Starting phenix.real_space_refine (version: dev) on Thu Dec 15 11:01:30 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0u_28781/12_2022/8f0u_28781.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0u_28781/12_2022/8f0u_28781.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0u_28781/12_2022/8f0u_28781.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0u_28781/12_2022/8f0u_28781.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0u_28781/12_2022/8f0u_28781.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0u_28781/12_2022/8f0u_28781.pdb" } resolution = 3.1 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= 0.001 sd= 0.203 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "X TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "X TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "X PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "X TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "X PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "X PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "X TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "0 TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "0 TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "0 PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "0 TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "0 PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "0 PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "0 TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "2 PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "3 TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "3 TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "3 PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "3 TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "3 PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "3 PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "3 TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "5 PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "6 TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "6 TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "6 PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "6 TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "6 PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "6 PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "6 TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "8 PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "9 TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "9 TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "9 PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "9 TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "9 PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "9 PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "9 TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "c PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 78260 Number of models: 1 Model: "" Number of chains: 39 Chain: "B" Number of atoms: 4468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 4468 Classifications: {'peptide': 302} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 290} Chain breaks: 1 Chain: "C" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1154 Classifications: {'peptide': 75} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "E" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 398 Classifications: {'peptide': 27} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 26} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "A" Number of atoms: 4468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 4468 Classifications: {'peptide': 302} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 290} Chain breaks: 1 Chain: "D" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1154 Classifications: {'peptide': 75} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "a" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 398 Classifications: {'peptide': 27} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 26} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "F" Number of atoms: 4468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 4468 Classifications: {'peptide': 302} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 290} Chain breaks: 1 Chain: "G" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1154 Classifications: {'peptide': 75} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "H" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 398 Classifications: {'peptide': 27} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 26} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "I" Number of atoms: 4468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 4468 Classifications: {'peptide': 302} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 290} Chain breaks: 1 Chain: "J" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1154 Classifications: {'peptide': 75} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "K" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 398 Classifications: {'peptide': 27} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 26} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "L" Number of atoms: 4468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 4468 Classifications: {'peptide': 302} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 290} Chain breaks: 1 Chain: "M" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1154 Classifications: {'peptide': 75} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "N" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 398 Classifications: {'peptide': 27} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 26} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "O" Number of atoms: 4468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 4468 Classifications: {'peptide': 302} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 290} Chain breaks: 1 Chain: "P" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1154 Classifications: {'peptide': 75} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "Q" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 398 Classifications: {'peptide': 27} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 26} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "R" Number of atoms: 4468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 4468 Classifications: {'peptide': 302} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 290} Chain breaks: 1 Chain: "S" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1154 Classifications: {'peptide': 75} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "T" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 398 Classifications: {'peptide': 27} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 26} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "U" Number of atoms: 4468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 4468 Classifications: {'peptide': 302} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 290} Chain breaks: 1 Chain: "V" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1154 Classifications: {'peptide': 75} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "W" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 398 Classifications: {'peptide': 27} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 26} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "X" Number of atoms: 4468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 4468 Classifications: {'peptide': 302} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 290} Chain breaks: 1 Chain: "Y" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1154 Classifications: {'peptide': 75} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "Z" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 398 Classifications: {'peptide': 27} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 26} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "0" Number of atoms: 4468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 4468 Classifications: {'peptide': 302} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 290} Chain breaks: 1 Chain: "1" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1154 Classifications: {'peptide': 75} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "2" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 398 Classifications: {'peptide': 27} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 26} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "3" Number of atoms: 4468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 4468 Classifications: {'peptide': 302} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 290} Chain breaks: 1 Chain: "4" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1154 Classifications: {'peptide': 75} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "5" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 398 Classifications: {'peptide': 27} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 26} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "6" Number of atoms: 4468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 4468 Classifications: {'peptide': 302} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 290} Chain breaks: 1 Chain: "7" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1154 Classifications: {'peptide': 75} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "8" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 398 Classifications: {'peptide': 27} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 26} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "9" Number of atoms: 4468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 4468 Classifications: {'peptide': 302} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 290} Chain breaks: 1 Chain: "b" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1154 Classifications: {'peptide': 75} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "c" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 398 Classifications: {'peptide': 27} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 26} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 21 Time building chain proxies: 27.67, per 1000 atoms: 0.35 Number of scatterers: 78260 At special positions: 0 Unit cell: (215.18, 258.64, 231.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 182 16.00 O 7436 8.00 N 6786 7.00 C 24037 6.00 H 39819 1.00 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: 54.41 Conformation dependent library (CDL) restraints added in 5.3 seconds 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9438 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 91 sheets defined 23.3% alpha, 42.