Starting phenix.real_space_refine on Sun Mar 17 07:05:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zja_11233/03_2024/6zja_11233_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zja_11233/03_2024/6zja_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_11233/03_2024/6zja_11233.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zja_11233/03_2024/6zja_11233.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zja_11233/03_2024/6zja_11233_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zja_11233/03_2024/6zja_11233_updated.pdb" } resolution = 2.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 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. 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: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 31.58, per 1000 atoms: 0.41 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: 24.65 Conformation dependent library (CDL) restraints added in 10.4 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: 12.05 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: 34.01 Time building geometry restraints manager: 26.95 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: 264 69.70 - 87.13: 216 Dihedral angle restraints: 45888 sinusoidal: 18456 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 45885 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 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: 4.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 23.920 Check model and map are aligned: 0.960 Set scattering table: 0.560 Process input model: 170.290 Find NCS groups from input model: 4.570 Set up NCS constraints: 0.630 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:12.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 217.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 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 : 14.309 87.130 28344 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 0.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.37 % Allowed : 4.70 % Favored : 93.93 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.004 TRP J 437 HIS 0.015 0.002 HIS R 248 PHE 0.023 0.003 PHE C 198 TYR 0.020 0.002 TYR S 15 ARG 0.006 0.001 ARG J 401 *********************** 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 : 6.986 Fit side-chains REVERT: A 1 MET cc_start: 0.8499 (mtm) cc_final: 0.8059 (mtm) REVERT: A 208 ASN cc_start: 0.8721 (m-40) cc_final: 0.8515 (m110) REVERT: B 262 MET cc_start: 0.8608 (mmm) cc_final: 0.8293 (mmm) REVERT: B 366 MET cc_start: 0.6843 (ttt) cc_final: 0.6585 (ttt) REVERT: B 527 MET cc_start: 0.9026 (mmp) cc_final: 0.8689 (mmp) REVERT: C 1 MET cc_start: 0.8516 (mtm) cc_final: 0.8294 (mtm) REVERT: C 58 MET cc_start: 0.7805 (mtt) cc_final: 0.7573 (mtp) REVERT: C 71 MET cc_start: 0.8747 (mtp) cc_final: 0.8481 (mtp) REVERT: G 1 MET cc_start: 0.8501 (mtm) cc_final: 0.8060 (mtm) REVERT: I 12 MET cc_start: 0.8431 (tmm) cc_final: 0.8221 (tmm) REVERT: I 86 MET cc_start: 0.8177 (ttm) cc_final: 0.7975 (ttp) REVERT: O 26 LYS cc_start: 0.6752 (mtmp) cc_final: 0.6488 (mmtt) REVERT: O 152 ARG cc_start: 0.8162 (ptm-80) cc_final: 0.7926 (ptt180) REVERT: Q 1 MET cc_start: 0.8570 (mtm) cc_final: 0.8297 (mtm) REVERT: U 1 MET cc_start: 0.8372 (mtm) cc_final: 0.8074 (mtm) REVERT: U 58 MET cc_start: 0.7858 (mtt) cc_final: 0.7550 (mtt) REVERT: W 77 MET cc_start: 0.9030 (mtp) cc_final: 0.8713 (mtp) REVERT: J 353 MET cc_start: 0.8613 (mtp) cc_final: 0.8390 (mtm) REVERT: J 366 MET cc_start: 0.6975 (ttt) cc_final: 0.6700 (ttt) REVERT: D 55 MET cc_start: 0.8424 (mtm) cc_final: 0.8120 (mtp) REVERT: D 191 MET cc_start: 0.9096 (tpp) cc_final: 0.8822 (tpp) REVERT: F 338 ARG cc_start: 0.8203 (mmm160) cc_final: 0.7989 (mmm160) REVERT: H 262 MET cc_start: 0.8656 (mmm) cc_final: 0.8397 (mmm) REVERT: H 270 MET cc_start: 0.8726 (tpp) cc_final: 0.8399 (tpp) REVERT: H 391 LYS cc_start: 0.8003 (pttm) cc_final: 0.7764 (pttm) REVERT: H 527 MET cc_start: 0.9099 (mmp) cc_final: 0.8803 (mmp) REVERT: N 182 MET cc_start: 0.9167 (mmm) cc_final: 0.8754 (mmm) REVERT: N 366 MET cc_start: 0.6960 (ttt) cc_final: 0.6578 (ttt) REVERT: N 467 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8605 (pt) REVERT: P 317 MET cc_start: 0.7977 (mtp) cc_final: 0.7642 (mtm) REVERT: R 55 MET cc_start: 0.8445 (mtm) cc_final: 0.8046 (mtp) REVERT: R 191 MET cc_start: 0.9124 (tpp) cc_final: 0.8642 (tpp) REVERT: T 27 ASP cc_start: 0.7379 (t0) cc_final: 0.7137 (t70) REVERT: T 55 MET cc_start: 0.8480 (mtm) cc_final: 0.7992 (mtp) REVERT: V 270 MET cc_start: 0.8723 (tpp) cc_final: 0.8245 (tpp) REVERT: V 478 MET cc_start: 0.9171 (mmp) cc_final: 0.8925 (mmp) outliers start: 108 outliers final: 10 residues processed: 1216 average time/residue: 1.9266 time to fit residues: 2981.2325 Evaluate side-chains 898 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 887 time to evaluate : 7.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 201 THR Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain N residue 467 ILE Chi-restraints excluded: chain P residue 201 THR Chi-restraints excluded: chain P residue 467 ILE Chi-restraints excluded: chain R residue 201 THR Chi-restraints excluded: chain T residue 467 ILE Chi-restraints excluded: chain V residue 201 THR Chi-restraints excluded: chain X residue 201 THR 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: 1.9990 chunk 287 optimal weight: 9.9990 chunk 451 optimal weight: 5.9990 chunk 553 optimal weight: 7.9990 chunk 860 optimal weight: 4.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 512 GLN H 512 GLN H 544 HIS H 558 ASN L 314 HIS L 322 HIS N 544 HIS P 544 HIS R 233 HIS R 314 HIS T 34 HIS T 314 HIS V 34 HIS V 512 GLN X 322 HIS X 544 HIS Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 76092 Z= 0.179 Angle : 0.608 8.752 102648 Z= 0.338 Chirality : 0.048 0.263 11400 Planarity : 0.005 0.052 13440 Dihedral : 6.884 65.523 10442 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.71 % Allowed : 7.56 % Favored : 91.73 % 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: 0.02 (0.08), residues: 9600 helix: 0.62 (0.09), residues: 3012 sheet: 1.01 (0.16), residues: 900 loop : -0.45 (0.08), residues: 5688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP F 437 HIS 0.012 0.001 HIS D 34 PHE 0.022 0.002 PHE C 198 TYR 0.021 0.002 TYR S 15 ARG 0.005 0.001 ARG S 21 *********************** 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 961 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 905 time to evaluate : 7.085 Fit side-chains REVERT: A 208 ASN cc_start: 0.8685 (m-40) cc_final: 0.8481 (m110) REVERT: B 262 MET cc_start: 