Starting phenix.real_space_refine (version: dev) on Thu Dec 15 10:58:57 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zja_11233/12_2022/6zja_11233_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zja_11233/12_2022/6zja_11233.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zja_11233/12_2022/6zja_11233.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zja_11233/12_2022/6zja_11233.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zja_11233/12_2022/6zja_11233_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zja_11233/12_2022/6zja_11233_updated.pdb" } resolution = 2.0 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= 0.000 sd= 0.005 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 "A GLU 18": "OE1" <-> "OE2" Residue "A ARG 62": "NH1" <-> "NH2" Residue "A GLU 110": "OE1" <-> "OE2" Residue "A GLU 116": "OE1" <-> "OE2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "A GLU 185": "OE1" <-> "OE2" Residue "B GLU 53": "OE1" <-> "OE2" Residue "B GLU 64": "OE1" <-> "OE2" Residue "B GLU 187": "OE1" <-> "OE2" Residue "B GLU 222": "OE1" <-> "OE2" Residue "B GLU 254": "OE1" <-> "OE2" Residue "B GLU 276": "OE1" <-> "OE2" Residue "B GLU 311": "OE1" <-> "OE2" Residue "B GLU 313": "OE1" <-> "OE2" Residue "B GLU 347": "OE1" <-> "OE2" Residue "B GLU 386": "OE1" <-> "OE2" Residue "B GLU 392": "OE1" <-> "OE2" Residue "B GLU 393": "OE1" <-> "OE2" Residue "B TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 421": "OE1" <-> "OE2" Residue "B TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 476": "NH1" <-> "NH2" Residue "B ASP 531": "OD1" <-> "OD2" Residue "C GLU 18": "OE1" <-> "OE2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "C GLU 110": "OE1" <-> "OE2" Residue "C GLU 116": "OE1" <-> "OE2" Residue "C GLU 159": "OE1" <-> "OE2" Residue "C GLU 185": "OE1" <-> "OE2" Residue "E GLU 18": "OE1" <-> "OE2" Residue "E ARG 62": "NH1" <-> "NH2" Residue "E GLU 110": "OE1" <-> "OE2" Residue "E GLU 116": "OE1" <-> "OE2" Residue "E GLU 159": "OE1" <-> "OE2" Residue "E GLU 185": "OE1" <-> "OE2" Residue "G GLU 18": "OE1" <-> "OE2" Residue "G ARG 62": "NH1" <-> "NH2" Residue "G GLU 110": "OE1" <-> "OE2" Residue "G GLU 116": "OE1" <-> "OE2" Residue "G GLU 159": "OE1" <-> "OE2" Residue "G GLU 185": "OE1" <-> "OE2" Residue "I GLU 18": "OE1" <-> "OE2" Residue "I ARG 62": "NH1" <-> "NH2" Residue "I GLU 110": "OE1" <-> "OE2" Residue "I GLU 116": "OE1" <-> "OE2" Residue "I GLU 159": "OE1" <-> "OE2" Residue "I GLU 185": "OE1" <-> "OE2" Residue "K GLU 18": "OE1" <-> "OE2" Residue "K ARG 62": "NH1" <-> "NH2" Residue "K GLU 110": "OE1" <-> "OE2" Residue "K GLU 116": "OE1" <-> "OE2" Residue "K GLU 159": "OE1" <-> "OE2" Residue "K GLU 185": "OE1" <-> "OE2" Residue "M GLU 18": "OE1" <-> "OE2" Residue "M ARG 62": "NH1" <-> "NH2" Residue "M GLU 110": "OE1" <-> "OE2" Residue "M GLU 116": "OE1" <-> "OE2" Residue "M GLU 159": "OE1" <-> "OE2" Residue "M GLU 185": "OE1" <-> "OE2" Residue "O GLU 18": "OE1" <-> "OE2" Residue "O ARG 62": "NH1" <-> "NH2" Residue "O GLU 110": "OE1" <-> "OE2" Residue "O GLU 116": "OE1" <-> "OE2" Residue "O GLU 159": "OE1" <-> "OE2" Residue "O GLU 185": "OE1" <-> "OE2" Residue "Q GLU 18": "OE1" <-> "OE2" Residue "Q ARG 62": "NH1" <-> "NH2" Residue "Q GLU 110": "OE1" <-> "OE2" Residue "Q GLU 116": "OE1" <-> "OE2" Residue "Q GLU 159": "OE1" <-> "OE2" Residue "Q GLU 185": "OE1" <-> "OE2" Residue "S GLU 18": "OE1" <-> "OE2" Residue "S ARG 62": "NH1" <-> "NH2" Residue "S GLU 110": "OE1" <-> "OE2" Residue "S GLU 116": "OE1" <-> "OE2" Residue "S GLU 159": "OE1" <-> "OE2" Residue "S GLU 185": "OE1" <-> "OE2" Residue "U GLU 18": "OE1" <-> "OE2" Residue "U ARG 62": "NH1" <-> "NH2" Residue "U GLU 110": "OE1" <-> "OE2" Residue "U GLU 116": "OE1" <-> "OE2" Residue "U GLU 159": "OE1" <-> "OE2" Residue "U GLU 185": "OE1" <-> "OE2" Residue "W GLU 18": "OE1" <-> "OE2" Residue "W ARG 62": "NH1" <-> "NH2" Residue "W GLU 110": "OE1" <-> "OE2" Residue "W GLU 116": "OE1" <-> "OE2" Residue "W GLU 159": "OE1" <-> "OE2" Residue "W GLU 185": "OE1" <-> "OE2" Residue "J GLU 53": "OE1" <-> "OE2" Residue "J GLU 64": "OE1" <-> "OE2" Residue "J GLU 187": "OE1" <-> "OE2" Residue "J GLU 222": "OE1" <-> "OE2" Residue "J GLU 254": "OE1" <-> "OE2" Residue "J GLU 276": "OE1" <-> "OE2" Residue "J GLU 311": "OE1" <-> "OE2" Residue "J GLU 313": "OE1" <-> "OE2" Residue "J GLU 347": "OE1" <-> "OE2" Residue "J GLU 386": "OE1" <-> "OE2" Residue "J GLU 392": "OE1" <-> "OE2" Residue "J GLU 393": "OE1" <-> "OE2" Residue "J TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 421": "OE1" <-> "OE2" Residue "J TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 476": "NH1" <-> "NH2" Residue "J ASP 531": "OD1" <-> "OD2" Residue "D GLU 53": "OE1" <-> "OE2" Residue "D GLU 64": "OE1" <-> "OE2" Residue "D GLU 187": "OE1" <-> "OE2" Residue "D GLU 222": "OE1" <-> "OE2" Residue "D GLU 254": "OE1" <-> "OE2" Residue "D GLU 276": "OE1" <-> "OE2" Residue "D GLU 311": "OE1" <-> "OE2" Residue "D GLU 313": "OE1" <-> "OE2" Residue "D GLU 347": "OE1" <-> "OE2" Residue "D GLU 386": "OE1" <-> "OE2" Residue "D GLU 392": "OE1" <-> "OE2" Residue "D GLU 393": "OE1" <-> "OE2" Residue "D TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 421": "OE1" <-> "OE2" Residue "D TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 476": "NH1" <-> "NH2" Residue "D ASP 531": "OD1" <-> "OD2" Residue "F GLU 53": "OE1" <-> "OE2" Residue "F GLU 64": "OE1" <-> "OE2" Residue "F GLU 187": "OE1" <-> "OE2" Residue "F GLU 222": "OE1" <-> "OE2" Residue "F GLU 254": "OE1" <-> "OE2" Residue "F GLU 276": "OE1" <-> "OE2" Residue "F GLU 311": "OE1" <-> "OE2" Residue "F GLU 313": "OE1" <-> "OE2" Residue "F GLU 347": "OE1" <-> "OE2" Residue "F GLU 386": "OE1" <-> "OE2" Residue "F GLU 392": "OE1" <-> "OE2" Residue "F GLU 393": "OE1" <-> "OE2" Residue "F TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 421": "OE1" <-> "OE2" Residue "F TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 476": "NH1" <-> "NH2" Residue "F ASP 531": "OD1" <-> "OD2" Residue "H GLU 53": "OE1" <-> "OE2" Residue "H GLU 64": "OE1" <-> "OE2" Residue "H GLU 187": "OE1" <-> "OE2" Residue "H GLU 222": "OE1" <-> "OE2" Residue "H GLU 254": "OE1" <-> "OE2" Residue "H GLU 276": "OE1" <-> "OE2" Residue "H GLU 311": "OE1" <-> "OE2" Residue "H GLU 313": "OE1" <-> "OE2" Residue "H GLU 347": "OE1" <-> "OE2" Residue "H GLU 386": "OE1" <-> "OE2" Residue "H GLU 392": "OE1" <-> "OE2" Residue "H GLU 393": "OE1" <-> "OE2" Residue "H TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 421": "OE1" <-> "OE2" Residue "H TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 476": "NH1" <-> "NH2" Residue "H ASP 531": "OD1" <-> "OD2" Residue "L GLU 53": "OE1" <-> "OE2" Residue "L GLU 64": "OE1" <-> "OE2" Residue "L GLU 187": "OE1" <-> "OE2" Residue "L GLU 222": "OE1" <-> "OE2" Residue "L GLU 254": "OE1" <-> "OE2" Residue "L GLU 276": "OE1" <-> "OE2" Residue "L GLU 311": "OE1" <-> "OE2" Residue "L GLU 313": "OE1" <-> "OE2" Residue "L GLU 347": "OE1" <-> "OE2" Residue "L GLU 386": "OE1" <-> "OE2" Residue "L GLU 392": "OE1" <-> "OE2" Residue "L GLU 393": "OE1" <-> "OE2" Residue "L TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 421": "OE1" <-> "OE2" Residue "L TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 476": "NH1" <-> "NH2" Residue "L ASP 531": "OD1" <-> "OD2" Residue "N GLU 53": "OE1" <-> "OE2" Residue "N GLU 64": "OE1" <-> "OE2" Residue "N GLU 187": "OE1" <-> "OE2" Residue "N GLU 222": "OE1" <-> "OE2" Residue "N GLU 254": "OE1" <-> "OE2" Residue "N GLU 276": "OE1" <-> "OE2" Residue "N GLU 311": "OE1" <-> "OE2" Residue "N GLU 313": "OE1" <-> "OE2" Residue "N GLU 347": "OE1" <-> "OE2" Residue "N GLU 386": "OE1" <-> "OE2" Residue "N GLU 392": "OE1" <-> "OE2" Residue "N GLU 393": "OE1" <-> "OE2" Residue "N TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 421": "OE1" <-> "OE2" Residue "N TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 476": "NH1" <-> "NH2" Residue "N ASP 531": "OD1" <-> "OD2" Residue "P GLU 53": "OE1" <-> "OE2" Residue "P GLU 64": "OE1" <-> "OE2" Residue "P GLU 187": "OE1" <-> "OE2" Residue "P GLU 222": "OE1" <-> "OE2" Residue "P GLU 254": "OE1" <-> "OE2" Residue "P GLU 276": "OE1" <-> "OE2" Residue "P GLU 311": "OE1" <-> "OE2" Residue "P GLU 313": "OE1" <-> "OE2" Residue "P GLU 347": "OE1" <-> "OE2" Residue "P GLU 386": "OE1" <-> "OE2" Residue "P GLU 392": "OE1" <-> "OE2" Residue "P GLU 393": "OE1" <-> "OE2" Residue "P TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 421": "OE1" <-> "OE2" Residue "P TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 476": "NH1" <-> "NH2" Residue "P ASP 531": "OD1" <-> "OD2" Residue "R GLU 53": "OE1" <-> "OE2" Residue "R GLU 64": "OE1" <-> "OE2" Residue "R GLU 187": "OE1" <-> "OE2" Residue "R GLU 222": "OE1" <-> "OE2" Residue "R GLU 254": "OE1" <-> "OE2" Residue "R GLU 276": "OE1" <-> "OE2" Residue "R GLU 311": "OE1" <-> "OE2" Residue "R GLU 313": "OE1" <-> "OE2" Residue "R GLU 347": "OE1" <-> "OE2" Residue "R GLU 386": "OE1" <-> "OE2" Residue "R GLU 392": "OE1" <-> "OE2" Residue "R GLU 393": "OE1" <-> "OE2" Residue "R TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 421": "OE1" <-> "OE2" Residue "R TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 476": "NH1" <-> "NH2" Residue "R ASP 531": "OD1" <-> "OD2" Residue "T GLU 53": "OE1" <-> "OE2" Residue "T GLU 64": "OE1" <-> "OE2" Residue "T GLU 187": "OE1" <-> "OE2" Residue "T GLU 222": "OE1" <-> "OE2" Residue "T GLU 254": "OE1" <-> "OE2" Residue "T GLU 276": "OE1" <-> "OE2" Residue "T GLU 311": "OE1" <-> "OE2" Residue "T GLU 313": "OE1" <-> "OE2" Residue "T GLU 347": "OE1" <-> "OE2" Residue "T GLU 386": "OE1" <-> "OE2" Residue "T GLU 392": "OE1" <-> "OE2" Residue "T GLU 393": "OE1" <-> "OE2" Residue "T TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 421": "OE1" <-> "OE2" Residue "T TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 476": "NH1" <-> "NH2" Residue "T ASP 531": "OD1" <-> "OD2" Residue "V GLU 53": "OE1" <-> "OE2" Residue "V GLU 64": "OE1" <-> "OE2" Residue "V GLU 187": "OE1" <-> "OE2" Residue "V GLU 222": "OE1" <-> "OE2" Residue "V GLU 254": "OE1" <-> "OE2" Residue "V GLU 276": "OE1" <-> "OE2" Residue "V GLU 311": "OE1" <-> "OE2" Residue "V GLU 313": "OE1" <-> "OE2" Residue "V GLU 347": "OE1" <-> "OE2" Residue "V GLU 386": "OE1" <-> "OE2" Residue "V GLU 392": "OE1" <-> "OE2" Residue "V GLU 393": "OE1" <-> "OE2" Residue "V TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 421": "OE1" <-> "OE2" Residue "V TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 476": "NH1" <-> "NH2" Residue "V ASP 531": "OD1" <-> "OD2" Residue "X GLU 53": "OE1" <-> "OE2" Residue "X GLU 64": "OE1" <-> "OE2" Residue "X GLU 187": "OE1" <-> "OE2" Residue "X GLU 222": "OE1" <-> "OE2" Residue "X GLU 254": "OE1" <-> "OE2" Residue "X GLU 276": "OE1" <-> "OE2" Residue "X GLU 311": "OE1" <-> "OE2" Residue "X GLU 313": "OE1" <-> "OE2" Residue "X GLU 347": "OE1" <-> "OE2" Residue "X GLU 386": "OE1" <-> "OE2" Residue "X GLU 392": "OE1" <-> "OE2" Residue "X GLU 393": "OE1" <-> "OE2" Residue "X TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 421": "OE1" <-> "OE2" Residue "X TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 476": "NH1" <-> "NH2" Residue "X ASP 531": "OD1" <-> "OD2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 77951 Number of models: 1 Model: "" Number of chains: 60 Chain: "A" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 230} Chain: "B" Number of atoms: 4340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4340 Classifications: {'peptide': 569} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 546} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 230} Chain: "E" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 230} Chain: "G" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 230} Chain: "I" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 230} Chain: "K" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 230} Chain: "M" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 230} Chain: "O" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 230} Chain: "Q" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 230} Chain: "S" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 230} Chain: "U" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 230} Chain: "W" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 230} Chain: "J" Number of atoms: 4340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4340 Classifications: {'peptide': 569} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 546} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 4340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4340 Classifications: {'peptide': 569} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 546} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 4340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4340 Classifications: {'peptide': 569} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 546} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 4340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4340 Classifications: {'peptide': 569} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 546} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 4340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4340 Classifications: {'peptide': 569} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 546} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 4340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4340 Classifications: {'peptide': 569} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 546} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 4340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4340 