Starting phenix.real_space_refine (version: dev) on Thu Dec 22 04:02:49 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bgl_7097/12_2022/6bgl_7097_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bgl_7097/12_2022/6bgl_7097.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bgl_7097/12_2022/6bgl_7097.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bgl_7097/12_2022/6bgl_7097.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bgl_7097/12_2022/6bgl_7097_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bgl_7097/12_2022/6bgl_7097_neut.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 144": "OD1" <-> "OD2" Residue "C TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 144": "OD1" <-> "OD2" Residue "D TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 144": "OD1" <-> "OD2" Residue "E TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 144": "OD1" <-> "OD2" Residue "F TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 144": "OD1" <-> "OD2" Residue "G TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 144": "OD1" <-> "OD2" Residue "H TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 144": "OD1" <-> "OD2" Residue "I TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 144": "OD1" <-> "OD2" Residue "J TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 144": "OD1" <-> "OD2" Residue "K TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 144": "OD1" <-> "OD2" Residue "L TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 144": "OD1" <-> "OD2" Residue "M TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 144": "OD1" <-> "OD2" Residue "N TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 144": "OD1" <-> "OD2" Residue "O TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 144": "OD1" <-> "OD2" Residue "P TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 433": "OE1" <-> "OE2" Residue "P GLU 434": "OE1" <-> "OE2" Residue "P TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 488": "NH1" <-> "NH2" Residue "P GLU 512": "OE1" <-> "OE2" Residue "Q TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 433": "OE1" <-> "OE2" Residue "Q GLU 434": "OE1" <-> "OE2" Residue "Q TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 488": "NH1" <-> "NH2" Residue "Q GLU 512": "OE1" <-> "OE2" Residue "R TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 433": "OE1" <-> "OE2" Residue "R GLU 434": "OE1" <-> "OE2" Residue "R TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 488": "NH1" <-> "NH2" Residue "R GLU 512": "OE1" <-> "OE2" Residue "S TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 433": "OE1" <-> "OE2" Residue "S GLU 434": "OE1" <-> "OE2" Residue "S TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 488": "NH1" <-> "NH2" Residue "S GLU 512": "OE1" <-> "OE2" Residue "T TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 433": "OE1" <-> "OE2" Residue "T GLU 434": "OE1" <-> "OE2" Residue "T TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 488": "NH1" <-> "NH2" Residue "T GLU 512": "OE1" <-> "OE2" Residue "U TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 433": "OE1" <-> "OE2" Residue "U GLU 434": "OE1" <-> "OE2" Residue "U TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 488": "NH1" <-> "NH2" Residue "U GLU 512": "OE1" <-> "OE2" Residue "V TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 433": "OE1" <-> "OE2" Residue "V GLU 434": "OE1" <-> "OE2" Residue "V TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 488": "NH1" <-> "NH2" Residue "V GLU 512": "OE1" <-> "OE2" Residue "W TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 433": "OE1" <-> "OE2" Residue "W GLU 434": "OE1" <-> "OE2" Residue "W TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 488": "NH1" <-> "NH2" Residue "W GLU 512": "OE1" <-> "OE2" Residue "X TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 433": "OE1" <-> "OE2" Residue "X GLU 434": "OE1" <-> "OE2" Residue "X TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 488": "NH1" <-> "NH2" Residue "X GLU 512": "OE1" <-> "OE2" Residue "Y TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 433": "OE1" <-> "OE2" Residue "Y GLU 434": "OE1" <-> "OE2" Residue "Y TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 488": "NH1" <-> "NH2" Residue "Y GLU 512": "OE1" <-> "OE2" Residue "Z TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 433": "OE1" <-> "OE2" Residue "Z GLU 434": "OE1" <-> "OE2" Residue "Z TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 488": "NH1" <-> "NH2" Residue "Z GLU 512": "OE1" <-> "OE2" Residue "a TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 433": "OE1" <-> "OE2" Residue "a GLU 434": "OE1" <-> "OE2" Residue "a TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 488": "NH1" <-> "NH2" Residue "a GLU 512": "OE1" <-> "OE2" Residue "b TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 433": "OE1" <-> "OE2" Residue "b GLU 434": "OE1" <-> "OE2" Residue "b TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 488": "NH1" <-> "NH2" Residue "b GLU 512": "OE1" <-> "OE2" Residue "c TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 433": "OE1" <-> "OE2" Residue "c GLU 434": "OE1" <-> "OE2" Residue "c TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 488": "NH1" <-> "NH2" Residue "c GLU 512": "OE1" <-> "OE2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 46618 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Chain: "C" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "D" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "E" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "F" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "G" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "H" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "I" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "J" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "K" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "L" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "M" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "N" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "O" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "P" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "Q" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "R" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "S" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "T" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1636 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "U" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "V" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "W" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "X" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "Y" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "Z" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "a" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "b" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "c" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "d" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Chain: "e" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Chain: "f" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Chain: "g" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Chain: "h" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Chain: "i" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Chain: "j" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Chain: "k" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Chain: "l" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Chain: "m" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Chain: "n" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Chain: "o" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Chain: "p" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Time building chain proxies: 25.75, per 1000 atoms: 0.55 Number of scatterers: 46618 At special positions: 0 Unit cell: (137.34, 139.52, 177.67, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 112 16.00 O 9015 8.00 N 8260 7.00 C 29231 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 19.46 Conformation dependent library (CDL) restraints added in 6.9 seconds 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11200 Finding SS restraints... Secondary structure from input PDB file: 210 helices and 80 sheets defined 46.8% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.19 Creating SS restraints... Processing helix chain 'A' and resid 8 through 26 Processing helix chain 'A' and resid 68 through 89 removed outlier: 3.516A pdb=" N THR A 84 " --> pdb=" O GLN A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 94 Processing helix chain 'A' and resid 95 through 114 Processing helix chain 'A' and resid 159 through 171 removed outlier: 4.611A pdb=" N ILE A 163 " --> pdb=" O THR A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 190 Processing helix chain 'A' and resid 226 through 234 removed outlier: 3.912A pdb=" N LEU A 230 " --> pdb=" O THR A 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 26 Processing helix chain 'C' and resid 68 through 89 removed outlier: 3.516A pdb=" N THR C 84 " --> pdb=" O GLN C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 94 Processing helix chain 'C' and resid 95 through 114 Processing helix chain 'C' and resid 159 through 171 removed outlier: 4.610A pdb=" N ILE C 163 " --> pdb=" O THR C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 190 Processing helix chain 'C' and resid 226 through 234 removed outlier: 3.911A