Starting phenix.real_space_refine (version: dev) on Thu Feb 23 03:25:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbx_13308/02_2023/7pbx_13308_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbx_13308/02_2023/7pbx_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_13308/02_2023/7pbx_13308.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbx_13308/02_2023/7pbx_13308.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbx_13308/02_2023/7pbx_13308_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbx_13308/02_2023/7pbx_13308_updated.pdb" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.023 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 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: 0.20s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 25.56, per 1000 atoms: 0.43 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: 19.71 Conformation dependent library (CDL) restraints added in 6.7 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: 5.31 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: 21.12 Time building geometry restraints manager: 21.27 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 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. 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: 2.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 14.480 Check model and map are aligned: 0.900 Process input model: 117.820 Find NCS groups from input model: 3.620 Set up NCS constraints: 0.520 Set refine NCS operators: 0.000 Set scattering table: 0.410 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:2.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 142.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6452 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 : 2.526 76.526 80955 Z= 1.709 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 % 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 *********************** 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 : 5.527 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 outliers start: 728 outliers final: 170 residues processed: 1131 average time/residue: 0.6043 time to fit residues: 1124.5648 Evaluate side-chains 542 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 372 time to evaluate : 5.291 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 170 outliers final: 10 residues processed: 170 average time/residue: 0.4749 time to fit residues: 151.8128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 404 optimal weight: 0.8980 chunk 320 optimal weight: 0.9980 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: 1.2782 ------------------------------------------------------------------------------- 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 432 GLN Ad 21 ASN 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 432 GLN Aj 21 ASN Aj 82 ASN Aj 146 GLN ** Aj 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 366 GLN Aj 453 GLN Aj 457 ASN Al 7 HIS Ao 21 ASN Ao 37 ASN Ao 432 GLN Ap 21 ASN 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 432 GLN Av 21 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 432 GLN Bb 21 ASN Bb 82 ASN Bb 146 GLN ** Bb 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bb 366 GLN Bg 21 ASN ** Bg 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 432 GLN Bh 21 ASN Bh 82 ASN Bh 146 GLN ** Bh 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bh 366 GLN ** Bj 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bm 21 ASN Bm 37 ASN Bm 432 GLN Bn 21 ASN Bn 82 ASN Bn 146 GLN ** Bn 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bn 366 GLN Bn 453 GLN Bn 457 ASN ** Bp 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6530 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.229 59906 Z= 0.468 Angle : 1.273 56.999 80955 Z= 0.628 Chirality : 0.067 1.518 9828 Planarity : 0.008 0.171 10542 Dihedral : 11.296 176.879 8617 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 20.53 Ramachandran Plot: Outliers : 0.59 % Allowed : 3.12 % Favored : 96.29 % Rotamer Outliers : 3.81 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.42 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.09), residues: 7973 helix: 1.94 (0.08), residues: 4032 sheet: 0.23 (0.14), residues: 1134 loop : -1.16 (0.12), residues: 2807 *********************** 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 607 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 370 time to evaluate : 6.509 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 outliers start: 237 outliers final: 61 residues processed: 580 average time/residue: 0.5869 time to fit residues: 591.3450 Evaluate side-chains 400 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 339 time to evaluate : 5.287 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 61 outliers final: 1 residues processed: 61 average time/residue: 0.4643 time to fit residues: 60.5563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 399 optimal weight: 6.9990 chunk 222 optimal weight: 8.9990 chunk 597 optimal weight: 5.9990 chunk 489 optimal weight: 9.9990 chunk 198 optimal weight: 20.0000 chunk 719 optimal weight: 2.9990 chunk 777 optimal weight: 4.9990 chunk 640 optimal weight: 4.9990 chunk 713 optimal weight: 3.9990 chunk 245 optimal weight: 20.0000 chunk 577 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ad 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Av 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bb 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bg 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bg 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bh 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bj 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bn 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bp 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bp 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6545 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.229 59906 Z= 0.468 Angle : 1.273 