Classifications: {'peptide': 569} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 546} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 4340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4340 Classifications: {'peptide': 569} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 546} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 4340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4340 Classifications: {'peptide': 569} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 546} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "V" Number of atoms: 4340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4340 Classifications: {'peptide': 569} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 546} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "X" Number of atoms: 4340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4340 Classifications: {'peptide': 569} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 546} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 21 Unusual residues: {' NI': 2, 'DJM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 21 Unusual residues: {' NI': 2, 'DJM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 21 Unusual residues: {' NI': 2, 'DJM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 21 Unusual residues: {' NI': 2, 'DJM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 21 Unusual residues: {' NI': 2, 'DJM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 21 Unusual residues: {' NI': 2, 'DJM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 21 Unusual residues: {' NI': 2, 'DJM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "P" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 21 Unusual residues: {' NI': 2, 'DJM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "R" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 21 Unusual residues: {' NI': 2, 'DJM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "T" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 21 Unusual residues: {' NI': 2, 'DJM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "V" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 21 Unusual residues: {' NI': 2, 'DJM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "X" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 21 Unusual residues: {' NI': 2, 'DJM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "B" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 206 Classifications: {'water': 206} Link IDs: {None: 205} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 62 Classifications: {'water': 62} Link IDs: {None: 61} Chain: "E" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "G" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 66 Classifications: {'water': 66} Link IDs: {None: 65} Chain: "I" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 63 Classifications: {'water': 63} Link IDs: {None: 62} Chain: "K" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 55 Classifications: {'water': 55} Link IDs: {None: 54} Chain: "M" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 62 Classifications: {'water': 62} Link IDs: {None: 61} Chain: "O" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 52 Classifications: {'water': 52} Link IDs: {None: 51} Chain: "Q" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Classifications: {'water': 51} Link IDs: {None: 50} Chain: "S" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 63 Classifications: {'water': 63} Link IDs: {None: 62} Chain: "U" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "W" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Chain: "J" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 223 Classifications: {'water': 223} Link IDs: {None: 222} Chain: "D" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 213 Classifications: {'water': 213} Link IDs: {None: 212} Chain: "F" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 206 Classifications: {'water': 206} Link IDs: {None: 205} Chain: "H" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 210 Classifications: {'water': 210} Link IDs: {None: 209} Chain: "L" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 201 Classifications: {'water': 201} Link IDs: {None: 200} Chain: "N" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 204 Classifications: {'water': 204} Link IDs: {None: 203} Chain: "P" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 213 Classifications: {'water': 213} Link IDs: {None: 212} Chain: "R" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 208 Classifications: {'water': 208} Link IDs: {None: 207} Chain: "T" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 204 Classifications: {'water': 204} Link IDs: {None: 203} Chain: "V" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 199 Classifications: {'water': 199} Link IDs: {None: 198} Chain: "X" Number of atoms: 209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 209 Classifications: {'water': 209} Link IDs: {None: 208} Time building chain proxies: 33.70, per 1000 atoms: 0.43 Number of scatterers: 77951 At special positions: 0 Unit cell: (172.733, 180.316, 171.89, 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) Ni 24 28.00 S 360 16.00 O 17639 8.00 N 13008 7.00 C 46920 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 27.14 Conformation dependent library (CDL) restraints added in 8.4 seconds 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17544 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 360 helices and 144 sheets defined 30.0% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.60 Creating SS restraints... Processing helix chain 'A' and resid 5 through 25 Processing helix chain 'A' and resid 32 through 49 Processing helix chain 'A' and resid 54 through 63 removed outlier: 3.577A pdb=" N GLN A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ARG A 62 " --> pdb=" O MET A 58 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N THR A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 69 No H-bonds generated for 'chain 'A' and resid 67 through 69' Processing helix chain 'A' and resid 74 through 77 No H-bonds generated for 'chain 'A' and resid 74 through 77' Processing helix chain 'A' and resid 147 through 149 No H-bonds generated for 'chain 'A' and resid 147 through 149' Processing helix chain 'A' and resid 158 through 161 Processing helix chain 'A' and resid 208 through 220 removed outlier: 3.797A pdb=" N LYS A 212 " --> pdb=" O ASN A 208 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE A 213 " --> pdb=" O GLU A 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 13 Processing helix chain 'B' and resid 110 through 112 No H-bonds generated for 'chain 'B' and resid 110 through 112' Processing helix chain 'B' and resid 142 through 151 Proline residue: B 146 - end of helix removed outlier: 3.573A pdb=" N ALA B 150 " --> pdb=" O THR B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 169 Processing helix chain 'B' and resid 176 through 188 removed outlier: 4.126A pdb=" N GLU B 187 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N GLU B 188 " --> pdb=" O ARG B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 212 removed outlier: 3.621A pdb=" N GLN B 210 " --> pdb=" O SER B 206 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE B 211 " --> pdb=" O LEU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 241 removed outlier: 3.515A pdb=" N LYS B 240 " --> pdb=" O ASP B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 265 Processing helix chain 'B' and resid 286 through 291 removed outlier: 3.542A pdb=" N GLY B 291 " --> pdb=" O LYS B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 303 No H-bonds generated for 'chain 'B' and resid 301 through 303' Processing helix chain 'B' and resid 310 through 321 Processing helix chain 'B' and resid 329 through 336 Processing helix chain 'B' and resid 341 through 352 removed outlier: 4.136A pdb=" N ASP B 348 " --> pdb=" O ILE B 344 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N THR B 349 " --> pdb=" O ALA B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 387 Processing helix chain 'B' and resid 399 through 408 removed outlier: 3.817A pdb=" N LYS B 408 " --> pdb=" O ARG B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 416 Processing helix chain 'B' and resid 439 through 441 No H-bonds generated for 'chain 'B' and resid 439 through 441' Processing helix chain 'B' and resid 479 through 481 No H-bonds generated for 'chain 'B' and resid 479 through 481' Processing helix chain 'B' and resid 485 through 488 No H-bonds generated for 'chain 'B' and resid 485 through 488' Processing helix chain 'B' and resid 496 through 500 Processing helix chain 'B' and resid 503 through 507 Processing helix chain 'B' and resid 524 through 526 No H-bonds generated for 'chain 'B' and resid 524 through 526' Processing helix chain 'C' and resid 5 through 25 Processing helix chain 'C' and resid 32 through 49 Processing helix chain 'C' and resid 54 through 63 removed outlier: 3.577A pdb=" N GLN C 59 " --> pdb=" O ALA C 55 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ARG C 62 " --> pdb=" O MET C 58 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N THR C 63 " --> pdb=" O GLN C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 69 No H-bonds generated for 'chain 'C' and resid 67 through 69' Processing helix chain 'C' and resid 74 through 77 No H-bonds generated for 'chain 'C' and resid 74 through 77' Processing helix chain 'C' and resid 147 through 149 No H-bonds generated for 'chain 'C' and resid 147 through 149' Processing helix chain 'C' and resid 158 through 161 Processing helix chain 'C' and resid 208 through 220 removed outlier: 3.797A pdb=" N LYS C 212 " --> pdb=" O ASN C 208 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE C 213 " --> pdb=" O GLU C 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 25 Processing helix chain 'E' and resid 32 through 49 Processing helix chain 'E' and resid 54 through 63 removed outlier: 3.577A pdb=" N GLN E 59 " --> pdb=" O ALA E 55 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ARG E 62 " --> pdb=" O MET E 58 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N THR E 63 " --> pdb=" O GLN E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 69 No H-bonds generated for 'chain 'E' and resid 67 through 69' Processing helix chain 'E' and resid 74 through 77 No H-bonds generated for 'chain 'E' and resid 74 through 77' Processing helix chain 'E' and resid 147 through 149 No H-bonds generated for 'chain 'E' and resid 147 through 149' Processing helix chain 'E' and resid 158 through 161 Processing helix chain 'E' and resid 208 through 220 removed outlier: 3.797A pdb=" N LYS E 212 " --> pdb=" O ASN E 208 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE E 213 " --> pdb=" O GLU E 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 25 Processing helix chain 'G' and resid 32 through 49 Processing helix chain 'G' and resid 54 through 63 removed outlier: 3.578A pdb=" N GLN G 59 " --> pdb=" O ALA G 55 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ARG G 62 " --> pdb=" O MET G 58 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N THR G 63 " --> pdb=" O GLN G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 69 No H-bonds generated for 'chain 'G' and resid 67 through 69' Processing helix chain 'G' and resid 74 through 77 No H-bonds generated for 'chain 'G' and resid 74 through 77' Processing helix chain 'G' and resid 147 through 149 No H-bonds generated for 'chain 'G' and resid 147 through 149' Processing helix chain 'G' and resid 158 through 161 Processing helix chain 'G' and resid 208 through 220 removed outlier: 3.798A pdb=" N LYS G 212 " --> pdb=" O ASN G 208 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE G 213 " --> pdb=" O GLU G 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 25 Processing helix chain 'I' and resid 32 through 49 Processing helix chain 'I' and resid 54 through 63 removed outlier: 3.577A pdb=" N GLN I 59 " --> pdb=" O ALA I 55 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ARG I 62 " --> pdb=" O MET I 58 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N THR I 63 " --> pdb=" O GLN I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 69 No H-bonds generated for 'chain 'I' and resid 67 through 69' Processing helix chain 'I' and resid 74 through 77 No H-bonds generated for 'chain 'I' and resid 74 through 77' Processing helix chain 'I' and resid 147 through 149 No H-bonds generated for 'chain 'I' and resid 147 through 149' Processing helix chain 'I' and resid 158 through 161 Processing helix chain 'I' and resid 208 through 220 removed outlier: 3.797A pdb=" N LYS I 212 " --> pdb=" O ASN I 208 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE I 213 " --> pdb=" O GLU I 209 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 25 Processing helix chain 'K' and resid 32 through 49 Processing helix chain 'K' and resid 54 through 63 removed outlier: 3.578A pdb=" N GLN K 59 " --> pdb=" O ALA K 55 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ARG K 62 " --> pdb=" O MET K 58 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N THR K 63 " --> pdb=" O GLN K 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 69 No H-bonds generated for 'chain 'K' and resid 67 through 69' Processing helix chain 'K' and resid 74 through 77 No H-bonds generated for 'chain 'K' and resid 74 through 77' Processing helix chain 'K' and resid 147 through 149 No H-bonds generated for 'chain 'K' and resid 147 through 149' Processing helix chain 'K' and resid 158 through 161 Processing helix chain 'K' and resid 208 through 220 removed outlier: 3.798A pdb=" N