Ai' and resid 488 through 491 No H-bonds generated for 'chain 'Ai' and resid 488 through 491' Processing helix chain 'Ai' and resid 497 through 515 Processing helix chain 'Aj' and resid 9 through 30 removed outlier: 4.138A pdb=" N THRAj 30 " --> pdb=" O ALAAj 26 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 53 through 59 Processing helix chain 'Aj' and resid 65 through 84 removed outlier: 3.621A pdb=" N GLYAj 70 " --> pdb=" O PHEAj 66 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLUAj 76 " --> pdb=" O GLNAj 72 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VALAj 77 " --> pdb=" O METAj 73 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALAAj 78 " --> pdb=" O VALAj 74 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 89 through 108 Processing helix chain 'Aj' and resid 113 through 134 Processing helix chain 'Aj' and resid 141 through 152 Processing helix chain 'Aj' and resid 156 through 169 Processing helix chain 'Aj' and resid 202 through 204 No H-bonds generated for 'chain 'Aj' and resid 202 through 204' Processing helix chain 'Aj' and resid 230 through 243 Proline residue: Aj 235 - end of helix Processing helix chain 'Aj' and resid 256 through 266 removed outlier: 4.072A pdb=" N THRAj 261 " --> pdb=" O GLUAj 257 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 282 through 296 removed outlier: 3.509A pdb=" N ASPAj 291 " --> pdb=" O ALAAj 287 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 309 through 311 No H-bonds generated for 'chain 'Aj' and resid 309 through 311' Processing helix chain 'Aj' and resid 339 through 354 Processing helix chain 'Aj' and resid 359 through 372 Processing helix chain 'Aj' and resid 386 through 409 Processing helix chain 'Aj' and resid 417 through 426 Processing helix chain 'Aj' and resid 434 through 458 removed outlier: 3.729A pdb=" N GLUAj 448 " --> pdb=" O LEUAj 444 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALAAj 449 " --> pdb=" O ARGAj 445 " (cutoff:3.500A) Proline residue: Aj 450 - end of helix Processing helix chain 'Aj' and resid 462 through 471 Processing helix chain 'Aj' and resid 488 through 491 No H-bonds generated for 'chain 'Aj' and resid 488 through 491' Processing helix chain 'Aj' and resid 497 through 515 Processing helix chain 'Al' and resid 22 through 24 No H-bonds generated for 'chain 'Al' and resid 22 through 24' Processing helix chain 'Al' and resid 49 through 51 No H-bonds generated for 'chain 'Al' and resid 49 through 51' Processing helix chain 'Al' and resid 88 through 90 No H-bonds generated for 'chain 'Al' and resid 88 through 90' Processing helix chain 'Ao' and resid 9 through 30 removed outlier: 4.212A pdb=" N THRAo 30 " --> pdb=" O ALAAo 26 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 53 through 59 Processing helix chain 'Ao' and resid 65 through 84 Processing helix chain 'Ao' and resid 89 through 109 Processing helix chain 'Ao' and resid 113 through 134 Processing helix chain 'Ao' and resid 141 through 151 removed outlier: 3.760A pdb=" N GLNAo 146 " --> pdb=" O LYSAo 142 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 156 through 168 removed outlier: 3.644A pdb=" N LEUAo 161 " --> pdb=" O THRAo 157 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 230 through 243 Proline residue: Ao 235 - end of helix removed outlier: 3.703A pdb=" N ALAAo 243 " --> pdb=" O ALAAo 239 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 256 through 267 removed outlier: 4.705A pdb=" N THRAo 261 " --> pdb=" O GLUAo 257 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N VALAo 264 " --> pdb=" O ALAAo 260 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASNAo 265 " --> pdb=" O THRAo 261 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 282 through 296 Processing helix chain 'Ao' and resid 339 through 354 removed outlier: 4.326A pdb=" N ARGAo 345 " --> pdb=" O ALAAo 341 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VALAo 346 " --> pdb=" O ILEAo 342 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ALAAo 347 " --> pdb=" O GLNAo 343 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLNAo 348 " --> pdb=" O GLYAo 344 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILEAo 353 " --> pdb=" O ILEAo 349 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLUAo 354 " --> pdb=" O ARGAo 350 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 359 through 374 removed outlier: 3.758A pdb=" N ALAAo 370 " --> pdb=" O GLNAo 366 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 386 through 409 removed outlier: 3.681A pdb=" N ALAAo 394 " --> pdb=" O LYSAo 390 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ARGAo 395 " --> pdb=" O GLUAo 391 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 417 through 428 removed outlier: 5.233A pdb=" N ASPAo 428 " --> pdb=" O SERAo 424 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 434 through 458 removed outlier: 3.687A pdb=" N GLUAo 448 " --> pdb=" O LEUAo 444 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALAAo 449 " --> pdb=" O ARGAo 445 " (cutoff:3.500A) Proline residue: Ao 450 - end of helix Processing helix chain 'Ao' and resid 462 through 471 Processing helix chain 'Ao' and resid 488 through 491 No H-bonds generated for 'chain 'Ao' and resid 488 through 491' Processing helix chain 'Ao' and resid 497 through 515 Processing helix chain 'Ap' and resid 9 through 30 removed outlier: 4.137A pdb=" N THRAp 30 " --> pdb=" O ALAAp 26 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 53 through 59 Processing helix chain 'Ap' and resid 65 through 84 removed outlier: 3.621A pdb=" N GLYAp 70 " --> pdb=" O PHEAp 66 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLUAp 76 " --> pdb=" O GLNAp 72 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VALAp 77 " --> pdb=" O METAp 73 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALAAp 78 " --> pdb=" O VALAp 74 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 89 through 108 Processing helix chain 'Ap' and resid 113 through 134 Processing helix chain 'Ap' and resid 141 through 152 Processing helix chain 'Ap' and resid 156 through 169 Processing helix chain 'Ap' and resid 202 through 204 No H-bonds generated for 'chain 'Ap' and resid 202 through 204' Processing helix chain 'Ap' and resid 230 through 243 Proline residue: Ap 235 - end of helix Processing helix chain 'Ap' and resid 256 through 266 removed outlier: 4.072A pdb=" N THRAp 261 " --> pdb=" O GLUAp 257 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 282 through 296 removed outlier: 3.509A pdb=" N ASPAp 291 " --> pdb=" O ALAAp 287 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 309 through 311 No H-bonds generated for 'chain 'Ap' and resid 309 through 311' Processing helix chain 'Ap' and resid 339 through 354 Processing helix chain 'Ap' and resid 359 through 372 Processing helix chain 'Ap' and resid 386 through 409 Processing helix chain 'Ap' and resid 417 through 426 Processing helix chain 'Ap' and resid 434 through 458 removed outlier: 3.728A pdb=" N GLUAp 448 " --> pdb=" O LEUAp 444 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALAAp 449 " --> pdb=" O ARGAp 445 " (cutoff:3.500A) Proline residue: Ap 450 - end of helix Processing helix chain 'Ap' and resid 462 through 471 Processing helix chain 'Ap' and resid 488 through 491 No H-bonds generated for 'chain 'Ap' and resid 488 through 491' Processing helix chain 'Ap' and resid 497 through 515 Processing helix chain 'Ar' and resid 22 through 24 No H-bonds generated for 'chain 'Ar' and resid 22 through 24' Processing helix chain 'Ar' and resid 49 through 51 No H-bonds generated for 'chain 'Ar' and resid 49 through 51' Processing helix chain 'Ar' and resid 88 through 90 No H-bonds generated for 'chain 'Ar' and resid 88 through 90' Processing helix chain 'Au' and resid 9 through 30 removed outlier: 4.211A pdb=" N THRAu 30 " --> pdb=" O ALAAu 26 " (cutoff:3.500A) Processing helix chain 'Au' and resid 53 through 59 Processing helix chain 'Au' and resid 65 through 84 Processing helix chain 'Au' and resid 89 through 109 Processing helix chain 'Au' and resid 113 through 134 Processing helix chain 'Au' and resid 141 through 151 removed outlier: 3.759A pdb=" N GLNAu 146 " --> pdb=" O LYSAu 142 " (cutoff:3.500A) Processing helix chain 'Au' and resid 156 through 168 removed outlier: 3.644A pdb=" N LEUAu 161 " --> pdb=" O THRAu 157 " (cutoff:3.500A) Processing helix chain 'Au' and resid 230 through 243 Proline residue: Au 235 - end of helix removed outlier: 3.703A pdb=" N ALAAu 243 " --> pdb=" O ALAAu 239 " (cutoff:3.500A) Processing helix chain 'Au' and resid 256 through 267 removed outlier: 4.705A pdb=" N THRAu 261 " --> pdb=" O GLUAu 257 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N VALAu 264 " --> pdb=" O ALAAu 260 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASNAu 265 " --> pdb=" O THRAu 261 " (cutoff:3.500A) Processing helix chain 'Au' and resid 282 through 296 Processing helix chain 'Au' and resid 339 through 354 removed outlier: 4.326A pdb=" N ARGAu 345 " --> pdb=" O ALAAu 341 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VALAu 346 " --> pdb=" O ILEAu 342 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ALAAu 347 " --> pdb=" O GLNAu 343 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLNAu 348 " --> pdb=" O GLYAu 344 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILEAu 353 " --> pdb=" O ILEAu 349 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLUAu 354 " --> pdb=" O ARGAu 350 " (cutoff:3.500A) Processing helix chain 'Au' and resid 359 through 374 removed outlier: 3.758A pdb=" N ALAAu 370 " --> pdb=" O GLNAu 366 " (cutoff:3.500A) Processing helix chain 'Au' and resid 386 through 409 removed outlier: 3.681A pdb=" N ALAAu 394 " --> pdb=" O LYSAu 390 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARGAu 395 " --> pdb=" O GLUAu 391 " (cutoff:3.500A) Processing helix chain 'Au' and resid 417 through 428 removed outlier: 5.233A pdb=" N ASPAu 428 " --> pdb=" O SERAu 424 " (cutoff:3.500A) Processing helix chain 'Au' and resid 434 through 458 removed outlier: 3.688A pdb=" N GLUAu 448 " --> pdb=" O LEUAu 444 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALAAu 449 " --> pdb=" O ARGAu 445 " (cutoff:3.500A) Proline residue: Au 450 - end of helix Processing helix chain 'Au' and resid 462 through 471 Processing helix chain 'Au' and resid 488 through 491 No H-bonds generated for 'chain 'Au' and resid 488 through 491' Processing helix chain 'Au' and resid 497 through 515 Processing helix chain 'Av' and resid 9 through 30 removed outlier: 4.138A pdb=" N THRAv 30 " --> pdb=" O ALAAv 26 " (cutoff:3.500A) Processing helix chain 'Av' and resid 53 through 59 Processing helix chain 'Av' and resid 65 through 84 removed outlier: 3.620A pdb=" N GLYAv 70 " --> pdb=" O PHEAv 66 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLUAv 76 " --> pdb=" O GLNAv 72 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VALAv 77 " --> pdb=" O METAv 73 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALAAv 78 " --> pdb=" O VALAv 74 " (cutoff:3.500A) Processing helix chain 'Av' and resid 89 through 108 Processing helix chain 'Av' and resid 113 through 134 Processing helix chain 'Av' and resid 141 through 152 Processing helix chain 'Av' and resid 156 through 169 Processing helix chain 'Av' and resid 202 through 204 No H-bonds generated for 'chain 'Av' and resid 202 through 204' Processing helix chain 'Av' and resid 230 through 243 Proline residue: Av 235 - end of helix Processing helix chain 'Av' and resid 256 through 266 removed outlier: 4.072A pdb=" N THRAv 261 " --> pdb=" O GLUAv 257 " (cutoff:3.500A) Processing helix chain 'Av' and resid 282 through 296 removed outlier: 3.509A pdb=" N ASPAv 291 " --> pdb=" O ALAAv 287 " (cutoff:3.500A) Processing helix chain 'Av' and resid 309 through 311 No H-bonds generated for 'chain 'Av' and resid 309 through 311' Processing helix chain 'Av' and resid 339 through 354 Processing helix chain 'Av' and resid 359 through 372 Processing helix chain 'Av' and resid 386 through 409 Processing helix chain 'Av' and resid 417 through 426 Processing helix chain 'Av' and resid 434 through 458 removed outlier: 3.728A pdb=" N GLUAv 448 " --> pdb=" O LEUAv 444 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALAAv 449 " --> pdb=" O ARGAv 445 " (cutoff:3.500A) Proline residue: Av 450 - end of helix Processing helix chain 'Av' and resid 462 through 471 Processing helix chain 'Av' and resid 488 through 491 No H-bonds generated for 'chain 'Av' and resid 488 through 491' Processing helix chain 'Av' and resid 497 through 515 Processing helix chain 'Ax' and resid 22 through 24 No H-bonds generated for 'chain 'Ax' and resid 22 through 24' Processing helix chain 'Ax' and resid 49 through 51 No H-bonds generated for 'chain 'Ax' and resid 49 through 51' Processing helix chain 'Ax' and resid 88 through 90 No H-bonds generated for 'chain 'Ax' and resid 88 through 90' Processing helix chain 'Ba' and resid 9 through 30 removed outlier: 4.212A pdb=" N THRBa 30 " --> pdb=" O ALABa 26 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 53 through 59 Processing helix chain 'Ba' and resid 65 through 84 Processing helix chain 'Ba' and resid 89 through 109 Processing helix chain 'Ba' and resid 113 through 134 Processing helix chain 'Ba' and resid 141 through 151 removed outlier: 3.760A pdb=" N GLNBa 146 " --> pdb=" O LYSBa 142 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 156 through 168 removed outlier: 3.644A pdb=" N LEUBa 161 " --> pdb=" O THRBa 157 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 230 through 243 Proline residue: Ba 235 - end of helix removed outlier: 3.702A pdb=" N ALABa 243 " --> pdb=" O ALABa 239 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 256 through 267 removed outlier: 4.705A pdb=" N THRBa 261 " --> pdb=" O GLUBa 257 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N VALBa 264 " --> pdb=" O ALABa 260 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASNBa 265 " --> pdb=" O THRBa 261 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 282 through 296 Processing helix chain 'Ba' and resid 339 through 354 removed outlier: 4.327A pdb=" N ARGBa 345 " --> pdb=" O ALABa 341 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N VALBa 346 " --> pdb=" O ILEBa 342 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ALABa 347 " --> pdb=" O GLNBa 343 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLNBa 348 " --> pdb=" O GLYBa 344 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILEBa 353 " --> pdb=" O ILEBa 349 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLUBa 354 " --> pdb=" O ARGBa 350 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 359 through 374 removed outlier: 3.758A pdb=" N ALABa 370 " --> pdb=" O GLNBa 366 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 386 through 409 removed outlier: 3.681A pdb=" N ALABa 394 " --> pdb=" O LYSBa 390 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ARGBa 395 " --> pdb=" O