57.000 80955 Z= 0.628 Chirality : 0.067 1.519 9828 Planarity : 0.008 0.171 10542 Dihedral : 11.279 176.879 8617 Min Nonbonded Distance : 1.542 Molprobity Statistics. All-atom Clashscore : 33.79 Ramachandran Plot: Outliers : 0.59 % Allowed : 3.12 % Favored : 96.29 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.42 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.09), residues: 7973 helix: 1.94 (0.08), residues: 4032 sheet: 0.23 (0.14), residues: 1134 loop : -1.17 (0.12), residues: 2807 *********************** 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 340 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 339 time to evaluate : 5.326 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 outliers start: 1 outliers final: 1 residues processed: 340 average time/residue: 0.5688 time to fit residues: 332.9475 Evaluate side-chains 339 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 338 time to evaluate : 5.322 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.4860 time to fit residues: 8.0039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 710 optimal weight: 6.9990 chunk 541 optimal weight: 8.9990 chunk 373 optimal weight: 9.9990 chunk 79 optimal weight: 7.9990 chunk 343 optimal weight: 2.9990 chunk 483 optimal weight: 40.0000 chunk 722 optimal weight: 0.9990 chunk 764 optimal weight: 1.9990 chunk 377 optimal weight: 30.0000 chunk 684 optimal weight: 1.9990 chunk 206 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ad 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Av 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bb 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bg 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bg 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bh 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bj 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bn 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bp 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bp 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6546 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.229 59906 Z= 0.468 Angle : 1.273 57.000 80955 Z= 0.628 Chirality : 0.067 1.519 9828 Planarity : 0.008 0.171 10542 Dihedral : 11.277 176.879 8617 Min Nonbonded Distance : 1.542 Molprobity Statistics. All-atom Clashscore : 33.80 Ramachandran Plot: Outliers : 0.59 % Allowed : 3.12 % Favored : 96.29 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.41 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.09), residues: 7973 helix: 1.94 (0.08), residues: 4032 sheet: 0.23 (0.14), residues: 1134 loop : -1.16 (0.12), residues: 2807 *********************** 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 339 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 338 time to evaluate : 5.472 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 outliers start: 1 outliers final: 1 residues processed: 339 average time/residue: 0.5834 time to fit residues: 342.6646 Evaluate side-chains 339 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 338 time to evaluate : 5.452 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.5059 time to fit residues: 8.1596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 636 optimal weight: 9.9990 chunk 434 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 chunk 569 optimal weight: 10.0000 chunk 315 optimal weight: 7.9990 chunk 652 optimal weight: 20.0000 chunk 528 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 390 optimal weight: 2.9990 chunk 686 optimal weight: 9.9990 chunk 192 optimal weight: 2.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ad 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Av 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bb 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bg 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bg 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bh 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bj 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bn 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bp 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bp 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6546 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.229 59906 Z= 0.468 Angle : 1.273 57.000 80955 Z= 0.628 Chirality : 0.067 1.519 9828 Planarity : 0.008 0.171 10542 Dihedral : 11.275 176.879 8617 Min Nonbonded Distance : 1.542 Molprobity Statistics. All-atom Clashscore : 33.85 Ramachandran Plot: Outliers : 0.59 % Allowed : 3.12 % Favored : 96.29 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.41 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.09), residues: 7973 helix: 1.94 (0.08), residues: 4032 sheet: 0.23 (0.14), residues: 1134 loop : -1.17 (0.12), residues: 2807 *********************** 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 339 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 338 time to evaluate : 5.468 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 outliers start: 1 outliers final: 1 residues processed: 339 average time/residue: 0.5791 time to fit residues: 338.9696 Evaluate side-chains 339 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 338 time to evaluate : 5.432 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.4927 time to fit residues: 8.1372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 257 optimal weight: 7.9990 chunk 688 optimal weight: 4.9990 chunk 151 optimal weight: 20.0000 chunk 448 optimal weight: 10.0000 chunk 188 optimal weight: 2.9990 chunk 765 optimal weight: 5.9990 chunk 635 optimal weight: 4.9990 chunk 354 optimal weight: 20.0000 chunk 63 optimal weight: 6.9990 chunk 253 optimal weight: 7.9990 chunk 401 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ad 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Av 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bb 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bg 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bg 