LYS K 212 " --> pdb=" O ASN K 208 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE K 213 " --> pdb=" O GLU K 209 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 25 Processing helix chain 'M' and resid 32 through 49 Processing helix chain 'M' and resid 54 through 63 removed outlier: 3.578A pdb=" N GLN M 59 " --> pdb=" O ALA M 55 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ARG M 62 " --> pdb=" O MET M 58 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N THR M 63 " --> pdb=" O GLN M 59 " (cutoff:3.500A) Processing helix chain 'M' and resid 67 through 69 No H-bonds generated for 'chain 'M' and resid 67 through 69' Processing helix chain 'M' and resid 74 through 77 No H-bonds generated for 'chain 'M' and resid 74 through 77' Processing helix chain 'M' and resid 147 through 149 No H-bonds generated for 'chain 'M' and resid 147 through 149' Processing helix chain 'M' and resid 158 through 161 Processing helix chain 'M' and resid 208 through 220 removed outlier: 3.797A pdb=" N LYS M 212 " --> pdb=" O ASN M 208 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE M 213 " --> pdb=" O GLU M 209 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 25 Processing helix chain 'O' and resid 32 through 49 Processing helix chain 'O' and resid 54 through 63 removed outlier: 3.578A pdb=" N GLN O 59 " --> pdb=" O ALA O 55 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ARG O 62 " --> pdb=" O MET O 58 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N THR O 63 " --> pdb=" O GLN O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 69 No H-bonds generated for 'chain 'O' and resid 67 through 69' Processing helix chain 'O' and resid 74 through 77 No H-bonds generated for 'chain 'O' and resid 74 through 77' Processing helix chain 'O' and resid 147 through 149 No H-bonds generated for 'chain 'O' and resid 147 through 149' Processing helix chain 'O' and resid 158 through 161 Processing helix chain 'O' and resid 208 through 220 removed outlier: 3.798A pdb=" N LYS O 212 " --> pdb=" O ASN O 208 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE O 213 " --> pdb=" O GLU O 209 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 25 Processing helix chain 'Q' and resid 32 through 49 Processing helix chain 'Q' and resid 54 through 63 removed outlier: 3.578A pdb=" N GLN Q 59 " --> pdb=" O ALA Q 55 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ARG Q 62 " --> pdb=" O MET Q 58 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N THR Q 63 " --> pdb=" O GLN Q 59 " (cutoff:3.500A) Processing helix chain 'Q' and resid 67 through 69 No H-bonds generated for 'chain 'Q' and resid 67 through 69' Processing helix chain 'Q' and resid 74 through 77 No H-bonds generated for 'chain 'Q' and resid 74 through 77' Processing helix chain 'Q' and resid 147 through 149 No H-bonds generated for 'chain 'Q' and resid 147 through 149' Processing helix chain 'Q' and resid 158 through 161 Processing helix chain 'Q' and resid 208 through 220 removed outlier: 3.798A pdb=" N LYS Q 212 " --> pdb=" O ASN Q 208 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE Q 213 " --> pdb=" O GLU Q 209 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 25 Processing helix chain 'S' and resid 32 through 49 Processing helix chain 'S' and resid 54 through 63 removed outlier: 3.577A pdb=" N GLN S 59 " --> pdb=" O ALA S 55 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ARG S 62 " --> pdb=" O MET S 58 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N THR S 63 " --> pdb=" O GLN S 59 " (cutoff:3.500A) Processing helix chain 'S' and resid 67 through 69 No H-bonds generated for 'chain 'S' and resid 67 through 69' Processing helix chain 'S' and resid 74 through 77 No H-bonds generated for 'chain 'S' and resid 74 through 77' Processing helix chain 'S' and resid 147 through 149 No H-bonds generated for 'chain 'S' and resid 147 through 149' Processing helix chain 'S' and resid 158 through 161 Processing helix chain 'S' and resid 208 through 220 removed outlier: 3.797A pdb=" N LYS S 212 " --> pdb=" O ASN S 208 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE S 213 " --> pdb=" O GLU S 209 " (cutoff:3.500A) Processing helix chain 'U' and resid 5 through 25 Processing helix chain 'U' and resid 32 through 49 Processing helix chain 'U' and resid 54 through 63 removed outlier: 3.577A pdb=" N GLN U 59 " --> pdb=" O ALA U 55 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ARG U 62 " --> pdb=" O MET U 58 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N THR U 63 " --> pdb=" O GLN U 59 " (cutoff:3.500A) Processing helix chain 'U' and resid 67 through 69 No H-bonds generated for 'chain 'U' and resid 67 through 69' Processing helix chain 'U' and resid 74 through 77 No H-bonds generated for 'chain 'U' and resid 74 through 77' Processing helix chain 'U' and resid 147 through 149 No H-bonds generated for 'chain 'U' and resid 147 through 149' Processing helix chain 'U' and resid 158 through 161 Processing helix chain 'U' and resid 208 through 220 removed outlier: 3.798A pdb=" N LYS U 212 " --> pdb=" O ASN U 208 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE U 213 " --> pdb=" O GLU U 209 " (cutoff:3.500A) Processing helix chain 'W' and resid 5 through 25 Processing helix chain 'W' and resid 32 through 49 Processing helix chain 'W' and resid 54 through 63 removed outlier: 3.578A pdb=" N GLN W 59 " --> pdb=" O ALA W 55 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ARG W 62 " --> pdb=" O MET W 58 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N THR W 63 " --> pdb=" O GLN W 59 " (cutoff:3.500A) Processing helix chain 'W' and resid 67 through 69 No H-bonds generated for 'chain 'W' and resid 67 through 69' Processing helix chain 'W' and resid 74 through 77 No H-bonds generated for 'chain 'W' and resid 74 through 77' Processing helix chain 'W' and resid 147 through 149 No H-bonds generated for 'chain 'W' and resid 147 through 149' Processing helix chain 'W' and resid 158 through 161 Processing helix chain 'W' and resid 208 through 220 removed outlier: 3.798A pdb=" N LYS W 212 " --> pdb=" O ASN W 208 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE W 213 " --> pdb=" O GLU W 209 " (cutoff:3.500A) Processing helix chain 'J' and resid 6 through 13 Processing helix chain 'J' and resid 110 through 112 No H-bonds generated for 'chain 'J' and resid 110 through 112' Processing helix chain 'J' and resid 142 through 151 Proline residue: J 146 - end of helix removed outlier: 3.574A pdb=" N ALA J 150 " --> pdb=" O THR J 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 165 through 169 Processing helix chain 'J' and resid 176 through 188 removed outlier: 4.126A pdb=" N GLU J 187 " --> pdb=" O LEU J 183 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLU J 188 " --> pdb=" O ARG J 184 " (cutoff:3.500A) Processing helix chain 'J' and resid 204 through 212 removed outlier: 3.622A pdb=" N GLN J 210 " --> pdb=" O SER J 206 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE J 211 " --> pdb=" O LEU J 207 " (cutoff:3.500A) Processing helix chain 'J' and resid 228 through 241 removed outlier: 3.514A pdb=" N LYS J 240 " --> pdb=" O ASP J 236 " (cutoff:3.500A) Processing helix chain 'J' and resid 258 through 265 Processing helix chain 'J' and resid 286 through 291 removed outlier: 3.542A pdb=" N GLY J 291 " --> pdb=" O LYS J 288 " (cutoff:3.500A) Processing helix chain 'J' and resid 301 through 303 No H-bonds generated for 'chain 'J' and resid 301 through 303' Processing helix chain 'J' and resid 310 through 321 Processing helix chain 'J' and resid 329 through 336 Processing helix chain 'J' and resid 341 through 352 removed outlier: 4.136A pdb=" N ASP J 348 " --> pdb=" O ILE J 344 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N THR J 349 " --> pdb=" O ALA J 345 " (cutoff:3.500A) Processing helix chain 'J' and resid 372 through 387 Processing helix chain 'J' and resid 399 through 408 removed outlier: 3.818A pdb=" N LYS J 408 " --> pdb=" O ARG J 404 " (cutoff:3.500A) Processing helix chain 'J' and resid 411 through 416 Processing helix chain 'J' and resid 439 through 441 No H-bonds generated for 'chain 'J' and resid 439 through 441' Processing helix chain 'J' and resid 479 through 481 No H-bonds generated for 'chain 'J' and resid 479 through 481' Processing helix chain 'J' and resid 485 through 488 No H-bonds generated for 'chain 'J' and resid 485 through 488' Processing helix chain 'J' and resid 496 through 500 Processing helix chain 'J' and resid 503 through 507 Processing helix chain 'J' and resid 524 through 526 No H-bonds generated for 'chain 'J' and resid 524 through 526' Processing helix chain 'D' and resid 6 through 13 Processing helix chain 'D' and resid 110 through 112 No H-bonds generated for 'chain 'D' and resid 110 through 112' Processing helix chain 'D' and resid 142 through 151 Proline residue: D 146 - end of helix removed outlier: 3.574A pdb=" N ALA D 150 " --> pdb=" O THR D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 169 Processing helix chain 'D' and resid 176 through 188 removed outlier: 4.127A pdb=" N GLU D 187 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLU D 188 " --> pdb=" O ARG D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 212 removed outlier: 3.621A pdb=" N GLN D 210 " --> pdb=" O SER D 206 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE D 211 " --> pdb=" O LEU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 241 removed outlier: 3.514A pdb=" N LYS D 240 " --> pdb=" O ASP D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 265 Processing helix chain 'D' and resid 286 through 291 removed outlier: 3.542A pdb=" N GLY D 291 " --> pdb=" O LYS D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 303 No H-bonds generated for 'chain 'D' and resid 301 through 303' Processing helix chain 'D' and resid 310 through 321 Processing helix chain 'D' and resid 329 through 336 Processing helix chain 'D' and resid 341 through 352 removed outlier: 4.136A pdb=" N ASP D 348 " --> pdb=" O ILE D 344 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N THR D 349 " --> pdb=" O ALA D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 387 Processing helix chain 'D' and resid 399 through 408 removed outlier: 3.818A pdb=" N LYS D 408 " --> pdb=" O ARG D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 416 Processing helix chain 'D' and resid 439 through 441 No H-bonds generated for 'chain 'D' and resid 439 through 441' Processing helix chain 'D' and resid 479 through 481 No H-bonds generated for 'chain 'D' and resid 479 through 481' Processing helix chain 'D' and resid 485 through 488 No H-bonds generated for 'chain 'D' and resid 485 through 488' Processing helix chain 'D' and resid 496 through 500 Processing helix chain 'D' and resid 503 through 507 Processing helix chain 'D' and resid 524 through 526 No H-bonds generated for 'chain 'D' and resid 524 through 526' Processing helix chain 'F' and resid 6 through 13 Processing helix chain 'F' and resid 110 through 112 No H-bonds generated for 'chain 'F' and resid 110 through 112' Processing helix chain 'F' and resid 142 through 151 Proline residue: F 146 - end of helix removed outlier: 3.574A pdb=" N ALA F 150 " --> pdb=" O THR F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 169 Processing helix chain 'F' and resid 176 through 188 removed outlier: 4.126A pdb=" N GLU F 187 " --> pdb=" O LEU F 183 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLU F 188 " --> pdb=" O ARG F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 212 removed outlier: 3.622A pdb=" N GLN F 210 " --> pdb=" O SER F 206 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE F 211 " --> pdb=" O LEU F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 241 removed outlier: 3.515A pdb=" N LYS F 240 " --> pdb=" O ASP F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 265 Processing helix chain 'F' and resid 286 through 291 removed outlier: 3.542A pdb=" N GLY F 291 " --> pdb=" O LYS F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 303 No H-bonds generated for 'chain 'F' and resid 301 through 303' Processing helix chain 'F' and resid 310 through 321 Processing helix chain 'F' and resid 329 through 336 Processing helix chain 'F' and resid 341 through 352 removed outlier: 4.136A pdb=" N ASP F 348 " --> pdb=" O ILE F 344 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N THR F 349 " --> pdb=" O ALA F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 387 Processing helix chain 'F' and resid 399 through 408 removed outlier: 3.817A pdb=" N LYS F 408 " --> pdb=" O ARG F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 411 through 416 Processing helix chain 'F' and resid 439 through 441 No H-bonds generated for 'chain 'F' and resid 439 through 441' Processing helix chain 'F' and resid 479 through 481 No H-bonds generated for 'chain 'F' and resid 479 through 481' Processing helix chain 'F' and resid 485 through 488 No H-bonds generated for 'chain 'F' and resid 485 through 488' Processing helix chain 'F' and resid 496 through 500 Processing helix chain 'F' and resid 503 through 507 Processing helix chain 'F' and resid 524 through 526 No H-bonds generated for 'chain 'F' and resid 524 through 526' Processing helix chain 'H' and resid 6 through 13 Processing helix chain 'H' and resid 110 through 112 No H-bonds generated for 'chain 'H' and resid 110 through 112' Processing helix chain 'H' and resid 142 through 151 Proline residue: H 146 - end of helix removed outlier: 3.573A pdb=" N ALA H 150 " --> pdb=" O THR H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 165 through 169 Processing helix chain 'H' and resid 176 through 188 