GLUBa 391 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 417 through 428 removed outlier: 5.233A pdb=" N ASPBa 428 " --> pdb=" O SERBa 424 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 434 through 458 removed outlier: 3.688A pdb=" N GLUBa 448 " --> pdb=" O LEUBa 444 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALABa 449 " --> pdb=" O ARGBa 445 " (cutoff:3.500A) Proline residue: Ba 450 - end of helix Processing helix chain 'Ba' and resid 462 through 471 Processing helix chain 'Ba' and resid 488 through 491 No H-bonds generated for 'chain 'Ba' and resid 488 through 491' Processing helix chain 'Ba' and resid 497 through 515 Processing helix chain 'Bb' and resid 9 through 30 removed outlier: 4.137A pdb=" N THRBb 30 " --> pdb=" O ALABb 26 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 53 through 59 Processing helix chain 'Bb' and resid 65 through 84 removed outlier: 3.620A pdb=" N GLYBb 70 " --> pdb=" O PHEBb 66 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLUBb 76 " --> pdb=" O GLNBb 72 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VALBb 77 " --> pdb=" O METBb 73 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALABb 78 " --> pdb=" O VALBb 74 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 89 through 108 Processing helix chain 'Bb' and resid 113 through 134 Processing helix chain 'Bb' and resid 141 through 152 Processing helix chain 'Bb' and resid 156 through 169 Processing helix chain 'Bb' and resid 202 through 204 No H-bonds generated for 'chain 'Bb' and resid 202 through 204' Processing helix chain 'Bb' and resid 230 through 243 Proline residue: Bb 235 - end of helix Processing helix chain 'Bb' and resid 256 through 266 removed outlier: 4.072A pdb=" N THRBb 261 " --> pdb=" O GLUBb 257 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 282 through 296 removed outlier: 3.509A pdb=" N ASPBb 291 " --> pdb=" O ALABb 287 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 309 through 311 No H-bonds generated for 'chain 'Bb' and resid 309 through 311' Processing helix chain 'Bb' and resid 339 through 354 Processing helix chain 'Bb' and resid 359 through 372 Processing helix chain 'Bb' and resid 386 through 409 Processing helix chain 'Bb' and resid 417 through 426 Processing helix chain 'Bb' and resid 434 through 458 removed outlier: 3.728A pdb=" N GLUBb 448 " --> pdb=" O LEUBb 444 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALABb 449 " --> pdb=" O ARGBb 445 " (cutoff:3.500A) Proline residue: Bb 450 - end of helix Processing helix chain 'Bb' and resid 462 through 471 Processing helix chain 'Bb' and resid 488 through 491 No H-bonds generated for 'chain 'Bb' and resid 488 through 491' Processing helix chain 'Bb' and resid 497 through 515 Processing helix chain 'Bd' and resid 22 through 24 No H-bonds generated for 'chain 'Bd' and resid 22 through 24' Processing helix chain 'Bd' and resid 49 through 51 No H-bonds generated for 'chain 'Bd' and resid 49 through 51' Processing helix chain 'Bd' and resid 88 through 90 No H-bonds generated for 'chain 'Bd' and resid 88 through 90' Processing helix chain 'Bg' and resid 9 through 30 removed outlier: 4.211A 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 Processing helix chain 'Bg' and resid 89 through 109 Processing helix chain 'Bg' and resid 113 through 134 Processing helix chain 'Bg' and resid 141 through 151 removed outlier: 3.760A pdb=" N GLNBg 146 " --> pdb=" O LYSBg 142 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 156 through 168 removed outlier: 3.644A pdb=" N LEUBg 161 " --> pdb=" O THRBg 157 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 230 through 243 Proline residue: Bg 235 - end of helix removed outlier: 3.702A pdb=" N ALABg 243 " --> pdb=" O ALABg 239 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 256 through 267 removed outlier: 4.706A pdb=" N THRBg 261 " --> pdb=" O GLUBg 257 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N VALBg 264 " --> pdb=" O ALABg 260 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASNBg 265 " --> pdb=" O THRBg 261 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 282 through 296 Processing helix chain 'Bg' and resid 339 through 354 removed outlier: 4.326A pdb=" N ARGBg 345 " --> pdb=" O ALABg 341 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N VALBg 346 " --> pdb=" O ILEBg 342 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ALABg 347 " --> pdb=" O GLNBg 343 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLNBg 348 " --> pdb=" O GLYBg 344 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILEBg 353 " --> pdb=" O ILEBg 349 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLUBg 354 " --> pdb=" O ARGBg 350 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 359 through 374 removed outlier: 3.758A pdb=" N ALABg 370 " --> pdb=" O GLNBg 366 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 386 through 409 removed outlier: 3.682A pdb=" N ALABg 394 " --> pdb=" O LYSBg 390 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARGBg 395 " --> pdb=" O GLUBg 391 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 417 through 428 removed outlier: 5.232A pdb=" N ASPBg 428 " --> pdb=" O SERBg 424 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 434 through 458 removed outlier: 3.687A pdb=" N GLUBg 448 " --> pdb=" O LEUBg 444 " (cutoff:3.500A) removed outlier: 3.700A 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 515 Processing helix chain 'Bh' and resid 9 through 30 removed outlier: 4.138A pdb=" N THRBh 30 " --> pdb=" O ALABh 26 " (cutoff:3.500A) Processing helix chain 'Bh' and resid 53 through 59 Processing helix chain 'Bh' and resid 65 through 84 removed outlier: 3.620A pdb=" N GLYBh 70 " --> pdb=" O PHEBh 66 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLUBh 76 " --> pdb=" O GLNBh 72 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VALBh 77 " --> pdb=" O METBh 73 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALABh 78 " --> pdb=" O VALBh 74 " (cutoff:3.500A) Processing helix chain 'Bh' and resid 89 through 108 Processing helix chain 'Bh' and resid 113 through 134 Processing helix chain 'Bh' and resid 141 through 152 Processing helix chain 'Bh' and resid 156 through 169 Processing helix chain 'Bh' and resid 202 through 204 No H-bonds generated for 'chain 'Bh' and resid 202 through 204' Processing helix chain 'Bh' and resid 230 through 243 Proline residue: Bh 235 - end of helix Processing helix chain 'Bh' and resid 256 through 266 removed outlier: 4.073A pdb=" N THRBh 261 " --> pdb=" O GLUBh 257 " (cutoff:3.500A) Processing helix chain 'Bh' and resid 282 through 296 removed outlier: 3.508A pdb=" N ASPBh 291 " --> pdb=" O ALABh 287 " (cutoff:3.500A) Processing helix chain 'Bh' and resid 309 through 311 No H-bonds generated for 'chain 'Bh' and resid 309 through 311' Processing helix chain 'Bh' and resid 339 through 354 Processing helix chain 'Bh' and resid 359 through 372 Processing helix chain 'Bh' and resid 386 through 409 Processing helix chain 'Bh' and resid 417 through 426 Processing helix chain 'Bh' and resid 434 through 458 removed outlier: 3.728A pdb=" N GLUBh 448 " --> pdb=" O LEUBh 444 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALABh 449 " --> pdb=" O ARGBh 445 " (cutoff:3.500A) Proline residue: Bh 450 - end of helix Processing helix chain 'Bh' and resid 462 through 471 Processing helix chain 'Bh' and resid 488 through 491 No H-bonds generated for 'chain 'Bh' and resid 488 through 491' Processing helix chain 'Bh' and resid 497 through 515 Processing helix chain 'Bj' and resid 22 through 24 No H-bonds generated for 'chain 'Bj' and resid 22 through 24' Processing helix chain 'Bj' and resid 49 through 51 No H-bonds generated for 'chain 'Bj' and resid 49 through 51' Processing helix chain 'Bj' and resid 88 through 90 No H-bonds generated for 'chain 'Bj' and resid 88 through 90' Processing helix chain 'Bm' and resid 9 through 30 removed outlier: 4.211A 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 removed outlier: 3.760A pdb=" N GLNBm 146 " --> pdb=" O LYSBm 142 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 156 through 168 removed outlier: 3.643A pdb=" N LEUBm 161 " --> pdb=" O THRBm 157 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 230 through 243 Proline residue: Bm 235 - end of helix removed outlier: 3.703A pdb=" N ALABm 243 " --> pdb=" O ALABm 239 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 256 through 267 removed outlier: 4.706A pdb=" N THRBm 261 " --> pdb=" O GLUBm 257 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N VALBm 264 " --> pdb=" O ALABm 260 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ASNBm 265 " --> pdb=" O THRBm 261 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 282 through 296 Processing helix chain 'Bm' and resid 339 through 354 removed outlier: 4.326A pdb=" N ARGBm 345 " --> pdb=" O ALABm 341 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VALBm 346 " --> pdb=" O ILEBm 342 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ALABm 347 " --> pdb=" O GLNBm 343 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLNBm 348 " --> pdb=" O GLYBm 344 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILEBm 353 " --> pdb=" O ILEBm 349 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLUBm 354 " --> pdb=" O ARGBm 350 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 359 through 374 removed outlier: 3.757A pdb=" N ALABm 370 " --> pdb=" O GLNBm 366 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 386 through 409 removed outlier: 3.682A pdb=" N ALABm 394 " --> pdb=" O LYSBm 390 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ARGBm 395 " --> pdb=" O GLUBm 391 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 417 through 428 removed outlier: 5.233A pdb=" N ASPBm 428 " --> pdb=" O SERBm 424 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 434 through 458 removed outlier: 3.688A pdb=" N GLUBm 448 " --> pdb=" O LEUBm 444 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALABm 449 " --> pdb=" O ARGBm 445 " (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 515 Processing helix chain 'Bn' and resid 9 through 30 removed outlier: 4.137A 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: 3.620A pdb=" N GLYBn 70 " --> pdb=" O PHEBn 66 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLUBn 76 " --> pdb=" O GLNBn 72 " (cutoff:3.500A) removed outlier: 4.215A 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 152 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 266 removed outlier: 4.072A pdb=" N THRBn 261 " --> pdb=" O GLUBn 257 " (cutoff:3.500A) Processing helix chain 'Bn' and resid 282 through 296 removed outlier: 3.508A pdb=" N ASPBn 291 " --> pdb=" O ALABn 287 " (cutoff:3.500A) 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 339 through 354 Processing helix chain 'Bn' and resid 359 through 372 Processing helix chain 'Bn' and resid 386 through 409 Processing helix chain 'Bn' and resid 417 through 426 Processing helix chain 'Bn' and resid 434 through 458 removed outlier: 3.728A pdb=" N GLUBn 448 " --> pdb=" O LEUBn 444 " (cutoff:3.500A) removed outlier: 3.966A 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 515 Processing helix chain 'Bp' and resid 22 through 24 No H-bonds generated for 'chain 'Bp' and resid 22 through 24' Processing helix chain 'Bp' and resid 49 through 51 No H-bonds generated for 'chain 'Bp' and resid 49 through 51' Processing helix chain 'Bp' and resid 88 through 90 No H-bonds generated for 'chain 'Bp' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'Ac' and resid 4 through 8 Processing sheet with id= B, first strand: chain 'Ac' and resid 38 through 40 Processing sheet with id= C, first strand: chain 'Ac' and resid 174 through 179 Processing sheet with id= D, first strand: chain 'Ac' and resid 193 through 195 Processing sheet with id= E, first strand: chain 'Ac' and resid 219 through 222 Processing sheet with id= F, first strand: chain 'Ac' and resid 411 through 413 Processing sheet with id= G, first strand: chain 'Ac' and resid 476 through 479 Processing sheet with id= H, first strand: chain 'Ad' and resid 4 through 8 Processing sheet with id= I, first strand: chain 'Ad' and resid 38 through 40 Processing sheet with id= J, first strand: chain 'Ad' and resid 174 through 180 removed outlier: 3.724A pdb=" N VALAd 376 " --> pdb=" O VALAd 190 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'Ad' and resid 193 through 195 removed outlier: 3.860A pdb=" N METAd 193 " --> pdb=" O ILEAd 332 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARGAd 322 " --> pdb=" O ILEAd 333 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'Ad' and resid 219 through 222 Processing sheet with id= M, first strand: chain 'Ad' and resid 411 through 413 Processing sheet with id= N, first strand: chain 'Ad' and resid 476 through 479 Processing sheet with id= O, first strand: chain 'Af' and resid 74 through 78 removed outlier: 8.475A pdb=" N GLUAf 82 " --> pdb=" O ARGAf 14 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ARGAf 14 " --> pdb=" O GLUAf 82 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LYSAf 13 " --> pdb=" O VALAf 40 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N VALAf 40 " --> pdb=" O LYSAf 13 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'Ai' and resid 4 through 8 Processing sheet with id= Q, first strand: chain 'Ai' and resid 38 through 40 Processing sheet with id= R, first strand: chain 'Ai' and resid 174 through 179 Processing sheet with id= S, first strand: chain 'Ai' and resid 193 through 195 Processing sheet with id= T, first strand: chain 'Ai' and resid 219 through 222 Processing sheet with id= U, first strand: chain 'Ai' and resid 411 through 413 Processing sheet with id= V, first strand: chain 'Ai' and resid 476 through 479 Processing sheet with id= W, first strand: chain 'Aj' and resid 4 through 8 Processing sheet with id= X, first strand: chain 'Aj' and resid 38 through 40 Processing sheet with id= Y, first strand: chain 'Aj' and resid 174 through 180 removed outlier: 3.724A pdb=" N VALAj 376 " --> pdb=" O VALAj 190 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'Aj' and resid 193 through 195 removed outlier: 3.859A pdb=" N METAj 193 " --> pdb=" O ILEAj 332 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARGAj 322 " --> pdb=" O ILEAj 333 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'Aj' and resid 219 through 222 Processing sheet with id= AB, first strand: chain 'Aj' and resid 411 through 413 Processing sheet with id= AC, first strand: chain 'Aj' and resid 476 through 479 Processing sheet with id= AD, first strand: chain 'Al' and resid 74 through 78 removed outlier: 8.475A pdb=" N GLUAl 82 " --> pdb=" O ARGAl 14 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ARGAl 14 " --> pdb=" O GLUAl 82 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LYSAl 13 " --> pdb=" O VALAl 40 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N VALAl 40 " --> pdb=" O LYSAl 13 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'Ao' and resid 4 through 8 Processing sheet with id= AF, first strand: chain 'Ao' and resid 38 through 40 Processing sheet with id= AG, first strand: chain 'Ao' and resid 174 through 179 Processing sheet with id= AH, first strand: chain 'Ao' and resid 193 through 195 Processing sheet with id= AI, first strand: chain 'Ao' and resid 219 through 222 Processing sheet with id= AJ, first strand: chain 'Ao' and resid 411 through 413 Processing sheet with id= AK, first strand: chain 'Ao' and resid 476 through 479 Processing sheet with id= AL, first strand: chain 'Ap' and resid 4 through 8 Processing sheet with id= AM, first strand: chain 'Ap' and resid 38 through 40 Processing sheet with id= AN, first strand: chain 'Ap' and resid 174 through 180 removed outlier: 3.723A pdb=" N VALAp 376 " --> pdb=" O VALAp 190 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'Ap' and resid 193 through 195 removed outlier: 3.860A pdb=" N METAp 193 " --> pdb=" O ILEAp 332 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARGAp 322 " --> pdb=" O ILEAp 333 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'Ap' and resid 219 through 222 Processing sheet with id= AQ, first strand: chain 'Ap' and resid 411 through 413 Processing sheet with id= AR, first strand: chain 'Ap' and resid 476 through 479 Processing sheet with id= AS, first strand: chain 'Ar' and resid 74 through 78 removed outlier: 8.474A pdb=" N GLUAr 82 " --> pdb=" O ARGAr 14 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ARGAr 14 " --> pdb=" O GLUAr 82 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LYSAr 13 " --> pdb=" O VALAr 40 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N VALAr 40 " --> pdb=" O LYSAr 13 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'Au' and resid 4 through 8 Processing sheet with id= AU, first strand: chain 'Au' and resid 38 through 40 Processing sheet with id= AV, first strand: chain 'Au' and resid 174 through 179 Processing sheet with id= AW, first strand: chain 'Au' and resid 193 through 195 Processing sheet with id= AX, first strand: chain 'Au' and resid 219 through 222 Processing sheet with id= AY, first strand: chain 'Au' and resid 411 through 413 Processing sheet with id= AZ, first strand: chain 'Au' and resid 476 through 479 Processing sheet with id= BA, first strand: chain 'Av' and resid 4 through 8 Processing sheet with id= BB, first strand: chain 'Av' and resid 38 through 40 Processing sheet with id= BC, first strand: chain 'Av' and resid 174 through 180 removed outlier: 3.724A pdb=" N VALAv 376 " --> pdb=" O VALAv 190 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'Av' and resid 193 through 195 removed outlier: 3.860A pdb=" N METAv 193 " --> pdb=" O ILEAv 332 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARGAv 322 " --> pdb=" O ILEAv 333 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'Av' and resid 219 through 222 Processing sheet with id= BF, first strand: chain 'Av' and resid 411 through 413 Processing sheet with id= BG, first strand: chain 'Av' and resid 476 through 479 Processing sheet with id= BH, first strand: chain 'Ax' and resid 74 through 78 removed outlier: 8.475A pdb=" N GLUAx 82 " --> pdb=" O ARGAx 14 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ARGAx 14 " --> pdb=" O GLUAx 82 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LYSAx 13 " --> pdb=" O VALAx 40 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N VALAx 40 " --> pdb=" O LYSAx 13 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'Ba' and resid 4 through 8 Processing sheet with id= BJ, first strand: chain 'Ba' and resid 38 through 40 Processing sheet with id= BK, first strand: chain 'Ba' and resid 174 through 179 Processing sheet with id= BL, first strand: chain 'Ba' and resid 193 through 195 Processing sheet with id= BM, first strand: chain 'Ba' and resid 219 through 222 Processing sheet with id= BN, first strand: chain 'Ba' and resid 411 through 413 Processing sheet with id= BO, first strand: chain 'Ba' and resid 476 through 479 Processing sheet with id= BP, first strand: chain 'Bb' and resid 4 through 8 Processing sheet with id= BQ, first strand: chain 'Bb' and resid 38 through 40 Processing sheet with id= BR, first strand: chain 'Bb' and resid 174 through 180 removed outlier: 3.724A pdb=" N VALBb 376 " --> pdb=" O VALBb 190 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'Bb' and resid 193 through 195 removed outlier: 3.860A pdb=" N METBb 193 " --> pdb=" O ILEBb 332 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARGBb 322 " --> pdb=" O ILEBb 333 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'Bb' and resid 219 through 222 Processing sheet with id= BU, first strand: chain 'Bb' and resid 411 through 413 Processing sheet with id= BV, first strand: chain 'Bb' and resid 476 through 479 Processing sheet with id= BW, first strand: chain 'Bd' and resid 74 through 78 removed outlier: 8.475A pdb=" N GLUBd 82 " --> pdb=" O ARGBd 14 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ARGBd 14 " --> pdb=" O GLUBd 82 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LYSBd 13 " --> pdb=" O VALBd 40 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N VALBd 40 " --> pdb=" O LYSBd 13 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'Bg' and resid 4 through 8 Processing sheet with id= BY, first strand: chain 'Bg' and resid 38 through 40 Processing sheet with id= BZ, first strand: chain 'Bg' and resid 174 through 179 Processing sheet with id= CA, first strand: chain 'Bg' and resid 193 through 195 Processing sheet with id= CB, first strand: chain 'Bg' and resid 219 through 222 Processing sheet with id= CC, first strand: chain 'Bg' and resid 411 through 413 Processing sheet with id= CD, first strand: chain 'Bg' and resid 476 through 479 Processing sheet with id= CE, first strand: chain 'Bh' and resid 4 through 8 Processing sheet with id= CF, first strand: chain 'Bh' and resid 38 through 40 Processing sheet with id= CG, first strand: chain 'Bh' and resid 174 through 180 removed outlier: 3.724A pdb=" N VALBh 376 " --> pdb=" O VALBh 190 " (cutoff:3.500A) Processing sheet with id= CH, first strand: chain 'Bh' and resid 193 through 195 removed outlier: 3.859A pdb=" N METBh 193 " --> pdb=" O ILEBh 332 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARGBh 322 " --> pdb=" O ILEBh 333 " (cutoff:3.500A) Processing sheet with id= CI, first strand: chain 'Bh' and resid 219 through 222 Processing sheet with id= CJ, first strand: chain 'Bh' and resid 411 through 413 Processing sheet with id= CK, first strand: chain 'Bh' and resid 476 through 479 Processing sheet with id= CL, first strand: chain 'Bj' and resid 74 through 78 removed outlier: 8.476A pdb=" N GLUBj 82 " --> pdb=" O ARGBj 14 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ARGBj 14 " --> pdb=" O GLUBj 82 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LYSBj 13 " --> pdb=" O VALBj 40 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N VALBj 40 " --> pdb=" O LYSBj 13 " (cutoff:3.500A) Processing sheet with id= CM, first strand: chain 'Bm' and resid 4 through 8 Processing sheet with id= CN, first strand: chain 'Bm' and resid 38 through 40 Processing sheet with id= CO, first strand: chain 'Bm' and resid 174 through 179 Processing sheet with id= CP, first strand: chain 'Bm' and resid 193 through 195 Processing sheet with id= CQ, first strand: chain 'Bm' and resid 219 through 222 Processing sheet with id= CR, first strand: chain 'Bm' and resid 411 through 413 Processing sheet with id= CS, first strand: chain 'Bm' and resid 476 through 479 Processing sheet with id= CT, first strand: chain 'Bn' and resid 4 through 8 Processing sheet with id= CU, first strand: chain 'Bn' and resid 38 through 40 Processing sheet with id= CV, first strand: chain 'Bn' and resid 174 through 180 removed outlier: 3.725A pdb=" N VALBn 376 " --> pdb=" O VALBn 190 " (cutoff:3.500A) Processing sheet with id= CW, first strand: chain 'Bn' and resid 193 through 195 removed outlier: 3.860A pdb=" N METBn 193 " --> pdb=" O ILEBn 332 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARGBn 322 " --> pdb=" O ILEBn 333 " (cutoff:3.500A) Processing sheet with id= CX, first strand: chain 'Bn' and resid 219 through 222 Processing sheet with id= CY, first strand: chain 'Bn' and resid 411 through 413 Processing sheet with id= CZ, first strand: chain 'Bn' and resid 476 through 479 Processing sheet with id= DA, first strand: chain 'Bp' and resid 74 through 78 removed outlier: 8.476A pdb=" N GLUBp 82 " --> pdb=" O ARGBp 14 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ARGBp 14 " --> pdb=" O GLUBp 82 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LYSBp 13 " --> pdb=" O VALBp 40 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N VALBp 40 " --> pdb=" O LYSBp 13 " (cutoff:3.500A) 3311 hydrogen bonds defined for protein. 9597 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: 24.50 Time building geometry restraints manager: 19.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.58: 59081 1.58 - 1.96: 776 1.96 - 2.33: 35 2.33 - 2.71: 7 2.71 - 3.09: 7 Bond restraints: 59906 Sorted by residual: bond pdb=" C PROBm 525 " pdb=" O PROBm 525 " ideal model delta sigma weight residual 1.231 2.610 -1.379 2.00e-02 2.50e+03 4.75e+03 bond pdb=" C PROBg 525 " pdb=" O PROBg 525 " ideal model delta sigma weight residual 1.231 2.609 -1.378 2.00e-02 2.50e+03 4.75e+03 bond pdb=" C PROAu 525 " pdb=" O PROAu 525 " ideal model delta sigma weight residual 1.231 2.609 -1.378 2.00e-02 2.50e+03 4.75e+03 bond pdb=" C PROAi 525 " pdb=" O PROAi 525 " ideal model delta sigma weight residual 1.231 2.609 -1.378 2.00e-02 2.50e+03 4.75e+03 bond pdb=" C PROBa 525 " pdb=" O PROBa 525 " ideal model delta sigma weight residual 1.231 2.609 -1.378 2.00e-02 2.50e+03 4.75e+03 ... (remaining 59901 not shown) Histogram of bond angle deviations from ideal: 41.47 - 64.45: 7 64.45 - 87.43: 0 87.43 - 110.41: 14167 110.41 - 133.39: 66669 133.39 - 156.36: 112 Bond angle restraints: 80955 Sorted by residual: angle pdb=" O PROAo 525 " pdb=" C PROAo 525 " pdb=" OXT PROAo 525 " ideal model delta sigma weight residual 118.00 41.47 76.53 3.00e+00 1.11e-01 6.51e+02 angle pdb=" O PROAu 525 " pdb=" C PROAu 525 " pdb=" OXT PROAu 525 " ideal model delta sigma weight residual 118.00 41.48 76.52 3.00e+00 1.11e-01 6.51e+02 angle pdb=" O PROBm 525 " pdb=" C PROBm 525 " pdb=" OXT PROBm 525 " ideal model delta sigma weight residual 118.00 41.49 76.51 3.00e+00 1.11e-01 6.50e+02 angle pdb=" O PROAi 525 " pdb=" C PROAi 525 " pdb=" OXT PROAi 525 " ideal model delta sigma weight residual 118.00 41.49 76.51 3.00e+00 1.11e-01 6.50e+02 angle pdb=" O PROAc 525 " pdb=" C PROAc 525 " pdb=" OXT PROAc 525 " ideal model delta sigma weight residual 118.00 41.49 76.51 3.00e+00 1.11e-01 6.50e+02 ... (remaining 80950 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.64: 35018 32.64 - 65.28: 1830 65.28 - 97.92: 245 97.92 - 130.56: 7 130.56 - 163.21: 21 Dihedral angle restraints: 37121 sinusoidal: 14532 harmonic: 22589 Sorted by residual: dihedral pdb=" CA ILEAx 3 " pdb=" C ILEAx 3 " pdb=" N ARGAx 4 " pdb=" CA ARGAx 4 " ideal model delta harmonic sigma weight residual -180.00 -48.77 -131.23 0 5.00e+00 4.00e-02 6.89e+02 dihedral pdb=" CA ILEAf 3 " pdb=" C ILEAf 3 " pdb=" N ARGAf 4 " pdb=" CA ARGAf 4 " ideal model delta harmonic sigma weight residual -180.00 -48.88 -131.12 0 5.00e+00 4.00e-02 6.88e+02 dihedral pdb=" CA ILEAr 3 " pdb=" C ILEAr 3 " pdb=" N ARGAr 4 " pdb=" CA ARGAr 4 " ideal model delta harmonic sigma weight residual -180.00 -48.93 -131.07 0 5.00e+00 4.00e-02 6.87e+02 ... (remaining 37118 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.915: 9786 0.915 - 1.830: 28 1.830 - 2.745: 7 2.745 - 3.660: 0 3.660 - 4.574: 7 Chirality restraints: 9828 Sorted by residual: chirality pdb=" C1' ADPAj 601 " pdb=" C2' ADPAj 601 " pdb=" N9 ADPAj 601 " pdb=" O4' ADPAj 601 " both_signs ideal model delta sigma weight residual False 2.48 -2.09 4.57 2.00e-01 2.50e+01 5.23e+02 chirality pdb=" C1' ADPBh 601 " pdb=" C2' ADPBh 601 " pdb=" N9 ADPBh 601 " pdb=" O4' ADPBh 601 " both_signs ideal model delta sigma weight residual False 2.48 -2.09 4.57 2.00e-01 2.50e+01 5.23e+02 chirality pdb=" C1' ADPAp 601 " pdb=" C2' ADPAp 601 " pdb=" N9 ADPAp 601 " pdb=" O4' ADPAp 601 " both_signs ideal model delta sigma weight residual False 2.48 -2.09 4.57 2.00e-01 2.50e+01 5.23e+02 ... (remaining 9825 not shown) Planarity restraints: 10542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PROBg 525 " 0.142 2.00e-02 2.50e+03 2.83e-01 8.02e+02 pdb=" C PROBg 525 " -0.404 2.00e-02 2.50e+03 pdb=" O PROBg 525 " -0.097 2.00e-02 2.50e+03 pdb=" OXT PROBg 525 " 0.358 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PROAu 525 " 0.142 2.00e-02 2.50e+03 2.83e-01 8.02e+02 pdb=" C PROAu 525 " -0.403 2.00e-02 2.50e+03 pdb=" O PROAu 525 " -0.097 2.00e-02 2.50e+03 pdb=" OXT PROAu 525 " 0.359 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PROAi 525 " 0.142 2.00e-02 2.50e+03 2.83e-01 8.01e+02 pdb=" C PROAi 525 " -0.403 2.00e-02 2.50e+03 pdb=" O PROAi 525 " -0.097 2.00e-02 2.50e+03 pdb=" OXT PROAi 525 " 0.358 2.00e-02 2.50e+03 ... (remaining 10539 not shown) Histogram of nonbonded interaction distances: 0.60 - 1.46: 75 1.46 - 2.32: 496 2.32 - 3.18: 53512 3.18 - 4.04: 166407 4.04 - 4.90: 282535 Warning: very small nonbonded interaction distances. Nonbonded interactions: 503025 Sorted by model distance: nonbonded pdb=" CD2 PHEAc 281 " pdb=" CD GLUAo 386 " model vdw 0.597 3.570 nonbonded pdb=" CD2 PHEBa 281 " pdb=" CD GLUBm 386 " model vdw 0.600 3.570 nonbonded pdb=" CD2 PHEAo 281 " pdb=" CD GLUBa 386 " model vdw 0.607 3.570 nonbonded pdb=" CD GLUAu 386 " pdb=" CD2 PHEBg 281 " model vdw 0.614 3.570 nonbonded pdb=" OE2 GLUAc 386 " pdb=" CD2 PHEAi 281 " model vdw 0.618 3.340 ... (remaining 503020 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 'Ac' selection = chain 'Ad' selection = chain 'Ai' selection = chain 'Aj' selection = chain 'Ao' selection = chain 'Ap' selection = chain 'Au' selection = chain 'Av' selection = chain 'Ba' selection = chain 'Bb' selection = chain 'Bg' selection = chain 'Bh' selection = chain 'Bm' selection = chain 'Bn' } ncs_group { reference = chain 'Af' selection = chain 'Al' selection = chain 'Ar' selection = chain 'Ax' selection = chain 'Bd' selection = chain 'Bj' selection = chain 'Bp' } 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: 2.070 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: 0.050 Extract box with map and model: 12.750 Check model and map are aligned: 0.670 Set scattering table: 0.420 Process input model: 126.190 Find NCS groups from input model: 3.520 Set up NCS constraints: 0.560 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:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 148.