0.8603 (mmm) cc_final: 0.8243 (mmm) REVERT: B 366 MET cc_start: 0.6813 (ttt) cc_final: 0.6601 (ttt) REVERT: B 501 LYS cc_start: 0.7844 (OUTLIER) cc_final: 0.7512 (mptt) REVERT: C 208 ASN cc_start: 0.8640 (m-40) cc_final: 0.8434 (m-40) REVERT: G 1 MET cc_start: 0.8712 (mtm) cc_final: 0.8249 (mtm) REVERT: U 152 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.8009 (ptt180) REVERT: J 317 MET cc_start: 0.8047 (mtp) cc_final: 0.7624 (mtp) REVERT: J 353 MET cc_start: 0.8651 (mtp) cc_final: 0.8447 (mtm) REVERT: J 366 MET cc_start: 0.7005 (ttt) cc_final: 0.6606 (ttt) REVERT: J 537 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6933 (mp0) REVERT: D 55 MET cc_start: 0.8259 (mtm) cc_final: 0.7974 (mtp) REVERT: D 338 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7216 (mmm-85) REVERT: F 338 ARG cc_start: 0.8113 (mmm160) cc_final: 0.7906 (mmm160) REVERT: F 541 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6632 (mt-10) REVERT: F 551 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7292 (tt0) REVERT: H 270 MET cc_start: 0.8787 (tpp) cc_final: 0.8372 (tpp) REVERT: H 391 LYS cc_start: 0.8058 (pttm) cc_final: 0.7752 (pttm) REVERT: N 182 MET cc_start: 0.9078 (mmm) cc_final: 0.8776 (mmm) REVERT: N 366 MET cc_start: 0.6967 (ttt) cc_final: 0.6636 (ttt) REVERT: N 467 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8400 (pt) REVERT: N 551 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7248 (tt0) REVERT: R 191 MET cc_start: 0.9017 (tpp) cc_final: 0.8579 (tpp) REVERT: T 27 ASP cc_start: 0.7418 (t0) cc_final: 0.7142 (t70) REVERT: T 55 MET cc_start: 0.8230 (mtm) cc_final: 0.7786 (mtp) REVERT: T 501 LYS cc_start: 0.7862 (mttp) cc_final: 0.7659 (mptt) REVERT: T 551 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7272 (tt0) REVERT: V 270 MET cc_start: 0.8753 (tpp) cc_final: 0.8246 (tpp) REVERT: V 478 MET cc_start: 0.8946 (mmp) cc_final: 0.8333 (mmp) REVERT: V 551 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7437 (tt0) REVERT: X 8 GLU cc_start: 0.7092 (pt0) cc_final: 0.6891 (tt0) REVERT: X 551 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7310 (tt0) outliers start: 56 outliers final: 20 residues processed: 939 average time/residue: 1.9417 time to fit residues: 2314.9007 Evaluate side-chains 896 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 865 time to evaluate : 6.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 501 LYS Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain O residue 125 LYS Chi-restraints excluded: chain U residue 152 ARG Chi-restraints excluded: chain W residue 105 LYS Chi-restraints excluded: chain J residue 201 THR Chi-restraints excluded: chain J residue 537 GLU Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 338 ARG Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 541 GLU Chi-restraints excluded: chain F residue 551 GLU Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain N residue 467 ILE Chi-restraints excluded: chain N residue 551 GLU Chi-restraints excluded: chain P residue 201 THR Chi-restraints excluded: chain R residue 201 THR Chi-restraints excluded: chain T residue 467 ILE Chi-restraints excluded: chain T residue 551 GLU Chi-restraints excluded: chain V residue 2 LYS Chi-restraints excluded: chain V residue 201 THR Chi-restraints excluded: chain V residue 467 ILE Chi-restraints excluded: chain V residue 551 GLU Chi-restraints excluded: chain X residue 201 THR Chi-restraints excluded: chain X residue 467 ILE Chi-restraints excluded: chain X residue 551 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 478 optimal weight: 20.0000 chunk 267 optimal weight: 10.0000 chunk 716 optimal weight: 6.9990 chunk 586 optimal weight: 0.5980 chunk 237 optimal weight: 9.9990 chunk 862 optimal weight: 2.9990 chunk 931 optimal weight: 9.9990 chunk 768 optimal weight: 0.9990 chunk 855 optimal weight: 0.9990 chunk 294 optimal weight: 7.9990 chunk 691 optimal weight: 5.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS B 34 HIS B 558 ASN C 97 HIS E 97 HIS G 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 535 HIS H 558 ASN 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: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1573 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= 0.181 Angle : 0.604 8.544 102648 Z= 0.337 Chirality : 0.048 0.256 11400 Planarity : 0.005 0.051 13440 Dihedral : 6.840 68.182 10440 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.87 % Allowed : 7.97 % Favored : 91.16 % 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: 0.16 (0.08), residues: 9600 helix: 0.87 (0.09), residues: 3024 sheet: 0.99 (0.16), residues: 900 loop : -0.44 (0.08), residues: 5676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP F 437 HIS 0.012 0.001 HIS D 34 PHE 0.023 0.002 PHE G 198 TYR 0.020 0.002 TYR I 15 ARG 0.007 0.000 ARG Q 21 *********************** 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 957 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 888 time to evaluate : 7.102 Fit side-chains REVERT: A 71 MET cc_start: 0.8850 (mtp) cc_final: 0.8556 (mtp) REVERT: B 262 MET cc_start: 0.8570 (mmm) cc_final: 0.8272 (mmm) REVERT: B 501 LYS cc_start: 0.7869 (OUTLIER) cc_final: 0.7565 (mptt) REVERT: C 208 ASN cc_start: 0.8668 (m-40) cc_final: 0.8437 (m-40) REVERT: G 1 MET cc_start: 0.8723 (mtm) cc_final: 0.8224 (mtm) REVERT: Q 152 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7971 (ptt-90) REVERT: U 152 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7965 (ptt-90) REVERT: J 317 MET cc_start: 0.8003 (mtp) cc_final: 0.7738 (mtp) REVERT: J 353 MET cc_start: 0.8666 (mtp) cc_final: 0.8465 (mtm) REVERT: J 366 MET cc_start: 0.7008 (ttt) cc_final: 0.6757 (ttt) REVERT: D 55 MET cc_start: 0.8236 (mtm) cc_final: 0.7936 (mtp) REVERT: D 338 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7114 (mmm-85) REVERT: F 338 ARG cc_start: 0.8077 (mmm160) cc_final: 0.7875 (mmm160) REVERT: F 551 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7295 (tt0) REVERT: H 270 MET cc_start: 0.8790 (tpp) cc_final: 0.8521 (tpp) REVERT: H 391 LYS cc_start: 0.8065 (pttm) cc_final: 0.7755 (pttm) REVERT: H 501 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7429 (mptt) REVERT: N 182 MET cc_start: 0.9067 (mmm) cc_final: 0.8786 (mmm) REVERT: N 366 MET cc_start: 0.6979 (ttt) cc_final: 0.6629 (ttt) REVERT: N 467 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8394 (pt) REVERT: N 551 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7258 (tt0) REVERT: T 55 MET cc_start: 0.8211 (mtm) cc_final: 0.7783 (mtp) REVERT: T 551 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7268 (tt0) REVERT: V 270 MET cc_start: 0.8754 (tpp) cc_final: 0.8215 (tpp) REVERT: V 322 HIS cc_start: 0.8032 (m-70) cc_final: 0.7816 (m90) REVERT: V 478 MET cc_start: 0.8985 (mmp) cc_final: 0.8423 (mmp) REVERT: X 551 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7250 (tt0) outliers start: 69 outliers final: 28 residues processed: 925 average time/residue: 1.9496 time to fit residues: 2293.1268 Evaluate side-chains 910 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 872 time to evaluate : 6.