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bh 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bj 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bn 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bp 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bp 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6546 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.229 59906 Z= 0.468 Angle : 1.273 57.000 80955 Z= 0.628 Chirality : 0.067 1.519 9828 Planarity : 0.008 0.171 10542 Dihedral : 11.275 176.879 8617 Min Nonbonded Distance : 1.542 Molprobity Statistics. All-atom Clashscore : 33.85 Ramachandran Plot: Outliers : 0.59 % Allowed : 3.12 % Favored : 96.29 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.41 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.09), residues: 7973 helix: 1.94 (0.08), residues: 4032 sheet: 0.23 (0.14), residues: 1134 loop : -1.17 (0.12), residues: 2807 *********************** 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 339 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 338 time to evaluate : 5.315 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 outliers start: 1 outliers final: 1 residues processed: 339 average time/residue: 0.5829 time to fit residues: 341.3636 Evaluate side-chains 339 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 338 time to evaluate : 5.341 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.5083 time to fit residues: 8.1401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 436 optimal weight: 4.9990 chunk 558 optimal weight: 7.9990 chunk 433 optimal weight: 2.9990 chunk 644 optimal weight: 20.0000 chunk 427 optimal weight: 4.9990 chunk 762 optimal weight: 0.9990 chunk 477 optimal weight: 8.9990 chunk 464 optimal weight: 2.9990 chunk 351 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ad 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Av 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bb 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bg 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bg 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bh 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bj 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bn 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bp 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bp 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6546 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.229 59906 Z= 0.468 Angle : 1.273 57.000 80955 Z= 0.628 Chirality : 0.067 1.519 9828 Planarity : 0.008 0.171 10542 Dihedral : 11.274 176.879 8617 Min Nonbonded Distance : 1.542 Molprobity Statistics. All-atom Clashscore : 33.85 Ramachandran Plot: Outliers : 0.59 % Allowed : 3.12 % Favored : 96.29 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.41 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.09), residues: 7973 helix: 1.94 (0.08), residues: 4032 sheet: 0.23 (0.14), residues: 1134 loop : -1.17 (0.12), residues: 2807 *********************** 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 339 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 338 time to evaluate : 5.367 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 outliers start: 1 outliers final: 1 residues processed: 339 average time/residue: 0.5807 time to fit residues: 339.1161 Evaluate side-chains 339 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 338 time to evaluate : 5.342 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.5011 time to fit residues: 8.0878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 471 optimal weight: 9.9990 chunk 304 optimal weight: 9.9990 chunk 455 optimal weight: 4.9990 chunk 229 optimal weight: 0.9980 chunk 149 optimal weight: 6.9990 chunk 147 optimal weight: 7.9990 chunk 484 optimal weight: 9.9990 chunk 519 optimal weight: 8.9990 chunk 376 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 599 optimal weight: 9.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ad 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Av 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bb 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bg 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bg 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bh 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bj 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bn 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bp 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bp 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6546 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.229 59906 Z= 0.468 Angle : 1.273 57.000 80955 Z= 0.628 Chirality : 0.067 1.519 9828 Planarity : 0.008 0.171 10542 Dihedral : 11.274 176.879 8617 Min Nonbonded Distance : 1.542 Molprobity Statistics. All-atom Clashscore : 33.85 Ramachandran Plot: Outliers : 0.59 % Allowed : 3.12 % Favored : 96.29 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.41 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.09), residues: 7973 helix: 1.94 (0.08), residues: 4032 sheet: 0.23 (0.14), residues: 1134 loop : -1.17 (0.12), residues: 2807 *********************** 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 339 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 338 time to evaluate : 5.351 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 outliers start: 1 outliers final: 1 residues processed: 339 average time/residue: 0.5780 time to fit residues: 337.6320 Evaluate side-chains 339 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 338 time to evaluate : 5.314 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.5017 time to fit residues: 8.0190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 693 optimal weight: 1.9990 chunk 730 optimal weight: 4.9990 chunk 666 optimal weight: 5.9990 chunk 710 optimal weight: 6.9990 chunk 427 optimal weight: 0.9980 chunk 309 optimal weight: 8.9990 chunk 557 optimal weight: 2.9990 chunk 218 optimal weight: 