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6324 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 : 0.032 1.566 59906 Z= 2.040 Angle : 2.527 76.526 80955 Z= 1.715 Chirality : 0.208 4.574 9828 Planarity : 0.016 0.283 10542 Dihedral : 19.429 163.205 22631 Min Nonbonded Distance : 0.597 Molprobity Statistics. All-atom Clashscore : 32.75 Ramachandran Plot: Outliers : 1.58 % Allowed : 3.11 % Favored : 95.31 % Rotamer: Outliers : 11.71 % Allowed : 13.84 % Favored : 74.45 % Cbeta Deviations : 2.84 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.54 % 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: 1.29 (0.09), residues: 7973 helix: 2.33 (0.08), residues: 4032 sheet: 0.07 (0.16), residues: 966 loop : -0.97 (0.11), residues: 2975 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HISBd 7 PHE 0.062 0.011 PHEAj 219 TYR 0.144 0.011 TYRBg 360 ARG 0.027 0.002 ARGAu 322 *********************** 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 1227 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 728 poor density : 499 time to evaluate : 5.033 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: Ad 389 MET cc_start: 0.7138 (tpp) cc_final: 0.6510 (tpp) REVERT: Aj 389 MET cc_start: 0.7111 (tpp) cc_final: 0.6857 (tpp) REVERT: Av 417 VAL cc_start: 0.8954 (OUTLIER) cc_final: 0.8716 (m) REVERT: Av 483 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6910 (mm-30) REVERT: Bn 483 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6981 (mm-30) outliers start: 728 outliers final: 170 residues processed: 1131 average time/residue: 0.5799 time to fit residues: 1078.3299 Evaluate side-chains 545 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 372 time to evaluate : 5.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ac residue 55 SER Chi-restraints excluded: chain Ac residue 77 VAL Chi-restraints excluded: chain Ac residue 79 SER Chi-restraints excluded: chain Ac residue 90 THR Chi-restraints excluded: chain Ac residue 116 LEU Chi-restraints excluded: chain Ac residue 184 GLN Chi-restraints excluded: chain Ac residue 358 SER Chi-restraints excluded: chain Ac residue 366 GLN Chi-restraints excluded: chain Ac residue 432 GLN Chi-restraints excluded: chain Ac residue 518 GLU Chi-restraints excluded: chain Ad residue 201 SER Chi-restraints excluded: chain Ad residue 313 THR Chi-restraints excluded: chain Ad residue 380 LYS Chi-restraints excluded: chain Ad residue 417 VAL Chi-restraints excluded: chain Ad residue 420 ILE Chi-restraints excluded: chain Ad residue 509 SER Chi-restraints excluded: chain Af residue 1 MET Chi-restraints excluded: chain Af residue 2 ASN Chi-restraints excluded: chain Af residue 34 LYS Chi-restraints excluded: chain Af residue 54 VAL Chi-restraints excluded: chain Af residue 77 LYS Chi-restraints excluded: chain Af residue 94 ILE Chi-restraints excluded: chain Af residue 96 GLU Chi-restraints excluded: chain Ai residue 55 SER Chi-restraints excluded: chain Ai residue 77 VAL Chi-restraints excluded: chain Ai residue 79 SER Chi-restraints excluded: chain Ai residue 89 THR Chi-restraints excluded: chain Ai residue 90 THR Chi-restraints excluded: chain Ai residue 139 SER Chi-restraints excluded: chain Ai residue 184 GLN Chi-restraints excluded: chain Ai residue 358 SER Chi-restraints excluded: chain Ai residue 366 GLN Chi-restraints excluded: chain Ai residue 432 GLN Chi-restraints excluded: chain Ai residue 518 GLU Chi-restraints excluded: chain Aj residue 87 ASP Chi-restraints excluded: chain Aj residue 201 SER Chi-restraints excluded: chain Aj residue 313 THR Chi-restraints excluded: chain Aj residue 379 ILE Chi-restraints excluded: chain Aj residue 380 LYS Chi-restraints excluded: chain Aj residue 417 VAL Chi-restraints excluded: chain Aj residue 420 ILE Chi-restraints excluded: chain Aj residue 483 GLU Chi-restraints excluded: chain Al residue 1 MET Chi-restraints excluded: chain Al residue 2 ASN Chi-restraints excluded: chain Al residue 3 ILE Chi-restraints excluded: chain Al residue 34 LYS Chi-restraints excluded: chain Al residue 54 VAL Chi-restraints excluded: chain Al residue 77 LYS Chi-restraints excluded: chain Al residue 78 ILE Chi-restraints excluded: chain Al residue 94 ILE Chi-restraints excluded: chain Al residue 96 GLU Chi-restraints excluded: chain Ao residue 55 SER Chi-restraints excluded: chain Ao residue 90 THR Chi-restraints excluded: chain Ao residue 184 GLN Chi-restraints excluded: chain Ao residue 358 SER Chi-restraints excluded: chain Ao residue 366 GLN Chi-restraints excluded: chain Ao residue 432 GLN Chi-restraints excluded: chain Ao residue 518 GLU Chi-restraints excluded: chain Ap residue 157 THR Chi-restraints excluded: chain Ap residue 201 SER Chi-restraints excluded: chain Ap residue 286 LYS Chi-restraints excluded: chain Ap residue 308 GLU Chi-restraints excluded: chain Ap residue 313 THR Chi-restraints excluded: chain Ap residue 380 LYS Chi-restraints excluded: chain Ap residue 417 VAL Chi-restraints excluded: chain Ap residue 420 ILE Chi-restraints excluded: chain Ap residue 483 GLU Chi-restraints excluded: chain Ap residue 509 SER Chi-restraints excluded: chain Ar residue 1 MET Chi-restraints excluded: chain Ar residue 2 ASN Chi-restraints excluded: chain Ar residue 13 LYS Chi-restraints excluded: chain Ar residue 54 VAL Chi-restraints excluded: chain Ar residue 64 ILE Chi-restraints excluded: chain Ar residue 77 LYS Chi-restraints excluded: chain Ar residue 78 ILE Chi-restraints excluded: chain Ar residue 96 GLU Chi-restraints excluded: chain Au residue 55 SER Chi-restraints excluded: chain Au residue 77 VAL Chi-restraints excluded: chain Au residue 89 THR Chi-restraints excluded: chain Au residue 90 THR Chi-restraints excluded: chain Au residue 184 GLN Chi-restraints excluded: chain Au residue 358 SER Chi-restraints excluded: chain Au residue 366 GLN Chi-restraints excluded: chain Au residue 432 GLN Chi-restraints excluded: chain Au residue 518 GLU Chi-restraints excluded: chain Av residue 87 ASP Chi-restraints excluded: chain Av residue 201 SER Chi-restraints excluded: chain Av residue 286 LYS Chi-restraints excluded: chain Av residue 308 GLU Chi-restraints excluded: chain Av residue 313 THR Chi-restraints excluded: chain Av residue 380 LYS Chi-restraints excluded: chain Av residue 417 VAL Chi-restraints excluded: chain Av residue 420 ILE Chi-restraints excluded: chain Av residue 483 GLU Chi-restraints excluded: chain Av residue 509 SER Chi-restraints excluded: chain Ax residue 1 MET Chi-restraints excluded: chain Ax residue 2 ASN Chi-restraints excluded: chain Ax residue 3 ILE Chi-restraints excluded: chain Ax residue 77 LYS Chi-restraints excluded: chain Ax residue 78 ILE Chi-restraints excluded: chain Ax residue 94 ILE Chi-restraints excluded: chain Ax residue 96 GLU Chi-restraints excluded: chain Ba residue 55 SER Chi-restraints excluded: chain Ba residue 77 VAL Chi-restraints excluded: chain Ba residue 89 THR Chi-restraints excluded: chain Ba residue 90 THR Chi-restraints excluded: chain Ba residue 139 SER Chi-restraints excluded: chain Ba residue 358 SER Chi-restraints excluded: chain Ba residue 366 GLN Chi-restraints excluded: chain Ba residue 432 GLN Chi-restraints excluded: chain Ba residue 518 GLU Chi-restraints excluded: chain Bb residue 157 THR Chi-restraints excluded: chain Bb residue 201 SER Chi-restraints excluded: chain Bb residue 313 THR Chi-restraints excluded: chain Bb residue 379 ILE Chi-restraints excluded: chain Bb residue 380 LYS Chi-restraints excluded: chain Bb residue 417 VAL Chi-restraints excluded: chain Bb residue 483 GLU Chi-restraints excluded: chain Bb residue 509 SER Chi-restraints excluded: chain Bd residue 1 MET Chi-restraints excluded: chain Bd residue 2 ASN Chi-restraints excluded: chain Bd residue 3 ILE Chi-restraints excluded: chain Bd residue 34 LYS Chi-restraints excluded: chain Bd residue 54 VAL Chi-restraints excluded: chain Bd residue 64 ILE Chi-restraints excluded: chain Bd residue 77 LYS Chi-restraints excluded: chain Bd residue 94 ILE Chi-restraints excluded: chain Bd residue 96 GLU Chi-restraints excluded: chain Bg residue 55 SER Chi-restraints excluded: chain Bg residue 77 VAL Chi-restraints excluded: chain Bg residue 90 THR Chi-restraints excluded: chain Bg residue 116 LEU Chi-restraints excluded: chain Bg residue 358 SER Chi-restraints excluded: chain Bg residue 366 GLN Chi-restraints excluded: chain Bg residue 432 GLN Chi-restraints excluded: chain Bg residue 518 GLU Chi-restraints excluded: chain Bh residue 87 ASP Chi-restraints excluded: chain Bh residue 201 SER Chi-restraints excluded: chain Bh residue 313 THR Chi-restraints excluded: chain Bh residue 380 LYS Chi-restraints excluded: chain Bh residue 417 VAL Chi-restraints excluded: chain Bh residue 420 ILE Chi-restraints excluded: chain Bh residue 483 GLU Chi-restraints excluded: chain Bj residue 1 MET Chi-restraints excluded: chain Bj residue 2 ASN Chi-restraints excluded: chain Bj residue 3 ILE Chi-restraints excluded: chain Bj residue 34 LYS Chi-restraints excluded: chain Bj residue 77 LYS Chi-restraints excluded: chain Bj residue 94 ILE Chi-restraints excluded: chain Bj residue 96 GLU Chi-restraints excluded: chain Bm residue 55 SER Chi-restraints excluded: chain Bm residue 77 VAL Chi-restraints excluded: chain Bm residue 89 THR Chi-restraints excluded: chain Bm residue 90 THR Chi-restraints excluded: chain Bm residue 184 GLN Chi-restraints excluded: chain Bm residue 358 SER Chi-restraints excluded: chain Bm residue 366 GLN Chi-restraints excluded: chain Bm residue 432 GLN Chi-restraints excluded: chain Bm residue 518 GLU Chi-restraints excluded: chain Bn residue 201 SER Chi-restraints excluded: chain Bn residue 308 GLU Chi-restraints excluded: chain Bn residue 313 THR Chi-restraints excluded: chain Bn residue 380 LYS Chi-restraints excluded: chain Bn residue 417 VAL Chi-restraints excluded: chain Bn residue 483 GLU Chi-restraints excluded: chain Bn residue 509 SER Chi-restraints excluded: chain Bp residue 1 MET Chi-restraints excluded: chain Bp residue 2 ASN Chi-restraints excluded: chain Bp residue 54 VAL Chi-restraints excluded: chain Bp residue 77 LYS Chi-restraints excluded: chain Bp residue 78 ILE Chi-restraints excluded: chain Bp residue 94 ILE Chi-restraints excluded: chain Bp residue 96 GLU 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: 8.9990 chunk 332 optimal weight: 20.0000 chunk 204 optimal weight: 0.9990 chunk 404 optimal weight: 0.8980 chunk 320 optimal weight: 0.7980 chunk 619 optimal weight: 0.4980 chunk 239 optimal weight: 2.9990 chunk 376 optimal weight: 6.9990 chunk 461 optimal weight: 2.9990 chunk 718 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ac 21 ASN Ac 37 ASN Ac 112 ASN Ac 366 GLN Ac 432 GLN ** Ad 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 82 ASN Ad 146 GLN ** Ad 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 366 GLN Ad 453 GLN Ad 457 ASN Ai 21 ASN Ai 366 GLN Ai 432 GLN ** Aj 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 82 ASN Aj 146 GLN ** Aj 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 366 GLN Aj 453 GLN Aj 457 ASN Ao 21 ASN Ao 37 ASN Ao 112 ASN Ao 366 GLN Ao 432 GLN ** Ap 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 82 ASN Ap 146 GLN ** Ap 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 366 GLN Ap 457 ASN Au 21 ASN Au 366 GLN Au 432 GLN ** Av 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Av 37 ASN Av 82 ASN Av 146 GLN ** Av 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Av 366 GLN Av 457 ASN Ba 21 ASN Ba 366 GLN Ba 432 GLN ** Bb 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 82 ASN Bb 146 GLN ** Bb 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 366 GLN Bb 457 ASN Bg 21 ASN Bg 112 ASN Bg 184 GLN Bg 366 GLN Bg 432 GLN ** Bh 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bh 82 ASN Bh 146 GLN ** Bh 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bh 366 GLN Bh 457 ASN Bm 21 ASN Bm 37 ASN Bm 366 GLN Bm 432 GLN ** Bn 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bn 82 ASN Bn 146 GLN ** Bn 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bn 366 GLN Bn 453 GLN Bn 457 ASN Total number of N/Q/H flips: 60 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6376 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.266 59906 Z= 0.356 Angle : 0.974 36.867 80955 Z= 0.516 Chirality : 0.072 1.851 9828 Planarity : 0.006 0.137 10542 Dihedral : 12.362 177.461 8986 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.45 % Allowed : 3.09 % Favored : 96.46 % Rotamer: Outliers : 4.26 % Allowed : 17.49 % Favored : 78.25 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.28 % 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: 1.47 (0.09), residues: 7973 helix: 2.45 (0.08), residues: 4039 sheet: -0.03 (0.14), residues: 1281 loop : -0.85 (0.12), residues: 2653 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.003 HISAr 7 PHE 0.019 0.002 PHEAj 66 TYR 0.029 0.002 TYRAc 360 ARG 0.012 0.001 ARGAf 4 *********************** 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 637 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 372 time to evaluate : 5.199 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: Ac 107 VAL cc_start: 0.8901 (OUTLIER) cc_final: 0.8686 (t) REVERT: Ad 491 MET cc_start: 0.7913 (mtm) cc_final: 0.7578 (mtm) REVERT: Af 19 THR cc_start: 0.3933 (p) cc_final: 0.3690 (p) REVERT: Ar 86 MET cc_start: 0.4476 (pmm) cc_final: 0.4231 (ptp) REVERT: Ba 491 MET cc_start: 0.7300 (mtm) cc_final: 0.7028 (mtm) REVERT: Bb 28 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.8162 (mtmt) REVERT: Bn 28 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7951 (mtpt) outliers start: 265 outliers final: 77 residues processed: 600 average time/residue: 0.5388 time to fit residues: 555.4386 Evaluate side-chains 416 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 336 time to evaluate : 5.