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 501 LYS Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain O residue 125 LYS Chi-restraints excluded: chain Q residue 128 SER Chi-restraints excluded: chain Q residue 152 ARG Chi-restraints excluded: chain S residue 170 SER Chi-restraints excluded: chain U residue 128 SER Chi-restraints excluded: chain U residue 152 ARG Chi-restraints excluded: chain J residue 201 THR Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 338 ARG Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 551 GLU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 501 LYS Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain N residue 467 ILE Chi-restraints excluded: chain N residue 551 GLU Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain P residue 201 THR Chi-restraints excluded: chain P residue 467 ILE Chi-restraints excluded: chain R residue 201 THR Chi-restraints excluded: chain T residue 37 THR Chi-restraints excluded: chain T residue 467 ILE Chi-restraints excluded: chain T residue 551 GLU Chi-restraints excluded: chain V residue 2 LYS Chi-restraints excluded: chain V residue 201 THR Chi-restraints excluded: chain X residue 201 THR Chi-restraints excluded: chain X residue 467 ILE Chi-restraints excluded: chain X residue 551 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 852 optimal weight: 3.9990 chunk 648 optimal weight: 6.9990 chunk 447 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 411 optimal weight: 3.9990 chunk 579 optimal weight: 4.9990 chunk 865 optimal weight: 9.9990 chunk 916 optimal weight: 1.9990 chunk 452 optimal weight: 2.9990 chunk 820 optimal weight: 7.9990 chunk 246 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 E 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 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: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1604 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= 0.201 Angle : 0.633 8.874 102648 Z= 0.352 Chirality : 0.049 0.263 11400 Planarity : 0.005 0.050 13440 Dihedral : 6.895 68.134 10440 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.02 % Allowed : 8.08 % Favored : 90.90 % 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: 0.15 (0.08), residues: 9600 helix: 0.91 (0.09), residues: 3024 sheet: 0.91 (0.16), residues: 900 loop : -0.45 (0.08), residues: 5676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP F 437 HIS 0.012 0.002 HIS D 34 PHE 0.025 0.002 PHE G 198 TYR 0.022 0.002 TYR Q 15 ARG 0.008 0.001 ARG Q 21 *********************** 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 973 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 892 time to evaluate : 7.105 Fit side-chains REVERT: B 248 HIS cc_start: 0.9069 (OUTLIER) cc_final: 0.8077 (t-170) REVERT: B 262 MET cc_start: 0.8555 (mmm) cc_final: 0.8285 (mmm) REVERT: B 501 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7562 (mptt) REVERT: I 86 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7856 (ttp) REVERT: Q 152 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7982 (ptt-90) REVERT: U 152 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7993 (ptt180) REVERT: J 317 MET cc_start: 0.8037 (mtp) cc_final: 0.7767 (mtp) REVERT: J 366 MET cc_start: 0.7031 (ttt) cc_final: 0.6734 (ttt) REVERT: D 55 MET cc_start: 0.8302 (mtm) cc_final: 0.7998 (mtp) REVERT: D 338 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7119 (mmm-85) REVERT: F 551 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7291 (tt0) REVERT: H 27 ASP cc_start: 0.7478 (OUTLIER) cc_final: 0.7093 (t0) REVERT: H 270 MET cc_start: 0.8792 (tpp) cc_final: 0.8492 (tpp) REVERT: H 391 LYS cc_start: 0.8091 (pttm) cc_final: 0.7808 (pttm) REVERT: H 501 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7682 (mptt) REVERT: L 156 MET cc_start: 0.8913 (mtp) cc_final: 0.8649 (mtp) REVERT: N 182 MET cc_start: 0.9076 (mmm) cc_final: 0.8783 (mmm) REVERT: N 366 MET cc_start: 0.6982 (ttt) cc_final: 0.6622 (ttt) REVERT: N 467 ILE cc_start: 0.8844 (OUTLIER) cc_final: 0.8461 (pt) REVERT: N 551 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7282 (tt0) REVERT: T 27 ASP cc_start: 0.7460 (OUTLIER) cc_final: 0.7135 (t70) REVERT: T 55 MET cc_start: 0.8276 (mtm) cc_final: 0.7821 (mtp) REVERT: T 551 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7277 (tt0) REVERT: V 248 HIS cc_start: 0.8943 (OUTLIER) cc_final: 0.8207 (t-170) REVERT: V 270 MET cc_start: 0.8754 (tpp) cc_final: 0.8244 (tpp) REVERT: V 338 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7675 (mmm160) REVERT: V 478 MET cc_start: 0.8998 (mmp) cc_final: 0.8444 (mmp) REVERT: X 248 HIS cc_start: 0.9181 (OUTLIER) cc_final: 0.8051 (t-170) REVERT: X 551 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7263 (tt0) outliers start: 81 outliers final: 44 residues processed: 943 average time/residue: 1.9841 time to fit residues: 2391.5424 Evaluate side-chains 943 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 882 time to evaluate : 6.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain B residue 248 HIS Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 501 LYS Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain I residue 86 MET Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain O residue 86 MET Chi-restraints excluded: chain O residue 125 LYS Chi-restraints excluded: chain Q residue 128 SER Chi-restraints excluded: chain Q residue 152 ARG Chi-restraints excluded: chain S residue 170 SER Chi-restraints excluded: chain U residue 128 SER Chi-restraints excluded: chain U residue 152 ARG Chi-restraints excluded: chain U residue 170 SER Chi-restraints excluded: chain W residue 22 LYS Chi-restraints excluded: chain J residue 201 THR Chi-restraints excluded: chain J residue 469 THR Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 338 ARG Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain D residue 469 THR Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 551 GLU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 501 LYS Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 469 THR