9.9990 chunk 641 optimal weight: 2.9990 chunk 671 optimal weight: 10.0000 chunk 707 optimal weight: 0.0980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ad 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Av 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bb 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bg 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bg 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bh 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bj 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bn 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bp 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bp 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6546 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.229 59906 Z= 0.468 Angle : 1.273 57.000 80955 Z= 0.628 Chirality : 0.067 1.519 9828 Planarity : 0.008 0.171 10542 Dihedral : 11.274 176.879 8617 Min Nonbonded Distance : 1.542 Molprobity Statistics. All-atom Clashscore : 33.85 Ramachandran Plot: Outliers : 0.59 % Allowed : 3.12 % Favored : 96.29 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.41 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.09), residues: 7973 helix: 1.94 (0.08), residues: 4032 sheet: 0.23 (0.14), residues: 1134 loop : -1.17 (0.12), residues: 2807 *********************** 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 339 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 338 time to evaluate : 5.406 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 outliers start: 1 outliers final: 1 residues processed: 339 average time/residue: 0.5801 time to fit residues: 338.8189 Evaluate side-chains 339 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 338 time to evaluate : 5.312 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.5069 time to fit residues: 8.0199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 458 optimal weight: 0.9980 chunk 356 optimal weight: 6.9990 chunk 522 optimal weight: 9.9990 chunk 788 optimal weight: 6.9990 chunk 725 optimal weight: 9.9990 chunk 627 optimal weight: 0.9990 chunk 65 optimal weight: 8.9990 chunk 484 optimal weight: 5.9990 chunk 384 optimal weight: 5.9990 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 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Av 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bb 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bg 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bg 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bh 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bj 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bn 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bp 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bp 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6546 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.229 59906 Z= 0.468 Angle : 1.273 57.000 80955 Z= 0.628 Chirality : 0.067 1.519 9828 Planarity : 0.008 0.171 10542 Dihedral : 11.274 176.879 8617 Min Nonbonded Distance : 1.542 Molprobity Statistics. All-atom Clashscore : 33.85 Ramachandran Plot: Outliers : 0.59 % Allowed : 3.12 % Favored : 96.29 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.41 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.09), residues: 7973 helix: 1.94 (0.08), residues: 4032 sheet: 0.23 (0.14), residues: 1134 loop : -1.17 (0.12), residues: 2807 ********************** 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 339 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 338 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 339 average time/residue: 0.5875 time to fit residues: 343.9806 Evaluate side-chains 339 residues out of total 6216 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 338 time to evaluate : 5.316 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.5072 time to fit residues: 8.0545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 791 random chunks: chunk 498 optimal weight: 2.9990 chunk 668 optimal weight: 6.9990 chunk 192 optimal weight: 3.9990 chunk 578 optimal weight: 0.5980 chunk 92 optimal weight: 5.9990 chunk 174 optimal weight: 4.9990 chunk 628 optimal weight: 1.9990 chunk 263 optimal weight: 3.9990 chunk 645 optimal weight: 7.9990 chunk 79 optimal weight: 8.9990 chunk 115 optimal weight: 5.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ad 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ap 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Av 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bb 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bg 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bg 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bh 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bj 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bn 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bp 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bp 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.065390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.049013 restraints weight = 324038.130| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 3.68 r_work: 0.3015 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.229 59906 Z= 0.468 Angle : 1.273 57.000 80955 Z= 0.628 Chirality : 0.067 1.519 9828 Planarity : 0.008 0.171 10542 Dihedral : 11.274 176.879 8617 Min Nonbonded Distance : 1.542 Molprobity Statistics. All-atom Clashscore : 33.85 Ramachandran Plot: Outliers : 0.59 % Allowed : 3.12 % Favored : 96.29 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.01 % Twisted Proline : 0.00 % Twisted General : 0.41 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.09), residues: 7973 helix: 1.94 (0.08), residues: 4032 sheet: 0.23 (0.14), residues: 1134 loop : -1.17 (0.12), residues: 2807 =============================================================================== Job complete usr+sys time: 9063.39 seconds wall clock time: 163 minutes 51.96 seconds (9831.96 seconds total)