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ac residue 77 VAL Chi-restraints excluded: chain Ac residue 107 VAL Chi-restraints excluded: chain Ac residue 252 GLU Chi-restraints excluded: chain Ac residue 358 SER Chi-restraints excluded: chain Ad residue 87 ASP Chi-restraints excluded: chain Ad residue 201 SER Chi-restraints excluded: chain Ad residue 379 ILE Chi-restraints excluded: chain Ad residue 380 LYS Chi-restraints excluded: chain Ad residue 417 VAL Chi-restraints excluded: chain Af residue 2 ASN Chi-restraints excluded: chain Af residue 3 ILE Chi-restraints excluded: chain Af residue 60 LYS Chi-restraints excluded: chain Af residue 64 ILE Chi-restraints excluded: chain Af residue 77 LYS Chi-restraints excluded: chain Ai residue 77 VAL Chi-restraints excluded: chain Ai residue 107 VAL Chi-restraints excluded: chain Ai residue 521 VAL Chi-restraints excluded: chain Aj residue 201 SER Chi-restraints excluded: chain Aj residue 417 VAL Chi-restraints excluded: chain Al residue 2 ASN Chi-restraints excluded: chain Al residue 3 ILE Chi-restraints excluded: chain Al residue 64 ILE Chi-restraints excluded: chain Ao residue 489 ILE Chi-restraints excluded: chain Ap residue 16 MET Chi-restraints excluded: chain Ap residue 77 VAL Chi-restraints excluded: chain Ap residue 201 SER Chi-restraints excluded: chain Ap residue 286 LYS Chi-restraints excluded: chain Ap residue 360 TYR Chi-restraints excluded: chain Ap residue 417 VAL Chi-restraints excluded: chain Ar residue 2 ASN Chi-restraints excluded: chain Ar residue 3 ILE Chi-restraints excluded: chain Ar residue 21 SER Chi-restraints excluded: chain Ar residue 65 VAL Chi-restraints excluded: chain Ar residue 77 LYS Chi-restraints excluded: chain Au residue 54 VAL Chi-restraints excluded: chain Au residue 77 VAL Chi-restraints excluded: chain Au residue 89 THR Chi-restraints excluded: chain Au residue 304 GLU Chi-restraints excluded: chain Au residue 521 VAL Chi-restraints excluded: chain Av residue 201 SER Chi-restraints excluded: chain Av residue 286 LYS Chi-restraints excluded: chain Av residue 360 TYR Chi-restraints excluded: chain Ax residue 2 ASN Chi-restraints excluded: chain Ax residue 3 ILE Chi-restraints excluded: chain Ax residue 27 LEU Chi-restraints excluded: chain Ax residue 64 ILE Chi-restraints excluded: chain Ax residue 75 SER Chi-restraints excluded: chain Ax residue 77 LYS Chi-restraints excluded: chain Ba residue 54 VAL Chi-restraints excluded: chain Ba residue 77 VAL Chi-restraints excluded: chain Ba residue 304 GLU Chi-restraints excluded: chain Bb residue 28 LYS Chi-restraints excluded: chain Bb residue 87 ASP Chi-restraints excluded: chain Bb residue 201 SER Chi-restraints excluded: chain Bb residue 417 VAL Chi-restraints excluded: chain Bd residue 2 ASN Chi-restraints excluded: chain Bd residue 3 ILE Chi-restraints excluded: chain Bd residue 65 VAL Chi-restraints excluded: chain Bd residue 78 ILE Chi-restraints excluded: chain Bg residue 77 VAL Chi-restraints excluded: chain Bg residue 79 SER Chi-restraints excluded: chain Bh residue 201 SER Chi-restraints excluded: chain Bh residue 360 TYR Chi-restraints excluded: chain Bh residue 417 VAL Chi-restraints excluded: chain Bj residue 2 ASN Chi-restraints excluded: chain Bj residue 3 ILE Chi-restraints excluded: chain Bj residue 77 LYS Chi-restraints excluded: chain Bj residue 78 ILE Chi-restraints excluded: chain Bm residue 77 VAL Chi-restraints excluded: chain Bm residue 107 VAL Chi-restraints excluded: chain Bm residue 304 GLU Chi-restraints excluded: chain Bn residue 28 LYS Chi-restraints excluded: chain Bn residue 87 ASP Chi-restraints excluded: chain Bn residue 201 SER Chi-restraints excluded: chain Bn residue 360 TYR Chi-restraints excluded: chain Bn residue 380 LYS Chi-restraints excluded: chain Bn residue 417 VAL Chi-restraints excluded: chain Bp residue 2 ASN Chi-restraints excluded: chain Bp residue 3 ILE Chi-restraints excluded: chain Bp residue 21 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 399 optimal weight: 5.9990 chunk 222 optimal weight: 0.7980 chunk 597 optimal weight: 6.9990 chunk 489 optimal weight: 7.9990 chunk 198 optimal weight: 7.9990 chunk 719 optimal weight: 8.9990 chunk 777 optimal weight: 0.9990 chunk 640 optimal weight: 10.0000 chunk 713 optimal weight: 2.9990 chunk 245 optimal weight: 30.0000 chunk 577 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ad 21 ASN Ad 37 ASN Ad 351 GLN Ai 453 GLN Aj 21 ASN Aj 351 GLN Ao 72 GLN Ap 21 ASN Ap 37 ASN Ap 351 GLN Au 343 GLN Av 21 ASN Av 351 GLN Bb 21 ASN Bb 37 ASN Bb 351 GLN Bg 37 ASN Bg 343 GLN Bh 21 ASN Bh 351 GLN Bh 453 GLN Bm 343 GLN Bn 21 ASN Bn 351 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6477 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 59906 Z= 0.292 Angle : 0.802 20.546 80955 Z= 0.418 Chirality : 0.066 1.844 9828 Planarity : 0.005 0.107 10542 Dihedral : 10.245 144.115 8692 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.61 % Favored : 96.00 % Rotamer: Outliers : 3.43 % Allowed : 18.60 % Favored : 77.98 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.35 % 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: 1.35 (0.09), residues: 7973 helix: 2.37 (0.08), residues: 3955 sheet: -0.04 (0.14), residues: 1288 loop : -0.86 (0.12), residues: 2730 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.003 HISAx 7 PHE 0.018 0.002 PHEBg 44 TYR 0.027 0.002 TYRBm 203 ARG 0.014 0.001 ARGBj 14 *********************** 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 561 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 348 time to evaluate : 6.333 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 491 MET cc_start: 0.8115 (mtm) cc_final: 0.7842 (mtm) REVERT: Ai 491 MET cc_start: 0.6678 (mtp) cc_final: 0.6443 (mtm) REVERT: Al 80 ASN cc_start: 0.4603 (p0) cc_final: 0.4345 (p0) REVERT: Ao 69 MET cc_start: 0.7798 (mtm) cc_final: 0.7586 (mtm) REVERT: Au 520 MET cc_start: 0.7579 (mtm) cc_final: 0.7357 (mtm) REVERT: Ba 491 MET cc_start: 0.7196 (mtm) cc_final: 0.6826 (mtm) REVERT: Bd 59 VAL cc_start: 0.5588 (OUTLIER) cc_final: 0.5131 (p) REVERT: Bh 491 MET cc_start: 0.8213 (mtm) cc_final: 0.7956 (mtm) REVERT: Bm 520 MET cc_start: 0.7829 (mtp) cc_final: 0.7561 (mtm) outliers start: 213 outliers final: 74 residues processed: 531 average time/residue: 0.5268 time to fit residues: 486.9585 Evaluate side-chains 405 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 330 time to evaluate : 5.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ac residue 77 VAL Chi-restraints excluded: chain Ac residue 358 SER Chi-restraints excluded: chain Ac residue 435 ASP Chi-restraints excluded: chain Ad residue 380 LYS Chi-restraints excluded: chain Ad residue 417 VAL Chi-restraints excluded: chain Af residue 60 LYS Chi-restraints excluded: chain Af residue 65 VAL Chi-restraints excluded: chain Ai residue 77 VAL Chi-restraints excluded: chain Ai residue 89 THR Chi-restraints excluded: chain Ai residue 157 THR Chi-restraints excluded: chain Ai residue 358 SER Chi-restraints excluded: chain Aj residue 385 THR Chi-restraints excluded: chain Aj residue 417 VAL Chi-restraints excluded: chain Al residue 2 ASN Chi-restraints excluded: chain Al residue 3 ILE Chi-restraints excluded: chain Al residue 65 VAL Chi-restraints excluded: chain Al residue 75 SER Chi-restraints excluded: chain Ao residue 358 SER Chi-restraints excluded: chain Ao residue 435 ASP Chi-restraints excluded: chain Ao residue 489 ILE Chi-restraints excluded: chain Ap residue 16 MET Chi-restraints excluded: chain Ap residue 77 VAL Chi-restraints excluded: chain Ap residue 179 ASP Chi-restraints excluded: chain Ap residue 201 SER Chi-restraints excluded: chain Ap residue 286 LYS Chi-restraints excluded: chain Ap residue 360 TYR Chi-restraints excluded: chain Ap residue 417 VAL Chi-restraints excluded: chain Ar residue 2 ASN Chi-restraints excluded: chain Ar residue 3 ILE Chi-restraints excluded: chain Ar residue 65 VAL Chi-restraints excluded: chain Ar residue 77 LYS Chi-restraints excluded: chain Ar residue 94 ILE Chi-restraints excluded: chain Au residue 40 LEU Chi-restraints excluded: chain Au residue 54 VAL Chi-restraints excluded: chain Au residue 77 VAL Chi-restraints excluded: chain Au residue 89 THR Chi-restraints excluded: chain Au residue 290 GLN Chi-restraints excluded: chain Au residue 358 SER Chi-restraints excluded: chain Au residue 435 ASP Chi-restraints excluded: chain Av residue 16 MET Chi-restraints excluded: chain Av residue 233 MET Chi-restraints excluded: chain Av residue 305 ILE Chi-restraints excluded: chain Av residue 360 TYR Chi-restraints excluded: chain Ax residue 3 ILE Chi-restraints excluded: chain Ax residue 65 VAL Chi-restraints excluded: chain Ax residue 77 LYS Chi-restraints excluded: chain Ba residue 77 VAL Chi-restraints excluded: chain Ba residue 89 THR Chi-restraints excluded: chain Ba residue 290 GLN Chi-restraints excluded: chain Ba residue 358 SER Chi-restraints excluded: chain Bb residue 16 MET Chi-restraints excluded: chain Bb residue 305 ILE Chi-restraints excluded: chain Bb residue 417 VAL Chi-restraints excluded: chain Bd residue 3 ILE Chi-restraints excluded: chain Bd residue 59 VAL Chi-restraints excluded: chain Bd residue 65 VAL Chi-restraints excluded: chain Bg residue 77 VAL Chi-restraints excluded: chain Bg residue 358 SER Chi-restraints excluded: chain Bg residue 435 ASP Chi-restraints excluded: chain Bh residue 360 TYR Chi-restraints excluded: chain Bj residue 3 ILE Chi-restraints excluded: chain Bj residue 60 LYS Chi-restraints excluded: chain Bj residue 65 VAL Chi-restraints excluded: chain Bj residue 77 LYS Chi-restraints excluded: chain Bm residue 77 VAL Chi-restraints excluded: chain Bm residue 89 THR Chi-restraints excluded: chain Bm residue 358 SER Chi-restraints excluded: chain Bn residue 201 SER Chi-restraints excluded: chain Bn residue 305 ILE Chi-restraints excluded: chain Bn residue 360 TYR Chi-restraints excluded: chain Bn residue 380 LYS Chi-restraints excluded: chain Bn residue 417 VAL Chi-restraints excluded: chain Bp residue 3 ILE Chi-restraints excluded: chain Bp residue 21 SER Chi-restraints excluded: chain Bp residue 65 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 710 optimal weight: 20.0000 chunk 541 optimal weight: 3.9990 chunk 373 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 343 optimal weight: 6.9990 chunk 483 optimal weight: 30.0000 chunk 722 optimal weight: 1.9990 chunk 764 optimal weight: 10.0000 chunk 377 optimal weight: 6.9990 chunk 684 optimal weight: 4.9990 chunk 206 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ac 194 GLN Ac 343 GLN Ac 453 GLN Ai 343 GLN Al 51 ASN Ao 343 GLN ** Ao 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Au 112 ASN Ax 7 HIS ** Ba 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ba 343 GLN Bb 453 GLN Bd 7 HIS Bd 51 ASN Bj 7 HIS Bm 112 ASN Bm 194 GLN Bp 7 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6550 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.113 59906 Z= 0.340 Angle : 0.767 18.178 80955 Z= 0.389 Chirality : 0.049 0.494 9828 Planarity : 0.005 0.110 10542 Dihedral : 9.215 139.065 8668 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.10 % Favored : 95.66 % Rotamer: Outliers : 3.07 % Allowed : 19.71 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % 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: 1.12 (0.09), residues: 7973 helix: 2.01 (0.08), residues: 4060 sheet: 0.08 (0.16), residues: 1078 loop : -0.87 (0.11), residues: 2835 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HISBd 7 PHE 0.018 0.002 PHEAd 66 TYR 0.022 0.002 TYRBa 199 ARG 0.012 0.001 ARGAx 14 *********************** 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 536 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 345 time to evaluate : 5.155 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: Al 2 ASN cc_start: 0.2965 (OUTLIER) cc_final: 0.2536 (m-40) REVERT: Al 80 ASN cc_start: 0.4742 (p0) cc_final: 0.4467 (p0) REVERT: Ao 69 MET cc_start: 0.7838 (mtm) cc_final: 0.7574 (mtm) REVERT: Av 389 MET cc_start: 0.7007 (tpp) cc_final: 0.6770 (tpp) REVERT: Bb 10 ASN cc_start: 0.7083 (m-40) cc_final: 0.6843 (m-40) REVERT: Bb 69 MET cc_start: 0.8068 (mtt) cc_final: 0.7483 (mtt) REVERT: Bm 520 MET cc_start: 0.8013 (mtp) cc_final: 0.7809 (mtm) REVERT: Bn 100 ILE cc_start: 0.9315 (OUTLIER) cc_final: 0.9020 (mt) outliers start: 191 outliers final: 105 residues processed: 515 average time/residue: 0.5374 time to fit residues: 478.6207 Evaluate side-chains 431 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 324 time to evaluate : 5.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ac residue 77 VAL Chi-restraints excluded: chain Ac residue 90 THR Chi-restraints excluded: chain Ac residue 358 SER Chi-restraints excluded: chain Ad residue 77 VAL Chi-restraints excluded: chain Ad residue 179 ASP Chi-restraints excluded: chain Ad residue 201 SER Chi-restraints excluded: chain Ad residue 417 VAL Chi-restraints excluded: chain Af residue 3 ILE Chi-restraints excluded: chain Af residue 51 ASN Chi-restraints excluded: chain Af residue 65 VAL Chi-restraints excluded: chain Ai residue 37 ASN Chi-restraints excluded: chain Ai residue 77 VAL Chi-restraints excluded: chain Ai residue 90 THR Chi-restraints excluded: chain Ai residue 358 SER Chi-restraints excluded: chain Ai residue 521 VAL Chi-restraints excluded: chain Aj residue 77 VAL Chi-restraints excluded: chain Aj residue 201 SER Chi-restraints excluded: chain Aj residue 385 THR Chi-restraints excluded: chain Aj residue 417 VAL Chi-restraints excluded: chain Aj residue 420 ILE Chi-restraints excluded: chain Aj residue 499 VAL Chi-restraints excluded: chain Al residue 2 ASN Chi-restraints excluded: chain Al residue 3 ILE Chi-restraints excluded: chain Al residue 65 VAL Chi-restraints excluded: chain Al residue 95 VAL Chi-restraints excluded: chain Ao residue 358 SER Chi-restraints excluded: chain Ap residue 16 MET Chi-restraints excluded: chain Ap residue 77 VAL Chi-restraints excluded: chain Ap residue 179 ASP Chi-restraints excluded: chain Ap residue 201 SER Chi-restraints excluded: chain Ap residue 210 THR Chi-restraints excluded: chain Ap residue 233 MET Chi-restraints excluded: chain Ap residue 286 LYS Chi-restraints excluded: chain Ap residue 417 VAL Chi-restraints excluded: chain Ap residue 420 ILE Chi-restraints excluded: chain Ap residue 499 VAL Chi-restraints excluded: chain Ar residue 1 MET Chi-restraints excluded: chain Ar residue 2 ASN Chi-restraints excluded: chain Ar residue 3 ILE Chi-restraints excluded: chain Ar residue 65 VAL Chi-restraints excluded: chain Ar residue 77 LYS Chi-restraints excluded: chain Ar residue 94 ILE Chi-restraints excluded: chain Au residue 37 ASN Chi-restraints excluded: chain Au residue 40 LEU Chi-restraints excluded: chain Au residue 54 VAL Chi-restraints excluded: chain Au residue 77 VAL Chi-restraints excluded: chain Au residue 89 THR Chi-restraints excluded: chain Au residue 358 SER Chi-restraints excluded: chain Au residue 497 THR Chi-restraints excluded: chain Au residue 521 VAL Chi-restraints excluded: chain Av residue 16 MET Chi-restraints excluded: chain Av residue 77 VAL Chi-restraints excluded: chain Av residue 179 ASP Chi-restraints excluded: chain Av residue 201 SER Chi-restraints excluded: chain Av residue 233 MET Chi-restraints excluded: chain Av residue 273 VAL Chi-restraints excluded: chain Av residue 360 TYR Chi-restraints excluded: chain Av residue 417 VAL Chi-restraints excluded: chain Ax residue 3 ILE Chi-restraints excluded: chain Ax residue 25 ILE Chi-restraints excluded: chain Ax residue 64 ILE Chi-restraints excluded: chain Ax residue 65 VAL Chi-restraints excluded: chain Ax residue 77 LYS Chi-restraints excluded: chain Ba residue 77 VAL Chi-restraints excluded: chain Ba residue 89 THR Chi-restraints excluded: chain Ba residue 358 SER Chi-restraints excluded: chain Ba residue 435 ASP Chi-restraints excluded: chain Ba residue 515 ILE Chi-restraints excluded: chain Bb residue 77 VAL Chi-restraints excluded: chain Bb residue 179 ASP Chi-restraints excluded: chain Bb residue 185 ASP Chi-restraints excluded: chain Bb residue 305 ILE Chi-restraints excluded: chain Bb residue 417 VAL Chi-restraints excluded: chain Bb residue 499 VAL Chi-restraints excluded: chain Bb residue 504 LEU Chi-restraints excluded: chain Bd residue 3 ILE Chi-restraints excluded: chain Bd residue 65 VAL Chi-restraints excluded: chain Bg residue 77 VAL Chi-restraints excluded: chain Bg residue 79 SER Chi-restraints excluded: chain Bg residue 358 SER Chi-restraints excluded: chain Bh residue 77 VAL Chi-restraints excluded: chain Bh residue 179 ASP Chi-restraints excluded: chain Bh residue 201 SER Chi-restraints excluded: chain Bh residue 417 VAL Chi-restraints excluded: chain Bh residue 420 ILE Chi-restraints excluded: chain Bh residue 499 VAL Chi-restraints excluded: chain Bh residue 504 LEU Chi-restraints excluded: chain Bj residue 2 ASN Chi-restraints excluded: chain Bj residue 3 ILE Chi-restraints excluded: chain Bj residue 77 LYS Chi-restraints excluded: chain Bj residue 95 VAL Chi-restraints excluded: chain Bm residue 77 VAL Chi-restraints excluded: chain Bm residue 89 THR Chi-restraints excluded: chain Bm residue 358 SER Chi-restraints excluded: chain Bm residue 435 ASP Chi-restraints excluded: chain Bn residue 100 ILE Chi-restraints excluded: chain Bn residue 179 ASP Chi-restraints excluded: chain Bn residue 201 SER Chi-restraints excluded: chain Bn residue 233 MET Chi-restraints excluded: chain Bn residue 305 ILE Chi-restraints excluded: chain Bn residue 360 TYR Chi-restraints excluded: chain Bn residue 417 VAL Chi-restraints excluded: chain Bn residue 499 VAL Chi-restraints excluded: chain Bp residue 3 ILE Chi-restraints excluded: chain Bp residue 25 ILE Chi-restraints excluded: chain Bp residue 65 VAL Chi-restraints excluded: chain Bp 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: 10.0000 chunk 434 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 569 optimal weight: 10.0000 chunk 315 optimal weight: 8.9990 chunk 652 optimal weight: 20.0000 chunk 528 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 390 optimal weight: 0.9980 chunk 686 optimal weight: 10.0000 chunk 192 optimal weight: 5.