pdb=" N LEU C 230 " --> pdb=" O THR C 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 26 Processing helix chain 'D' and resid 68 through 89 removed outlier: 3.516A pdb=" N THR D 84 " --> pdb=" O GLN D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 94 Processing helix chain 'D' and resid 95 through 114 Processing helix chain 'D' and resid 159 through 171 removed outlier: 4.611A pdb=" N ILE D 163 " --> pdb=" O THR D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 190 Processing helix chain 'D' and resid 226 through 234 removed outlier: 3.911A pdb=" N LEU D 230 " --> pdb=" O THR D 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 26 Processing helix chain 'E' and resid 67 through 89 removed outlier: 3.515A pdb=" N THR E 84 " --> pdb=" O GLN E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 94 Processing helix chain 'E' and resid 95 through 114 Processing helix chain 'E' and resid 159 through 171 removed outlier: 4.610A pdb=" N ILE E 163 " --> pdb=" O THR E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 190 Processing helix chain 'E' and resid 226 through 234 removed outlier: 3.911A pdb=" N LEU E 230 " --> pdb=" O THR E 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 26 Processing helix chain 'F' and resid 68 through 89 removed outlier: 3.516A pdb=" N THR F 84 " --> pdb=" O GLN F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 94 Processing helix chain 'F' and resid 95 through 114 Processing helix chain 'F' and resid 159 through 171 removed outlier: 4.611A pdb=" N ILE F 163 " --> pdb=" O THR F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 190 Processing helix chain 'F' and resid 226 through 234 removed outlier: 3.912A pdb=" N LEU F 230 " --> pdb=" O THR F 226 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 26 Processing helix chain 'G' and resid 68 through 89 removed outlier: 3.516A pdb=" N THR G 84 " --> pdb=" O GLN G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 94 Processing helix chain 'G' and resid 95 through 114 Processing helix chain 'G' and resid 159 through 171 removed outlier: 4.611A pdb=" N ILE G 163 " --> pdb=" O THR G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 190 Processing helix chain 'G' and resid 226 through 234 removed outlier: 3.912A pdb=" N LEU G 230 " --> pdb=" O THR G 226 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 26 Processing helix chain 'H' and resid 67 through 89 removed outlier: 3.516A pdb=" N THR H 84 " --> pdb=" O GLN H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 94 Processing helix chain 'H' and resid 95 through 114 Processing helix chain 'H' and resid 159 through 171 removed outlier: 4.610A pdb=" N ILE H 163 " --> pdb=" O THR H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 190 Processing helix chain 'H' and resid 226 through 234 removed outlier: 3.911A pdb=" N LEU H 230 " --> pdb=" O THR H 226 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 26 Processing helix chain 'I' and resid 68 through 89 removed outlier: 3.516A pdb=" N THR I 84 " --> pdb=" O GLN I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 94 Processing helix chain 'I' and resid 95 through 114 Processing helix chain 'I' and resid 159 through 171 removed outlier: 4.612A pdb=" N ILE I 163 " --> pdb=" O THR I 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 190 Processing helix chain 'I' and resid 226 through 234 removed outlier: 3.911A pdb=" N LEU I 230 " --> pdb=" O THR I 226 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 26 Processing helix chain 'J' and resid 68 through 89 removed outlier: 3.516A pdb=" N THR J 84 " --> pdb=" O GLN J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 90 through 94 Processing helix chain 'J' and resid 95 through 114 Processing helix chain 'J' and resid 159 through 171 removed outlier: 4.611A pdb=" N ILE J 163 " --> pdb=" O THR J 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 176 through 190 Processing helix chain 'J' and resid 226 through 234 removed outlier: 3.911A pdb=" N LEU J 230 " --> pdb=" O THR J 226 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 26 Processing helix chain 'K' and resid 67 through 89 removed outlier: 3.517A pdb=" N THR K 84 " --> pdb=" O GLN K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 94 Processing helix chain 'K' and resid 95 through 114 Processing helix chain 'K' and resid 159 through 171 removed outlier: 4.611A pdb=" N ILE K 163 " --> pdb=" O THR K 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 176 through 190 Processing helix chain 'K' and resid 226 through 234 removed outlier: 3.912A pdb=" N LEU K 230 " --> pdb=" O THR K 226 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 26 Processing helix chain 'L' and resid 68 through 89 removed outlier: 