removed outlier: 4.126A pdb=" N GLU H 187 " --> pdb=" O LEU H 183 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLU H 188 " --> pdb=" O ARG H 184 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 212 removed outlier: 3.621A pdb=" N GLN H 210 " --> pdb=" O SER H 206 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE H 211 " --> pdb=" O LEU H 207 " (cutoff:3.500A) Processing helix chain 'H' and resid 228 through 241 removed outlier: 3.515A pdb=" N LYS H 240 " --> pdb=" O ASP H 236 " (cutoff:3.500A) Processing helix chain 'H' and resid 258 through 265 Processing helix chain 'H' and resid 286 through 291 removed outlier: 3.542A pdb=" N GLY H 291 " --> pdb=" O LYS H 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 301 through 303 No H-bonds generated for 'chain 'H' and resid 301 through 303' Processing helix chain 'H' and resid 310 through 321 Processing helix chain 'H' and resid 329 through 336 Processing helix chain 'H' and resid 341 through 352 removed outlier: 4.136A pdb=" N ASP H 348 " --> pdb=" O ILE H 344 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N THR H 349 " --> pdb=" O ALA H 345 " (cutoff:3.500A) Processing helix chain 'H' and resid 372 through 387 Processing helix chain 'H' and resid 399 through 408 removed outlier: 3.818A pdb=" N LYS H 408 " --> pdb=" O ARG H 404 " (cutoff:3.500A) Processing helix chain 'H' and resid 411 through 416 Processing helix chain 'H' and resid 439 through 441 No H-bonds generated for 'chain 'H' and resid 439 through 441' Processing helix chain 'H' and resid 479 through 481 No H-bonds generated for 'chain 'H' and resid 479 through 481' Processing helix chain 'H' and resid 485 through 488 No H-bonds generated for 'chain 'H' and resid 485 through 488' Processing helix chain 'H' and resid 496 through 500 Processing helix chain 'H' and resid 503 through 507 Processing helix chain 'H' and resid 524 through 526 No H-bonds generated for 'chain 'H' and resid 524 through 526' Processing helix chain 'L' and resid 6 through 13 Processing helix chain 'L' and resid 110 through 112 No H-bonds generated for 'chain 'L' and resid 110 through 112' Processing helix chain 'L' and resid 142 through 151 Proline residue: L 146 - end of helix removed outlier: 3.574A pdb=" N ALA L 150 " --> pdb=" O THR L 147 " (cutoff:3.500A) Processing helix chain 'L' and resid 165 through 169 Processing helix chain 'L' and resid 176 through 188 removed outlier: 4.126A pdb=" N GLU L 187 " --> pdb=" O LEU L 183 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLU L 188 " --> pdb=" O ARG L 184 " (cutoff:3.500A) Processing helix chain 'L' and resid 204 through 212 removed outlier: 3.621A pdb=" N GLN L 210 " --> pdb=" O SER L 206 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE L 211 " --> pdb=" O LEU L 207 " (cutoff:3.500A) Processing helix chain 'L' and resid 228 through 241 removed outlier: 3.515A pdb=" N LYS L 240 " --> pdb=" O ASP L 236 " (cutoff:3.500A) Processing helix chain 'L' and resid 258 through 265 Processing helix chain 'L' and resid 286 through 291 removed outlier: 3.542A pdb=" N GLY L 291 " --> pdb=" O LYS L 288 " (cutoff:3.500A) Processing helix chain 'L' and resid 301 through 303 No H-bonds generated for 'chain 'L' and resid 301 through 303' Processing helix chain 'L' and resid 310 through 321 Processing helix chain 'L' and resid 329 through 336 Processing helix chain 'L' and resid 341 through 352 removed outlier: 4.136A pdb=" N ASP L 348 " --> pdb=" O ILE L 344 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N THR L 349 " --> pdb=" O ALA L 345 " (cutoff:3.500A) Processing helix chain 'L' and resid 372 through 387 Processing helix chain 'L' and resid 399 through 408 removed outlier: 3.817A pdb=" N LYS L 408 " --> pdb=" O ARG L 404 " (cutoff:3.500A) Processing helix chain 'L' and resid 411 through 416 Processing helix chain 'L' and resid 439 through 441 No H-bonds generated for 'chain 'L' and resid 439 through 441' Processing helix chain 'L' and resid 479 through 481 No H-bonds generated for 'chain 'L' and resid 479 through 481' Processing helix chain 'L' and resid 485 through 488 No H-bonds generated for 'chain 'L' and resid 485 through 488' Processing helix chain 'L' and resid 496 through 500 Processing helix chain 'L' and resid 503 through 507 Processing helix chain 'L' and resid 524 through 526 No H-bonds generated for 'chain 'L' and resid 524 through 526' Processing helix chain 'N' and resid 6 through 13 Processing helix chain 'N' and resid 110 through 112 No H-bonds generated for 'chain 'N' and resid 110 through 112' Processing helix chain 'N' and resid 142 through 151 Proline residue: N 146 - end of helix removed outlier: 3.573A pdb=" N ALA N 150 " --> pdb=" O THR N 147 " (cutoff:3.500A) Processing helix chain 'N' and resid 165 through 169 Processing helix chain 'N' and resid 176 through 188 removed outlier: 4.126A pdb=" N GLU N 187 " --> pdb=" O LEU N 183 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLU N 188 " --> pdb=" O ARG N 184 " (cutoff:3.500A) Processing helix chain 'N' and resid 204 through 212 removed outlier: 3.621A pdb=" N GLN N 210 " --> pdb=" O SER N 206 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE N 211 " --> pdb=" O LEU N 207 " (cutoff:3.500A) Processing helix chain 'N' and resid 228 through 241 removed outlier: 3.514A pdb=" N LYS N 240 " --> pdb=" O ASP N 236 " (cutoff:3.500A) Processing helix chain 'N' and resid 258 through 265 Processing helix chain 'N' and resid 286 through 291 removed outlier: 3.542A pdb=" N GLY N 291 " --> pdb=" O LYS N 288 " (cutoff:3.500A) Processing helix chain 'N' and resid 301 through 303 No H-bonds generated for 'chain 'N' and resid 301 through 303' Processing helix chain 'N' and resid 310 through 321 Processing helix chain 'N' and resid 329 through 336 Processing helix chain 'N' and resid 341 through 352 removed outlier: 4.136A pdb=" N ASP N 348 " --> pdb=" O ILE N 344 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N THR N 349 " --> pdb=" O ALA N 345 " (cutoff:3.500A) Processing helix chain 'N' and resid 372 through 387 Processing helix chain 'N' and resid 399 through 408 removed outlier: 3.817A pdb=" N LYS N 408 " --> pdb=" O ARG N 404 " (cutoff:3.500A) Processing helix chain 'N' and resid 411 through 416 Processing helix chain 'N' and resid 439 through 441 No H-bonds generated for 'chain 'N' and resid 439 through 441' Processing helix chain 'N' and resid 479 through 481 No H-bonds generated for 'chain 'N' and resid 479 through 481' Processing helix chain 'N' and resid 485 through 488 No H-bonds generated for 'chain 'N' and resid 485 through 488' Processing helix chain 'N' and resid 496 through 500 Processing helix chain 'N' and resid 503 through 507 Processing helix chain 'N' and resid 524 through 526 No H-bonds generated for 'chain 'N' and resid 524 through 526' Processing helix chain 'P' and resid 6 through 13 Processing helix chain 'P' and resid 110 through 112 No H-bonds generated for 'chain 'P' and resid 110 through 112' Processing helix chain 'P' and resid 142 through 151 Proline residue: P 146 - end of helix removed outlier: 3.574A pdb=" N ALA P 150 " --> pdb=" O THR P 147 " (cutoff:3.500A) Processing helix chain 'P' and resid 165 through 169 Processing helix chain 'P' and resid 176 through 188 removed outlier: 4.126A pdb=" N GLU P 187 " --> pdb=" O LEU P 183 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N GLU P 188 " --> pdb=" O ARG P 184 " (cutoff:3.500A) Processing helix chain 'P' and resid 204 through 212 removed outlier: 3.621A pdb=" N GLN P 210 " --> pdb=" O SER P 206 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE P 211 " --> pdb=" O LEU P 207 " (cutoff:3.500A) Processing helix chain 'P' and resid 228 through 241 removed outlier: 3.515A pdb=" N LYS P 240 " --> pdb=" O ASP P 236 " (cutoff:3.500A) Processing helix chain 'P' and resid 258 through 265 Processing helix chain 'P' and resid 286 through 291 removed outlier: 3.542A pdb=" N GLY P 291 " --> pdb=" O LYS P 288 " (cutoff:3.500A) Processing helix chain 'P' and resid 301 through 303 No H-bonds generated for 'chain 'P' and resid 301 through 303' Processing helix chain 'P' and resid 310 through 321 Processing helix chain 'P' and resid 329 through 336 Processing helix chain 'P' and resid 341 through 352 removed outlier: 4.136A pdb=" N ASP P 348 " --> pdb=" O ILE P 344 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N THR P 349 " --> pdb=" O ALA P 345 " (cutoff:3.500A) Processing helix chain 'P' and resid 372 through 387 Processing helix chain 'P' and resid 399 through 408 removed outlier: 3.818A pdb=" N LYS P 408 " --> pdb=" O ARG P 404 " (cutoff:3.500A) Processing helix chain 'P' and resid 411 through 416 Processing helix chain 'P' and resid 439 through 441 No H-bonds generated for 'chain 'P' and resid 439 through 441' Processing helix chain 'P' and resid 479 through 481 No H-bonds generated for 'chain 'P' and resid 479 through 481' Processing helix chain 'P' and resid 485 through 488 No H-bonds generated for 'chain 'P' and resid 485 through 488' Processing helix chain 'P' and resid 496 through 500 Processing helix chain 'P' and resid 503 through 507 Processing helix chain 'P' and resid 524 through 526 No H-bonds generated for 'chain 'P' and resid 524 through 526' Processing helix chain 'R' and resid 6 through 13 Processing helix chain 'R' and resid 110 through 112 No H-bonds generated for 'chain 'R' and resid 110 through 112' Processing helix chain 'R' and resid 142 through 151 Proline residue: R 146 - end of helix removed outlier: 3.574A pdb=" N ALA R 150 " --> pdb=" O THR R 147 " (cutoff:3.500A) Processing helix chain 'R' and resid 165 through 169 Processing helix chain 'R' and resid 176 through 188 removed outlier: 4.126A pdb=" N GLU R 187 " --> pdb=" O LEU R 183 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLU R 188 " --> pdb=" O ARG R 184 " (cutoff:3.500A) Processing helix chain 'R' and resid 204 through 212 removed outlier: 3.621A pdb=" N GLN R 210 " --> pdb=" O SER R 206 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE R 211 " --> pdb=" O LEU R 207 " (cutoff:3.500A) Processing helix chain 'R' and resid 228 through 241 removed outlier: 3.514A pdb=" N LYS R 240 " --> pdb=" O ASP R 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 258 through 265 Processing helix chain 'R' and resid 286 through 291 removed outlier: 3.541A pdb=" N GLY R 291 " --> pdb=" O LYS R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 301 through 303 No H-bonds generated for 'chain 'R' and resid 301 through 303' Processing helix chain 'R' and resid 310 through 321 Processing helix chain 'R' and resid 329 through 336 Processing helix chain 'R' and resid 341 through 352 removed outlier: 4.136A pdb=" N ASP R 348 " --> pdb=" O ILE R 344 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N THR R 349 " --> pdb=" O ALA R 345 " (cutoff:3.500A) Processing helix chain 'R' and resid 372 through 387 Processing helix chain 'R' and resid 399 through 408 removed outlier: 3.817A pdb=" N LYS R 408 " --> pdb=" O ARG R 404 " (cutoff:3.500A) Processing helix chain 'R' and resid 411 through 416 Processing helix chain 'R' and resid 439 through 441 No H-bonds generated for 'chain 'R' and resid 439 through 441' Processing helix chain 'R' and resid 479 through 481 No H-bonds generated for 'chain 'R' and resid 479 through 481' Processing helix chain 'R' and resid 485 through 488 No H-bonds generated for 'chain 'R' and resid 485 through 488' Processing helix chain 'R' and resid 496 through 500 Processing helix chain 'R' and resid 503 through 507 Processing helix chain 'R' and resid 524 through 526 No H-bonds generated for 'chain 'R' and resid 524 through 526' Processing helix chain 'T' and resid 6 through 13 Processing helix chain 'T' and resid 110 through 112 No H-bonds generated for 'chain 'T' and resid 110 through 112' Processing helix chain 'T' and resid 142 through 151 Proline residue: T 146 - end of helix removed outlier: 3.573A pdb=" N ALA T 150 " --> pdb=" O THR T 147 " (cutoff:3.500A) Processing helix chain 'T' and resid 165 through 169 Processing helix chain 'T' and resid 176 through 188 removed outlier: 4.126A pdb=" N GLU T 187 " --> pdb=" O LEU T 183 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLU T 188 " --> pdb=" O ARG T 184 " (cutoff:3.500A) Processing helix chain 'T' and resid 204 through 212 removed outlier: 3.621A pdb=" N GLN T 210 " --> pdb=" O SER T 206 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE T 211 " --> pdb=" O LEU T 207 " (cutoff:3.500A) Processing helix chain 'T' and resid 228 through 241 removed outlier: 3.515A pdb=" N LYS T 240 " --> pdb=" O ASP T 236 " (cutoff:3.500A) Processing helix chain 'T' and resid 258 through 265 Processing helix chain 'T' and resid 286 through 291 removed outlier: 3.541A pdb=" N GLY T 291 " --> pdb=" O LYS T 288 " (cutoff:3.500A) Processing helix chain 'T' and resid 301 through 303 No H-bonds generated for 'chain 'T' and resid 301 through 303' Processing helix chain 'T' and resid 310 through 321 Processing helix chain 'T' and resid 329 through 336 Processing helix chain 'T' and resid 341 through 352 removed outlier: 4.135A pdb=" N ASP T 348 " --> pdb=" O ILE T 344 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N THR T 349 " --> pdb=" O ALA T 345 " (cutoff:3.500A) Processing helix chain 'T' and resid 372 through 387 Processing helix chain 'T' and resid 399 through 408 removed outlier: 3.818A pdb=" N LYS T 408 " --> pdb=" O ARG T 404 " (cutoff:3.500A) Processing helix chain 'T' and resid 411 through 416 Processing helix chain 'T' and resid 439 through 441 No H-bonds generated for 'chain 'T' and resid 439 through 441' Processing helix