Chi-restraints excluded: chain N residue 467 ILE Chi-restraints excluded: chain N residue 469 THR Chi-restraints excluded: chain N residue 551 GLU Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain P residue 201 THR Chi-restraints excluded: chain P residue 467 ILE Chi-restraints excluded: chain P residue 469 THR Chi-restraints excluded: chain R residue 201 THR Chi-restraints excluded: chain R residue 338 ARG Chi-restraints excluded: chain R residue 469 THR Chi-restraints excluded: chain T residue 27 ASP Chi-restraints excluded: chain T residue 37 THR Chi-restraints excluded: chain T residue 551 GLU Chi-restraints excluded: chain V residue 2 LYS Chi-restraints excluded: chain V residue 201 THR Chi-restraints excluded: chain V residue 248 HIS Chi-restraints excluded: chain V residue 338 ARG Chi-restraints excluded: chain V residue 467 ILE Chi-restraints excluded: chain X residue 201 THR Chi-restraints excluded: chain X residue 248 HIS Chi-restraints excluded: chain X residue 391 LYS Chi-restraints excluded: chain X residue 467 ILE Chi-restraints excluded: chain X residue 469 THR Chi-restraints excluded: chain X residue 551 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 763 optimal weight: 1.9990 chunk 520 optimal weight: 0.9990 chunk 13 optimal weight: 8.9990 chunk 682 optimal weight: 0.8980 chunk 378 optimal weight: 2.9990 chunk 781 optimal weight: 0.5980 chunk 633 optimal weight: 0.0970 chunk 1 optimal weight: 7.9990 chunk 467 optimal weight: 4.9990 chunk 822 optimal weight: 1.9990 chunk 231 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 E 97 HIS G 97 HIS K 79 HIS M 79 HIS M 97 HIS O 208 ASN J 544 HIS D 34 HIS D 314 HIS D 496 GLN H 233 HIS H 535 HIS L 314 HIS N 322 HIS N 496 GLN N 512 GLN N 544 HIS 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: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1833 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= 0.116 Angle : 0.483 8.168 102648 Z= 0.266 Chirality : 0.045 0.239 11400 Planarity : 0.004 0.053 13440 Dihedral : 6.267 67.331 10438 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.48 % Allowed : 8.94 % Favored : 90.58 % 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: 0.87 (0.15), residues: 1020 loop : -0.36 (0.08), residues: 5568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP T 181 HIS 0.010 0.001 HIS X 34 PHE 0.016 0.001 PHE S 198 TYR 0.015 0.001 TYR A 15 ARG 0.005 0.000 ARG C 21 *********************** 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 947 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 909 time to evaluate : 7.157 Fit side-chains REVERT: B 316 ASP cc_start: 0.7936 (t70) cc_final: 0.7677 (t70) REVERT: W 22 LYS cc_start: 0.7850 (mtpt) cc_final: 0.7613 (mtmt) REVERT: J 366 MET cc_start: 0.6937 (ttt) cc_final: 0.6651 (ttt) REVERT: D 55 MET cc_start: 0.8001 (mtm) cc_final: 0.7715 (mtp) REVERT: D 338 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7012 (mmm-85) REVERT: F 551 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7260 (tt0) REVERT: H 27 ASP cc_start: 0.7443 (OUTLIER) cc_final: 0.7075 (t0) REVERT: H 270 MET cc_start: 0.8767 (tpp) cc_final: 0.8397 (tpp) REVERT: H 391 LYS cc_start: 0.8066 (pttm) cc_final: 0.7789 (pttm) REVERT: L 348 ASP cc_start: 0.7873 (m-30) cc_final: 0.7662 (m-30) REVERT: N 366 MET cc_start: 0.6932 (ttt) cc_final: 0.6620 (ttt) REVERT: T 55 MET cc_start: 0.8003 (mtm) cc_final: 0.7608 (mtp) REVERT: T 551 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7234 (tt0) outliers start: 38 outliers final: 20 residues processed: 936 average time/residue: 1.9362 time to fit residues: 2307.1496 Evaluate side-chains 907 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 883 time to evaluate : 6.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain O residue 125 LYS Chi-restraints excluded: chain Q residue 128 SER Chi-restraints excluded: chain U residue 128 SER Chi-restraints excluded: chain D residue 338 ARG Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain F residue 467 ILE Chi-restraints excluded: chain F residue 551 GLU Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 467 ILE Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain N residue 467 ILE Chi-restraints excluded: chain N residue 469 THR Chi-restraints excluded: chain P residue 467 ILE Chi-restraints excluded: chain R residue 469 THR Chi-restraints excluded: chain T residue 467 ILE Chi-restraints excluded: chain T residue 469 THR Chi-restraints excluded: chain T residue 551 GLU Chi-restraints excluded: chain V residue 467 ILE Chi-restraints excluded: chain X residue 467 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 308 optimal weight: 9.9990 chunk 825 optimal weight: 8.9990 chunk 181 optimal weight: 7.9990 chunk 538 optimal weight: 8.9990 chunk 226 optimal weight: 20.0000 chunk 917 optimal weight: 10.0000 chunk 761 optimal weight: 4.9990 chunk 424 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 chunk 303 optimal weight: 2.9990 chunk 481 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 C 224 HIS E 97 HIS G 42 HIS G 208 ASN M 97 HIS O 208 ASN J 544 HIS D 34 HIS D 314 HIS F 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: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 76092 Z= 0.363 Angle : 0.823 10.644 102648 Z= 0.460 Chirality : 0.056 0.281 11400 Planarity : 0.006 0.053 13440 Dihedral : 7.182 71.900 10430 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.05 % Allowed : 8.41 % Favored : 90.54 % 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: 0.06 (0.08), residues: 9600 helix: 0.77 (0.09), residues: 3012 sheet: 0.90 (0.16), residues: 888 loop : -0.47 (0.08), residues: 5700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.005 TRP F 437 HIS 0.013 0.002 HIS F 417 PHE 0.034 0.003 PHE I 198 TYR 0.028 0.003 TYR I 15 ARG 0.009 0.001 ARG Q 21 *********************** 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 970 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 887 time to evaluate : 7.146 Fit side-chains REVERT: G 1 MET cc_start: 0.8588 (mtm) cc_final: 0.8202 (mtm) REVERT: I 86 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.7758 (ttp) REVERT: O 86 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7907 (ttp) REVERT: Q 152 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7996 (ptt-90) REVERT: U 152 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.8029 (ptt180) REVERT: D 55 MET cc_start: 0.8653 (mtm) cc_final: 0.8400 (mtp) REVERT: D 248 HIS cc_start: 0.9189 (OUTLIER) cc_final: 0.8808 (t-170) REVERT: D 338 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7749 (mmm160) REVERT: F 248 HIS cc_start: 0.9153 (OUTLIER) cc_final: 0.8198 (t-170) REVERT: F 551 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7345 (tt0) REVERT: H 27 ASP cc_start: 0.7561 (OUTLIER) cc_final: 0.7126 (t0) REVERT: H 270 MET cc_start: 0.8802 (tpp) cc_final: 0.8453 (tpp) REVERT: H 391 LYS cc_start: 0.8127 (pttm) cc_final: 0.7844 (pttm) REVERT: N 366 MET cc_start: 0.6994 (ttt) cc_final: 0.6643 (ttt) REVERT: N 467 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8636 (pt) REVERT: N 551 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7290 (tt0) REVERT: P 8 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6949 (pt0) REVERT: R 248 HIS cc_start: 0.9170 (OUTLIER) cc_final: 0.8229 (t-170) REVERT: T 27 ASP cc_start: 0.7515 (OUTLIER) cc_final: 0.7157 (t70) REVERT: T 248 HIS cc_start: 0.8920 (OUTLIER) cc_final: 0.8592 (t-170) REVERT: T 551 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7318 (tt0) REVERT: V 248 HIS cc_start: 0.8973 (OUTLIER) cc_final: 0.8522 (t-170) REVERT: V 338 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7522 (mmm160) REVERT: V 551 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7273 (tt0) REVERT: X 248 HIS cc_start: 0.9235 (OUTLIER) cc_final: 0.8272 (t-170) REVERT: X 551 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7287 (tt0) outliers start: 83 outliers final: 39 residues processed: 935 average time/residue: 1.9413 time to fit residues: 2304.4533 Evaluate side-chains 935 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 875 time to evaluate : 7.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain I residue 86 MET Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain O residue 86 MET Chi-restraints excluded: chain Q residue 128 SER Chi-restraints excluded: chain Q residue 152 ARG Chi-restraints excluded: chain S residue 170 SER Chi-restraints excluded: chain U residue 128 SER Chi-restraints excluded: chain U residue 152 ARG Chi-restraints excluded: chain U residue 170 SER Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 248 HIS Chi-restraints excluded: chain D residue 338 ARG Chi-restraints excluded: chain F residue 248 HIS Chi-restraints excluded: chain F residue 551 GLU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 469 THR Chi-restraints excluded: chain N residue 467 ILE Chi-restraints excluded: chain N residue 469 THR Chi-restraints excluded: chain N residue 551 GLU Chi-restraints excluded: chain P residue 8 GLU Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain P residue 201 THR Chi-restraints excluded: chain P residue 288 LYS Chi-restraints excluded: chain P residue 467 ILE Chi-restraints excluded: chain R residue 201 THR Chi-restraints excluded: chain R residue 248 HIS Chi-restraints excluded: chain R residue 338 ARG Chi-restraints excluded: chain R residue 469 THR Chi-restraints excluded: chain T residue 27 ASP Chi-restraints excluded: chain T residue 37 THR Chi-restraints excluded: chain T residue 248 HIS Chi-restraints excluded: chain T residue 469 THR Chi-restraints excluded: chain T residue 551 GLU Chi-restraints excluded: chain V residue 2 LYS Chi-restraints excluded: chain V residue 201 THR Chi-restraints excluded: chain V residue 248 HIS Chi-restraints excluded: chain V residue 338 ARG Chi-restraints excluded: chain V residue 503 ILE Chi-restraints excluded: chain V residue 551 GLU Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain X residue 201 THR Chi-restraints excluded: chain X residue 248 HIS Chi-restraints excluded: chain X residue 391 LYS Chi-restraints excluded: chain X residue 467 ILE Chi-restraints excluded: chain X residue 551 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 884 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 522 optimal weight: 6.9990 chunk 669 optimal weight: 1.9990 chunk 518 optimal weight: 0.5980 chunk 772 optimal weight: 2.9990 chunk 512 optimal weight: 10.0000 chunk 913 optimal weight: 6.9990 chunk 571 optimal weight: 6.9990 chunk 557 optimal weight: 6.9990 chunk 421 optimal weight: 20.0000 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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 79 HIS C 97 HIS C 208 ASN E 97 HIS G 97 HIS M 97 HIS O 208 ASN J 544 HIS D 34 HIS D 314 HIS H 535 HIS H 544 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: 0.8448 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 76092 Z= 0.184 Angle : 0.611 8.536 102648 Z= 0.340 Chirality : 0.048 0.266 11400 Planarity : 0.005 0.050 13440 Dihedral : 6.864 72.334 10430 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.75 % Allowed : 8.86 % Favored : 90.39 % 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: 0.19 (0.08), residues: 9600 helix: 1.00 (0.09), residues: 3024 sheet: 0.86 (0.16), residues: 900 loop : -0.45 (0.08), residues: 5676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP F 437 HIS 0.011 0.001 HIS D 34 PHE 0.023 0.002 PHE I 198 TYR 0.021 0.002 TYR Q 15 ARG 0.008 0.000 ARG Q 21 *********************** 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 952 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 893 time to evaluate : 8.157 Fit side-chains REVERT: G 1 MET cc_start: 0.8590 (mtm) cc_final: 0.8190 (mtm) REVERT: Q 152 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7974 (ptt-90) REVERT: J 366 MET cc_start: 0.7002 (ttt) cc_final: 0.6712 (ttt) REVERT: D 55 MET cc_start: 0.8309 (mtm) cc_final: 0.8015 (mtp) REVERT: D 338 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7110 (mmm-85) REVERT: F 551 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7286 (tt0) REVERT: H 27 ASP cc_start: 0.7508 (OUTLIER) cc_final: 0.7082 (t0) REVERT: H 391 LYS cc_start: 0.8105 (pttm) cc_final: 0.7824 (pttm) REVERT: N 366 MET cc_start: 0.6992 (ttt) cc_final: 0.6625 (ttt) REVERT: N 467 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8419 (pt) REVERT: N 551 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7319 (tt0) REVERT: T 27 ASP cc_start: 0.7468 (OUTLIER) cc_final: 0.7143 (t70) REVERT: T 55 MET cc_start: 0.8278 (mtm) cc_final: 0.7867 (mtp) REVERT: T 551 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7278 (tt0) REVERT: V 338 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7638 (mmm160) REVERT: X 551 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7257 (tt0) outliers start: 59 outliers final: 34 residues processed: 932 average time/residue: 1.9410 time to fit residues: 2298.1905 Evaluate side-chains 923 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 879 time to evaluate : 7.