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.89 Creating SS restraints... Processing helix chain 'A' and resid 15 through 20 Processing helix chain 'A' and resid 21 through 24 Proline residue: A 24 - end of helix No H-bonds generated for 'chain 'A' and resid 21 through 24' Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 154 through 158 Processing helix chain 'A' and resid 169 through 173 Processing helix chain 'A' and resid 244 through 258 removed outlier: 3.612A pdb=" N GLN A 253 " --> pdb=" O ASN A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 280 Processing helix chain 'A' and resid 297 through 303 Processing helix chain 'A' and resid 320 through 329 Processing helix chain 'D' and resid 394 through 399 Processing helix chain 'D' and resid 417 through 426 Processing helix chain 'a' and resid 37 through 49 Processing helix chain 'B' and resid 15 through 20 Processing helix chain 'B' and resid 21 through 24 Proline residue: B 24 - end of helix No H-bonds generated for 'chain 'B' and resid 21 through 24' Processing helix chain 'B' and resid 104 through 108 Processing helix chain 'B' and resid 154 through 158 Processing helix chain 'B' and resid 169 through 173 Processing helix chain 'B' and resid 244 through 258 removed outlier: 3.612A pdb=" N GLN B 253 " --> pdb=" O ASN B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 280 Processing helix chain 'B' and resid 297 through 303 Processing helix chain 'B' and resid 320 through 329 Processing helix chain 'C' and resid 394 through 399 Processing helix chain 'C' and resid 417 through 426 Processing helix chain 'E' and resid 37 through 49 Processing helix chain 'F' and resid 15 through 20 Processing helix chain 'F' and resid 21 through 24 Proline residue: F 24 - end of helix No H-bonds generated for 'chain 'F' and resid 21 through 24' Processing helix chain 'F' and resid 104 through 108 Processing helix chain 'F' and resid 154 through 158 Processing helix chain 'F' and resid 169 through 173 Processing helix chain 'F' and resid 244 through 258 removed outlier: 3.612A pdb=" N GLN F 253 " --> pdb=" O ASN F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 280 Processing helix chain 'F' and resid 297 through 303 Processing helix chain 'F' and resid 320 through 329 Processing helix chain 'G' and resid 394 through 399 Processing helix chain 'G' and resid 417 through 426 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'I' and resid 15 through 20 Processing helix chain 'I' and resid 21 through 24 Proline residue: I 24 - end of helix No H-bonds generated for 'chain 'I' and resid 21 through 24' Processing helix chain 'I' and resid 104 through 108 Processing helix chain 'I' and resid 154 through 158 Processing helix chain 'I' and resid 169 through 173 Processing helix chain 'I' and resid 244 through 258 removed outlier: 3.612A pdb=" N GLN I 253 " --> pdb=" O ASN I 249 " (cutoff:3.500A) Processing helix chain 'I' and resid 273 through 280 Processing helix chain 'I' and resid 297 through 303 Processing helix chain 'I' and resid 320 through 329 Processing helix chain 'J' and resid 394 through 399 Processing helix chain 'J' and resid 417 through 426 Processing helix chain 'K' and resid 37 through 49 Processing helix chain 'L' and resid 15 through 20 Processing helix chain 'L' and resid 21 through 24 Proline residue: L 24 - end of helix No H-bonds generated for 'chain 'L' and resid 21 through 24' Processing helix chain 'L' and resid 104 through 108 Processing helix chain 'L' and resid 154 through 158 Processing helix chain 'L' and resid 169 through 173 Processing helix chain 'L' and resid 244 through 258 removed outlier: 3.611A pdb=" N GLN L 253 " --> pdb=" O ASN L 249 " (cutoff:3.500A) Processing helix chain 'L' and resid 273 through 280 Processing helix chain 'L' and resid 297 through 303 Processing helix chain 'L' and resid 320 through 329 Processing helix chain 'M' and resid 394 through 399 Processing helix chain 'M' and resid 417 through 426 Processing helix chain 'N' and resid 37 through 49 Processing helix chain 'O' and resid 15 through 20 Processing helix chain 'O' and resid 21 through 24 Proline residue: O 24 - end of helix No H-bonds generated for 'chain 'O' and resid 21 through 24' Processing helix chain 'O' and resid 104 through 108 Processing helix chain 'O' and resid 154 through 158 Processing helix chain 'O' and resid 169 through 173 Processing helix chain 'O' and resid 244 through 258 removed outlier: 3.612A pdb=" N GLN O 253 " --> pdb=" O ASN O 249 " (cutoff:3.500A) Processing helix chain 'O' and resid 273 through 280 Processing helix chain 'O' and resid 297 through 303 Processing helix chain 'O' and resid 320 through 329 Processing helix chain 'P' and resid 394 through 399 Processing helix chain 'P' and resid 417 through 426 Processing helix chain 'Q' and resid 37 through 49 Processing helix chain 'R' and resid 15 through 20 Processing helix chain 'R' and resid 21 through 24 Proline residue: R 24 - end of helix No H-bonds generated for 'chain 'R' and resid 21 through 24' Processing helix chain 'R' and resid 104 through 108 Processing helix chain 'R' and resid 154 through 158 Processing helix chain 'R' and resid 169 through 173 Processing helix chain 'R' and resid 244 through 258 removed outlier: 3.613A pdb=" N GLN R 253 " --> pdb=" O ASN R 249 " (cutoff:3.500A) Processing helix chain 'R' and resid 273 through 280 Processing helix chain 'R' and resid 297 through 303 Processing helix chain 'R' and resid 320 through 329 Processing helix chain 'S' and resid 394 through 399 Processing helix chain 'S' and resid 417 through 426 Processing helix chain 'T' and resid 37 through 49 Processing helix chain 'U' and resid 15 through 20 Processing helix chain 'U' and resid 21 through 24 Proline residue: U 24 - end of helix No H-bonds generated for 'chain 'U' and resid 21 through 24' Processing helix chain 'U' and resid 104 through 108 Processing helix chain 'U' and resid 154 through 158 Processing helix chain 'U' and resid 169 through 173 Processing helix chain 'U' and resid 244 through 258 removed outlier: 3.612A pdb=" N GLN U 253 " --> pdb=" O ASN U 249 " (cutoff:3.500A) Processing helix chain 'U' and resid 273 through 280 Processing helix chain 'U' and resid 297 through 303 Processing helix chain 'U' and resid 320 through 329 Processing helix chain 'V' and resid 394 through 399 Processing helix chain 'V' and resid 417 through 426 Processing helix chain 'W' and resid 37 through 49 Processing helix chain 'X' and resid 15 through 20 Processing helix chain 'X' and resid 21 through 24 Proline residue: X 24 - end of helix No H-bonds generated for 'chain 'X' and resid 21 through 24' Processing helix chain 'X' and resid 104 through 108 Processing helix chain 'X' and resid 154 through 158 Processing helix chain 'X' and resid 169 through 173 Processing helix chain 'X' and resid 244 through 258 removed outlier: 3.612A pdb=" N GLN X 253 " --> pdb=" O ASN X 249 " (cutoff:3.500A) Processing helix chain 'X' and resid 273 through 280 Processing helix chain 'X' and resid 297 through 303 Processing helix chain 'X' and resid 320 through 329 Processing helix chain 'Y' and resid 394 through 399 Processing helix chain 'Y' and resid 417 through 426 Processing helix chain 'Z' and resid 37 through 49 Processing helix chain '0' and resid 15 through 20 Processing helix chain '0' and resid 21 through 24 Proline residue: 0 24 - end of helix No H-bonds generated for 'chain '0' and resid 21 through 24' Processing helix chain '0' and resid 104 through 108 Processing helix chain '0' and resid 154 through 158 Processing helix chain '0' and resid 169 through 173 Processing helix chain '0' and resid 244 through 258 removed outlier: 3.612A pdb=" N GLN 0 253 " --> pdb=" O ASN 0 249 " (cutoff:3.500A) Processing helix chain '0' and resid 273 through 280 Processing helix chain '0' and resid 297 through 303 Processing helix chain '0' and resid 320 through 329 Processing helix chain '1' and resid 394 through 399 Processing helix chain '1' and resid 417 through 426 Processing helix chain '2' and resid 37 through 49 Processing helix chain '3' and resid 15 through 20 Processing helix chain '3' and resid 21 through 24 Proline residue: 3 24 - end of helix No H-bonds generated for 'chain '3' and resid 21 through 24' Processing helix chain '3' and resid 104 through 108 Processing helix chain '3' and resid 154 through 158 Processing helix chain '3' and resid 169 through 173 Processing helix chain '3' and resid 244 through 258 removed outlier: 3.612A pdb=" N GLN 3 253 " --> pdb=" O ASN 3 249 " (cutoff:3.500A) Processing helix chain '3' and resid 273 through 280 Processing helix chain '3' and resid 297 through 303 Processing helix chain '3' and resid 320 through 329 Processing helix chain '4' and resid 394 through 399 Processing helix chain '4' and resid 417 through 426 Processing helix chain '5' and resid 37 through 49 Processing helix chain '6' and resid 15 through 20 Processing helix chain '6' and resid 21 through 24 Proline residue: 6 24 - end of helix No H-bonds generated for 'chain '6' and resid 21 through 24' Processing helix chain '6' and resid 104 through 108 Processing helix chain '6' and resid 154 through 158 Processing helix chain '6' and resid 169 through 173 Processing helix chain '6' and resid 244 through 258 removed outlier: 3.611A pdb=" N GLN 6 253 " --> pdb=" O ASN 6 249 " (cutoff:3.500A) Processing helix chain '6' and resid 273 through 280 Processing helix chain '6' and resid 297 through 303 Processing helix chain '6' and resid 320 through 329 Processing helix chain '7' and resid 394 through 399 Processing helix chain '7' and resid 417 through 426 Processing helix chain '8' and resid 37 through 49 Processing helix chain '9' and resid 15 through 20 Processing helix chain '9' and resid 21 through 24 Proline residue: 9 24 - end of helix No H-bonds generated for 'chain '9' and resid 21 through 24' Processing helix chain '9' and resid 104 through 108 Processing helix chain '9' and resid 154 through 158 Processing helix chain '9' and resid 169 through 173 Processing helix chain '9' and resid 244 through 258 removed outlier: 3.612A pdb=" N GLN 9 253 " --> pdb=" O ASN 9 249 " (cutoff:3.500A) Processing helix chain '9' and resid 273 through 280 Processing helix chain '9' and resid 297 through 303 Processing helix