chain 'T' and resid 479 through 481 No H-bonds generated for 'chain 'T' and resid 479 through 481' Processing helix chain 'T' and resid 485 through 488 No H-bonds generated for 'chain 'T' and resid 485 through 488' Processing helix chain 'T' and resid 496 through 500 Processing helix chain 'T' and resid 503 through 507 Processing helix chain 'T' and resid 524 through 526 No H-bonds generated for 'chain 'T' and resid 524 through 526' Processing helix chain 'V' and resid 6 through 13 Processing helix chain 'V' and resid 110 through 112 No H-bonds generated for 'chain 'V' and resid 110 through 112' Processing helix chain 'V' and resid 142 through 151 Proline residue: V 146 - end of helix removed outlier: 3.573A pdb=" N ALA V 150 " --> pdb=" O THR V 147 " (cutoff:3.500A) Processing helix chain 'V' and resid 165 through 169 Processing helix chain 'V' and resid 176 through 188 removed outlier: 4.126A pdb=" N GLU V 187 " --> pdb=" O LEU V 183 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N GLU V 188 " --> pdb=" O ARG V 184 " (cutoff:3.500A) Processing helix chain 'V' and resid 204 through 212 removed outlier: 3.621A pdb=" N GLN V 210 " --> pdb=" O SER V 206 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE V 211 " --> pdb=" O LEU V 207 " (cutoff:3.500A) Processing helix chain 'V' and resid 228 through 241 removed outlier: 3.515A pdb=" N LYS V 240 " --> pdb=" O ASP V 236 " (cutoff:3.500A) Processing helix chain 'V' and resid 258 through 265 Processing helix chain 'V' and resid 286 through 291 removed outlier: 3.541A pdb=" N GLY V 291 " --> pdb=" O LYS V 288 " (cutoff:3.500A) Processing helix chain 'V' and resid 301 through 303 No H-bonds generated for 'chain 'V' and resid 301 through 303' Processing helix chain 'V' and resid 310 through 321 Processing helix chain 'V' and resid 329 through 336 Processing helix chain 'V' and resid 341 through 352 removed outlier: 4.136A pdb=" N ASP V 348 " --> pdb=" O ILE V 344 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N THR V 349 " --> pdb=" O ALA V 345 " (cutoff:3.500A) Processing helix chain 'V' and resid 372 through 387 Processing helix chain 'V' and resid 399 through 408 removed outlier: 3.818A pdb=" N LYS V 408 " --> pdb=" O ARG V 404 " (cutoff:3.500A) Processing helix chain 'V' and resid 411 through 416 Processing helix chain 'V' and resid 439 through 441 No H-bonds generated for 'chain 'V' and resid 439 through 441' Processing helix chain 'V' and resid 479 through 481 No H-bonds generated for 'chain 'V' and resid 479 through 481' Processing helix chain 'V' and resid 485 through 488 No H-bonds generated for 'chain 'V' and resid 485 through 488' Processing helix chain 'V' and resid 496 through 500 Processing helix chain 'V' and resid 503 through 507 Processing helix chain 'V' and resid 524 through 526 No H-bonds generated for 'chain 'V' and resid 524 through 526' Processing helix chain 'X' and resid 6 through 13 Processing helix chain 'X' and resid 110 through 112 No H-bonds generated for 'chain 'X' and resid 110 through 112' Processing helix chain 'X' and resid 142 through 151 Proline residue: X 146 - end of helix removed outlier: 3.573A pdb=" N ALA X 150 " --> pdb=" O THR X 147 " (cutoff:3.500A) Processing helix chain 'X' and resid 165 through 169 Processing helix chain 'X' and resid 176 through 188 removed outlier: 4.125A pdb=" N GLU X 187 " --> pdb=" O LEU X 183 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N GLU X 188 " --> pdb=" O ARG X 184 " (cutoff:3.500A) Processing helix chain 'X' and resid 204 through 212 removed outlier: 3.621A pdb=" N GLN X 210 " --> pdb=" O SER X 206 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE X 211 " --> pdb=" O LEU X 207 " (cutoff:3.500A) Processing helix chain 'X' and resid 228 through 241 removed outlier: 3.515A pdb=" N LYS X 240 " --> pdb=" O ASP X 236 " (cutoff:3.500A) Processing helix chain 'X' and resid 258 through 265 Processing helix chain 'X' and resid 286 through 291 removed outlier: 3.541A pdb=" N GLY X 291 " --> pdb=" O LYS X 288 " (cutoff:3.500A) Processing helix chain 'X' and resid 301 through 303 No H-bonds generated for 'chain 'X' and resid 301 through 303' Processing helix chain 'X' and resid 310 through 321 Processing helix chain 'X' and resid 329 through 336 Processing helix chain 'X' and resid 341 through 352 removed outlier: 4.136A pdb=" N ASP X 348 " --> pdb=" O ILE X 344 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N THR X 349 " --> pdb=" O ALA X 345 " (cutoff:3.500A) Processing helix chain 'X' and resid 372 through 387 Processing helix chain 'X' and resid 399 through 408 removed outlier: 3.817A pdb=" N LYS X 408 " --> pdb=" O ARG X 404 " (cutoff:3.500A) Processing helix chain 'X' and resid 411 through 416 Processing helix chain 'X' and resid 439 through 441 No H-bonds generated for 'chain 'X' and resid 439 through 441' Processing helix chain 'X' and resid 479 through 481 No H-bonds generated for 'chain 'X' and resid 479 through 481' Processing helix chain 'X' and resid 485 through 488 No H-bonds generated for 'chain 'X' and resid 485 through 488' Processing helix chain 'X' and resid 496 through 500 Processing helix chain 'X' and resid 503 through 507 Processing helix chain 'X' and resid 524 through 526 No H-bonds generated for 'chain 'X' and resid 524 through 526' Processing sheet with id= A, first strand: chain 'A' and resid 80 through 87 Processing sheet with id= B, first strand: chain 'A' and resid 127 through 132 Processing sheet with id= C, first strand: chain 'A' and resid 139 through 142 Processing sheet with id= D, first strand: chain 'B' and resid 20 through 22 Processing sheet with id= E, first strand: chain 'B' and resid 119 through 122 removed outlier: 6.105A pdb=" N LYS B 89 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ILE B 93 " --> pdb=" O LYS B 89 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 73 through 77 Processing sheet with id= G, first strand: chain 'B' and resid 126 through 130 removed outlier: 3.620A pdb=" N MET B 448 " --> pdb=" O LEU B 436 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU B 457 " --> pdb=" O ILE B 449 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LYS B 451 " --> pdb=" O ILE B 455 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ILE B 455 " --> pdb=" O LYS B 451 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 192 through 195 removed outlier: 6.866A pdb=" N GLY B 132 " --> pdb=" O THR B 154 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N MET B 156 " --> pdb=" O GLY B 132 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASP B 134 " --> pdb=" O MET B 156 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N GLY B 158 " --> pdb=" O ASP B 134 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 270 through 272 Processing sheet with id= J, first strand: chain 'B' and resid 298 through 300 removed outlier: 6.526A pdb=" N ILE B 358 " --> pdb=" O SER B 299 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'B' and resid 491 through 494 removed outlier: 6.428A pdb=" N GLN B 512 " --> pdb=" O THR B 492 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N VAL B 494 " --> pdb=" O GLN B 512 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU B 514 " --> pdb=" O VAL B 494 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'B' and resid 536 through 538 Processing sheet with id= M, first strand: chain 'C' and resid 80 through 87 Processing sheet with id= N, first strand: chain 'C' and resid 127 through 132 Processing sheet with id= O, first strand: chain 'C' and resid 139 through 142 Processing sheet with id= P, first strand: chain 'E' and resid 80 through 87 Processing sheet with id= Q, first strand: chain 'E' and resid 127 through 132 Processing sheet with id= R, first strand: chain 'E' and resid 139 through 142 Processing sheet with id= S, first strand: chain 'G' and resid 80 through 87 Processing sheet with id= T, first strand: chain 'G' and resid 127 through 132 Processing sheet with id= U, first strand: chain 'G' and resid 139 through 142 Processing sheet with id= V, first strand: chain 'I' and resid 80 through 87 Processing sheet with id= W, first strand: chain 'I' and resid 127 through 132 Processing sheet with id= X, first strand: chain 'I' and resid 139 through 142 Processing sheet with id= Y, first strand: chain 'K' and resid 80 through 87 Processing sheet with id= Z, first strand: chain 'K' and resid 127 through 132 Processing sheet with id= AA, first strand: chain 'K' and resid 139 through 142 Processing sheet with id= AB, first strand: chain 'M' and resid 80 through 87 Processing sheet with id= AC, first strand: chain 'M' and resid 127 through 132 Processing sheet with id= AD, first strand: chain 'M' and resid 139 through 142 Processing sheet with id= AE, first strand: chain 'O' and resid 80 through 87 Processing sheet with id= AF, first strand: chain 'O' and resid 127 through 132 Processing sheet with id= AG, first strand: chain 'O' and resid 139 through 142 Processing sheet with id= AH, first strand: chain 'Q' and resid 80 through 87 Processing sheet with id= AI, first strand: chain 'Q' and resid 127 through 132 Processing sheet with id= AJ, first strand: chain 'Q' and resid 139 through 142 Processing sheet with id= AK, first strand: chain 'S' and resid 80 through 87 Processing sheet with id= AL, first strand: chain 'S' and resid 127 through 132 Processing sheet with id= AM, first strand: chain 'S' and resid 139 through 142 Processing sheet with id= AN, first strand: chain 'U' and resid 80 through 87 Processing sheet with id= AO, first strand: chain 'U' and resid 127 through 132 Processing sheet with id= AP, first strand: chain 'U' and resid 139 through 142 Processing sheet with id= AQ, first strand: chain 'W' and resid 80 through 87 Processing sheet with id= AR, first strand: chain 'W' and resid 127 through 132 Processing sheet with id= AS, first strand: chain 'W' and resid 139 through 142 Processing sheet with id= AT, first strand: chain 'J' and resid 20 through 22 Processing sheet with id= AU, first strand: chain 'J' and resid 119 through 122 removed outlier: 6.106A pdb=" N LYS J 89 " --> pdb=" O ILE J 93 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ILE J 93 " --> pdb=" O LYS J 89 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'J' and resid 73 through 77 Processing sheet with id= AW, first strand: chain 'J' and resid 126 through 130 removed outlier: 3.621A pdb=" N MET J 448 " --> pdb=" O LEU J 436 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU J 457 " --> pdb=" O ILE J 449 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LYS J 451 " --> pdb=" O ILE J 455 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ILE J 455 " --> pdb=" O LYS J 451 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'J' and resid 192 through 195 removed outlier: 6.867A pdb=" N GLY J 132 " --> pdb=" O THR J 154 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N MET J 156 " --> pdb=" O GLY J 132 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASP J 134 " --> pdb=" O MET J 156 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N GLY J 158 " --> pdb=" O ASP J 134 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'J' and resid 270 through 272 Processing sheet with id= AZ, first strand: chain 'J' and resid 298 through 300 removed outlier: 6.526A pdb=" N ILE J 358 " --> pdb=" O SER J 299 " (cutoff:3.500A) No H-bonds generated for sheet with id= AZ Processing sheet with id= BA, first strand: chain 'J' and resid 491 through 494 removed outlier: 6.428A pdb=" N GLN J 512 " --> pdb=" O THR J 492 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N VAL J 494 " --> pdb=" O GLN J 512 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU J 514 " --> pdb=" O VAL J 494 " (cutoff:3.500A) No H-bonds generated for sheet with id= BA Processing sheet with id= BB, first strand: chain 'J' and resid 536 through 538 Processing sheet with id= BC, first strand: chain 'D' and resid 20 through 22 Processing sheet with id= BD, first strand: chain 'D' and resid 119 through 122 removed outlier: 6.105A pdb=" N LYS D 89 " --> pdb=" O ILE D 93 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ILE D 93 " --> pdb=" O LYS D 89 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'D' and resid 73 through 77 Processing sheet with id= BF, first strand: chain 'D' and resid 126 through 130 removed outlier: 3.620A pdb=" N MET D 448 " --> pdb=" O LEU D 436 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU D 457 " --> pdb=" O ILE D 449 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LYS D 451 " --> pdb=" O ILE D 455 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ILE D 455 " --> pdb=" O LYS D 451 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'D' and resid 192 through 195 removed outlier: 6.867A pdb=" N GLY D 132 " --> pdb=" O THR D 154 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N MET D 156 " --> pdb=" O GLY D 132 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASP D 134 " --> pdb=" O MET D 156 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N GLY D 158 " --> pdb=" O ASP D 134 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'D' and resid 270 through 272 Processing sheet with id= BI, first strand: chain 'D' and resid 298 through 300 removed outlier: 6.526A pdb=" N ILE D 358 " --> pdb=" O SER D 299 " (cutoff:3.500A) No H-bonds generated for sheet with id= BI Processing sheet with id= BJ, first strand: chain 'D' and resid 491 through 494 removed outlier: 6.428A pdb=" N GLN D 512 " --> pdb=" O THR D 492 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N VAL D 494 " --> pdb=" O GLN D 512 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU D 514 " --> pdb=" O VAL D 494 " (cutoff:3.500A) No H-bonds generated for sheet with id= BJ Processing sheet with id= BK, first strand: chain 'D' and resid 536 through 538 Processing sheet with id= BL, first strand: chain 'F' and resid 20 through 22 Processing sheet with id= BM, first strand: chain 'F' and resid 119 through 122 removed outlier: 6.106A pdb=" N LYS F 89 " --> pdb=" O ILE F 93 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ILE F 93 " --> pdb=" O LYS F 89 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'F' and resid 73 through 77 Processing sheet with id= BO, first strand: chain 'F' and resid 126 through 130 removed outlier: 3.620A pdb=" N MET F 448 " --> pdb=" O LEU F 436 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU F 457 " --> pdb=" O ILE F 449 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LYS F 451 " --> pdb=" O ILE F 455 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ILE F 455 " --> pdb=" O LYS F 451 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'F' and resid 192 through 195 removed outlier: 6.867A pdb=" N GLY F 132 " --> pdb=" O THR F 154 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N MET F 156 " --> pdb=" O GLY F 132 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASP F 134 " --> pdb=" O MET F 156 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N GLY F 158 " --> pdb=" O ASP F 134 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'F' and resid 270 through 272 Processing sheet with id= BR, first strand: chain 'F' and resid 298 through 300 removed outlier: 6.526A pdb=" N ILE F 358 " --> pdb=" O SER F 299 " (cutoff:3.500A) No H-bonds generated for sheet with id= BR Processing sheet with id= BS, first strand: chain 'F' and resid 491 through 494 removed outlier: 6.428A pdb=" N GLN F 512 " --> pdb=" O THR F 492 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N VAL F 494 " --> pdb=" O GLN F 512 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU F 514 " --> pdb=" O VAL F 494 " (cutoff:3.500A) No H-bonds generated for sheet with id= BS Processing sheet with id= BT, first strand: chain 'F' and resid 536 through 538 Processing sheet with id= BU, first strand: chain 'H' and resid 20 through 22 Processing sheet with id= BV, first strand: chain 'H' and resid 119 through 122 removed outlier: 6.105A pdb=" N LYS H 89 " --> pdb=" O ILE H 93 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ILE H 93 " --> pdb=" O LYS H 89 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'H' and resid 73 through 77 Processing sheet with id= BX, first strand: chain 'H' and resid 126 through 130 removed outlier: 3.620A pdb=" N MET H 448 " --> pdb=" O LEU H 436 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU H 457 " --> pdb=" O ILE H 449 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LYS H 451 " --> pdb=" O ILE H 455 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ILE H 455 " --> pdb=" O LYS H 451 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'H' and resid 192 through 195 removed outlier: 6.866A pdb=" N GLY H 132 " --> pdb=" O THR H 154 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N MET H 156 " --> pdb=" O GLY H 132 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ASP H 134 " --> pdb=" O MET H 156 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N GLY H 158 " --> pdb=" O ASP H 134 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'H' and resid 270 through 272 Processing sheet with id= CA, first strand: chain 'H' and resid 298 through 300 removed outlier: 6.526A pdb=" N ILE H 358 " --> pdb=" O SER H 299 " (cutoff:3.500A) No H-bonds generated for sheet with id= CA Processing sheet with id= CB, first strand: chain 'H' and resid 491 through 494 removed outlier: 6.429A pdb=" N GLN H 512 " --> pdb=" O THR H 492 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N VAL H 494 " --> pdb=" O GLN H 512 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LEU H 514 " --> pdb=" O VAL H 494 " (cutoff:3.500A) No H-bonds generated for sheet with id= CB Processing sheet with id= CC, first strand: chain 'H' and resid 536 through 538 Processing sheet with id= CD, first strand: chain 'L' and resid 20 through 22 Processing sheet with id= CE, first strand: chain 'L' and resid 119 through 122 removed outlier: 6.106A pdb=" N LYS L 89 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ILE L 93 " --> pdb=" O LYS L 89 " (cutoff:3.500A) Processing sheet with id= CF, first strand: chain 'L' and resid 73 through 77 Processing sheet with id= CG, first strand: chain 'L' and resid 126 through 130 removed outlier: 3.619A pdb=" N MET L 448 " --> pdb=" O LEU L 436 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU L 457 " --> pdb=" O ILE L 449 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LYS L 451 " --> pdb=" O ILE L 455 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ILE L 455 " --> pdb=" O LYS L 451 " (cutoff:3.500A) Processing sheet with id= CH, first strand: chain 'L' and resid 192 through 195 removed outlier: 6.868A pdb=" N GLY L 132 " --> pdb=" O THR L 154 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N MET L 156 " --> pdb=" O GLY L 132 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASP L 134 " --> pdb=" O MET L 156 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N GLY L 158 " --> pdb=" O ASP L 134 " (cutoff:3.500A) Processing sheet with id= CI, first strand: chain 'L' and resid 270 through 272 Processing sheet with id= CJ, first strand: chain 'L' and resid 298 through 300 removed outlier: 6.525A pdb=" N ILE L 358 " --> pdb=" O SER L 299 " (cutoff:3.500A) No H-bonds generated for sheet with id= CJ Processing sheet with id= CK, first strand: chain 'L' and resid 491 through 494 removed outlier: 6.427A pdb=" N GLN L 512 " --> pdb=" O THR L 492 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N VAL L 494 " --> pdb=" O GLN L 512 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU L 514 " --> pdb=" O VAL L 494 " (cutoff:3.500A) No H-bonds generated for sheet with id= CK Processing sheet with id= CL, first strand: chain 'L' and resid 536 through 538 Processing sheet with id= CM, first strand: chain 'N' and resid 20 through 22 Processing sheet with id= CN, first strand: chain 'N' and resid 119 through 122 removed outlier: 6.106A pdb=" N LYS N 89 " --> pdb=" O ILE N 93 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ILE N 93 " --> pdb=" O LYS N 89 " (cutoff:3.500A) Processing sheet with id= CO, first strand: chain 'N' and resid 73 through 77 Processing sheet with id= CP, first strand: chain 'N' and resid 126 through 130 removed outlier: 3.620A pdb=" N MET N 448 " --> pdb=" O LEU N 436 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU N 457 " --> pdb=" O ILE N 449 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LYS N 451 " --> pdb=" O ILE N 455 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ILE N 455 " --> pdb=" O LYS N 451 " (cutoff:3.500A) Processing sheet with id= CQ, first strand: chain 'N' and resid 192 through 195 removed outlier: 6.867A pdb=" N GLY N 132 " --> pdb=" O THR N 154 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N MET N 156 " --> pdb=" O GLY N 132 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASP N 134 " --> pdb=" O MET N 156 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N GLY N 158 " --> pdb=" O ASP N 134 " (cutoff:3.500A) Processing sheet with id= CR, first strand: chain 'N' and resid 270 through 272 Processing sheet with id= CS, first strand: chain 'N' and resid 298 through 300 removed outlier: 6.526A pdb=" N ILE N 358 " --> pdb=" O SER N 299 " (cutoff:3.500A) No H-bonds generated for sheet with id= CS Processing sheet with id= CT, first strand: chain 'N' and resid 491 through 494 removed outlier: 6.429A pdb=" N GLN N 512 " --> pdb=" O THR N 492 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL N 494 " --> pdb=" O GLN N 512 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU N 514 " --> pdb=" O VAL N 494 " (cutoff:3.500A) No H-bonds generated for sheet with id= CT Processing sheet with id= CU, first strand: chain 'N' and resid 536 through 538 Processing sheet with id= CV, first strand: chain 'P' and resid 20 through 22 Processing sheet with id= CW, first strand: chain 'P' and resid 119 through 122 removed outlier: 6.106A pdb=" N LYS P 89 " --> pdb=" O ILE P 93 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ILE P 93 " --> pdb=" O LYS P 89 " (cutoff:3.500A) Processing sheet with id= CX, first strand: chain 'P' and resid 73 through 77 Processing sheet with id= CY, first strand: chain 'P' and resid 126 through 130 removed outlier: 3.620A pdb=" N MET P 448 " --> pdb=" O LEU P 436 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU P 457 " --> pdb=" O ILE P 449 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N LYS P 451 " --> pdb=" O ILE P 455 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ILE P 455 " --> pdb=" O LYS P 451 " (cutoff:3.500A) Processing sheet with id= CZ, first strand: chain 'P' and resid 192 through 195 removed outlier: 6.867A pdb=" N GLY P 132 " --> pdb=" O THR P 154 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N MET P 156 " --> pdb=" O GLY P 132 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASP P 134 " --> pdb=" O MET P 156 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N GLY P 158 " --> pdb=" O ASP P 134 " (cutoff:3.500A) Processing sheet with id= DA, first strand: chain 'P' and resid 270 through 272 Processing sheet with id= DB, first strand: chain 'P' and resid 298 through 300 removed outlier: 6.526A pdb=" N ILE P 358 " --> pdb=" O SER P 299 " (cutoff:3.500A) No H-bonds generated for sheet with id= DB Processing sheet with id= DC, first strand: chain 'P' and resid 491 through 494 removed outlier: 6.427A pdb=" N GLN P 512 " --> pdb=" O THR P 492 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N VAL P 494 " --> pdb=" O GLN P 512 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU P 514 " --> pdb=" O VAL P 494 " (cutoff:3.500A) No H-bonds generated for sheet with id= DC Processing sheet with id= DD, first strand: chain 'P' and resid 536 through 538 Processing sheet with id= DE, first strand: chain 'R' and resid 20 through 22 Processing sheet with id= DF, first strand: chain 'R' and resid 119 through 122 removed outlier: 6.105A pdb=" N LYS R 89 " --> pdb=" O ILE R 93 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ILE R 93 " --> pdb=" O LYS R 89 " (cutoff:3.500A) Processing sheet with id= DG, first strand: chain 'R' and resid 73 through 77 Processing sheet with id= DH, first strand: chain 'R' and resid 126 through 130 removed outlier: 3.619A pdb=" N MET R 448 " --> pdb=" O LEU R 436 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU R 457 " --> pdb=" O ILE R 449 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LYS R 451 " --> pdb=" O ILE R 455 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ILE R 455 " --> pdb=" O LYS R 451 " (cutoff:3.500A) Processing sheet with id= DI, first strand: chain 'R' and resid 192 through 195 removed outlier: 6.867A pdb=" N GLY R 132 " --> pdb=" O THR R 154 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N MET R 156 " --> pdb=" O GLY R 132 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASP R 134 " --> pdb=" O MET R 156 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N GLY R 158 " --> pdb=" O ASP R 134 " (cutoff:3.500A) Processing sheet with id= DJ, first strand: chain 'R' and resid 270 through 272 Processing sheet with id= DK, first strand: chain 'R' and resid 298 through 300 removed outlier: 6.526A pdb=" N ILE R 358 " --> pdb=" O SER R 299 " (cutoff:3.500A) No H-bonds generated for sheet with id= DK Processing sheet with id= DL, first strand: chain 'R' and resid 491 through 494 removed outlier: 6.429A pdb=" N GLN R 512 " --> pdb=" O THR R 492 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N VAL R 494 " --> pdb=" O GLN R 512 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU R 514 " --> pdb=" O VAL R 494 " (cutoff:3.500A) No H-bonds generated for sheet with id= DL Processing sheet with id= DM, first strand: chain 'R' and resid 536 through 538 Processing sheet with id= DN, first strand: chain 'T' and resid 20 through 22 Processing sheet with id= DO, first strand: chain 'T' and resid 119 through 122 removed outlier: 6.105A pdb=" N LYS T 89 " --> pdb=" O ILE T 93 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ILE T 93 " --> pdb=" O LYS T 89 " (cutoff:3.500A) Processing sheet with id= DP, first strand: chain 'T' and resid 73 through 77 Processing sheet with id= DQ, first strand: chain 'T' and resid 126 through 130 removed outlier: 3.620A pdb=" N MET T 448 " --> pdb=" O LEU T 436 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU T 457 " --> pdb=" O ILE T 449 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LYS T 451 " --> pdb=" O ILE T 455 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ILE T 455 " --> pdb=" O LYS T 451 " (cutoff:3.500A) Processing sheet with id= DR, first strand: chain 'T' and resid 192 through 195 removed outlier: 6.867A pdb=" N GLY T 132 " --> pdb=" O THR T 154 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N MET T 156 " --> pdb=" O GLY T 132 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ASP T 134 " --> pdb=" O MET T 156 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N GLY T 158 " --> pdb=" O ASP T 134 " (cutoff:3.500A) Processing sheet with id= DS, first strand: chain 'T' and resid 270 through 272 Processing sheet with id= DT, first strand: chain 'T' and resid 298 through 300 removed outlier: 6.527A pdb=" N ILE T 358 " --> pdb=" O SER T 299 " (cutoff:3.500A) No H-bonds generated for sheet with id= DT Processing sheet with