3.516A pdb=" N THR L 84 " --> pdb=" O GLN L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 90 through 94 Processing helix chain 'L' and resid 95 through 114 Processing helix chain 'L' and resid 159 through 171 removed outlier: 4.610A pdb=" N ILE L 163 " --> pdb=" O THR L 159 " (cutoff:3.500A) Processing helix chain 'L' and resid 176 through 190 Processing helix chain 'L' and resid 226 through 234 removed outlier: 3.911A pdb=" N LEU L 230 " --> pdb=" O THR L 226 " (cutoff:3.500A) Processing helix chain 'M' and resid 9 through 26 Processing helix chain 'M' and resid 67 through 89 removed outlier: 3.515A pdb=" N THR M 84 " --> pdb=" O GLN M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 90 through 94 Processing helix chain 'M' and resid 95 through 114 Processing helix chain 'M' and resid 159 through 171 removed outlier: 4.610A pdb=" N ILE M 163 " --> pdb=" O THR M 159 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 190 Processing helix chain 'M' and resid 226 through 234 removed outlier: 3.911A pdb=" N LEU M 230 " --> pdb=" O THR M 226 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 26 Processing helix chain 'N' and resid 68 through 89 removed outlier: 3.516A pdb=" N THR N 84 " --> pdb=" O GLN N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 90 through 94 Processing helix chain 'N' and resid 95 through 114 Processing helix chain 'N' and resid 159 through 171 removed outlier: 4.611A pdb=" N ILE N 163 " --> pdb=" O THR N 159 " (cutoff:3.500A) Processing helix chain 'N' and resid 176 through 190 Processing helix chain 'N' and resid 226 through 234 removed outlier: 3.911A pdb=" N LEU N 230 " --> pdb=" O THR N 226 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 26 Processing helix chain 'O' and resid 68 through 89 removed outlier: 3.516A pdb=" N THR O 84 " --> pdb=" O GLN O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 90 through 94 Processing helix chain 'O' and resid 95 through 114 Processing helix chain 'O' and resid 159 through 171 removed outlier: 4.611A pdb=" N ILE O 163 " --> pdb=" O THR O 159 " (cutoff:3.500A) Processing helix chain 'O' and resid 176 through 190 Processing helix chain 'O' and resid 226 through 234 removed outlier: 3.911A pdb=" N LEU O 230 " --> pdb=" O THR O 226 " (cutoff:3.500A) Processing helix chain 'P' and resid 348 through 371 Processing helix chain 'P' and resid 375 through 390 Processing helix chain 'P' and resid 390 through 396 Processing helix chain 'P' and resid 413 through 416 Processing helix chain 'P' and resid 442 through 454 removed outlier: 4.023A pdb=" N LYS P 452 " --> pdb=" O SER P 448 " (cutoff:3.500A) Processing helix chain 'P' and resid 455 through 457 No H-bonds generated for 'chain 'P' and resid 455 through 457' Processing helix chain 'P' and resid 459 through 478 Processing helix chain 'P' and resid 506 through 522 removed outlier: 3.834A pdb=" N ILE P 510 " --> pdb=" O PRO P 506 " (cutoff:3.500A) Processing helix chain 'Q' and resid 348 through 371 Processing helix chain 'Q' and resid 375 through 390 Processing helix chain 'Q' and resid 390 through 396 Processing helix chain 'Q' and resid 413 through 416 Processing helix chain 'Q' and resid 442 through 454 removed outlier: 4.023A pdb=" N LYS Q 452 " --> pdb=" O SER Q 448 " (cutoff:3.500A) Processing helix chain 'Q' and resid 455 through 457 No H-bonds generated for 'chain 'Q' and resid 455 through 457' Processing helix chain 'Q' and resid 459 through 478 Processing helix chain 'Q' and resid 506 through 522 removed outlier: 3.833A pdb=" N ILE Q 510 " --> pdb=" O PRO Q 506 " (cutoff:3.500A) Processing helix chain 'R' and resid 348 through 371 Processing helix chain 'R' and resid 375 through 390 Processing helix chain 'R' and resid 390 through 396 Processing helix chain 'R' and resid 413 through 416 Processing helix chain 'R' and resid 442 through 454 removed outlier: 4.023A pdb=" N LYS R 452 " --> pdb=" O SER R 448 " (cutoff:3.500A) Processing helix chain 'R' and resid 455 through 457 No H-bonds generated for 'chain 'R' and resid 455 through 457' Processing helix chain 'R' and resid 459 through 478 Processing helix chain 'R' and resid 506 through 522 removed outlier: 3.833A pdb=" N ILE R 510 " --> pdb=" O PRO R 506 " (cutoff:3.500A) Processing helix chain 'S' and resid 348 through 371 Processing helix chain 'S' and resid 375 through 390 Processing helix chain 'S' and resid 390 through 396 Processing helix chain 'S' and resid 413 through 416 Processing helix chain 'S' and resid 442 through 454 removed outlier: 4.023A pdb=" N LYS S 452 " --> pdb=" O SER S 448 " (cutoff:3.500A) Processing helix chain 'S' and resid 455 through 457 No H-bonds generated for 'chain 'S' and resid 455 through 457' Processing helix chain 'S' and