chain '9' and resid 320 through 329 Processing helix chain 'b' and resid 394 through 399 Processing helix chain 'b' and resid 417 through 426 Processing helix chain 'c' and resid 37 through 49 Processing sheet with id= 1, first strand: chain 'a' and resid 34 through 36 removed outlier: 4.251A pdb=" N MET A 85 " --> pdb=" O PHE a 36 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N SER A 89 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ASN A 103 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TYR A 99 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE A 136 " --> pdb=" O LYS A 130 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LYS A 130 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU A 138 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE A 113 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N MET A 127 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 11.689A pdb=" N THR A 111 " --> pdb=" O MET A 127 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLU A 32 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE A 113 " --> pdb=" O ASN A 30 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN A 30 " --> pdb=" O ILE A 113 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL A 115 " --> pdb=" O SER A 28 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N SER A 28 " --> pdb=" O VAL A 115 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'a' and resid 29 through 31 removed outlier: 5.791A pdb=" N ASN A 225 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ILE A 242 " --> pdb=" O ASN A 225 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLN A 200 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N LEU A 185 " --> pdb=" O GLN A 200 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU A 214 " --> pdb=" O ILE A 222 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 263 through 264 Processing sheet with id= 4, first strand: chain 'A' and resid 267 through 271 removed outlier: 6.661A pdb=" N MET A 268 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'A' and resid 267 through 271 removed outlier: 6.661A pdb=" N MET A 268 " --> pdb=" O SER A 291 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY A 340 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU A 313 " --> pdb=" O THR A 338 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N THR A 338 " --> pdb=" O LEU A 313 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'D' and resid 375 through 378 removed outlier: 6.507A pdb=" N GLU D 375 " --> pdb=" O ASN D 388 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'D' and resid 375 through 378 removed outlier: 6.507A pdb=" N GLU D 375 " --> pdb=" O ASN D 388 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN D 435 " --> pdb=" O ILE D 408 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ALA D 410 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ALA D 433 " --> pdb=" O ALA D 410 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'E' and resid 34 through 36 removed outlier: 4.251A pdb=" N MET B 85 " --> pdb=" O PHE E 36 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N SER B 89 " --> pdb=" O ASN B 103 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ASN B 103 " --> pdb=" O SER B 89 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TYR B 99 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE B 136 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LYS B 130 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU B 138 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE B 113 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N MET B 127 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 11.689A pdb=" N THR B 111 " --> pdb=" O MET B 127 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLU B 32 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE B 113 " --> pdb=" O ASN B 30 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASN B 30 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N VAL B 115 " --> pdb=" O SER B 28 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N SER B 28 " --> pdb=" O VAL B 115 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'E' and resid 29 through 31 removed outlier: 5.791A pdb=" N ASN B 225 " --> pdb=" O ILE B 242 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE B 242 " --> pdb=" O ASN B 225 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLN B 200 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N LEU B 185 " --> pdb=" O GLN B 200 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU B 214 " --> pdb=" O ILE B 222 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'B' and resid 263 through 264 Processing sheet with id= 11, first strand: chain 'B' and resid 267 through 271 removed outlier: 6.661A pdb=" N MET B 268 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'B' and resid 267 through 271 removed outlier: 6.661A pdb=" N MET B 268 " --> pdb=" O SER B 291 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY B 340 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU B 313 " --> pdb=" O THR B 338 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N THR B 338 " --> pdb=" O LEU B 313 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'C' and resid 375 through 378 removed outlier: 6.507A pdb=" N GLU C 375 " --> pdb=" O ASN C 388 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'C' and resid 375 through 378 removed outlier: 6.507A pdb=" N GLU C 375 " --> pdb=" O ASN C 388 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN C 435 " --> pdb=" O ILE C 408 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ALA C 410 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ALA C 433 " --> pdb=" O ALA C 410 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'H' and resid 34 through 36 removed outlier: 4.252A pdb=" N MET F 85 " --> pdb=" O PHE H 36 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N SER F 89 " --> pdb=" O ASN F 103 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ASN F 103 " --> pdb=" O SER F 89 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TYR F 99 " --> pdb=" O ILE F 93 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE F 136 " --> pdb=" O LYS F 130 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LYS F 130 " --> pdb=" O ILE F 136 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU F 138 " --> pdb=" O VAL F 128 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE F 113 " --> pdb=" O ALA F 125 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N MET F 127 " --> pdb=" O THR F 111 " (cutoff:3.500A) removed outlier: 11.689A pdb=" N THR F 111 " --> pdb=" O MET F 127 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLU F 32 " --> pdb=" O THR F 111 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE F 113 " --> pdb=" O ASN F 30 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN F 30 " --> pdb=" O ILE F 113 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL F 115 " --> pdb=" O SER F 28 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N SER F 28 " --> pdb=" O VAL F 115 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'H' and resid 29 through 31 removed outlier: 5.791A pdb=" N ASN F 225 " --> pdb=" O ILE F 242 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ILE F 242 " --> pdb=" O ASN F 225 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLN F 200 " --> pdb=" O LEU F 185 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N LEU F 185 " --> pdb=" O GLN F 200 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU F 214 " --> pdb=" O ILE F 222 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'F' and resid 263 through 264 Processing sheet with id= 18, first strand: chain 'F' and resid 267 through 271 removed outlier: 6.662A pdb=" N MET F 268 " --> pdb=" O SER F 291 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'F' and resid 267 through 271 removed outlier: 6.662A pdb=" N MET F 268 " --> pdb=" O SER F 291 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY F 340 " --> pdb=" O THR F 311 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU F 313 " --> pdb=" O THR F 338 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR F 338 " --> pdb=" O LEU F 313 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'G' and resid 375 through 378 removed outlier: 6.507A pdb=" N GLU G 375 " --> pdb=" O ASN G 388 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'G' and resid 375 through 378 removed outlier: 6.507A pdb=" N GLU G 375 " --> pdb=" O ASN G 388 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN G 435 " --> pdb=" O ILE G 408 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ALA G 410 " --> pdb=" O ALA G 433 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ALA G 433 " --> pdb=" O ALA G 410 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'K' and resid 34 through 36 removed outlier: 4.251A pdb=" N MET I 85 " --> pdb=" O PHE K 36 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N SER I 89 " --> pdb=" O ASN I 103 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ASN I 103 " --> pdb=" O SER I 89 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TYR I 99 " --> pdb=" O ILE I 93 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE I 136 " --> pdb=" O LYS I 130 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LYS I 130 " --> pdb=" O ILE I 136 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU I 138 " --> pdb=" O VAL I 128 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE I 113 " --> pdb=" O ALA I 125 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N MET I 127 " --> pdb=" O THR I 111 " (cutoff:3.500A) removed outlier: 11.689A pdb=" N THR I 111 " --> pdb=" O MET I 127 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLU I 32 " --> pdb=" O THR I 111 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE I 113 " --> pdb=" O ASN I 30 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASN I 30 " --> pdb=" O ILE I 113 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL I 115 " --> pdb=" O SER I 28 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N SER I 28 " --> pdb=" O VAL I 115 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'K' and resid 29 through 31 removed outlier: 5.791A pdb=" N ASN I 225 " --> pdb=" O ILE I 242 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ILE I 242 " --> pdb=" O ASN I 225 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLN I 200 " --> pdb=" O LEU I 185 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N LEU I 185 " --> pdb=" O GLN I 200 