id= DU, first strand: chain 'T' and resid 491 through 494 removed outlier: 6.428A pdb=" N GLN T 512 " --> pdb=" O THR T 492 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N VAL T 494 " --> pdb=" O GLN T 512 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU T 514 " --> pdb=" O VAL T 494 " (cutoff:3.500A) No H-bonds generated for sheet with id= DU Processing sheet with id= DV, first strand: chain 'T' and resid 536 through 538 Processing sheet with id= DW, first strand: chain 'V' and resid 20 through 22 Processing sheet with id= DX, first strand: chain 'V' and resid 119 through 122 removed outlier: 6.106A pdb=" N LYS V 89 " --> pdb=" O ILE V 93 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ILE V 93 " --> pdb=" O LYS V 89 " (cutoff:3.500A) Processing sheet with id= DY, first strand: chain 'V' and resid 73 through 77 Processing sheet with id= DZ, first strand: chain 'V' and resid 126 through 130 removed outlier: 3.619A pdb=" N MET V 448 " --> pdb=" O LEU V 436 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU V 457 " --> pdb=" O ILE V 449 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LYS V 451 " --> pdb=" O ILE V 455 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ILE V 455 " --> pdb=" O LYS V 451 " (cutoff:3.500A) Processing sheet with id= EA, first strand: chain 'V' and resid 192 through 195 removed outlier: 6.867A pdb=" N GLY V 132 " --> pdb=" O THR V 154 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N MET V 156 " --> pdb=" O GLY V 132 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASP V 134 " --> pdb=" O MET V 156 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N GLY V 158 " --> pdb=" O ASP V 134 " (cutoff:3.500A) Processing sheet with id= EB, first strand: chain 'V' and resid 270 through 272 Processing sheet with id= EC, first strand: chain 'V' and resid 298 through 300 removed outlier: 6.526A pdb=" N ILE V 358 " --> pdb=" O SER V 299 " (cutoff:3.500A) No H-bonds generated for sheet with id= EC Processing sheet with id= ED, first strand: chain 'V' and resid 491 through 494 removed outlier: 6.428A pdb=" N GLN V 512 " --> pdb=" O THR V 492 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N VAL V 494 " --> pdb=" O GLN V 512 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU V 514 " --> pdb=" O VAL V 494 " (cutoff:3.500A) No H-bonds generated for sheet with id= ED Processing sheet with id= EE, first strand: chain 'V' and resid 536 through 538 Processing sheet with id= 0, first strand: chain 'X' and resid 20 through 22 Processing sheet with id= 1, first strand: chain 'X' and resid 119 through 122 removed outlier: 6.106A pdb=" N LYS X 89 " --> pdb=" O ILE X 93 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ILE X 93 " --> pdb=" O LYS X 89 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'X' and resid 73 through 77 Processing sheet with id= 3, first strand: chain 'X' and resid 126 through 130 removed outlier: 3.620A pdb=" N MET X 448 " --> pdb=" O LEU X 436 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU X 457 " --> pdb=" O ILE X 449 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N LYS X 451 " --> pdb=" O ILE X 455 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ILE X 455 " --> pdb=" O LYS X 451 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'X' and resid 192 through 195 removed outlier: 6.866A pdb=" N GLY X 132 " --> pdb=" O THR X 154 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N MET X 156 " --> pdb=" O GLY X 132 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASP X 134 " --> pdb=" O MET X 156 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N GLY X 158 " --> pdb=" O ASP X 134 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'X' and resid 270 through 272 Processing sheet with id= 6, first strand: chain 'X' and resid 298 through 300 removed outlier: 6.526A pdb=" N ILE X 358 " --> pdb=" O SER X 299 " (cutoff:3.500A) No H-bonds generated for sheet with id= 6 Processing sheet with id= 7, first strand: chain 'X' and resid 491 through 494 removed outlier: 6.428A pdb=" N GLN X 512 " --> pdb=" O THR X 492 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL X 494 " --> pdb=" O GLN X 512 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU X 514 " --> pdb=" O VAL X 494 " (cutoff:3.500A) No H-bonds generated for sheet with id= 7 Processing sheet with id= 8, first strand: chain 'X' and resid 536 through 538 2076 hydrogen bonds defined for protein. 5652 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: 40.96 Time building geometry restraints manager: 29.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 13139 1.32 - 1.45: 19023 1.45 - 1.58: 43234 1.58 - 1.71: 24 1.71 - 1.84: 672 Bond restraints: 76092 Sorted by residual: bond pdb=" C16 DJM L 603 " pdb=" N18 DJM L 603 " ideal model delta sigma weight residual 1.347 1.489 -0.142 2.00e-02 2.50e+03 5.04e+01 bond pdb=" C16 DJM D 603 " pdb=" N18 DJM D 603 " ideal model delta sigma weight residual 1.347 1.489 -0.142 2.00e-02 2.50e+03 5.04e+01 bond pdb=" C16 DJM B 603 " pdb=" N18 DJM B 603 " ideal model delta sigma weight residual 1.347 1.489 -0.142 2.00e-02 2.50e+03 5.03e+01 bond pdb=" C16 DJM F 603 " pdb=" N18 DJM F 603 " ideal model delta sigma weight residual 1.347 1.489 -0.142 2.00e-02 2.50e+03 5.03e+01 bond pdb=" C16 DJM H 603 " pdb=" N18 DJM H 603 " ideal model delta sigma weight residual 1.347 1.489 -0.142 2.00e-02 2.50e+03 5.02e+01 ... (remaining 76087 not shown) Histogram of bond angle deviations from ideal: 100.02 - 106.85: 2052 106.85 - 113.68: 41303 113.68 - 120.50: 30446 120.50 - 127.33: 28150 127.33 - 134.16: 697 Bond angle restraints: 102648 Sorted by residual: angle pdb=" C GLY U 197 " pdb=" N PHE U 198 " pdb=" CA PHE U 198 " ideal model delta sigma weight residual 121.54 131.81 -10.27 1.91e+00 2.74e-01 2.89e+01 angle pdb=" C GLY E 197 " pdb=" N PHE E 198 " pdb=" CA PHE E 198 " ideal model delta sigma weight residual 121.54 131.79 -10.25 1.91e+00 2.74e-01 2.88e+01 angle pdb=" C GLY O 197 " pdb=" N PHE O 198 " pdb=" CA PHE O 198 " ideal model delta sigma weight residual 121.54 131.77 -10.23 1.91e+00 2.74e-01 2.87e+01 angle pdb=" C GLY W 197 " pdb=" N PHE W 198 " pdb=" CA PHE W 198 " ideal model delta sigma weight residual 121.54 131.77 -10.23 1.91e+00 2.74e-01 2.87e+01 angle pdb=" C GLY Q 197 " pdb=" N PHE Q 198 " pdb=" CA PHE Q 198 " ideal model delta sigma weight residual 121.54 131.77 -10.23 1.91e+00 2.74e-01 2.87e+01 ... (remaining 102643 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 42413 17.43 - 34.85: 2431 34.85 - 52.28: 564 52.28 - 69.70: 216 69.70 - 87.13: 216 Dihedral angle restraints: 45840 sinusoidal: 18408 harmonic: 27432 Sorted by residual: dihedral pdb=" CA GLU X 188 " pdb=" C GLU X 188 " pdb=" N TYR X 189 " pdb=" CA TYR X 189 " ideal model delta harmonic sigma weight residual -180.00 -151.12 -28.88 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA GLU J 188 " pdb=" C GLU J 188 " pdb=" N TYR J 189 " pdb=" CA TYR J 189 " ideal model delta harmonic sigma weight residual -180.00 -151.15 -28.85 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA GLU H 188 " pdb=" C GLU H 188 " pdb=" N TYR H 189 " pdb=" CA TYR H 189 " ideal model delta harmonic sigma weight residual -180.00 -151.15 -28.85 0 5.00e+00 4.00e-02 3.33e+01 ... (remaining 45837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 9483 0.074 - 0.148: 1777 0.148 - 0.222: 116 0.222 - 0.296: 12 0.296 - 0.370: 12 Chirality restraints: 11400 Sorted by residual: chirality pdb=" CA ASN B 301 " pdb=" N ASN B 301 " pdb=" C ASN B 301 " pdb=" CB ASN B 301 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" CA ASN P 301 " pdb=" N ASN P 301 " pdb=" C ASN P 301 " pdb=" CB ASN P 301 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" CA ASN N 301 " pdb=" N ASN N 301 " pdb=" C ASN N 301 " pdb=" CB ASN N 301 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.41e+00 ... (remaining 11397 not shown) Planarity restraints: 13440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE O 87 " -0.037 5.00e-02 4.00e+02 5.59e-02 4.99e+00 pdb=" N PRO O 88 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO O 88 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO O 88 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE G 87 " 0.037 5.00e-02 4.00e+02 5.59e-02 4.99e+00 pdb=" N PRO G 88 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO G 88 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO G 88 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 87 " -0.037 5.00e-02 4.00e+02 5.57e-02 4.97e+00 pdb=" N PRO C 88 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO C 88 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 88 " -0.031 5.00e-02 4.00e+02 ... (remaining 13437 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 575 2.56 - 3.14: 61248 3.14 - 3.73: 127596 3.73 - 4.31: 197812 4.31 - 4.90: 304839 Nonbonded interactions: 692070 Sorted by model distance: nonbonded pdb="NI NI H 601 " pdb=" O19 DJM H 603 " model vdw 1.974 2.180 nonbonded pdb="NI NI P 601 " pdb=" O19 DJM P 603 " model vdw 1.974 2.180 nonbonded pdb="NI NI D 601 " pdb=" O19 DJM D 603 " model vdw 1.974 2.180 nonbonded pdb="NI NI N 601 " pdb=" O19 DJM N 603 " model vdw 1.974 2.180 nonbonded pdb="NI NI F 601 " pdb=" O19 DJM F 603 " model vdw 1.975 2.180 ... (remaining 692065 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' } 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 Ni 24 6.56 5 S 360 5.16 5 C 46920 2.51 5 N 13008 2.21 5 O 17639 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 27.520 Check model and map are aligned: 0.880 Convert atoms to be neutral: 0.520 Process input model: 171.480 Find NCS groups from input model: 4.770 Set up NCS constraints: 0.690 Set refine NCS operators: 0.000 Set scattering table: 0.050 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:13.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 223.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 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 : 0.006 0.142 76092 Z= 0.410 Angle : 0.863 11.815 102648 Z= 0.494 Chirality : 0.057 0.370 11400 Planarity : 0.006 0.056 13440 Dihedral : 14.136 87.130 28296 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 0.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer Outliers : 1.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: -0.40 (0.08), residues: 9600 helix: -0.14 (0.09), residues: 2868 sheet: 0.82 (0.15), residues: 996 loop : -0.48 (0.08), residues: 5736 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1297 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 1189 time to evaluate : 6.906 Fit side-chains outliers start: 108 outliers final: 10 residues processed: 1216 average time/residue: 1.8424 time to fit residues: 2859.3574 Evaluate side-chains 896 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 886 time to evaluate : 6.812 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 10 residues processed: 0 time to fit residues: 9.1831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 800 optimal weight: 7.9990 chunk 718 optimal weight: 0.9990 chunk 398 optimal weight: 2.9990 chunk 245 optimal weight: 7.9990 chunk 484 optimal weight: 7.9990 chunk 383 optimal weight: 0.0870 chunk 743 optimal weight: 0.0970 chunk 287 optimal weight: 9.9990 chunk 451 optimal weight: 5.9990 chunk 553 optimal weight: 7.9990 chunk 860 optimal weight: 2.9990 overall best weight: 1.4362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS A 208 ASN B 322 HIS C 97 HIS E 97 HIS G 97 HIS I 97 HIS K 42 HIS K 97 HIS M 97 HIS O 42 HIS O 208 ASN Q 208 ASN S 97 HIS U 97 HIS W 42 HIS W 97 HIS J 544 HIS D 34 HIS D 233 HIS D 314 HIS D 322 HIS D 512 GLN F 322 HIS H 322 HIS H 544 HIS H 558 ASN L 314 HIS L 322 HIS L 544 HIS N 322 HIS N 544 HIS P 322 HIS P 544 HIS R 233 HIS R 314 HIS T 34 HIS T 314 HIS V 34 HIS X 322 HIS X 544 HIS Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 76092 Z= 0.146 Angle : 0.550 8.561 102648 Z= 0.305 Chirality : 0.046 0.251 11400 Planarity : 0.005 0.053 13440 Dihedral : 5.707 61.172 10380 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.08 (0.08), residues: 9600 helix: 0.67 (0.09), residues: 3012 sheet: 1.08 (0.16), residues: 900 loop : -0.42 (0.08), residues: 5688 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 975 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 926 time to evaluate : 6.950 Fit side-chains outliers start: 49 outliers final: 19 residues processed: 956 average time/residue: 1.8166 time to fit residues: 2232.0147 Evaluate side-chains 902 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 883 time to evaluate : 7.028 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 18 residues processed: 1 average time/residue: 0.6956 time to fit residues: 10.6374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 478 optimal weight: 10.0000 chunk 267 optimal weight: 1.9990 chunk 716 optimal weight: 10.0000 chunk 586 optimal weight: 9.9990 chunk 237 optimal weight: 10.0000 chunk 862 optimal weight: 6.9990 chunk 931 optimal weight: 0.9980 chunk 768 optimal weight: 9.9990 chunk 855 optimal weight: 0.0000 chunk 294 optimal weight: 5.9990 chunk 691 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN B 34 HIS B 558 ASN C 97 HIS C 208 ASN E 97 HIS I 97 HIS M 42 HIS M 97 HIS O 208 ASN U 97 HIS J 544 HIS D 34 HIS D 314 HIS H 512 GLN H 535 HIS H 558 ASN L 314 HIS P 544 HIS R 314 HIS T 34 HIS T 314 HIS V 34 HIS V 512 GLN X 34 HIS X 544 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 76092 Z= 0.212 Angle : 0.648 8.883 102648 Z= 0.361 Chirality : 0.050 0.262 11400 Planarity : 0.005 0.050 13440 Dihedral : 6.015 65.563 10380 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.10 (0.08), residues: 9600 helix: 0.79 (0.09), residues: 3036 sheet: 0.96 (0.16), residues: 900 loop : -0.46 (0.08), residues: 5664 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 960 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 894 time to evaluate : 6.936 Fit side-chains outliers start: 66 outliers final: 30 residues processed: 930 average time/residue: 1.8533 time to fit residues: 2198.8233 Evaluate side-chains 905 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 875 time to evaluate : 6.935 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 24 residues processed: 6 average time/residue: 0.9346 time to fit residues: 17.7443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 852 optimal weight: 0.8980 chunk 648 optimal weight: 9.9990 chunk 447 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 411 optimal weight: 3.9990 chunk 579 optimal weight: 4.9990 chunk 865 optimal weight: 0.9980 chunk 916 optimal weight: 1.9990 chunk 452 optimal weight: 10.0000 chunk 820 optimal weight: 5.9990 chunk 246 optimal weight: 5.