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 469 THR Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain O residue 125 LYS Chi-restraints excluded: chain Q residue 128 SER Chi-restraints excluded: chain Q residue 152 ARG Chi-restraints excluded: chain S residue 170 SER Chi-restraints excluded: chain U residue 128 SER Chi-restraints excluded: chain U residue 170 SER Chi-restraints excluded: chain J residue 469 THR Chi-restraints excluded: chain D residue 338 ARG Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain F residue 551 GLU Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 469 THR Chi-restraints excluded: chain N residue 467 ILE Chi-restraints excluded: chain N residue 469 THR Chi-restraints excluded: chain N residue 551 GLU Chi-restraints excluded: chain P residue 201 THR Chi-restraints excluded: chain P residue 467 ILE Chi-restraints excluded: chain R residue 201 THR Chi-restraints excluded: chain R residue 469 THR Chi-restraints excluded: chain T residue 27 ASP Chi-restraints excluded: chain T residue 467 ILE Chi-restraints excluded: chain T residue 469 THR Chi-restraints excluded: chain T residue 551 GLU Chi-restraints excluded: chain V residue 2 LYS Chi-restraints excluded: chain V residue 322 HIS Chi-restraints excluded: chain V residue 338 ARG Chi-restraints excluded: chain V residue 467 ILE Chi-restraints excluded: chain X residue 467 ILE Chi-restraints excluded: chain X residue 551 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 565 optimal weight: 7.9990 chunk 364 optimal weight: 10.0000 chunk 545 optimal weight: 3.9990 chunk 275 optimal weight: 7.9990 chunk 179 optimal weight: 9.9990 chunk 177 optimal weight: 10.0000 chunk 580 optimal weight: 9.9990 chunk 622 optimal weight: 7.9990 chunk 451 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 718 optimal weight: 0.8980 overall best weight: 5.5788 ------------------------------------------------------------------------------- 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 C 224 HIS E 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 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: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 76092 Z= 0.321 Angle : 0.789 10.241 102648 Z= 0.441 Chirality : 0.055 0.288 11400 Planarity : 0.006 0.051 13440 Dihedral : 7.203 73.166 10430 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.90 % Allowed : 8.78 % Favored : 90.33 % 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: 0.00 (0.08), residues: 9600 helix: 0.74 (0.09), residues: 3012 sheet: 0.85 (0.16), residues: 888 loop : -0.51 (0.08), residues: 5700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.005 TRP F 437 HIS 0.012 0.002 HIS D 34 PHE 0.032 0.003 PHE I 198 TYR 0.026 0.003 TYR Q 15 ARG 0.010 0.001 ARG Q 21 *********************** 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 951 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 880 time to evaluate : 7.181 Fit side-chains REVERT: G 1 MET cc_start: 0.8649 (mtm) cc_final: 0.8240 (mtm) REVERT: I 86 MET cc_start: 0.8074 (OUTLIER) cc_final: 0.7747 (ttp) REVERT: Q 152 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7998 (ptt-90) REVERT: U 152 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.8014 (ptt180) REVERT: J 248 HIS cc_start: 0.9192 (OUTLIER) cc_final: 0.8176 (t-170) REVERT: D 8 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6794 (pt0) REVERT: D 55 MET cc_start: 0.8567 (mtm) cc_final: 0.8284 (mtp) REVERT: D 338 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7175 (mmm-85) REVERT: F 551 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7336 (tt0) REVERT: H 27 ASP cc_start: 0.7569 (OUTLIER) cc_final: 0.7136 (t0) REVERT: H 248 HIS cc_start: 0.9088 (OUTLIER) cc_final: 0.8046 (t-170) REVERT: H 391 LYS cc_start: 0.8142 (pttm) cc_final: 0.7858 (pttm) REVERT: N 366 MET cc_start: 0.7008 (ttt) cc_final: 0.6681 (ttt) REVERT: N 467 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8617 (pt) REVERT: N 551 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7331 (tt0) REVERT: T 27 ASP cc_start: 0.7498 (OUTLIER) cc_final: 0.7141 (t70) REVERT: T 55 MET cc_start: 0.8481 (mtm) cc_final: 0.8145 (mtp) REVERT: T 551 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7310 (tt0) REVERT: V 338 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7680 (mmm160) REVERT: V 551 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7265 (tt0) REVERT: X 551 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7268 (tt0) outliers start: 71 outliers final: 36 residues processed: 925 average time/residue: 2.0217 time to fit residues: 2369.7339 Evaluate side-chains 921 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 869 time to evaluate : 7.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain I residue 86 MET Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain O residue 86 MET Chi-restraints excluded: chain Q residue 128 SER Chi-restraints excluded: chain Q residue 152 ARG Chi-restraints excluded: chain S residue 170 SER Chi-restraints excluded: chain U residue 128 SER Chi-restraints excluded: chain U residue 152 ARG Chi-restraints excluded: chain U residue 170 SER Chi-restraints excluded: chain J residue 201 THR Chi-restraints excluded: chain J residue 248 HIS Chi-restraints excluded: chain J residue 469 THR Chi-restraints excluded: chain J residue 501 LYS Chi-restraints excluded: chain D residue 8 GLU Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 338 ARG Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain F residue 551 GLU Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 248 HIS Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 469 THR Chi-restraints excluded: chain N residue 467 ILE Chi-restraints excluded: chain N residue 469 THR Chi-restraints excluded: chain N residue 551 GLU Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain P residue 201 THR Chi-restraints excluded: chain P residue 288 LYS Chi-restraints excluded: chain P residue 467 ILE Chi-restraints excluded: chain R residue 201 THR Chi-restraints excluded: chain R residue 469 THR Chi-restraints excluded: chain T residue 27 ASP Chi-restraints excluded: chain T residue 37 THR Chi-restraints excluded: chain T residue 469 THR Chi-restraints excluded: chain T residue 551 GLU Chi-restraints excluded: chain V residue 2 LYS Chi-restraints excluded: chain V residue 201 THR Chi-restraints excluded: chain V residue 338 ARG Chi-restraints excluded: chain V residue 551 GLU Chi-restraints excluded: chain X residue 467 ILE Chi-restraints excluded: chain X residue 551 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 831 optimal weight: 0.9990 chunk 875 optimal weight: 6.9990 chunk 798 optimal weight: 0.6980 