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU I 214 " --> pdb=" O ILE I 222 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'I' and resid 263 through 264 Processing sheet with id= 25, first strand: chain 'I' and resid 267 through 271 removed outlier: 6.661A pdb=" N MET I 268 " --> pdb=" O SER I 291 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'I' and resid 267 through 271 removed outlier: 6.661A pdb=" N MET I 268 " --> pdb=" O SER I 291 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY I 340 " --> pdb=" O THR I 311 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU I 313 " --> pdb=" O THR I 338 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N THR I 338 " --> pdb=" O LEU I 313 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'J' and resid 375 through 378 removed outlier: 6.507A pdb=" N GLU J 375 " --> pdb=" O ASN J 388 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'J' and resid 375 through 378 removed outlier: 6.507A pdb=" N GLU J 375 " --> pdb=" O ASN J 388 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN J 435 " --> pdb=" O ILE J 408 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ALA J 410 " --> pdb=" O ALA J 433 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ALA J 433 " --> pdb=" O ALA J 410 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'N' and resid 34 through 36 removed outlier: 4.251A pdb=" N MET L 85 " --> pdb=" O PHE N 36 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N SER L 89 " --> pdb=" O ASN L 103 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ASN L 103 " --> pdb=" O SER L 89 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TYR L 99 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE L 136 " --> pdb=" O LYS L 130 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LYS L 130 " --> pdb=" O ILE L 136 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU L 138 " --> pdb=" O VAL L 128 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE L 113 " --> pdb=" O ALA L 125 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N MET L 127 " --> pdb=" O THR L 111 " (cutoff:3.500A) removed outlier: 11.689A pdb=" N THR L 111 " --> pdb=" O MET L 127 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLU L 32 " --> pdb=" O THR L 111 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE L 113 " --> pdb=" O ASN L 30 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN L 30 " --> pdb=" O ILE L 113 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL L 115 " --> pdb=" O SER L 28 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N SER L 28 " --> pdb=" O VAL L 115 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'N' and resid 29 through 31 removed outlier: 5.792A pdb=" N ASN L 225 " --> pdb=" O ILE L 242 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE L 242 " --> pdb=" O ASN L 225 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLN L 200 " --> pdb=" O LEU L 185 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N LEU L 185 " --> pdb=" O GLN L 200 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU L 214 " --> pdb=" O ILE L 222 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'L' and resid 263 through 264 Processing sheet with id= 32, first strand: chain 'L' and resid 267 through 271 removed outlier: 6.662A pdb=" N MET L 268 " --> pdb=" O SER L 291 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'L' and resid 267 through 271 removed outlier: 6.662A pdb=" N MET L 268 " --> pdb=" O SER L 291 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLY L 340 " --> pdb=" O THR L 311 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU L 313 " --> pdb=" O THR L 338 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N THR L 338 " --> pdb=" O LEU L 313 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'M' and resid 375 through 378 removed outlier: 6.507A pdb=" N GLU M 375 " --> pdb=" O ASN M 388 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'M' and resid 375 through 378 removed outlier: 6.507A pdb=" N GLU M 375 " --> pdb=" O ASN M 388 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASN M 435 " --> pdb=" O ILE M 408 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ALA M 410 " --> pdb=" O ALA M 433 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ALA M 433 " --> pdb=" O ALA M 410 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'Q' and resid 34 through 36 removed outlier: 4.251A pdb=" N MET O 85 " --> pdb=" O PHE Q 36 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N SER O 89 " --> pdb=" O ASN O 103 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ASN O 103 " --> pdb=" O SER O 89 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TYR O 99 " --> pdb=" O ILE O 93 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ILE O 136 " --> pdb=" O LYS O 130 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LYS O 130 " --> pdb=" O ILE O 136 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU O 138 " --> pdb=" O VAL O 128 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE O 113 " --> pdb=" O ALA O 125 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N MET O 127 " --> pdb=" O THR O 111 " (cutoff:3.500A) removed outlier: 11.689A pdb=" N THR O 111 " --> pdb=" O MET O 127 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLU O 32 " --> pdb=" O THR O 111 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE O 113 " --> pdb=" O ASN O 30 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASN O 30 " --> pdb=" O ILE O 113 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL O 115 " --> pdb=" O SER O 28 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N SER O 28 " --> pdb=" O VAL O 115 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'Q' and resid 29 through 31 removed outlier: 5.792A pdb=" N ASN O 225 " --> pdb=" O ILE O 242 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE O 242 " --> pdb=" O ASN O 225 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLN O 200 " --> pdb=" O LEU O 185 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N LEU O 185 " --> pdb=" O GLN O 200 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU O 214 " --> pdb=" O ILE O 222 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'O' and resid 263 through 264 Processing sheet with id= 39, first strand: chain 'O' and resid 267 through 271 removed outlier: 6.661A pdb=" N MET O 268 " --> pdb=" O SER O 291 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'O' and resid 267 through 271 removed outlier: 6.661A pdb=" N MET O 268 " --> pdb=" O SER O 291 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY O 340 " --> pdb=" O THR O 311 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LEU O 313 " --> pdb=" O THR O 338 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR O 338 " --> pdb=" O LEU O 313 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'P' and resid 375 through 378 removed outlier: 6.507A pdb=" N GLU P 375 " --> pdb=" O ASN P 388 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'P' and resid 375 through 378 removed outlier: 6.507A pdb=" N GLU P 375 " --> pdb=" O ASN P 388 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASN P 435 " --> pdb=" O ILE P 408 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ALA P 410 " --> pdb=" O ALA P 433 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ALA P 433 " --> pdb=" O ALA P 410 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'T' and resid 34 through 36 removed outlier: 4.251A pdb=" N MET R 85 " --> pdb=" O PHE T 36 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N SER R 89 " --> pdb=" O ASN R 103 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ASN R 103 " --> pdb=" O SER R 89 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TYR R 99 " --> pdb=" O ILE R 93 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE R 136 " --> pdb=" O LYS R 130 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LYS R 130 " --> pdb=" O ILE R 136 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU R 138 " --> pdb=" O VAL R 128 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE R 113 " --> pdb=" O ALA R 125 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N MET R 127 " --> pdb=" O THR R 111 " (cutoff:3.500A) removed outlier: 11.689A pdb=" N THR R 111 " --> pdb=" O MET R 127 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLU R 32 " --> pdb=" O THR R 111 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE R 113 " --> pdb=" O ASN R 30 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN R 30 " --> pdb=" O ILE R 113 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N VAL R 115 " --> pdb=" O SER R 28 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N SER R 28 " --> pdb=" O VAL R 115 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'T' and resid 29 through 31 removed outlier: 5.790A pdb=" N ASN R 225 " --> pdb=" O ILE R 242 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE R 242 " --> pdb=" O ASN R 225 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLN R 200 " --> pdb=" O LEU R 185 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N LEU R 185 " --> pdb=" O GLN R 200 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU R 214 " --> pdb=" O ILE R 222 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'R' and resid 263 through 264 Processing sheet with id= 46, first strand: chain 'R' and resid 267 through 271 removed outlier: 6.661A pdb=" N MET R 268 " --> pdb=" O SER R 291 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'R' and resid 267 through 271 removed outlier: 6.661A pdb=" N MET R 268 " --> pdb=" O SER R 291 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY R 340 " --> pdb=" O THR R 311 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LEU R 313 " --> pdb=" O THR R 338 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR R 338 " --> pdb=" O LEU R 313 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'S' and resid 375 through 378 removed outlier: 6.507A pdb=" N GLU S 375 " --> pdb=" O ASN S 388 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'S' and resid 375 through 378 removed outlier: 6.507A pdb=" N GLU S 375 " --> pdb=" O ASN S 388 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASN S 435 " --> pdb=" O ILE S 408 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ALA S 410 " --> pdb=" O ALA S 433 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ALA S 433 " --> pdb=" O ALA S 410 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'W' and resid 34 through 36 removed outlier: 4.251A pdb=" N MET U 85 " --> pdb=" O PHE W 36 