resid 459 through 478 Processing helix chain 'S' and resid 506 through 522 removed outlier: 3.834A pdb=" N ILE S 510 " --> pdb=" O PRO S 506 " (cutoff:3.500A) Processing helix chain 'T' and resid 348 through 371 Processing helix chain 'T' and resid 375 through 390 Processing helix chain 'T' and resid 390 through 396 Processing helix chain 'T' and resid 413 through 416 Processing helix chain 'T' and resid 442 through 454 removed outlier: 4.023A pdb=" N LYS T 452 " --> pdb=" O SER T 448 " (cutoff:3.500A) Processing helix chain 'T' and resid 455 through 457 No H-bonds generated for 'chain 'T' and resid 455 through 457' Processing helix chain 'T' and resid 459 through 478 Processing helix chain 'T' and resid 506 through 522 removed outlier: 3.834A pdb=" N ILE T 510 " --> pdb=" O PRO T 506 " (cutoff:3.500A) Processing helix chain 'U' and resid 348 through 371 Processing helix chain 'U' and resid 375 through 390 Processing helix chain 'U' and resid 390 through 396 Processing helix chain 'U' and resid 413 through 416 Processing helix chain 'U' and resid 442 through 454 removed outlier: 4.023A pdb=" N LYS U 452 " --> pdb=" O SER U 448 " (cutoff:3.500A) Processing helix chain 'U' and resid 455 through 457 No H-bonds generated for 'chain 'U' and resid 455 through 457' Processing helix chain 'U' and resid 459 through 478 Processing helix chain 'U' and resid 506 through 522 removed outlier: 3.833A pdb=" N ILE U 510 " --> pdb=" O PRO U 506 " (cutoff:3.500A) Processing helix chain 'V' and resid 348 through 371 Processing helix chain 'V' and resid 375 through 390 Processing helix chain 'V' and resid 390 through 396 Processing helix chain 'V' and resid 413 through 416 Processing helix chain 'V' and resid 442 through 454 removed outlier: 4.023A pdb=" N LYS V 452 " --> pdb=" O SER V 448 " (cutoff:3.500A) Processing helix chain 'V' and resid 455 through 457 No H-bonds generated for 'chain 'V' and resid 455 through 457' Processing helix chain 'V' and resid 459 through 478 Processing helix chain 'V' and resid 506 through 522 removed outlier: 3.834A pdb=" N ILE V 510 " --> pdb=" O PRO V 506 " (cutoff:3.500A) Processing helix chain 'W' and resid 348 through 371 Processing helix chain 'W' and resid 375 through 390 Processing helix chain 'W' and resid 390 through 396 Processing helix chain 'W' and resid 413 through 416 Processing helix chain 'W' and resid 442 through 454 removed outlier: 4.023A pdb=" N LYS W 452 " --> pdb=" O SER W 448 " (cutoff:3.500A) Processing helix chain 'W' and resid 455 through 457 No H-bonds generated for 'chain 'W' and resid 455 through 457' Processing helix chain 'W' and resid 459 through 478 Processing helix chain 'W' and resid 506 through 522 removed outlier: 3.834A pdb=" N ILE W 510 " --> pdb=" O PRO W 506 " (cutoff:3.500A) Processing helix chain 'X' and resid 348 through 371 Processing helix chain 'X' and resid 375 through 390 Processing helix chain 'X' and resid 390 through 396 Processing helix chain 'X' and resid 413 through 416 Processing helix chain 'X' and resid 442 through 454 removed outlier: 4.023A pdb=" N LYS X 452 " --> pdb=" O SER X 448 " (cutoff:3.500A) Processing helix chain 'X' and resid 455 through 457 No H-bonds generated for 'chain 'X' and resid 455 through 457' Processing helix chain 'X' and resid 459 through 478 Processing helix chain 'X' and resid 506 through 522 removed outlier: 3.834A pdb=" N ILE X 510 " --> pdb=" O PRO X 506 " (cutoff:3.500A) Processing helix chain 'Y' and resid 348 through 371 Processing helix chain 'Y' and resid 375 through 390 Processing helix chain 'Y' and resid 390 through 396 Processing helix chain 'Y' and resid 413 through 416 Processing helix chain 'Y' and resid 442 through 454 removed outlier: 4.023A pdb=" N LYS Y 452 " --> pdb=" O SER Y 448 " (cutoff:3.500A) Processing helix chain 'Y' and resid 455 through 457 No H-bonds generated for 'chain 'Y' and resid 455 through 457' Processing helix chain 'Y' and resid 459 through 478 Processing helix chain 'Y' and resid 506 through 522 removed outlier: 3.834A pdb=" N ILE Y 510 " --> pdb=" O PRO Y 506 " (cutoff:3.500A) Processing helix chain 'Z' and resid 348 through 371 Processing helix chain 'Z' and resid 375 through 390 Processing helix chain 'Z' and resid 390 through 396 Processing helix chain 'Z' and resid 413 through 416 Processing helix chain 'Z' and resid 442 through 454 removed outlier: 4.023A pdb=" N LYS Z 452 " --> pdb=" O SER Z 448 " (cutoff:3.500A) Processing helix chain 'Z' and resid 455 through 457 No H-bonds generated for 'chain 'Z' and resid 455 through 457' Processing helix chain 'Z' and resid 459 through 478 Processing helix chain 'Z' and resid 506 through 522 removed outlier: 3.834A pdb=" N ILE Z 510 " --> pdb=" O PRO Z 506 " (cutoff:3.500A) Processing helix chain 'a' and resid 348 through 371 Processing helix chain 'a' and resid 375 through 390 Processing helix chain 'a' and resid 390 through 396 Processing helix chain 'a' and resid 413 through 416 Processing helix chain 'a' and resid 442 through 454 removed outlier: 4.023A pdb=" N LYS a 452 " --> pdb=" O SER a 448 " (cutoff:3.500A) Processing helix chain 'a' and resid 455 through 457 No H-bonds generated for 'chain 'a' and resid 455 through 457' Processing helix chain 'a' and resid 459 through 478 Processing helix chain 'a' and resid 506 through 522 removed outlier: 3.834A pdb=" N ILE a 510 " --> pdb=" O PRO a 506 " (cutoff:3.500A) Processing helix chain 'b' and resid 348 through 371 Processing helix chain 'b' and resid 375 through 390 Processing helix chain 'b' and resid 390 through 396 Processing helix chain 'b' and resid 413 through 416 Processing helix chain 'b' and resid 442 through 454 removed outlier: 4.022A pdb=" N LYS b 452 " --> pdb=" O SER b 448 " (cutoff:3.500A) Processing helix chain 'b' and resid 455 through 457 No H-bonds generated for 'chain 'b' and resid 455 through 457' Processing helix chain 'b' and resid 459 through 478 Processing helix chain 'b' and resid 506 through 522 removed outlier: 3.834A pdb=" N ILE b 510 " --> pdb=" O PRO b 506 " (cutoff:3.500A) Processing helix chain 'c' and resid 348 through 371 Processing helix chain 'c' and resid 375 through 390 Processing helix chain 'c' and resid 390 through 396 Processing helix chain 'c' and resid 413 through 416 Processing helix chain 'c' and resid 442 through 454 removed outlier: 4.023A pdb=" N LYS c 452 " --> pdb=" O SER c 448 " (cutoff:3.500A) Processing helix chain 'c' and resid 455 through 457 No H-bonds generated for 'chain 'c' and resid 455 through 457' Processing helix chain 'c' and resid 459 through 478 Processing helix chain 'c' and resid 506 through 522 removed outlier: 3.833A pdb=" N ILE c 510 " --> pdb=" O PRO c 506 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 153 through 156 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 57 removed outlier: 6.495A pdb=" N VAL A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU A 138 " --> pdb=" O GLU A 150 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 57 removed outlier: 6.495A pdb=" N VAL A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 173 through 174 removed outlier: 6.495A pdb=" N VAL N 60 " --> pdb=" O LEU N 56 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 173 through 174 removed outlier: 3.742A pdb=" N LEU N 138 " --> pdb=" O GLU N 150 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 153 through 156 Processing sheet with id=AA7, first strand: chain 'C' and resid 53 through 57 removed outlier: 6.495A pdb=" N VAL C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU C 138 " --> pdb=" O GLU C 150 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 53 through 57 removed outlier: 6.495A pdb=" N VAL C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 153 through 156 Processing sheet with id=AB1, first strand: chain 'D' and resid 53 through 57 removed outlier: 6.495A pdb=" N VAL D 60 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU D 138 " --> pdb=" O GLU D 150 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 53 through 57 removed outlier: 6.495A pdb=" N VAL D 60 " --> pdb=" O LEU D 56 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 153 through 156 Processing sheet with id=AB4, first strand: chain 'E' and resid 53 through 57 removed outlier: 6.494A pdb=" N VAL E 60 " --> pdb=" O LEU E 56 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU E 138 " --> pdb=" O GLU E 150 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 153 through 156 Processing sheet with id=AB6, first strand: chain 'F' and resid 53 through 57 removed outlier: 6.494A pdb=" N VAL F 60 " --> pdb=" O LEU F 56 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU F 138 " --> pdb=" O GLU F 150 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 53 through 57 removed outlier: 6.494A pdb=" N VAL F 60 " --> pdb=" O LEU F 56 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 153 through 156 Processing sheet with id=AB9, first strand: chain 'G' and resid 53 through 57 removed outlier: 6.495A pdb=" N VAL G 60 " --> pdb=" O LEU G 56 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU G 138 " --> pdb=" O GLU G 150 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 53 through 57 removed outlier: 6.495A pdb=" N VAL G 60 " --> pdb=" O LEU G 56 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 153 through 156 Processing sheet with id=AC3, first strand: chain 'H' and resid 53 through 57 removed outlier: 6.495A pdb=" N VAL H 60 " --> pdb=" O LEU H 56 