chunk 851 optimal weight: 10.0000 chunk 512 optimal weight: 9.9990 chunk 370 optimal weight: 9.9990 chunk 668 optimal weight: 7.9990 chunk 261 optimal weight: 6.9990 chunk 769 optimal weight: 9.9990 chunk 805 optimal weight: 4.9990 chunk 848 optimal weight: 10.0000 overall best weight: 4.1388 ------------------------------------------------------------------------------- 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 M 79 HIS M 97 HIS O 208 ASN J 544 HIS D 314 HIS H 535 HIS H 544 HIS L 314 HIS P 544 HIS R 314 HIS T 34 HIS T 314 HIS V 34 HIS X 34 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 76092 Z= 0.260 Angle : 0.709 9.321 102648 Z= 0.396 Chirality : 0.052 0.276 11400 Planarity : 0.005 0.049 13440 Dihedral : 7.125 74.169 10430 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.87 % Allowed : 8.83 % Favored : 90.30 % 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: -0.03 (0.08), residues: 9600 helix: 0.82 (0.09), residues: 3000 sheet: 0.45 (0.16), residues: 960 loop : -0.54 (0.08), residues: 5640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP F 437 HIS 0.012 0.002 HIS H 417 PHE 0.026 0.002 PHE K 198 TYR 0.025 0.002 TYR C 15 ARG 0.010 0.001 ARG Q 21 *********************** 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 952 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 883 time to evaluate : 7.225 Fit side-chains REVERT: B 248 HIS cc_start: 0.9109 (OUTLIER) cc_final: 0.8266 (t-170) REVERT: B 527 MET cc_start: 0.8809 (mmp) cc_final: 0.8532 (mmp) REVERT: G 1 MET cc_start: 0.8641 (mtm) cc_final: 0.8222 (mtm) REVERT: I 86 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.7849 (ttp) REVERT: Q 152 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.7996 (ptt-90) REVERT: U 152 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7999 (ptt180) REVERT: W 86 MET cc_start: 0.8065 (ttp) cc_final: 0.7838 (ttp) REVERT: J 248 HIS cc_start: 0.9168 (OUTLIER) cc_final: 0.8148 (t-170) REVERT: D 55 MET cc_start: 0.8394 (mtm) cc_final: 0.8100 (mtp) REVERT: D 248 HIS cc_start: 0.9175 (OUTLIER) cc_final: 0.8681 (t-170) REVERT: D 338 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7074 (mmm-85) REVERT: F 248 HIS cc_start: 0.9126 (OUTLIER) cc_final: 0.8146 (t-170) REVERT: F 551 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7329 (tt0) REVERT: H 27 ASP cc_start: 0.7524 (OUTLIER) cc_final: 0.7093 (t0) REVERT: H 248 HIS cc_start: 0.9077 (OUTLIER) cc_final: 0.8135 (t-170) REVERT: H 391 LYS cc_start: 0.8142 (pttm) cc_final: 0.7858 (pttm) REVERT: N 366 MET cc_start: 0.6994 (ttt) cc_final: 0.6643 (ttt) REVERT: N 467 ILE cc_start: 0.8929 (OUTLIER) cc_final: 0.8551 (pt) REVERT: N 551 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7318 (tt0) REVERT: T 27 ASP cc_start: 0.7495 (OUTLIER) cc_final: 0.7168 (t70) REVERT: T 551 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7303 (tt0) REVERT: V 338 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7644 (mmm160) REVERT: V 551 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7265 (tt0) REVERT: X 248 HIS cc_start: 0.9214 (OUTLIER) cc_final: 0.8189 (t-170) REVERT: X 551 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7277 (tt0) outliers start: 69 outliers final: 40 residues processed: 931 average time/residue: 1.9511 time to fit residues: 2306.6676 Evaluate side-chains 933 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 874 time to evaluate : 6.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain B residue 248 HIS Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain I residue 86 MET Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain Q residue 128 SER Chi-restraints excluded: chain Q residue 152 ARG Chi-restraints excluded: chain S residue 170 SER Chi-restraints excluded: chain U residue 128 SER Chi-restraints excluded: chain U residue 152 ARG Chi-restraints excluded: chain U residue 170 SER Chi-restraints excluded: chain J residue 201 THR Chi-restraints excluded: chain J residue 248 HIS Chi-restraints excluded: chain J residue 469 THR Chi-restraints excluded: chain J residue 501 LYS Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 248 HIS Chi-restraints excluded: chain D residue 338 ARG Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 248 HIS Chi-restraints excluded: chain F residue 551 GLU Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 248 HIS Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 469 THR Chi-restraints excluded: chain N residue 467 ILE Chi-restraints excluded: chain N residue 469 THR Chi-restraints excluded: chain N residue 551 GLU Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain P residue 201 THR Chi-restraints excluded: chain P residue 467 ILE Chi-restraints excluded: chain R residue 201 THR Chi-restraints excluded: chain R residue 469 THR Chi-restraints excluded: chain T residue 27 ASP Chi-restraints excluded: chain T residue 37 THR Chi-restraints excluded: chain T residue 469 THR Chi-restraints excluded: chain T residue 551 GLU Chi-restraints excluded: chain V residue 2 LYS Chi-restraints excluded: chain V residue 201 THR Chi-restraints excluded: chain V residue 338 ARG Chi-restraints excluded: chain V residue 503 ILE Chi-restraints excluded: chain V residue 551 GLU Chi-restraints excluded: chain X residue 201 THR Chi-restraints excluded: chain X residue 248 HIS Chi-restraints excluded: chain X residue 467 ILE Chi-restraints excluded: chain X residue 469 THR Chi-restraints excluded: chain X residue 551 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 559 optimal weight: 10.0000 chunk 900 optimal weight: 10.0000 chunk 549 optimal weight: 0.6980 chunk 427 optimal weight: 4.9990 chunk 625 optimal weight: 1.9990 chunk 944 optimal weight: 1.9990 chunk 869 optimal weight: 20.0000 chunk 752 optimal weight: 9.9990 chunk 78 optimal weight: 8.9990 chunk 580 optimal weight: 9.9990 chunk 461 optimal weight: 5.