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ac 290 GLN Af 7 HIS Ai 290 GLN Al 7 HIS Ao 290 GLN Ao 453 GLN Ar 51 ASN Ax 51 ASN Ba 112 ASN Bg 290 GLN Bj 51 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6532 moved from start: 0.4894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 59906 Z= 0.274 Angle : 0.708 16.939 80955 Z= 0.359 Chirality : 0.046 0.410 9828 Planarity : 0.004 0.106 10542 Dihedral : 8.863 138.770 8660 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.06 % Favored : 95.72 % Rotamer: Outliers : 2.40 % Allowed : 21.03 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: 1.21 (0.09), residues: 7973 helix: 2.11 (0.08), residues: 4039 sheet: 0.03 (0.16), residues: 1092 loop : -0.79 (0.12), residues: 2842 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HISAf 7 PHE 0.015 0.001 PHEBm 44 TYR 0.031 0.002 TYRAc 203 ARG 0.011 0.000 ARGAr 4 *********************** 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 489 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 340 time to evaluate : 5.821 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: Ad 491 MET cc_start: 0.8169 (mtm) cc_final: 0.7615 (mtm) REVERT: Al 80 ASN cc_start: 0.4722 (p0) cc_final: 0.4469 (p0) REVERT: Av 389 MET cc_start: 0.6993 (tpp) cc_final: 0.6773 (tpp) REVERT: Bb 10 ASN cc_start: 0.7050 (m-40) cc_final: 0.6826 (m-40) REVERT: Bb 69 MET cc_start: 0.8003 (mtt) cc_final: 0.7484 (mtt) REVERT: Bm 520 MET cc_start: 0.7968 (mtp) cc_final: 0.7763 (mtm) outliers start: 149 outliers final: 97 residues processed: 471 average time/residue: 0.5235 time to fit residues: 431.8851 Evaluate side-chains 419 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 322 time to evaluate : 5.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ac residue 77 VAL Chi-restraints excluded: chain Ac residue 358 SER Chi-restraints excluded: chain Ac residue 494 LEU Chi-restraints excluded: chain Ac residue 497 THR Chi-restraints excluded: chain Ad residue 16 MET Chi-restraints excluded: chain Ad residue 77 VAL Chi-restraints excluded: chain Ad residue 179 ASP Chi-restraints excluded: chain Ad residue 185 ASP Chi-restraints excluded: chain Ad residue 201 SER Chi-restraints excluded: chain Ad residue 417 VAL Chi-restraints excluded: chain Ad residue 420 ILE Chi-restraints excluded: chain Af residue 2 ASN Chi-restraints excluded: chain Af residue 3 ILE Chi-restraints excluded: chain Af residue 65 VAL Chi-restraints excluded: chain Ai residue 77 VAL Chi-restraints excluded: chain Ai residue 157 THR Chi-restraints excluded: chain Ai residue 358 SER Chi-restraints excluded: chain Ai residue 494 LEU Chi-restraints excluded: chain Aj residue 49 ILE Chi-restraints excluded: chain Aj residue 77 VAL Chi-restraints excluded: chain Aj residue 134 LEU Chi-restraints excluded: chain Aj residue 185 ASP Chi-restraints excluded: chain Aj residue 385 THR Chi-restraints excluded: chain Aj residue 417 VAL Chi-restraints excluded: chain Aj residue 420 ILE Chi-restraints excluded: chain Al residue 2 ASN Chi-restraints excluded: chain Al residue 3 ILE Chi-restraints excluded: chain Al residue 65 VAL Chi-restraints excluded: chain Al residue 75 SER Chi-restraints excluded: chain Ao residue 90 THR Chi-restraints excluded: chain Ao residue 358 SER Chi-restraints excluded: chain Ap residue 16 MET Chi-restraints excluded: chain Ap residue 77 VAL Chi-restraints excluded: chain Ap residue 286 LYS Chi-restraints excluded: chain Ap residue 417 VAL Chi-restraints excluded: chain Ar residue 1 MET Chi-restraints excluded: chain Ar residue 2 ASN Chi-restraints excluded: chain Ar residue 6 LEU Chi-restraints excluded: chain Ar residue 65 VAL Chi-restraints excluded: chain Ar residue 77 LYS Chi-restraints excluded: chain Ar residue 94 ILE Chi-restraints excluded: chain Au residue 40 LEU Chi-restraints excluded: chain Au residue 54 VAL Chi-restraints excluded: chain Au residue 77 VAL Chi-restraints excluded: chain Au residue 89 THR Chi-restraints excluded: chain Au residue 358 SER Chi-restraints excluded: chain Av residue 16 MET Chi-restraints excluded: chain Av residue 179 ASP Chi-restraints excluded: chain Av residue 185 ASP Chi-restraints excluded: chain Av residue 201 SER Chi-restraints excluded: chain Av residue 233 MET Chi-restraints excluded: chain Av residue 360 TYR Chi-restraints excluded: chain Av residue 417 VAL Chi-restraints excluded: chain Ax residue 3 ILE Chi-restraints excluded: chain Ax residue 25 ILE Chi-restraints excluded: chain Ax residue 65 VAL Chi-restraints excluded: chain Ax residue 77 LYS Chi-restraints excluded: chain Ba residue 77 VAL Chi-restraints excluded: chain Ba residue 89 THR Chi-restraints excluded: chain Ba residue 358 SER Chi-restraints excluded: chain Ba residue 497 THR Chi-restraints excluded: chain Bb residue 16 MET Chi-restraints excluded: chain Bb residue 179 ASP Chi-restraints excluded: chain Bb residue 201 SER Chi-restraints excluded: chain Bb residue 305 ILE Chi-restraints excluded: chain Bb residue 417 VAL Chi-restraints excluded: chain Bb residue 504 LEU Chi-restraints excluded: chain Bd residue 3 ILE Chi-restraints excluded: chain Bd residue 65 VAL Chi-restraints excluded: chain Bg residue 77 VAL Chi-restraints excluded: chain Bg residue 79 SER Chi-restraints excluded: chain Bg residue 358 SER Chi-restraints excluded: chain Bg residue 494 LEU Chi-restraints excluded: chain Bh residue 77 VAL Chi-restraints excluded: chain Bh residue 179 ASP Chi-restraints excluded: chain Bh residue 201 SER Chi-restraints excluded: chain Bh residue 417 VAL Chi-restraints excluded: chain Bh residue 420 ILE Chi-restraints excluded: chain Bh residue 504 LEU Chi-restraints excluded: chain Bj residue 3 ILE Chi-restraints excluded: chain Bm residue 77 VAL Chi-restraints excluded: chain Bm residue 89 THR Chi-restraints excluded: chain Bm residue 107 VAL Chi-restraints excluded: chain Bm residue 358 SER Chi-restraints excluded: chain Bm residue 494 LEU Chi-restraints excluded: chain Bm residue 497 THR Chi-restraints excluded: chain Bn residue 49 ILE Chi-restraints excluded: chain Bn residue 77 VAL Chi-restraints excluded: chain Bn residue 179 ASP Chi-restraints excluded: chain Bn residue 201 SER Chi-restraints excluded: chain Bn residue 213 VAL Chi-restraints excluded: chain Bn residue 233 MET Chi-restraints excluded: chain Bn residue 360 TYR Chi-restraints excluded: chain Bn residue 417 VAL Chi-restraints excluded: chain Bp residue 25 ILE Chi-restraints excluded: chain Bp residue 65 VAL Chi-restraints excluded: chain Bp 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: 50.0000 chunk 688 optimal weight: 4.9990 chunk 151 optimal weight: 9.9990 chunk 448 optimal weight: 30.0000 chunk 188 optimal weight: 1.9990 chunk 765 optimal weight: 0.9980 chunk 635 optimal weight: 5.9990 chunk 354 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 253 optimal weight: 8.9990 chunk 401 optimal weight: 0.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ad 82 ASN Ar 7 HIS Au 194 GLN Av 82 ASN Bn 82 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6554 moved from start: 0.5121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 59906 Z= 0.300 Angle : 0.710 17.257 80955 Z= 0.357 Chirality : 0.046 0.415 9828 Planarity : 0.004 0.103 10542 Dihedral : 8.708 139.669 8655 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.34 % Favored : 95.45 % Rotamer: Outliers : 2.61 % Allowed : 21.57 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: 1.22 (0.09), residues: 7973 helix: 2.05 (0.08), residues: 4046 sheet: 0.25 (0.17), residues: 1029 loop : -0.77 (0.12), residues: 2898 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HISBd 7 PHE 0.014 0.002 PHEAv 44 TYR 0.016 0.001 TYRBm 199 ARG 0.005 0.000 ARGAr 4 *********************** 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 494 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 332 time to evaluate : 5.371 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: Ad 491 MET cc_start: 0.8263 (mtm) cc_final: 0.7822 (mtm) REVERT: Al 80 ASN cc_start: 0.4753 (p0) cc_final: 0.4527 (p0) REVERT: Av 389 MET cc_start: 0.7004 (tpp) cc_final: 0.6772 (tpp) REVERT: Bg 183 LEU cc_start: 0.4086 (OUTLIER) cc_final: 0.3881 (mt) REVERT: Bh 491 MET cc_start: 0.8166 (mtm) cc_final: 0.7712 (mtm) REVERT: Bm 520 MET cc_start: 0.7982 (mtp) cc_final: 0.7669 (mtp) outliers start: 162 outliers final: 110 residues processed: 477 average time/residue: 0.5067 time to fit residues: 427.4484 Evaluate side-chains 436 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 325 time to evaluate : 5.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ac residue 77 VAL Chi-restraints excluded: chain Ac residue 358 SER Chi-restraints excluded: chain Ac residue 494 LEU Chi-restraints excluded: chain Ad residue 77 VAL Chi-restraints excluded: chain Ad residue 179 ASP Chi-restraints excluded: chain Ad residue 185 ASP Chi-restraints excluded: chain Ad residue 201 SER Chi-restraints excluded: chain Ad residue 417 VAL Chi-restraints excluded: chain Ad residue 420 ILE Chi-restraints excluded: chain Af residue 2 ASN Chi-restraints excluded: chain Af residue 3 ILE Chi-restraints excluded: chain Af residue 65 VAL Chi-restraints excluded: chain Ai residue 37 ASN Chi-restraints excluded: chain Ai residue 77 VAL Chi-restraints excluded: chain Ai residue 157 THR Chi-restraints excluded: chain Ai residue 358 SER Chi-restraints excluded: chain Ai residue 494 LEU Chi-restraints excluded: chain Ai residue 521 VAL Chi-restraints excluded: chain Aj residue 49 ILE Chi-restraints excluded: chain Aj residue 77 VAL Chi-restraints excluded: chain Aj residue 134 LEU Chi-restraints excluded: chain Aj residue 185 ASP Chi-restraints excluded: chain Aj residue 201 SER Chi-restraints excluded: chain Aj residue 385 THR Chi-restraints excluded: chain Aj residue 417 VAL Chi-restraints excluded: chain Aj residue 420 ILE Chi-restraints excluded: chain Aj residue 524 LEU Chi-restraints excluded: chain Al residue 2 ASN Chi-restraints excluded: chain Al residue 3 ILE Chi-restraints excluded: chain Al residue 65 VAL Chi-restraints excluded: chain Ap residue 77 VAL Chi-restraints excluded: chain Ap residue 179 ASP Chi-restraints excluded: chain Ap residue 201 SER Chi-restraints excluded: chain Ap residue 417 VAL Chi-restraints excluded: chain Ap residue 420 ILE Chi-restraints excluded: chain Ap residue 499 VAL Chi-restraints excluded: chain Ar residue 2 ASN Chi-restraints excluded: chain Ar residue 3 ILE Chi-restraints excluded: chain Ar residue 25 ILE Chi-restraints excluded: chain Ar residue 65 VAL Chi-restraints excluded: chain Ar residue 94 ILE Chi-restraints excluded: chain Ar residue 95 VAL Chi-restraints excluded: chain Au residue 40 LEU Chi-restraints excluded: chain Au residue 54 VAL Chi-restraints excluded: chain Au residue 77 VAL Chi-restraints excluded: chain Au residue 89 THR Chi-restraints excluded: chain Au residue 358 SER Chi-restraints excluded: chain Au residue 494 LEU Chi-restraints excluded: chain Au residue 497 THR Chi-restraints excluded: chain Au residue 521 VAL Chi-restraints excluded: chain Av residue 16 MET Chi-restraints excluded: chain Av residue 77 VAL Chi-restraints excluded: chain Av residue 134 LEU Chi-restraints excluded: chain Av residue 179 ASP Chi-restraints excluded: chain Av residue 185 ASP Chi-restraints excluded: chain Av residue 201 SER Chi-restraints excluded: chain Av residue 233 MET Chi-restraints excluded: chain Av residue 360 TYR Chi-restraints excluded: chain Av residue 417 VAL Chi-restraints excluded: chain Ax residue 3 ILE Chi-restraints excluded: chain Ax residue 25 ILE Chi-restraints excluded: chain Ax residue 65 VAL Chi-restraints excluded: chain Ba residue 77 VAL Chi-restraints excluded: chain Ba residue 89 THR Chi-restraints excluded: chain Ba residue 494 LEU Chi-restraints excluded: chain Ba residue 497 THR Chi-restraints excluded: chain Bb residue 16 MET Chi-restraints excluded: chain Bb residue 77 VAL Chi-restraints excluded: chain Bb residue 179 ASP Chi-restraints excluded: chain Bb residue 185 ASP Chi-restraints excluded: chain Bb residue 201 SER Chi-restraints excluded: chain Bb residue 417 VAL Chi-restraints excluded: chain Bb residue 504 LEU Chi-restraints excluded: chain Bd residue 2 ASN Chi-restraints excluded: chain Bd residue 3 ILE Chi-restraints excluded: chain Bd residue 6 LEU Chi-restraints excluded: chain Bd residue 65 VAL Chi-restraints excluded: chain Bg residue 77 VAL Chi-restraints excluded: chain Bg residue 79 SER Chi-restraints excluded: chain Bg residue 183 LEU Chi-restraints excluded: chain Bg residue 358 SER Chi-restraints excluded: chain Bg residue 494 LEU Chi-restraints excluded: chain Bh residue 77 VAL Chi-restraints excluded: chain Bh residue 179 ASP Chi-restraints excluded: chain Bh residue 201 SER Chi-restraints excluded: chain Bh residue 417 VAL Chi-restraints excluded: chain Bh residue 420 ILE Chi-restraints excluded: chain Bh residue 483 GLU Chi-restraints excluded: chain Bh residue 499 VAL Chi-restraints excluded: chain Bh residue 504 LEU Chi-restraints excluded: chain Bj residue 3 ILE Chi-restraints excluded: chain Bj residue 65 VAL Chi-restraints excluded: chain Bm residue 77 VAL Chi-restraints excluded: chain Bm residue 89 THR Chi-restraints excluded: chain Bm residue 107 VAL Chi-restraints excluded: chain Bm residue 358 SER Chi-restraints excluded: chain Bm residue 494 LEU Chi-restraints excluded: chain Bn residue 44 PHE Chi-restraints excluded: chain Bn residue 49 ILE Chi-restraints excluded: chain Bn residue 77 VAL Chi-restraints excluded: chain Bn residue 179 ASP Chi-restraints excluded: chain Bn residue 201 SER Chi-restraints excluded: chain Bn residue 213 VAL Chi-restraints excluded: chain Bn residue 233 MET Chi-restraints excluded: chain Bn residue 360 TYR Chi-restraints excluded: chain Bn residue 417 VAL Chi-restraints excluded: chain Bn residue 499 VAL Chi-restraints excluded: chain Bp residue 2 ASN Chi-restraints excluded: chain Bp residue 3 ILE Chi-restraints excluded: chain Bp residue 25 ILE Chi-restraints excluded: chain Bp residue 65 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 737 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 436 optimal weight: 6.9990 chunk 558 optimal weight: 0.8980 chunk 433 optimal weight: 1.9990 chunk 644 optimal weight: 1.9990 chunk 427 optimal weight: 0.0980 chunk 762 optimal weight: 10.0000 chunk 477 optimal weight: 9.9990 chunk 464 optimal weight: 7.9990 chunk 351 optimal weight: 7.