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N SER U 89 " --> pdb=" O ASN U 103 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ASN U 103 " --> pdb=" O SER U 89 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TYR U 99 " --> pdb=" O ILE U 93 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE U 136 " --> pdb=" O LYS U 130 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LYS U 130 " --> pdb=" O ILE U 136 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU U 138 " --> pdb=" O VAL U 128 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE U 113 " --> pdb=" O ALA U 125 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N MET U 127 " --> pdb=" O THR U 111 " (cutoff:3.500A) removed outlier: 11.689A pdb=" N THR U 111 " --> pdb=" O MET U 127 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLU U 32 " --> pdb=" O THR U 111 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE U 113 " --> pdb=" O ASN U 30 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN U 30 " --> pdb=" O ILE U 113 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL U 115 " --> pdb=" O SER U 28 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N SER U 28 " --> pdb=" O VAL U 115 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'W' and resid 29 through 31 removed outlier: 5.791A pdb=" N ASN U 225 " --> pdb=" O ILE U 242 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ILE U 242 " --> pdb=" O ASN U 225 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLN U 200 " --> pdb=" O LEU U 185 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N LEU U 185 " --> pdb=" O GLN U 200 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU U 214 " --> pdb=" O ILE U 222 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'U' and resid 263 through 264 Processing sheet with id= 53, first strand: chain 'U' and resid 267 through 271 removed outlier: 6.661A pdb=" N MET U 268 " --> pdb=" O SER U 291 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'U' and resid 267 through 271 removed outlier: 6.661A pdb=" N MET U 268 " --> pdb=" O SER U 291 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY U 340 " --> pdb=" O THR U 311 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU U 313 " --> pdb=" O THR U 338 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR U 338 " --> pdb=" O LEU U 313 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'V' and resid 375 through 378 removed outlier: 6.508A pdb=" N GLU V 375 " --> pdb=" O ASN V 388 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'V' and resid 375 through 378 removed outlier: 6.508A pdb=" N GLU V 375 " --> pdb=" O ASN V 388 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASN V 435 " --> pdb=" O ILE V 408 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ALA V 410 " --> pdb=" O ALA V 433 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ALA V 433 " --> pdb=" O ALA V 410 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'Z' and resid 34 through 36 removed outlier: 4.251A pdb=" N MET X 85 " --> pdb=" O PHE Z 36 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N SER X 89 " --> pdb=" O ASN X 103 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ASN X 103 " --> pdb=" O SER X 89 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TYR X 99 " --> pdb=" O ILE X 93 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ILE X 136 " --> pdb=" O LYS X 130 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LYS X 130 " --> pdb=" O ILE X 136 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU X 138 " --> pdb=" O VAL X 128 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE X 113 " --> pdb=" O ALA X 125 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N MET X 127 " --> pdb=" O THR X 111 " (cutoff:3.500A) removed outlier: 11.689A pdb=" N THR X 111 " --> pdb=" O MET X 127 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLU X 32 " --> pdb=" O THR X 111 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE X 113 " --> pdb=" O ASN X 30 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASN X 30 " --> pdb=" O ILE X 113 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL X 115 " --> pdb=" O SER X 28 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N SER X 28 " --> pdb=" O VAL X 115 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'Z' and resid 29 through 31 removed outlier: 5.792A pdb=" N ASN X 225 " --> pdb=" O ILE X 242 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ILE X 242 " --> pdb=" O ASN X 225 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLN X 200 " --> pdb=" O LEU X 185 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N LEU X 185 " --> pdb=" O GLN X 200 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU X 214 " --> pdb=" O ILE X 222 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'X' and resid 263 through 264 Processing sheet with id= 60, first strand: chain 'X' and resid 267 through 271 removed outlier: 6.660A pdb=" N MET X 268 " --> pdb=" O SER X 291 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'X' and resid 267 through 271 removed outlier: 6.660A pdb=" N MET X 268 " --> pdb=" O SER X 291 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLY X 340 " --> pdb=" O THR X 311 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU X 313 " --> pdb=" O THR X 338 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N THR X 338 " --> pdb=" O LEU X 313 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'Y' and resid 375 through 378 removed outlier: 6.507A pdb=" N GLU Y 375 " --> pdb=" O ASN Y 388 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'Y' and resid 375 through 378 removed outlier: 6.507A pdb=" N GLU Y 375 " --> pdb=" O ASN Y 388 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASN Y 435 " --> pdb=" O ILE Y 408 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ALA Y 410 " --> pdb=" O ALA Y 433 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ALA Y 433 " --> pdb=" O ALA Y 410 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain '2' and resid 34 through 36 removed outlier: 4.251A pdb=" N MET 0 85 " --> pdb=" O PHE 2 36 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N SER 0 89 " --> pdb=" O ASN 0 103 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASN 0 103 " --> pdb=" O SER 0 89 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TYR 0 99 " --> pdb=" O ILE 0 93 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE 0 136 " --> pdb=" O LYS 0 130 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LYS 0 130 " --> pdb=" O ILE 0 136 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU 0 138 " --> pdb=" O VAL 0 128 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE 0 113 " --> pdb=" O ALA 0 125 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N MET 0 127 " --> pdb=" O THR 0 111 " (cutoff:3.500A) removed outlier: 11.689A pdb=" N THR 0 111 " --> pdb=" O MET 0 127 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLU 0 32 " --> pdb=" O THR 0 111 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE 0 113 " --> pdb=" O ASN 0 30 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN 0 30 " --> pdb=" O ILE 0 113 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL 0 115 " --> pdb=" O SER 0 28 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N SER 0 28 " --> pdb=" O VAL 0 115 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain '2' and resid 29 through 31 removed outlier: 5.792A pdb=" N ASN 0 225 " --> pdb=" O ILE 0 242 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ILE 0 242 " --> pdb=" O ASN 0 225 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLN 0 200 " --> pdb=" O LEU 0 185 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N LEU 0 185 " --> pdb=" O GLN 0 200 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU 0 214 " --> pdb=" O ILE 0 222 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain '0' and resid 263 through 264 Processing sheet with id= 67, first strand: chain '0' and resid 267 through 271 removed outlier: 6.660A pdb=" N MET 0 268 " --> pdb=" O SER 0 291 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain '0' and resid 267 through 271 removed outlier: 6.660A pdb=" N MET 0 268 " --> pdb=" O SER 0 291 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLY 0 340 " --> pdb=" O THR 0 311 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU 0 313 " --> pdb=" O THR 0 338 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N THR 0 338 " --> pdb=" O LEU 0 313 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain '1' and resid 375 through 378 removed outlier: 6.507A pdb=" N GLU 1 375 " --> pdb=" O ASN 1 388 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain '1' and resid 375 through 378 removed outlier: 6.507A pdb=" N GLU 1 375 " --> pdb=" O ASN 1 388 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASN 1 435 " --> pdb=" O ILE 1 408 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ALA 1 410 " --> pdb=" O ALA 1 433 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ALA 1 433 " --> pdb=" O ALA 1 410 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain '5' and resid 34 through 36 removed outlier: 4.251A pdb=" N MET 3 85 " --> pdb=" O PHE 5 36 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N SER 3 89 " --> pdb=" O ASN 3 103 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ASN 3 103 " --> pdb=" O SER 3 89 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TYR 3 99 " --> pdb=" O ILE 3 93 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE 3 136 " --> pdb=" O LYS 3 130 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LYS 3 130 " --> pdb=" O ILE 3 136 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU 3 138 " --> pdb=" O VAL 3 128 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE 3 113 " --> pdb=" O ALA 3 125 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N MET 3 127 " --> pdb=" O THR 3 111 " (cutoff:3.500A) removed outlier: 11.690A pdb=" N THR 3 111 " --> pdb=" O MET 3 127 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLU 3 32 " --> pdb=" O THR 3 111 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE 3 113 " --> pdb=" O ASN 3 30 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN 3 30 " --> pdb=" O ILE 3 113 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL 3 115 " --> pdb=" O SER 3 28 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N SER 3 28 " --> pdb=" O VAL 3 115 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain '5' and resid 29 through 31 removed outlier: 5.792A pdb=" N ASN 3 225 " --> pdb=" O ILE 3 242 