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS A 208 ASN B 34 HIS B 558 ASN C 97 HIS C 208 ASN E 97 HIS G 97 HIS I 97 HIS M 97 HIS O 208 ASN J 544 HIS D 34 HIS D 314 HIS H 535 HIS L 314 HIS P 544 HIS R 314 HIS T 34 HIS T 314 HIS V 34 HIS X 34 HIS X 544 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 76092 Z= 0.192 Angle : 0.616 8.600 102648 Z= 0.343 Chirality : 0.049 0.262 11400 Planarity : 0.005 0.050 13440 Dihedral : 5.946 66.392 10380 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.18 (0.08), residues: 9600 helix: 0.95 (0.09), residues: 3024 sheet: 0.92 (0.16), residues: 900 loop : -0.45 (0.08), residues: 5676 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 946 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 883 time to evaluate : 6.907 Fit side-chains revert: symmetry clash outliers start: 63 outliers final: 38 residues processed: 929 average time/residue: 1.8404 time to fit residues: 2193.1093 Evaluate side-chains 912 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 874 time to evaluate : 6.770 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 32 residues processed: 6 average time/residue: 1.0522 time to fit residues: 18.5534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 763 optimal weight: 10.0000 chunk 520 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 682 optimal weight: 0.6980 chunk 378 optimal weight: 2.9990 chunk 781 optimal weight: 0.9990 chunk 633 optimal weight: 0.0770 chunk 1 optimal weight: 7.9990 chunk 467 optimal weight: 4.9990 chunk 822 optimal weight: 0.9980 chunk 231 optimal weight: 0.9980 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS A 208 ASN B 34 HIS B 558 ASN C 97 HIS C 208 ASN E 97 HIS G 97 HIS I 97 HIS M 79 HIS M 97 HIS O 208 ASN J 544 HIS D 34 HIS D 314 HIS H 535 HIS L 314 HIS L 544 HIS N 512 GLN P 512 GLN P 544 HIS R 314 HIS T 34 HIS T 314 HIS T 512 GLN V 34 HIS X 34 HIS X 544 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 76092 Z= 0.118 Angle : 0.487 8.213 102648 Z= 0.268 Chirality : 0.045 0.239 11400 Planarity : 0.004 0.052 13440 Dihedral : 5.389 63.348 10380 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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 (0.08), residues: 9600 helix: 1.35 (0.10), residues: 3012 sheet: 0.88 (0.15), residues: 1020 loop : -0.37 (0.08), residues: 5568 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 965 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 908 time to evaluate : 7.029 Fit side-chains outliers start: 57 outliers final: 39 residues processed: 954 average time/residue: 1.8440 time to fit residues: 2278.6442 Evaluate side-chains 909 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 870 time to evaluate : 6.865 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 38 residues processed: 1 average time/residue: 0.5435 time to fit residues: 10.1846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 308 optimal weight: 0.0570 chunk 825 optimal weight: 8.9990 chunk 181 optimal weight: 0.7980 chunk 538 optimal weight: 7.9990 chunk 226 optimal weight: 0.6980 chunk 917 optimal weight: 10.0000 chunk 761 optimal weight: 0.9980 chunk 424 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 303 optimal weight: 2.9990 chunk 481 optimal weight: 9.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS A 208 ASN B 34 HIS B 558 ASN C 97 HIS C 208 ASN E 97 HIS G 97 HIS I 97 HIS K 208 ASN M 79 HIS M 97 HIS O 208 ASN J 544 HIS D 34 HIS D 314 HIS D 496 GLN F 314 HIS H 535 HIS L 314 HIS L 544 HIS N 496 GLN P 544 HIS R 314 HIS T 34 HIS T 314 HIS V 34 HIS X 34 HIS X 544 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 76092 Z= 0.112 Angle : 0.471 8.135 102648 Z= 0.258 Chirality : 0.044 0.233 11400 Planarity : 0.004 0.052 13440 Dihedral : 5.137 60.169 10380 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.61 (0.09), residues: 9600 helix: 1.52 (0.10), residues: 3012 sheet: 0.92 (0.15), residues: 1020 loop : -0.28 (0.08), residues: 5568 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 954 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 902 time to evaluate : 7.048 Fit side-chains outliers start: 52 outliers final: 38 residues processed: 945 average time/residue: 1.8522 time to fit residues: 2253.9937 Evaluate side-chains 916 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 878 time to evaluate : 6.940 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 36 residues processed: 2 average time/residue: 0.5375 time to fit residues: 11.2886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 884 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 522 optimal weight: 6.9990 chunk 669 optimal weight: 6.9990 chunk 518 optimal weight: 5.9990 chunk 772 optimal weight: 2.9990 chunk 512 optimal weight: 3.9990 chunk 913 optimal weight: 4.9990 chunk 571 optimal weight: 5.9990 chunk 557 optimal weight: 0.9980 chunk 421 optimal weight: 20.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN B 34 HIS B 558 ASN C 79 HIS C 97 HIS C 208 ASN E 97 HIS I 97 HIS K 208 ASN M 97 HIS O 208 ASN J 544 HIS D 34 HIS D 314 HIS F 314 HIS H 535 HIS L 34 HIS L 314 HIS P 544 HIS R 314 HIS T 34 HIS T 314 HIS V 34 HIS X 34 HIS X 544 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 76092 Z= 0.236 Angle : 0.670 9.261 102648 Z= 0.373 Chirality : 0.051 0.260 11400 Planarity : 0.005 0.048 13440 Dihedral : 5.944 64.596 10380 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.25 (0.08), residues: 9600 helix: 1.07 (0.09), residues: 3012 sheet: 0.60 (0.16), residues: 960 loop : -0.38 (0.08), residues: 5628 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 956 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 890 time to evaluate : 7.259 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 40 residues processed: 936 average time/residue: 1.8682 time to fit residues: 2248.5754 Evaluate side-chains 924 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 884 time to evaluate : 7.046 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 36 residues processed: 4 average time/residue: 1.6734 time to fit residues: 18.0538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 565 optimal weight: 4.9990 chunk 364 optimal weight: 0.3980 chunk 545 optimal weight: 8.9990 chunk 275 optimal weight: 9.9990 chunk 179 optimal weight: 10.0000 chunk 177 optimal weight: 9.9990 chunk 580 optimal weight: 8.9990 chunk 622 optimal weight: 7.9990 chunk 451 optimal weight: 2.9990 chunk 85 optimal weight: 9.9990 chunk 718 optimal weight: 0.7980 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN B 34 HIS B 558 ASN C 79 HIS C 97 HIS C 208 ASN E 97 HIS I 97 HIS K 79 HIS M 97 HIS O 208 ASN J 544 HIS D 34 HIS D 314 HIS H 535 HIS L 34 HIS L 314 HIS P 544 HIS R 314 HIS T 34 HIS T 314 HIS V 34 HIS X 34 HIS X 544 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 76092 Z= 0.229 Angle : 0.671 9.175 102648 Z= 0.374 Chirality : 0.050 0.267 11400 Planarity : 0.005 0.049 13440 Dihedral : 6.027 65.629 10380 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.12 (0.08), residues: 9600 helix: 0.96 (0.09), residues: 3024 sheet: 0.51 (0.16), residues: 960 loop : -0.46 (0.08), residues: 5616 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 941 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 884 time to evaluate : 7.376 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 44 residues processed: 924 average time/residue: 1.9213 time to fit residues: 2283.4152 Evaluate side-chains 921 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 877 time to evaluate : 6.996 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 36 residues processed: 8 average time/residue: 1.1378 time to fit residues: 22.9734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 831 optimal weight: 6.9990 chunk 875 optimal weight: 5.9990 chunk 798 optimal weight: 0.5980 chunk 851 optimal weight: 3.9990 chunk 512 optimal weight: 10.0000 chunk 370 optimal weight: 9.9990 chunk 668 optimal weight: 9.9990 chunk 261 optimal weight: 9.9990 chunk 769 optimal weight: 9.9990 chunk 805 optimal weight: 0.9990 chunk 848 optimal weight: 4.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN B 34 HIS B 558 ASN C 79 HIS C 97 HIS C 208 ASN G 208 ASN K 79 HIS M 97 HIS O 208 ASN J 544 HIS D 34 HIS D 314 HIS H 535 HIS L 34 HIS L 314 HIS N 544 HIS P 544 HIS R 314 HIS T 34 HIS T 314 HIS V 34 HIS X 34 HIS X 544 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 76092 Z= 0.224 Angle : 0.663 9.107 102648 Z= 0.369 Chirality : 0.050 0.261 11400 Planarity : 0.005 0.049 13440 Dihedral : 6.032 67.379 10380 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.11 (0.08), residues: 9600 helix: 0.96 (0.09), residues: 3024 sheet: 0.51 (0.16), residues: 960 loop : -0.47 (0.08), residues: 5616 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 928 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 881 time to evaluate : 7.530 Fit side-chains outliers start: 47 outliers final: 37 residues processed: 925 average time/residue: 1.8964 time to fit residues: 2267.8291 Evaluate side-chains 910 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 873 time to evaluate : 6.943 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 37 residues processed: 0 time to fit residues: 9.3557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 559 optimal weight: 8.9990 chunk 900 optimal weight: 0.6980 chunk 549 optimal weight: 9.9990 chunk 427 optimal weight: 5.9990 chunk 625 optimal weight: 2.9990 chunk 944 optimal weight: 8.9990 chunk 869 optimal weight: 20.0000 chunk 752 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 chunk 580 optimal weight: 8.9990 chunk 461 optimal weight: 3.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN B 34 HIS B 558 ASN C 79 HIS C 97 HIS C 208 ASN K 79 HIS M 79 HIS M 97 HIS O 208 ASN J 544 HIS D 34 HIS D 314 HIS H 535 HIS L 34 HIS L 314 HIS N 544 HIS P 544 HIS R 314 HIS T 34 HIS T 314 HIS V 34 HIS X 34 HIS X 544 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 76092 Z= 0.198 Angle : 0.628 8.770 102648 Z= 0.349 Chirality : 0.049 0.257 11400 Planarity : 0.005 0.050 13440 Dihedral : 5.986 69.231 10380 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer Outliers : 0.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.14 (0.08), residues: 9600 helix: 1.01 (0.09), residues: 3024 sheet: 0.52 (0.16), residues: 960 loop : -0.47 (0.08), residues: 5616 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19200 Ramachandran restraints generated. 9600 Oldfield, 0 Emsley, 9600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 923 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 882 time to evaluate : 8.103 Fit side-chains outliers start: 41 outliers final: 39 residues processed: 920 average time/residue: 1.9240 time to fit residues: 2277.3184 Evaluate side-chains 913 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 874 time to evaluate : 7.067 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 38 residues processed: 1 average time/residue: 2.0824 time to fit residues: 12.0095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 597 optimal weight: 10.0000 chunk 801 optimal weight: 9.9990 chunk 230 optimal weight: 8.9990 chunk 693 optimal weight: 10.0000 chunk 111 optimal weight: 0.9990 chunk 208 optimal weight: 9.9990 chunk 753 optimal weight: 6.9990 chunk 315 optimal weight: 0.5980 chunk 773 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 138 optimal weight: 20.0000 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN B 34 HIS B 558 ASN C 79 HIS C 97 HIS C 208 ASN K 79 HIS M 79 HIS M 97 HIS O 208 ASN J 544 HIS D 34 HIS D 314 HIS H 535 HIS L 34 HIS L 314 HIS P 544 HIS R 314 HIS R 528 GLN T 34 HIS T 314 HIS V 34 HIS X 34 HIS X 544 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.126035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.104622 restraints weight = 57982.062| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 0.80 r_work: 0.3027 rms_B_bonded: 1.18 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 1.96 restraints_weight: 0.2500 r_work: 0.2724 rms_B_bonded: 4.91 restraints_weight: 0.1250 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 76092 Z= 0.200 Angle : 0.633 8.832 102648 Z= 0.352 Chirality : 0.049 0.256 11400 Planarity : 0.005 0.049 13440 Dihedral : 5.980 69.696 10380 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.14 (0.08), residues: 9600 helix: 1.01 (0.09), residues: 3024 sheet: 0.52 (0.16), residues: 960 loop : -0.46 (0.08), residues: 5616 =============================================================================== Job complete usr+sys time: 31478.99 seconds wall clock time: 546 minutes 2.04 seconds (32762.04 seconds total)