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ap 82 ASN Au 37 ASN Bb 82 ASN Bh 82 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6524 moved from start: 0.5321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 59906 Z= 0.237 Angle : 0.682 18.469 80955 Z= 0.343 Chirality : 0.045 0.424 9828 Planarity : 0.004 0.099 10542 Dihedral : 8.424 139.033 8643 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.47 % Favored : 95.33 % Rotamer: Outliers : 2.32 % Allowed : 22.51 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: 1.28 (0.09), residues: 7973 helix: 2.19 (0.08), residues: 4004 sheet: 0.15 (0.16), residues: 1078 loop : -0.81 (0.12), residues: 2891 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HISBp 7 PHE 0.009 0.001 PHEAv 195 TYR 0.020 0.002 TYRBd 71 ARG 0.003 0.000 ARGBa 285 *********************** 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 477 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 333 time to evaluate : 5.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ad 491 MET cc_start: 0.8254 (mtm) cc_final: 0.7814 (mtm) REVERT: Aj 389 MET cc_start: 0.7352 (tpp) cc_final: 0.7134 (tpt) REVERT: Al 80 ASN cc_start: 0.4746 (p0) cc_final: 0.4506 (p0) REVERT: Ao 69 MET cc_start: 0.7635 (mtm) cc_final: 0.7327 (mtm) REVERT: Av 267 MET cc_start: 0.5451 (pmm) cc_final: 0.5191 (pmm) REVERT: Av 389 MET cc_start: 0.6972 (tpp) cc_final: 0.6765 (tpp) REVERT: Ax 1 MET cc_start: 0.2926 (mmm) cc_final: 0.2635 (mpp) REVERT: Bm 520 MET cc_start: 0.7951 (mtp) cc_final: 0.7641 (mtp) outliers start: 144 outliers final: 93 residues processed: 464 average time/residue: 0.5045 time to fit residues: 414.4840 Evaluate side-chains 413 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 320 time to evaluate : 5.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ac residue 77 VAL Chi-restraints excluded: chain Ac residue 494 LEU Chi-restraints excluded: chain Ad residue 77 VAL Chi-restraints excluded: chain Ad residue 179 ASP Chi-restraints excluded: chain Ad residue 185 ASP Chi-restraints excluded: chain Ad residue 201 SER Chi-restraints excluded: chain Ad residue 417 VAL Chi-restraints excluded: chain Af residue 2 ASN Chi-restraints excluded: chain Af residue 3 ILE Chi-restraints excluded: chain Af residue 25 ILE Chi-restraints excluded: chain Af residue 65 VAL Chi-restraints excluded: chain Ai residue 77 VAL Chi-restraints excluded: chain Ai residue 157 THR Chi-restraints excluded: chain Ai residue 494 LEU Chi-restraints excluded: chain Ai residue 521 VAL Chi-restraints excluded: chain Aj residue 49 ILE Chi-restraints excluded: chain Aj residue 77 VAL Chi-restraints excluded: chain Aj residue 134 LEU Chi-restraints excluded: chain Aj residue 185 ASP Chi-restraints excluded: chain Aj residue 201 SER Chi-restraints excluded: chain Aj residue 417 VAL Chi-restraints excluded: chain Aj residue 420 ILE Chi-restraints excluded: chain Aj residue 524 LEU Chi-restraints excluded: chain Al residue 2 ASN Chi-restraints excluded: chain Al residue 3 ILE Chi-restraints excluded: chain Al residue 6 LEU Chi-restraints excluded: chain Al residue 57 LEU Chi-restraints excluded: chain Al residue 65 VAL Chi-restraints excluded: chain Al residue 75 SER Chi-restraints excluded: chain Ap residue 77 VAL Chi-restraints excluded: chain Ap residue 179 ASP Chi-restraints excluded: chain Ap residue 201 SER Chi-restraints excluded: chain Ap residue 417 VAL Chi-restraints excluded: chain Ar residue 3 ILE Chi-restraints excluded: chain Ar residue 25 ILE Chi-restraints excluded: chain Ar residue 65 VAL Chi-restraints excluded: chain Ar residue 94 ILE Chi-restraints excluded: chain Ar residue 95 VAL Chi-restraints excluded: chain Au residue 37 ASN Chi-restraints excluded: chain Au residue 40 LEU Chi-restraints excluded: chain Au residue 77 VAL Chi-restraints excluded: chain Au residue 89 THR Chi-restraints excluded: chain Au residue 497 THR Chi-restraints excluded: chain Av residue 16 MET Chi-restraints excluded: chain Av residue 77 VAL Chi-restraints excluded: chain Av residue 134 LEU Chi-restraints excluded: chain Av residue 179 ASP Chi-restraints excluded: chain Av residue 185 ASP Chi-restraints excluded: chain Av residue 201 SER Chi-restraints excluded: chain Av residue 233 MET Chi-restraints excluded: chain Av residue 417 VAL Chi-restraints excluded: chain Av residue 524 LEU Chi-restraints excluded: chain Ax residue 3 ILE Chi-restraints excluded: chain Ax residue 25 ILE Chi-restraints excluded: chain Ax residue 65 VAL Chi-restraints excluded: chain Ba residue 77 VAL Chi-restraints excluded: chain Ba residue 89 THR Chi-restraints excluded: chain Ba residue 494 LEU Chi-restraints excluded: chain Ba residue 497 THR Chi-restraints excluded: chain Bb residue 16 MET Chi-restraints excluded: chain Bb residue 77 VAL Chi-restraints excluded: chain Bb residue 179 ASP Chi-restraints excluded: chain Bb residue 201 SER Chi-restraints excluded: chain Bb residue 417 VAL Chi-restraints excluded: chain Bd residue 3 ILE Chi-restraints excluded: chain Bd residue 6 LEU Chi-restraints excluded: chain Bd residue 65 VAL Chi-restraints excluded: chain Bg residue 77 VAL Chi-restraints excluded: chain Bg residue 494 LEU Chi-restraints excluded: chain Bh residue 179 ASP Chi-restraints excluded: chain Bh residue 201 SER Chi-restraints excluded: chain Bh residue 213 VAL Chi-restraints excluded: chain Bh residue 420 ILE Chi-restraints excluded: chain Bh residue 504 LEU Chi-restraints excluded: chain Bj residue 3 ILE Chi-restraints excluded: chain Bj residue 65 VAL Chi-restraints excluded: chain Bm residue 77 VAL Chi-restraints excluded: chain Bm residue 89 THR Chi-restraints excluded: chain Bm residue 107 VAL Chi-restraints excluded: chain Bm residue 358 SER Chi-restraints excluded: chain Bm residue 494 LEU Chi-restraints excluded: chain Bn residue 77 VAL Chi-restraints excluded: chain Bn residue 179 ASP Chi-restraints excluded: chain Bn residue 201 SER Chi-restraints excluded: chain Bn residue 213 VAL Chi-restraints excluded: chain Bn residue 233 MET Chi-restraints excluded: chain Bn residue 307 MET Chi-restraints excluded: chain Bn residue 417 VAL Chi-restraints excluded: chain Bn residue 442 VAL Chi-restraints excluded: chain Bp residue 2 ASN Chi-restraints excluded: chain Bp residue 3 ILE Chi-restraints excluded: chain Bp residue 25 ILE Chi-restraints excluded: chain Bp residue 65 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 471 optimal weight: 2.9990 chunk 304 optimal weight: 10.0000 chunk 455 optimal weight: 3.9990 chunk 229 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 chunk 147 optimal weight: 9.9990 chunk 484 optimal weight: 6.9990 chunk 519 optimal weight: 8.9990 chunk 376 optimal weight: 10.0000 chunk 71 optimal weight: 20.0000 chunk 599 optimal weight: 0.2980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ac 37 ASN Ai 112 ASN Bm 37 ASN Bm 72 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6536 moved from start: 0.5459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 59906 Z= 0.253 Angle : 0.690 17.368 80955 Z= 0.347 Chirality : 0.045 0.418 9828 Planarity : 0.004 0.096 10542 Dihedral : 8.271 138.969 8640 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.57 % Favored : 95.25 % Rotamer: Outliers : 2.27 % Allowed : 23.01 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 1.23 (0.09), residues: 7973 helix: 2.15 (0.08), residues: 4004 sheet: 0.14 (0.16), residues: 1148 loop : -0.87 (0.12), residues: 2821 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HISBj 7 PHE 0.009 0.001 PHEAu 44 TYR 0.017 0.001 TYRBa 203 ARG 0.005 0.000 ARGBn 268 *********************** 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 470 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 329 time to evaluate : 5.125 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: Ad 491 MET cc_start: 0.8251 (mtm) cc_final: 0.8022 (mtm) REVERT: Al 80 ASN cc_start: 0.4802 (p0) cc_final: 0.4545 (p0) REVERT: Av 389 MET cc_start: 0.6981 (tpp) cc_final: 0.6776 (tpp) REVERT: Ax 1 MET cc_start: 0.3458 (mmm) cc_final: 0.3007 (mpp) REVERT: Bh 302 SER cc_start: 0.7197 (OUTLIER) cc_final: 0.6987 (p) REVERT: Bm 520 MET cc_start: 0.7980 (mtp) cc_final: 0.7749 (mtm) outliers start: 141 outliers final: 102 residues processed: 457 average time/residue: 0.5102 time to fit residues: 412.2648 Evaluate side-chains 427 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 324 time to evaluate : 5.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ac residue 77 VAL Chi-restraints excluded: chain Ac residue 494 LEU Chi-restraints excluded: chain Ad residue 77 VAL Chi-restraints excluded: chain Ad residue 179 ASP Chi-restraints excluded: chain Ad residue 185 ASP Chi-restraints excluded: chain Ad residue 201 SER Chi-restraints excluded: chain Ad residue 417 VAL Chi-restraints excluded: chain Ad residue 420 ILE Chi-restraints excluded: chain Af residue 3 ILE Chi-restraints excluded: chain Af residue 65 VAL Chi-restraints excluded: chain Ai residue 77 VAL Chi-restraints excluded: chain Ai residue 157 THR Chi-restraints excluded: chain Ai residue 494 LEU Chi-restraints excluded: chain Ai residue 521 VAL Chi-restraints excluded: chain Aj residue 49 ILE Chi-restraints excluded: chain Aj residue 77 VAL Chi-restraints excluded: chain Aj residue 134 LEU Chi-restraints excluded: chain Aj residue 185 ASP Chi-restraints excluded: chain Aj residue 201 SER Chi-restraints excluded: chain Aj residue 272 LYS Chi-restraints excluded: chain Aj residue 417 VAL Chi-restraints excluded: chain Aj residue 420 ILE Chi-restraints excluded: chain Aj residue 524 LEU Chi-restraints excluded: chain Al residue 2 ASN Chi-restraints excluded: chain Al residue 3 ILE Chi-restraints excluded: chain Al residue 6 LEU Chi-restraints excluded: chain Al residue 65 VAL Chi-restraints excluded: chain Ap residue 77 VAL Chi-restraints excluded: chain Ap residue 179 ASP Chi-restraints excluded: chain Ap residue 201 SER Chi-restraints excluded: chain Ap residue 417 VAL Chi-restraints excluded: chain Ap residue 420 ILE Chi-restraints excluded: chain Ar residue 6 LEU Chi-restraints excluded: chain Ar residue 25 ILE Chi-restraints excluded: chain Ar residue 65 VAL Chi-restraints excluded: chain Ar residue 94 ILE Chi-restraints excluded: chain Ar residue 95 VAL Chi-restraints excluded: chain Au residue 37 ASN Chi-restraints excluded: chain Au residue 40 LEU Chi-restraints excluded: chain Au residue 77 VAL Chi-restraints excluded: chain Au residue 89 THR Chi-restraints excluded: chain Au residue 494 LEU Chi-restraints excluded: chain Au residue 497 THR Chi-restraints excluded: chain Av residue 16 MET Chi-restraints excluded: chain Av residue 77 VAL Chi-restraints excluded: chain Av residue 179 ASP Chi-restraints excluded: chain Av residue 185 ASP Chi-restraints excluded: chain Av residue 201 SER Chi-restraints excluded: chain Av residue 233 MET Chi-restraints excluded: chain Av residue 417 VAL Chi-restraints excluded: chain Av residue 483 GLU Chi-restraints excluded: chain Av residue 524 LEU Chi-restraints excluded: chain Ax residue 3 ILE Chi-restraints excluded: chain Ax residue 25 ILE Chi-restraints excluded: chain Ax residue 65 VAL Chi-restraints excluded: chain Ba residue 77 VAL Chi-restraints excluded: chain Ba residue 89 THR Chi-restraints excluded: chain Ba residue 494 LEU Chi-restraints excluded: chain Ba residue 497 THR Chi-restraints excluded: chain Bb residue 16 MET Chi-restraints excluded: chain Bb residue 77 VAL Chi-restraints excluded: chain Bb residue 179 ASP Chi-restraints excluded: chain Bb residue 185 ASP Chi-restraints excluded: chain Bb residue 201 SER Chi-restraints excluded: chain Bb residue 213 VAL Chi-restraints excluded: chain Bb residue 417 VAL Chi-restraints excluded: chain Bd residue 2 ASN Chi-restraints excluded: chain Bd residue 3 ILE Chi-restraints excluded: chain Bd residue 6 LEU Chi-restraints excluded: chain Bd residue 65 VAL Chi-restraints excluded: chain Bg residue 77 VAL Chi-restraints excluded: chain Bg residue 199 TYR Chi-restraints excluded: chain Bg residue 494 LEU Chi-restraints excluded: chain Bh residue 77 VAL Chi-restraints excluded: chain Bh residue 179 ASP Chi-restraints excluded: chain Bh residue 201 SER Chi-restraints excluded: chain Bh residue 213 VAL Chi-restraints excluded: chain Bh residue 302 SER Chi-restraints excluded: chain Bh residue 417 VAL Chi-restraints excluded: chain Bh residue 420 ILE Chi-restraints excluded: chain Bh residue 483 GLU Chi-restraints excluded: chain Bh residue 504 LEU Chi-restraints excluded: chain Bj residue 3 ILE Chi-restraints excluded: chain Bj residue 6 LEU Chi-restraints excluded: chain Bj residue 65 VAL Chi-restraints excluded: chain Bm residue 77 VAL Chi-restraints excluded: chain Bm residue 89 THR Chi-restraints excluded: chain Bm residue 107 VAL Chi-restraints excluded: chain Bm residue 199 TYR Chi-restraints excluded: chain Bm residue 494 LEU Chi-restraints excluded: chain Bn residue 16 MET Chi-restraints excluded: chain Bn residue 44 PHE Chi-restraints excluded: chain Bn residue 77 VAL Chi-restraints excluded: chain Bn residue 179 ASP Chi-restraints excluded: chain Bn residue 201 SER Chi-restraints excluded: chain Bn residue 213 VAL Chi-restraints excluded: chain Bn residue 233 MET Chi-restraints excluded: chain Bn residue 417 VAL Chi-restraints excluded: chain Bn residue 442 VAL Chi-restraints excluded: chain Bp residue 2 ASN Chi-restraints excluded: chain Bp residue 3 ILE Chi-restraints excluded: chain Bp residue 25 ILE Chi-restraints excluded: chain Bp residue 65 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 693 optimal weight: 0.9980 chunk 730 optimal weight: 1.9990 chunk 666 optimal weight: 2.9990 chunk 710 optimal weight: 6.9990 chunk 427 optimal weight: 6.9990 chunk 309 optimal weight: 8.9990 chunk 557 optimal weight: 5.9990 chunk 218 optimal weight: 4.9990 chunk 641 optimal weight: 3.9990 chunk 671 optimal weight: 10.0000 chunk 707 optimal weight: 50.