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- 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 224 HIS G 97 HIS K 79 HIS M 79 HIS M 97 HIS O 208 ASN J 544 HIS D 314 HIS H 535 HIS H 544 HIS L 314 HIS P 544 HIS R 314 HIS T 34 HIS T 314 HIS V 34 HIS X 34 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1695 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= 0.219 Angle : 0.661 9.039 102648 Z= 0.368 Chirality : 0.050 0.266 11400 Planarity : 0.005 0.049 13440 Dihedral : 7.023 74.671 10430 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.78 % Allowed : 9.00 % Favored : 90.21 % 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: 0.06 (0.08), residues: 9600 helix: 0.95 (0.09), residues: 2952 sheet: 0.49 (0.16), residues: 960 loop : -0.51 (0.08), residues: 5688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.004 TRP F 437 HIS 0.011 0.002 HIS X 34 PHE 0.025 0.002 PHE G 198 TYR 0.023 0.002 TYR Q 15 ARG 0.009 0.001 ARG Q 21 ********************** 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 945 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 883 time to evaluate : 7.101 Fit side-chains REVERT: B 248 HIS cc_start: 0.9106 (OUTLIER) cc_final: 0.8237 (t-170) REVERT: B 527 MET cc_start: 0.8881 (mmp) cc_final: 0.8614 (mmp) REVERT: G 1 MET cc_start: 0.8636 (mtm) cc_final: 0.8215 (mtm) REVERT: I 86 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.7801 (ttp) REVERT: Q 152 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.8000 (ptt-90) REVERT: U 152 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7993 (ptt-90) REVERT: D 55 MET cc_start: 0.8319 (mtm) cc_final: 0.8019 (mtp) REVERT: D 248 HIS cc_start: 0.9151 (OUTLIER) cc_final: 0.8648 (t-170) REVERT: D 338 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7169 (mmm-85) REVERT: F 248 HIS cc_start: 0.9110 (OUTLIER) cc_final: 0.8119 (t-170) REVERT: F 551 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7310 (tt0) REVERT: H 27 ASP cc_start: 0.7536 (OUTLIER) cc_final: 0.7109 (t0) REVERT: H 248 HIS cc_start: 0.9070 (OUTLIER) cc_final: 0.8091 (t-170) REVERT: H 391 LYS cc_start: 0.8134 (pttm) cc_final: 0.7852 (pttm) REVERT: N 366 MET cc_start: 0.7001 (ttt) cc_final: 0.6661 (ttt) REVERT: N 467 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8467 (pt) REVERT: N 551 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7312 (tt0) REVERT: T 27 ASP cc_start: 0.7470 (OUTLIER) cc_final: 0.7140 (t70) REVERT: T 55 MET cc_start: 0.8312 (mtm) cc_final: 0.7863 (mtp) REVERT: T 551 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7295 (tt0) REVERT: V 248 HIS cc_start: 0.8933 (OUTLIER) cc_final: 0.8279 (t-170) REVERT: V 338 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7622 (mmm160) REVERT: X 248 HIS cc_start: 0.9175 (OUTLIER) cc_final: 0.8053 (t-170) REVERT: X 551 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7235 (tt0) outliers start: 62 outliers final: 40 residues processed: 927 average time/residue: 1.9363 time to fit residues: 2280.0085 Evaluate side-chains 938 residues out of total 7908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 880 time to evaluate : 6.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain B residue 248 HIS Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 567 SER Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain G residue 128 SER Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain I residue 86 MET Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 170 SER Chi-restraints excluded: chain M residue 89 ASP Chi-restraints excluded: chain O residue 125 LYS Chi-restraints excluded: chain Q residue 128 SER Chi-restraints excluded: chain Q residue 152 ARG Chi-restraints excluded: chain S residue 170 SER Chi-restraints excluded: chain U residue 128 SER Chi-restraints excluded: chain U residue 152 ARG Chi-restraints excluded: chain U residue 170 SER Chi-restraints excluded: chain J residue 201 THR Chi-restraints excluded: chain J residue 469 THR Chi-restraints excluded: chain J residue 501 LYS Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 248 HIS Chi-restraints excluded: chain D residue 338 ARG Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 248 HIS Chi-restraints excluded: chain F residue 551 GLU Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 248 HIS Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain N residue 467 ILE Chi-restraints excluded: chain N residue 469 THR Chi-restraints excluded: chain N residue 551 GLU Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain P residue 201 THR Chi-restraints excluded: chain P residue 467 ILE Chi-restraints excluded: chain R residue 201 THR Chi-restraints excluded: chain T residue 27 ASP Chi-restraints excluded: chain T residue 37 THR Chi-restraints excluded: chain T residue 469 THR Chi-restraints excluded: chain T residue 551 GLU Chi-restraints excluded: chain V residue 2 LYS Chi-restraints excluded: chain V residue 201 THR Chi-restraints excluded: chain V residue 248 HIS Chi-restraints excluded: chain V residue 338 ARG Chi-restraints excluded: chain V residue 467 ILE Chi-restraints excluded: chain V residue 503 ILE Chi-restraints excluded: chain X residue 201 THR Chi-restraints excluded: chain X residue 248 HIS Chi-restraints excluded: chain X residue 467 ILE Chi-restraints excluded: chain X residue 469 THR Chi-restraints excluded: chain X residue 551 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 597 optimal weight: 2.9990 chunk 801 optimal weight: 10.0000 chunk 230 optimal weight: 8.9990 chunk 693 optimal weight: 3.9990 chunk 111 optimal weight: 20.0000 chunk 208 optimal weight: 10.0000 chunk 753 optimal weight: 6.9990 chunk 315 optimal weight: 0.0770 chunk 773 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 138 optimal weight: 20.0000 overall best weight: 2.6146 ------------------------------------------------------------------------------- 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 224 HIS G 97 HIS K 79 HIS M 79 HIS M 97 HIS O 208 ASN J 544 HIS D 314 HIS H 535 HIS H 544 HIS L 314 HIS P 544 HIS R 314 HIS T 34 HIS T 314 HIS V 34 HIS X 34 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.125942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.104495 restraints weight = 57779.363| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 0.80 r_work: 0.3025 rms_B_bonded: 1.18 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 1.96 restraints_weight: 0.2500 r_work: 0.2721 rms_B_bonded: 4.92 restraints_weight: 0.1250 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 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 0.035 76092 Z= 0.199 Angle : 0.637 8.940 102648 Z= 0.354 Chirality : 0.049 0.265 11400 Planarity : 0.005 0.049 13440 Dihedral : 6.960 74.890 10430 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.78 % Allowed : 9.02 % Favored : 90.20 % 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: 0.09 (0.08), residues: 9600 helix: 1.00 (0.09), residues: 2952 sheet: 0.51 (0.16), residues: 960 loop : -0.50 (0.08), residues: 5688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP F 437 HIS 0.011 0.001 HIS X 34 PHE 0.024 0.002 PHE G 198 TYR 0.022 0.002 TYR Q 15 ARG 0.009 0.000 ARG Q 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 32891.02 seconds wall clock time: 571 minutes 20.04 seconds (34280.04 seconds total)