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE 3 242 " --> pdb=" O ASN 3 225 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLN 3 200 " --> pdb=" O LEU 3 185 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N LEU 3 185 " --> pdb=" O GLN 3 200 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU 3 214 " --> pdb=" O ILE 3 222 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain '3' and resid 263 through 264 Processing sheet with id= 74, first strand: chain '3' and resid 267 through 271 removed outlier: 6.661A pdb=" N MET 3 268 " --> pdb=" O SER 3 291 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain '3' and resid 267 through 271 removed outlier: 6.661A pdb=" N MET 3 268 " --> pdb=" O SER 3 291 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY 3 340 " --> pdb=" O THR 3 311 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU 3 313 " --> pdb=" O THR 3 338 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N THR 3 338 " --> pdb=" O LEU 3 313 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain '4' and resid 375 through 378 removed outlier: 6.508A pdb=" N GLU 4 375 " --> pdb=" O ASN 4 388 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain '4' and resid 375 through 378 removed outlier: 6.508A pdb=" N GLU 4 375 " --> pdb=" O ASN 4 388 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASN 4 435 " --> pdb=" O ILE 4 408 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ALA 4 410 " --> pdb=" O ALA 4 433 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ALA 4 433 " --> pdb=" O ALA 4 410 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain '8' and resid 34 through 36 removed outlier: 4.251A pdb=" N MET 6 85 " --> pdb=" O PHE 8 36 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N SER 6 89 " --> pdb=" O ASN 6 103 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ASN 6 103 " --> pdb=" O SER 6 89 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TYR 6 99 " --> pdb=" O ILE 6 93 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE 6 136 " --> pdb=" O LYS 6 130 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LYS 6 130 " --> pdb=" O ILE 6 136 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU 6 138 " --> pdb=" O VAL 6 128 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE 6 113 " --> pdb=" O ALA 6 125 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N MET 6 127 " --> pdb=" O THR 6 111 " (cutoff:3.500A) removed outlier: 11.690A pdb=" N THR 6 111 " --> pdb=" O MET 6 127 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLU 6 32 " --> pdb=" O THR 6 111 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ILE 6 113 " --> pdb=" O ASN 6 30 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN 6 30 " --> pdb=" O ILE 6 113 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N VAL 6 115 " --> pdb=" O SER 6 28 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N SER 6 28 " --> pdb=" O VAL 6 115 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain '8' and resid 29 through 31 removed outlier: 5.791A pdb=" N ASN 6 225 " --> pdb=" O ILE 6 242 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ILE 6 242 " --> pdb=" O ASN 6 225 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLN 6 200 " --> pdb=" O LEU 6 185 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N LEU 6 185 " --> pdb=" O GLN 6 200 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU 6 214 " --> pdb=" O ILE 6 222 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain '6' and resid 263 through 264 Processing sheet with id= 81, first strand: chain '6' and resid 267 through 271 removed outlier: 6.661A pdb=" N MET 6 268 " --> pdb=" O SER 6 291 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain '6' and resid 267 through 271 removed outlier: 6.661A pdb=" N MET 6 268 " --> pdb=" O SER 6 291 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLY 6 340 " --> pdb=" O THR 6 311 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU 6 313 " --> pdb=" O THR 6 338 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N THR 6 338 " --> pdb=" O LEU 6 313 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain '7' and resid 375 through 378 removed outlier: 6.507A pdb=" N GLU 7 375 " --> pdb=" O ASN 7 388 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain '7' and resid 375 through 378 removed outlier: 6.507A pdb=" N GLU 7 375 " --> pdb=" O ASN 7 388 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASN 7 435 " --> pdb=" O ILE 7 408 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ALA 7 410 " --> pdb=" O ALA 7 433 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ALA 7 433 " --> pdb=" O ALA 7 410 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'c' and resid 34 through 36 removed outlier: 4.251A pdb=" N MET 9 85 " --> pdb=" O PHE c 36 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N SER 9 89 " --> pdb=" O ASN 9 103 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ASN 9 103 " --> pdb=" O SER 9 89 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N TYR 9 99 " --> pdb=" O ILE 9 93 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE 9 136 " --> pdb=" O LYS 9 130 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N LYS 9 130 " --> pdb=" O ILE 9 136 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU 9 138 " --> pdb=" O VAL 9 128 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE 9 113 " --> pdb=" O ALA 9 125 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N MET 9 127 " --> pdb=" O THR 9 111 " (cutoff:3.500A) removed outlier: 11.689A pdb=" N THR 9 111 " --> pdb=" O MET 9 127 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLU 9 32 " --> pdb=" O THR 9 111 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE 9 113 " --> pdb=" O ASN 9 30 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN 9 30 " --> pdb=" O ILE 9 113 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL 9 115 " --> pdb=" O SER 9 28 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N SER 9 28 " --> pdb=" O VAL 9 115 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'c' and resid 29 through 31 removed outlier: 5.791A pdb=" N ASN 9 225 " --> pdb=" O ILE 9 242 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE 9 242 " --> pdb=" O ASN 9 225 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLN 9 200 " --> pdb=" O LEU 9 185 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N LEU 9 185 " --> pdb=" O GLN 9 200 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU 9 214 " --> pdb=" O ILE 9 222 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain '9' and resid 263 through 264 Processing sheet with id= 88, first strand: chain '9' and resid 267 through 271 removed outlier: 6.662A pdb=" N MET 9 268 " --> pdb=" O SER 9 291 " (cutoff:3.500A) Processing sheet with id= 89, first strand: chain '9' and resid 267 through 271 removed outlier: 6.662A pdb=" N MET 9 268 " --> pdb=" O SER 9 291 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLY 9 340 " --> pdb=" O THR 9 311 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU 9 313 " --> pdb=" O THR 9 338 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N THR 9 338 " --> pdb=" O LEU 9 313 " (cutoff:3.500A) Processing sheet with id= 90, first strand: chain 'b' and resid 375 through 378 removed outlier: 6.507A pdb=" N GLU b 375 " --> pdb=" O ASN b 388 " (cutoff:3.500A) Processing sheet with id= 91, first strand: chain 'b' and resid 375 through 378 removed outlier: 6.507A pdb=" N GLU b 375 " --> pdb=" O ASN b 388 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN b 435 " --> pdb=" O ILE b 408 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ALA b 410 " --> pdb=" O ALA b 433 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ALA b 433 " --> pdb=" O ALA b 410 " (cutoff:3.500A) 1833 hydrogen bonds defined for protein. 4641 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: 39.06 Time building geometry restraints manager: 57.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.13: 39819 1.13 - 1.30: 7625 1.30 - 1.48: 16285 1.48 - 1.65: 14518 1.65 - 1.83: 364 Bond restraints: 78611 Sorted by residual: bond pdb=" CB HIS c 33 " pdb=" CG HIS c 33 " ideal model delta sigma weight residual 1.497 1.339 0.158 1.40e-02 5.10e+03 1.27e+02 bond pdb=" CB HIS W 33 " pdb=" CG HIS W 33 " ideal model delta sigma weight residual 1.497 1.340 0.157 1.40e-02 5.10e+03 1.27e+02 bond pdb=" CB HIS Q 33 " pdb=" CG HIS Q 33 " ideal model delta sigma weight residual 1.497 1.340 0.157 1.40e-02 5.10e+03 1.26e+02 bond pdb=" CB HIS Z 33 " pdb=" CG HIS Z 33 " ideal model delta sigma weight residual 1.497 1.340 0.157 1.40e-02 5.10e+03 1.26e+02 bond pdb=" CB HIS H 33 " pdb=" CG HIS H 33 " ideal model delta sigma weight residual 1.497 1.340 0.157 1.40e-02 5.10e+03 1.26e+02 ... (remaining 78606 not shown) Histogram of bond angle deviations from ideal: 98.85 - 105.92: 2113 105.92 - 112.98: 93574 112.98 - 120.04: 25420 120.04 - 127.11: 21518 127.11 - 134.17: 219 Bond angle restraints: 142844 Sorted by residual: angle pdb=" C ASP O 131 " pdb=" N PRO O 132 " pdb=" CA PRO O 132 " ideal model delta sigma weight residual 119.56 127.72 -8.16 1.02e+00 9.61e-01 6.40e+01 angle pdb=" C ASP 6 131 " pdb=" N PRO 6 132 " pdb=" CA PRO 6 132 " ideal model delta sigma weight residual 119.56 127.70 -8.14 1.02e+00 9.61e-01 6.36e+01 angle pdb=" C ASP 9 131 " pdb=" N PRO 9 132 " pdb=" CA PRO 9 132 " ideal model delta sigma weight residual 119.56 127.69 -8.13 1.02e+00 9.61e-01 6.35e+01 angle pdb=" C ASP 3 131 " pdb=" N PRO 3 132 " pdb=" CA PRO 3 132 " ideal model delta sigma weight residual 119.56 127.69 -8.13 1.02e+00 9.61e-01 6.35e+01 angle pdb=" C ASP R 131 " pdb=" N PRO R 132 " pdb=" CA PRO R 132 " ideal model delta sigma weight residual 119.56 127.68 -8.12 1.02e+00 9.61e-01 6.34e+01 ... (remaining 142839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 29437 16.52 - 33.05: 632 33.05 - 49.57: 190 49.57 - 66.10: 83 66.10 - 82.62: 39 Dihedral angle restraints: 30381 sinusoidal: 14677 harmonic: 15704 Sorted by residual: dihedral pdb=" CD2 HIS B 105 " pdb=" CG HIS B 105 " pdb=" ND1 HIS B 105 " pdb=" HD1 HIS B 105 " ideal model delta harmonic sigma weight residual 180.00 159.13 20.87 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CD2 HIS L 105 " pdb=" CG HIS L 105 " pdb=" ND1 HIS L 105 " pdb=" HD1 HIS L 105 " ideal model delta harmonic sigma weight residual 180.00 159.17 20.83 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CD2 HIS 6 105 " pdb=" CG HIS 6 105 " pdb=" ND1 HIS 6 105 " pdb=" HD1 HIS 6 105 " ideal model delta harmonic sigma weight residual 180.00 