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aj 72 GLN ** Ao 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Au 37 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6565 moved from start: 0.5597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 59906 Z= 0.292 Angle : 0.703 16.234 80955 Z= 0.353 Chirality : 0.045 0.418 9828 Planarity : 0.004 0.096 10542 Dihedral : 8.264 139.801 8640 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.63 % Favored : 95.18 % Rotamer: Outliers : 2.12 % Allowed : 23.25 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: 1.20 (0.09), residues: 7973 helix: 2.07 (0.08), residues: 4011 sheet: 0.48 (0.17), residues: 959 loop : -0.88 (0.11), residues: 3003 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HISBd 7 PHE 0.011 0.001 PHEAd 66 TYR 0.046 0.002 TYRBg 203 ARG 0.004 0.000 ARGAd 421 *********************** 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 459 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 327 time to evaluate : 5.139 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: Ac 69 MET cc_start: 0.7928 (mtm) cc_final: 0.7495 (mtm) REVERT: Ac 488 MET cc_start: 0.8083 (mmm) cc_final: 0.7835 (mmm) REVERT: Ad 491 MET cc_start: 0.8300 (mtm) cc_final: 0.7939 (mtm) REVERT: Aj 389 MET cc_start: 0.7486 (tpp) cc_final: 0.7251 (tpt) REVERT: Al 80 ASN cc_start: 0.4876 (p0) cc_final: 0.4596 (p0) REVERT: Au 488 MET cc_start: 0.7713 (mmm) cc_final: 0.7458 (mmm) REVERT: Ax 1 MET cc_start: 0.2531 (mmm) cc_final: 0.2264 (mpp) REVERT: Ax 2 ASN cc_start: 0.3102 (OUTLIER) cc_final: 0.2023 (m-40) REVERT: Bm 520 MET cc_start: 0.7999 (mtp) cc_final: 0.7669 (mtp) outliers start: 132 outliers final: 106 residues processed: 444 average time/residue: 0.5125 time to fit residues: 400.4447 Evaluate side-chains 432 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 325 time to evaluate : 5.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ac residue 77 VAL Chi-restraints excluded: chain Ac residue 494 LEU Chi-restraints excluded: chain Ad residue 77 VAL Chi-restraints excluded: chain Ad residue 179 ASP Chi-restraints excluded: chain Ad residue 185 ASP Chi-restraints excluded: chain Ad residue 201 SER Chi-restraints excluded: chain Ad residue 417 VAL Chi-restraints excluded: chain Ad residue 420 ILE Chi-restraints excluded: chain Af residue 2 ASN Chi-restraints excluded: chain Af residue 3 ILE Chi-restraints excluded: chain Af residue 25 ILE Chi-restraints excluded: chain Af residue 65 VAL Chi-restraints excluded: chain Ai residue 77 VAL Chi-restraints excluded: chain Ai residue 157 THR Chi-restraints excluded: chain Ai residue 494 LEU Chi-restraints excluded: chain Ai residue 521 VAL Chi-restraints excluded: chain Aj residue 49 ILE Chi-restraints excluded: chain Aj residue 77 VAL Chi-restraints excluded: chain Aj residue 134 LEU Chi-restraints excluded: chain Aj residue 185 ASP Chi-restraints excluded: chain Aj residue 201 SER Chi-restraints excluded: chain Aj residue 385 THR Chi-restraints excluded: chain Aj residue 417 VAL Chi-restraints excluded: chain Aj residue 420 ILE Chi-restraints excluded: chain Aj residue 524 LEU Chi-restraints excluded: chain Al residue 3 ILE Chi-restraints excluded: chain Al residue 6 LEU Chi-restraints excluded: chain Al residue 25 ILE Chi-restraints excluded: chain Al residue 65 VAL Chi-restraints excluded: chain Ap residue 77 VAL Chi-restraints excluded: chain Ap residue 179 ASP Chi-restraints excluded: chain Ap residue 201 SER Chi-restraints excluded: chain Ap residue 417 VAL Chi-restraints excluded: chain Ap residue 420 ILE Chi-restraints excluded: chain Ap residue 499 VAL Chi-restraints excluded: chain Ar residue 6 LEU Chi-restraints excluded: chain Ar residue 25 ILE Chi-restraints excluded: chain Ar residue 65 VAL Chi-restraints excluded: chain Ar residue 94 ILE Chi-restraints excluded: chain Ar residue 95 VAL Chi-restraints excluded: chain Au residue 37 ASN Chi-restraints excluded: chain Au residue 40 LEU Chi-restraints excluded: chain Au residue 54 VAL Chi-restraints excluded: chain Au residue 77 VAL Chi-restraints excluded: chain Au residue 89 THR Chi-restraints excluded: chain Au residue 494 LEU Chi-restraints excluded: chain Au residue 497 THR Chi-restraints excluded: chain Av residue 16 MET Chi-restraints excluded: chain Av residue 77 VAL Chi-restraints excluded: chain Av residue 179 ASP Chi-restraints excluded: chain Av residue 185 ASP Chi-restraints excluded: chain Av residue 201 SER Chi-restraints excluded: chain Av residue 233 MET Chi-restraints excluded: chain Av residue 417 VAL Chi-restraints excluded: chain Av residue 420 ILE Chi-restraints excluded: chain Av residue 483 GLU Chi-restraints excluded: chain Av residue 524 LEU Chi-restraints excluded: chain Ax residue 2 ASN Chi-restraints excluded: chain Ax residue 3 ILE Chi-restraints excluded: chain Ax residue 25 ILE Chi-restraints excluded: chain Ax residue 65 VAL Chi-restraints excluded: chain Ba residue 77 VAL Chi-restraints excluded: chain Ba residue 89 THR Chi-restraints excluded: chain Ba residue 494 LEU Chi-restraints excluded: chain Ba residue 497 THR Chi-restraints excluded: chain Bb residue 16 MET Chi-restraints excluded: chain Bb residue 77 VAL Chi-restraints excluded: chain Bb residue 179 ASP Chi-restraints excluded: chain Bb residue 185 ASP Chi-restraints excluded: chain Bb residue 201 SER Chi-restraints excluded: chain Bb residue 213 VAL Chi-restraints excluded: chain Bb residue 417 VAL Chi-restraints excluded: chain Bd residue 2 ASN Chi-restraints excluded: chain Bd residue 3 ILE Chi-restraints excluded: chain Bd residue 6 LEU Chi-restraints excluded: chain Bd residue 65 VAL Chi-restraints excluded: chain Bg residue 77 VAL Chi-restraints excluded: chain Bg residue 79 SER Chi-restraints excluded: chain Bg residue 199 TYR Chi-restraints excluded: chain Bg residue 494 LEU Chi-restraints excluded: chain Bh residue 77 VAL Chi-restraints excluded: chain Bh residue 179 ASP Chi-restraints excluded: chain Bh residue 201 SER Chi-restraints excluded: chain Bh residue 213 VAL Chi-restraints excluded: chain Bh residue 417 VAL Chi-restraints excluded: chain Bh residue 420 ILE Chi-restraints excluded: chain Bh residue 483 GLU Chi-restraints excluded: chain Bh residue 499 VAL Chi-restraints excluded: chain Bh residue 504 LEU Chi-restraints excluded: chain Bj residue 3 ILE Chi-restraints excluded: chain Bj residue 65 VAL Chi-restraints excluded: chain Bm residue 77 VAL Chi-restraints excluded: chain Bm residue 89 THR Chi-restraints excluded: chain Bm residue 107 VAL Chi-restraints excluded: chain Bm residue 199 TYR Chi-restraints excluded: chain Bm residue 494 LEU Chi-restraints excluded: chain Bn residue 44 PHE Chi-restraints excluded: chain Bn residue 77 VAL Chi-restraints excluded: chain Bn residue 179 ASP Chi-restraints excluded: chain Bn residue 201 SER Chi-restraints excluded: chain Bn residue 213 VAL Chi-restraints excluded: chain Bn residue 233 MET Chi-restraints excluded: chain Bn residue 417 VAL Chi-restraints excluded: chain Bn residue 442 VAL Chi-restraints excluded: chain Bp residue 3 ILE Chi-restraints excluded: chain Bp residue 25 ILE Chi-restraints excluded: chain Bp residue 65 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 466 optimal weight: 6.9990 chunk 751 optimal weight: 0.0470 chunk 458 optimal weight: 0.9990 chunk 356 optimal weight: 0.0770 chunk 522 optimal weight: 8.9990 chunk 788 optimal weight: 7.9990 chunk 725 optimal weight: 7.9990 chunk 627 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 484 optimal weight: 7.9990 chunk 384 optimal weight: 0.9980 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ac 72 GLN Ad 72 GLN Ai 72 GLN Aj 82 ASN ** Ao 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Au 37 ASN Au 72 GLN Av 72 GLN Ba 72 GLN Bb 72 GLN Bd 2 ASN Bg 72 GLN Bg 453 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6468 moved from start: 0.5773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 59906 Z= 0.171 Angle : 0.667 16.337 80955 Z= 0.333 Chirality : 0.044 0.428 9828 Planarity : 0.004 0.092 10542 Dihedral : 7.823 132.918 8638 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.57 % Favored : 95.27 % Rotamer: Outliers : 1.54 % Allowed : 23.62 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 1.36 (0.09), residues: 7973 helix: 2.29 (0.08), residues: 3997 sheet: 0.19 (0.16), residues: 1071 loop : -0.82 (0.11), residues: 2905 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HISAr 7 PHE 0.011 0.001 PHEBh 281 TYR 0.032 0.001 TYRBm 203 ARG 0.013 0.000 ARGAu 36 ********************** 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 427 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 331 time to evaluate : 5.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ad 491 MET cc_start: 0.8231 (mtm) cc_final: 0.7761 (mtm) REVERT: Al 80 ASN cc_start: 0.4642 (p0) cc_final: 0.4399 (p0) REVERT: Bm 520 MET cc_start: 0.7807 (mtp) cc_final: 0.7588 (mtm) outliers start: 96 outliers final: 73 residues processed: 418 average time/residue: 0.5347 time to fit residues: 393.4628 Evaluate side-chains 399 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 326 time to evaluate : 5.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ac residue 77 VAL Chi-restraints excluded: chain Ac residue 494 LEU Chi-restraints excluded: chain Ad residue 77 VAL Chi-restraints excluded: chain Ad residue 185 ASP Chi-restraints excluded: chain Ad residue 201 SER Chi-restraints excluded: chain Af residue 3 ILE Chi-restraints excluded: chain Af residue 64 ILE Chi-restraints excluded: chain Af residue 65 VAL Chi-restraints excluded: chain Ai residue 77 VAL Chi-restraints excluded: chain Ai residue 157 THR Chi-restraints excluded: chain Aj residue 77 VAL Chi-restraints excluded: chain Aj residue 185 ASP Chi-restraints excluded: chain Aj residue 201 SER Chi-restraints excluded: chain Aj residue 417 VAL Chi-restraints excluded: chain Al residue 3 ILE Chi-restraints excluded: chain Al residue 6 LEU Chi-restraints excluded: chain Al residue 65 VAL Chi-restraints excluded: chain Ap residue 179 ASP Chi-restraints excluded: chain Ap residue 201 SER Chi-restraints excluded: chain Ar residue 6 LEU Chi-restraints excluded: chain Ar residue 25 ILE Chi-restraints excluded: chain Ar residue 65 VAL Chi-restraints excluded: chain Ar residue 94 ILE Chi-restraints excluded: chain Au residue 37 ASN Chi-restraints excluded: chain Au residue 40 LEU Chi-restraints excluded: chain Au residue 54 VAL Chi-restraints excluded: chain Au residue 77 VAL Chi-restraints excluded: chain Au residue 89 THR Chi-restraints excluded: chain Au residue 494 LEU Chi-restraints excluded: chain Au residue 497 THR Chi-restraints excluded: chain Av residue 16 MET Chi-restraints excluded: chain Av residue 179 ASP Chi-restraints excluded: chain Av residue 185 ASP Chi-restraints excluded: chain Av residue 233 MET Chi-restraints excluded: chain Av residue 302 SER Chi-restraints excluded: chain Av residue 420 ILE Chi-restraints excluded: chain Av residue 524 LEU Chi-restraints excluded: chain Ax residue 3 ILE Chi-restraints excluded: chain Ax residue 25 ILE Chi-restraints excluded: chain Ax residue 65 VAL Chi-restraints excluded: chain Ba residue 77 VAL Chi-restraints excluded: chain Ba residue 89 THR Chi-restraints excluded: chain Ba residue 494 LEU Chi-restraints excluded: chain Ba residue 497 THR Chi-restraints excluded: chain Bb residue 77 VAL Chi-restraints excluded: chain Bb residue 179 ASP Chi-restraints excluded: chain Bb residue 185 ASP Chi-restraints excluded: chain Bb residue 201 SER Chi-restraints excluded: chain Bb residue 417 VAL Chi-restraints excluded: chain Bd residue 2 ASN Chi-restraints excluded: chain Bd residue 3 ILE Chi-restraints excluded: chain Bd residue 65 VAL Chi-restraints excluded: chain Bg residue 77 VAL Chi-restraints excluded: chain Bg residue 79 SER Chi-restraints excluded: chain Bg residue 199 TYR Chi-restraints excluded: chain Bg residue 494 LEU Chi-restraints excluded: chain Bh residue 77 VAL Chi-restraints excluded: chain Bh residue 179 ASP Chi-restraints excluded: chain Bh residue 201 SER Chi-restraints excluded: chain Bj residue 3 ILE Chi-restraints excluded: chain Bm residue 77 VAL Chi-restraints excluded: chain Bm residue 89 THR Chi-restraints excluded: chain Bm residue 107 VAL Chi-restraints excluded: chain Bm residue 199 TYR Chi-restraints excluded: chain Bm residue 494 LEU Chi-restraints excluded: chain Bn residue 77 VAL Chi-restraints excluded: chain Bn residue 201 SER Chi-restraints excluded: chain Bn residue 213 VAL Chi-restraints excluded: chain Bn residue 233 MET Chi-restraints excluded: chain Bn residue 442 VAL Chi-restraints excluded: chain Bp residue 3 ILE Chi-restraints excluded: chain Bp residue 25 ILE Chi-restraints excluded: chain Bp residue 65 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 498 optimal weight: 1.9990 chunk 668 optimal weight: 2.9990 chunk 192 optimal weight: 0.8980 chunk 578 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 174 optimal weight: 5.9990 chunk 628 optimal weight: 6.9990 chunk 263 optimal weight: 40.0000 chunk 645 optimal weight: 3.9990 chunk 79 optimal weight: 0.1980 chunk 115 optimal weight: 0.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ai 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bd 2 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.062736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.046532 restraints weight = 321640.200| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 3.51 r_work: 0.2942 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.5829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 59906 Z= 0.197 Angle : 0.668 16.948 80955 Z= 0.333 Chirality : 0.044 0.418 9828 Planarity : 0.004 0.091 10542 Dihedral : 7.697 134.555 8635 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.53 % Favored : 95.37 % Rotamer: Outliers : 1.24 % Allowed : 23.95 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: 1.35 (0.09), residues: 7973 helix: 2.30 (0.08), residues: 3997 sheet: 0.24 (0.16), residues: 1113 loop : -0.88 (0.11), residues: 2863 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HISAr 7 PHE 0.011 0.001 PHEBh 281 TYR 0.030 0.001 TYRBg 203 ARG 0.005 0.000 ARGAu 36 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10454.12 seconds wall clock time: 187 minutes 5.11 seconds (11225.11 seconds total)