159.17 20.83 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 30378 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 3750 0.110 - 0.219: 1943 0.219 - 0.329: 471 0.329 - 0.438: 76 0.438 - 0.548: 39 Chirality restraints: 6279 Sorted by residual: chirality pdb=" CG LEU 6 87 " pdb=" CB LEU 6 87 " pdb=" CD1 LEU 6 87 " pdb=" CD2 LEU 6 87 " both_signs ideal model delta sigma weight residual False -2.59 -2.04 -0.55 2.00e-01 2.50e+01 7.50e+00 chirality pdb=" CG LEU F 87 " pdb=" CB LEU F 87 " pdb=" CD1 LEU F 87 " pdb=" CD2 LEU F 87 " both_signs ideal model delta sigma weight residual False -2.59 -2.04 -0.55 2.00e-01 2.50e+01 7.49e+00 chirality pdb=" CG LEU R 87 " pdb=" CB LEU R 87 " pdb=" CD1 LEU R 87 " pdb=" CD2 LEU R 87 " both_signs ideal model delta sigma weight residual False -2.59 -2.04 -0.55 2.00e-01 2.50e+01 7.47e+00 ... (remaining 6276 not shown) Planarity restraints: 11869 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS B 105 " 0.076 2.00e-02 2.50e+03 7.50e-02 1.27e+02 pdb=" CG HIS B 105 " 0.030 2.00e-02 2.50e+03 pdb=" ND1 HIS B 105 " 0.073 2.00e-02 2.50e+03 pdb=" CD2 HIS B 105 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 HIS B 105 " 0.036 2.00e-02 2.50e+03 pdb=" NE2 HIS B 105 " -0.010 2.00e-02 2.50e+03 pdb=" HD1 HIS B 105 " -0.172 2.00e-02 2.50e+03 pdb=" HD2 HIS B 105 " -0.063 2.00e-02 2.50e+03 pdb=" HE1 HIS B 105 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS 6 105 " 0.076 2.00e-02 2.50e+03 7.50e-02 1.26e+02 pdb=" CG HIS 6 105 " 0.030 2.00e-02 2.50e+03 pdb=" ND1 HIS 6 105 " 0.072 2.00e-02 2.50e+03 pdb=" CD2 HIS 6 105 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 HIS 6 105 " 0.035 2.00e-02 2.50e+03 pdb=" NE2 HIS 6 105 " -0.010 2.00e-02 2.50e+03 pdb=" HD1 HIS 6 105 " -0.172 2.00e-02 2.50e+03 pdb=" HD2 HIS 6 105 " -0.063 2.00e-02 2.50e+03 pdb=" HE1 HIS 6 105 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS L 105 " 0.076 2.00e-02 2.50e+03 7.49e-02 1.26e+02 pdb=" CG HIS L 105 " 0.029 2.00e-02 2.50e+03 pdb=" ND1 HIS L 105 " 0.072 2.00e-02 2.50e+03 pdb=" CD2 HIS L 105 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 HIS L 105 " 0.036 2.00e-02 2.50e+03 pdb=" NE2 HIS L 105 " -0.010 2.00e-02 2.50e+03 pdb=" HD1 HIS L 105 " -0.172 2.00e-02 2.50e+03 pdb=" HD2 HIS L 105 " -0.063 2.00e-02 2.50e+03 pdb=" HE1 HIS L 105 " 0.057 2.00e-02 2.50e+03 ... (remaining 11866 not shown) Histogram of nonbonded interaction distances: 1.35 - 2.00: 1743 2.00 - 2.65: 107088 2.65 - 3.30: 227653 3.30 - 3.95: 306178 3.95 - 4.60: 475364 Nonbonded interactions: 1118026 Sorted by model distance: nonbonded pdb=" H SER 0 134 " pdb=" H ASP 0 135 " model vdw 1.354 2.100 nonbonded pdb=" H SER I 134 " pdb=" H ASP I 135 " model vdw 1.354 2.100 nonbonded pdb=" H SER F 134 " pdb=" H ASP F 135 " model vdw 1.354 2.100 nonbonded pdb=" H SER B 134 " pdb=" H ASP B 135 " model vdw 1.354 2.100 nonbonded pdb=" H SER 6 134 " pdb=" H ASP 6 135 " model vdw 1.354 2.100 ... (remaining 1118021 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 '0' selection = chain '3' selection = chain '6' selection = chain '9' selection = chain 'A' selection = chain 'B' selection = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'O' selection = chain 'R' selection = chain 'U' selection = chain 'X' } ncs_group { reference = chain '1' selection = chain '4' selection = chain '7' selection = chain 'C' selection = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'M' selection = chain 'P' selection = chain 'S' selection = chain 'V' selection = chain 'Y' selection = chain 'b' } ncs_group { reference = chain '2' selection = chain '5' selection = chain '8' selection = chain 'E' selection = chain 'H' selection = chain 'K' selection = chain 'N' selection = chain 'Q' selection = chain 'T' selection = chain 'W' selection = chain 'Z' selection = chain 'a' selection = chain 'c' } 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: 5 Type Number sf(0) Gaussians S 182 5.16 5 C 24037 2.51 5 N 6786 2.21 5 O 7436 1.98 5 H 39819 0.53 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: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.940 Extract box with map and model: 9.760 Check model and map are aligned: 0.930 Convert atoms to be neutral: 0.560 Process input model: 210.750 Find NCS groups from input model: 3.100 Set up NCS constraints: 0.650 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 231.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2951 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 : 0.031 0.202 38792 Z= 2.053 Angle : 1.769 11.026 52364 Z= 1.184 Chirality : 0.132 0.548 6279 Planarity : 0.010 0.075 6838 Dihedral : 9.860 82.622 14417 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 0.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.11), residues: 5148 helix: -0.93 (0.14), residues: 1001 sheet: 1.04 (0.13), residues: 1586 loop : 0.92 (0.12), residues: 2561 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Evaluate side-chains 766 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 766 time to evaluate : 4.822 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 outliers start: 0 outliers final: 0 residues processed: 766 average time/residue: 1.0306 time to fit residues: 1253.5772 Evaluate side-chains 509 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 509 time to evaluate : 4.926 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.1297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 428 optimal weight: 10.0000 chunk 384 optimal weight: 6.9990 chunk 213 optimal weight: 0.8980 chunk 131 optimal weight: 0.8980 chunk 259 optimal weight: 5.9990 chunk 205 optimal weight: 2.9990 chunk 397 optimal weight: 5.9990 chunk 153 optimal weight: 7.9990 chunk 241 optimal weight: 4.9990 chunk 295 optimal weight: 6.9990 chunk 460 optimal weight: 7.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 33 HIS a 33 HIS F 314 ASN I 206 ASN Q 33 HIS R 314 ASN T 33 HIS W 33 HIS X 314 ASN 2 33 HIS 3 235 ASN ** 6 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 200 GLN 9 314 ASN 9 355 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3183 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.059 38792 Z= 0.359 Angle : 0.711 5.415 52364 Z= 0.398 Chirality : 0.053 0.203 6279 Planarity : 0.005 0.072 6838 Dihedral : 7.087 85.001 5460 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.12 % Allowed : 0.97 % Favored : 98.91 % Rotamer Outliers : 1.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.11), residues: 5148 helix: 0.42 (0.16), residues: 988 sheet: 0.30 (0.13), residues: 1599 loop : 0.26 (0.11), residues: 2561 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Evaluate side-chains 611 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 557 time to evaluate : 4.928 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 outliers start: 54 outliers final: 34 residues processed: 589 average time/residue: 1.0503 time to fit residues: 980.1613 Evaluate side-chains 520 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 486 time to evaluate : 5.476 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.7777 time to fit residues: 55.6394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 255 optimal weight: 10.0000 chunk 142 optimal weight: 5.9990 chunk 383 optimal weight: 0.6980 chunk 313 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 chunk 461 optimal weight: 1.9990 chunk 498 optimal weight: 20.0000 chunk 410 optimal weight: 8.9990 chunk 457 optimal weight: 10.0000 chunk 157 optimal weight: 1.9990 chunk 370 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 200 GLN F 314 ASN L 194 ASN ** U 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 216 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3202 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 38792 Z= 0.200 Angle : 0.532 4.675 52364 Z= 0.298 Chirality : 0.046 0.245 6279 Planarity : 0.003 0.051 6838 Dihedral : 6.601 83.986 5460 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.12), residues: 5148 helix: 1.29 (0.18), residues: 988 sheet: 0.15 (0.13), residues: 1599 loop : 0.29 (0.12), residues: 2561 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Evaluate side-chains 514 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 497 time to evaluate : 5.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 17 outliers final: 10 residues processed: 511 average time/residue: 1.0330 time to fit residues: 829.7454 Evaluate side-chains 459 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 449 time to evaluate : 5.221 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.7525 time to fit residues: 19.5964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 455 optimal weight: 0.9980 chunk 346 optimal weight: 10.0000 chunk 239 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 220 optimal weight: 9.9990 chunk 309 optimal weight: 8.9990 chunk 462 optimal weight: 20.0000 chunk 490 optimal weight: 7.9990 chunk 241 optimal weight: 5.9990 chunk 438 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 314 ASN I 259 GLN L 105 HIS ** O 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 314 ASN 0 103 ASN 0 105 HIS ** 3 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 200 GLN 9 314 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3271 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 38792 Z= 0.268 Angle : 0.561 6.072 52364 Z= 0.311 Chirality : 0.049 0.185 6279 Planarity : 0.004 0.060 6838 Dihedral : 6.523 81.983 5460 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer Outliers : 0.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.12), residues: 5148 helix: 1.17 (0.17), residues: 988 sheet: -0.06 (0.13), residues: 1573 loop : -0.09 (0.12), residues: 2587 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Evaluate side-chains 510 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 473 time to evaluate : 4.800 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: 37 outliers final: 25 residues processed: 487 average time/residue: 1.0743 time to fit residues: 826.8555 Evaluate side-chains 456 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 431 time to evaluate : 4.832 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.6966 time to fit residues: 38.6195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 408 optimal weight: 1.9990 chunk 278 optimal weight: 6.9990 chunk 7 optimal weight: 40.0000 chunk 364 optimal weight: 8.9990 chunk 202 optimal weight: 5.9990 chunk 418 optimal weight: 9.9990 chunk 338 optimal weight: 10.0000 chunk 0 optimal weight: 100.0000 chunk 250 optimal weight: 3.9990 chunk 439 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 GLN I 200 GLN L 105 HIS ** R 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 355 GLN X 103 ASN 0 216 ASN ** 3 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3319 moved from start: 0.5524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.079 38792 Z= 0.332 Angle : 0.575 4.940 52364 Z= 0.320 Chirality : 0.050 0.169 6279 Planarity : 0.004 0.059 6838 Dihedral : 6.465 80.704 5460 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer Outliers : 0.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.12), residues: 5148 helix: 0.73 (0.16), residues: 1001 sheet: -0.31 (0.13), residues: 1573 loop : -0.57 (0.12), residues: 2574 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Evaluate side-chains 504 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 465 time to evaluate : 4.922 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: 39 outliers final: 23 residues processed: 492 average time/residue: 1.0166 time to fit residues: 794.0730 Evaluate side-chains 447 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 424 time to evaluate : 4.842 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.6678 time to fit residues: 34.6448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 164 optimal weight: 1.9990 chunk 441 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 287 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 490 optimal weight: 10.0000 chunk 407 optimal weight: 2.9990 chunk 227 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 chunk 257 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 314 ASN ** J 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 200 GLN U 103 ASN ** 3 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 225 ASN ** 6 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 314 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3309 moved from start: 0.5715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 38792 Z= 0.195 Angle : 0.497 4.552 52364 Z= 0.273 Chirality : 0.047 0.161 6279 Planarity : 0.003 0.058 6838 Dihedral : 6.177 79.577 5460 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.12), residues: 5148 helix: 1.01 (0.17), residues: 1001 sheet: -0.25 (0.13), residues: 1573 loop : -0.46 (0.12), residues: 2574 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Evaluate side-chains 475 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 449 time to evaluate : 4.860 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 outliers start: 26 outliers final: 17 residues processed: 460 average time/residue: 1.0484 time to fit residues: 762.5770 Evaluate side-chains 443 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 426 time to evaluate : 4.880 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.6691 time to fit residues: 27.9337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 472 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 279 optimal weight: 7.9990 chunk 358 optimal weight: 7.9990 chunk 277 optimal weight: 5.9990 chunk 412 optimal weight: 0.0980 chunk 273 optimal weight: 3.9990 chunk 488 optimal weight: 10.0000 chunk 305 optimal weight: 8.9990 chunk 297 optimal weight: 20.0000 chunk 225 optimal weight: 30.0000 overall best weight: 3.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 200 GLN ** 3 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3340 moved from start: 0.6097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.059 38792 Z= 0.317 Angle : 0.563 5.190 52364 Z= 0.312 Chirality : 0.049 0.178 6279 Planarity : 0.004 0.070 6838 Dihedral : 6.281 79.318 5460 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.12), residues: 5148 helix: 0.74 (0.16), residues: 1001 sheet: -0.46 (0.13), residues: 1573 loop : -0.76 (0.12), residues: 2574 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Evaluate side-chains 487 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 452 time to evaluate : 4.903 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 outliers start: 35 outliers final: 20 residues processed: 476 average time/residue: 1.0584 time to fit residues: 791.2272 Evaluate side-chains 457 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 437 time to evaluate : 4.795 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.6706 time to fit residues: 31.3540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 302 optimal weight: 4.9990 chunk 195 optimal weight: 3.9990 chunk 291 optimal weight: 1.9990 chunk 147 optimal weight: 0.4980 chunk 96 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 310 optimal weight: 5.9990 chunk 332 optimal weight: 10.0000 chunk 241 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 384 optimal weight: 20.0000 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 437 GLN 9 314 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3332 moved from start: 0.6256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 38792 Z= 0.214 Angle : 0.497 6.354 52364 Z= 0.273 Chirality : 0.047 0.161 6279 Planarity : 0.003 0.066 6838 Dihedral : 6.026 78.118 5460 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.12), residues: 5148 helix: 1.00 (0.17), residues: 1001 sheet: -0.39 (0.13), residues: 1573 loop : -0.67 (0.12), residues: 2574 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Evaluate side-chains 455 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 439 time to evaluate : 4.910 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: 16 outliers final: 11 residues processed: 446 average time/residue: 1.0278 time to fit residues: 720.9172 Evaluate side-chains 439 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 428 time to evaluate : 4.782 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.6623 time to fit residues: 19.6714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 444 optimal weight: 4.9990 chunk 468 optimal weight: 0.1980 chunk 427 optimal weight: 6.9990 chunk 455 optimal weight: 2.9990 chunk 274 optimal weight: 0.9990 chunk 198 optimal weight: 5.9990 chunk 357 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 411 optimal weight: 9.9990 chunk 430 optimal weight: 2.9990 chunk 453 optimal weight: 20.0000 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3341 moved from start: 0.6463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 38792 Z= 0.228 Angle : 0.505 5.514 52364 Z= 0.277 Chirality : 0.047 0.160 6279 Planarity : 0.003 0.077 6838 Dihedral : 5.904 76.056 5460 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.12), residues: 5148 helix: 1.06 (0.17), residues: 1001 sheet: -0.26 (0.13), residues: 1508 loop : -0.82 (0.12), residues: 2639 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Evaluate side-chains 465 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 448 time to evaluate : 4.886 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 outliers start: 17 outliers final: 12 residues processed: 457 average time/residue: 1.0481 time to fit residues: 760.1727 Evaluate side-chains 446 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 434 time to evaluate : 4.900 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.6621 time to fit residues: 21.3383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 299 optimal weight: 1.9990 chunk 481 optimal weight: 0.0270 chunk 293 optimal weight: 9.9990 chunk 228 optimal weight: 20.0000 chunk 334 optimal weight: 3.9990 chunk 505 optimal weight: 6.9990 chunk 464 optimal weight: 9.9990 chunk 402 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 310 optimal weight: 5.9990 chunk 246 optimal weight: 1.9990 overall best weight: 2.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 194 ASN ** 3 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 437 GLN 9 314 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3337 moved from start: 0.6581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 38792 Z= 0.192 Angle : 0.483 5.721 52364 Z= 0.264 Chirality : 0.046 0.187 6279 Planarity : 0.003 0.070 6838 Dihedral : 5.760 73.730 5460 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.12), residues: 5148 helix: 1.22 (0.17), residues: 1001 sheet: -0.37 (0.13), residues: 1573 loop : -0.61 (0.12), residues: 2574 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10296 Ramachandran restraints generated. 5148 Oldfield, 0 Emsley, 5148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue SER 28 is missing expected H atoms. Skipping. Residue THR 40 is missing expected H atoms. Skipping. Residue SER 41 is missing expected H atoms. Skipping. Residue VAL 42 is missing expected H atoms. Skipping. Residue MET 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Evaluate side-chains 443 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 439 time to evaluate : 5.010 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 outliers start: 4 outliers final: 2 residues processed: 440 average time/residue: 1.0311 time to fit residues: 721.2356 Evaluate side-chains 428 residues out of total 4238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 426 time to evaluate : 4.816 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.6544 time to fit residues: 8.5194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 507 random chunks: chunk 319 optimal weight: 2.9990 chunk 428 optimal weight: 40.0000 chunk 123 optimal weight: 6.9990 chunk 370 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 chunk 111 optimal weight: 20.0000 chunk 402 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 413 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 355 GLN ** R 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4901 r_free = 0.4901 target = 0.274093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.185133 restraints weight = 128754.255| |-----------------------------------------------------------------------------| r_work (start): 0.4118 rms_B_bonded: 4.19 r_work: 0.3876 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6617 moved from start: 0.6769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 38792 Z= 0.277 Angle : 0.531 4.953 52364 Z= 0.293 Chirality : 0.049 0.166 6279 Planarity : 0.004 0.075 6838 Dihedral : 5.905 72.096 5460 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.12), residues: 5148 helix: 1.05 (0.16), residues: 1001 sheet: -0.49 (0.13), residues: 1573 loop : -0.78 (0.12), residues: 2574 =============================================================================== Job complete usr+sys time: 16169.45 seconds wall clock time: 279 minutes 57.34 seconds (16797.34 seconds total)