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU H 138 " --> pdb=" O GLU H 150 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 153 through 156 Processing sheet with id=AC5, first strand: chain 'I' and resid 53 through 57 removed outlier: 6.494A pdb=" N VAL I 60 " --> pdb=" O LEU I 56 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU I 138 " --> pdb=" O GLU I 150 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 53 through 57 removed outlier: 6.494A pdb=" N VAL I 60 " --> pdb=" O LEU I 56 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 153 through 156 Processing sheet with id=AC8, first strand: chain 'J' and resid 53 through 57 removed outlier: 6.495A pdb=" N VAL J 60 " --> pdb=" O LEU J 56 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU J 138 " --> pdb=" O GLU J 150 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 53 through 57 removed outlier: 6.495A pdb=" N VAL J 60 " --> pdb=" O LEU J 56 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 153 through 156 Processing sheet with id=AD2, first strand: chain 'K' and resid 53 through 57 removed outlier: 6.494A pdb=" N VAL K 60 " --> pdb=" O LEU K 56 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU K 138 " --> pdb=" O GLU K 150 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 153 through 156 Processing sheet with id=AD4, first strand: chain 'L' and resid 53 through 57 removed outlier: 6.495A pdb=" N VAL L 60 " --> pdb=" O LEU L 56 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU L 138 " --> pdb=" O GLU L 150 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 53 through 57 removed outlier: 6.495A pdb=" N VAL L 60 " --> pdb=" O LEU L 56 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 153 through 156 Processing sheet with id=AD7, first strand: chain 'M' and resid 53 through 57 removed outlier: 6.495A pdb=" N VAL M 60 " --> pdb=" O LEU M 56 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU M 138 " --> pdb=" O GLU M 150 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 153 through 156 Processing sheet with id=AD9, first strand: chain 'O' and resid 153 through 156 Processing sheet with id=AE1, first strand: chain 'O' and resid 53 through 57 removed outlier: 6.494A pdb=" N VAL O 60 " --> pdb=" O LEU O 56 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU O 138 " --> pdb=" O GLU O 150 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'O' and resid 53 through 57 removed outlier: 6.494A pdb=" N VAL O 60 " --> pdb=" O LEU O 56 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'P' and resid 436 through 439 Processing sheet with id=AE4, first strand: chain 'P' and resid 320 through 322 removed outlier: 6.385A pdb=" N SER P 320 " --> pdb=" O SER P 327 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'P' and resid 334 through 338 removed outlier: 6.495A pdb=" N THR P 341 " --> pdb=" O THR P 337 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE P 423 " --> pdb=" O PRO P 402 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Q' and resid 436 through 439 Processing sheet with id=AE7, first strand: chain 'Q' and resid 320 through 322 removed outlier: 6.385A pdb=" N SER Q 320 " --> pdb=" O SER Q 327 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Q' and resid 334 through 338 removed outlier: 6.495A pdb=" N THR Q 341 " --> pdb=" O THR Q 337 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE Q 423 " --> pdb=" O PRO Q 402 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'R' and resid 436 through 439 Processing sheet with id=AF1, first strand: chain 'R' and resid 320 through 322 removed outlier: 6.384A pdb=" N SER R 320 " --> pdb=" O SER R 327 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'R' and resid 334 through 338 removed outlier: 6.495A pdb=" N THR R 341 " --> pdb=" O THR R 337 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE R 423 " --> pdb=" O PRO R 402 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'S' and resid 436 through 439 Processing sheet with id=AF4, first strand: chain 'S' and resid 320 through 322 removed outlier: 6.384A pdb=" N SER S 320 " --> pdb=" O SER S 327 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'S' and resid 334 through 338 removed outlier: 6.496A pdb=" N THR S 341 " --> pdb=" O THR S 337 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE S 423 " --> pdb=" O PRO S 402 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'T' and resid 436 through 439 Processing sheet with id=AF7, first strand: chain 'T' and resid 320 through 322 removed outlier: 6.385A pdb=" N SER T 320 " --> pdb=" O SER T 327 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'T' and resid 334 through 338 removed outlier: 6.496A pdb=" N THR T 341 " --> pdb=" O THR T 337 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE T 423 " --> pdb=" O PRO T 402 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'U' and resid 436 through 439 Processing sheet with id=AG1, first strand: chain 'U' and resid 320 through 322 removed outlier: 6.385A pdb=" N SER U 320 " --> pdb=" O SER U 327 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'U' and resid 334 through 338 removed outlier: 6.496A pdb=" N THR U 341 " --> pdb=" O THR U 337 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE U 423 " --> pdb=" O PRO U 402 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'V' and resid 436 through 439 Processing sheet with id=AG4, first strand: chain 'V' and resid 320 through 322 removed outlier: 6.385A pdb=" N SER V 320 " --> pdb=" O SER V 327 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'V' and resid 334 through 338 removed outlier: 6.495A pdb=" N THR V 341 " --> pdb=" O THR V 337 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE V 423 " --> pdb=" O PRO V 402 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'W' and resid 436 through 439 Processing sheet with id=AG7, first strand: chain 'W' and resid 320 through 322 removed outlier: 6.384A pdb=" N SER W 320 " --> pdb=" O SER W 327 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'W' and resid 334 through 338 removed outlier: 6.495A pdb=" N THR W 341 " --> pdb=" O THR W 337 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE W 423 " --> pdb=" O PRO W 402 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'X' and resid 436 through 439 Processing sheet with id=AH1, first strand: chain 'X' and resid 320 through 322 removed outlier: 6.384A pdb=" N SER X 320 " --> pdb=" O SER X 327 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'X' and resid 334 through 338 removed outlier: 6.495A pdb=" N THR X 341 " --> pdb=" O THR X 337 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE X 423 " --> pdb=" O PRO X 402 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Y' and resid 436 through 439 Processing sheet with id=AH4, first strand: chain 'Y' and resid 320 through 322 removed outlier: 6.385A pdb=" N SER Y 320 " --> pdb=" O SER Y 327 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'Y' and resid 334 through 338 removed outlier: 6.495A pdb=" N THR Y 341 " --> pdb=" O THR Y 337 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE Y 423 " --> pdb=" O PRO Y 402 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'Z' and resid 436 through 439 Processing sheet with id=AH7, first strand: chain 'Z' and resid 320 through 322 removed outlier: 6.385A pdb=" N SER Z 320 " --> pdb=" O SER Z 327 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'Z' and resid 334 through 338 removed outlier: 6.495A pdb=" N THR Z 341 " --> pdb=" O THR Z 337 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE Z 423 " --> pdb=" O PRO Z 402 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'a' and resid 436 through 439 Processing sheet with id=AI1, first strand: chain 'a' and resid 320 through 322 removed outlier: 6.384A pdb=" N SER a 320 " --> pdb=" O SER a 327 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'a' and resid 334 through 338 removed outlier: 6.495A pdb=" N THR a 341 " --> pdb=" O THR a 337 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE a 423 " --> pdb=" O PRO a 402 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'b' and resid 436 through 439 Processing sheet with id=AI4, first strand: chain 'b' and resid 320 through 322 removed outlier: 6.384A pdb=" N SER b 320 " --> pdb=" O SER b 327 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'b' and resid 334 through 338 removed outlier: 6.495A pdb=" N THR b 341 " --> pdb=" O THR b 337 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE b 423 " --> pdb=" O PRO b 402 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'c' and resid 436 through 439 Processing sheet with id=AI7, first strand: chain 'c' and resid 320 through 322 removed outlier: 6.384A pdb=" N SER c 320 " --> pdb=" O SER c 327 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'c' and resid 334 through 338 removed outlier: 6.495A pdb=" N THR c 341 " --> pdb=" O THR c 337 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE c 423 " --> pdb=" O PRO c 402 " (cutoff:3.500A) 3106 hydrogen bonds defined for protein. 8856 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: 22.07 Time building geometry restraints manager: 20.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 8074 1.31 - 1.44: 12027 1.44 - 1.56: 26979 1.56 - 1.69: 14 1.69 - 1.81: 210 Bond restraints: 47304 Sorted by residual: bond pdb=" C ILE M 110 " pdb=" O ILE M 110 " ideal model delta sigma weight residual 1.237 1.190 0.047 1.13e-02 7.83e+03 1.71e+01 bond pdb=" C ILE D 110 " pdb=" O ILE D 110 " ideal model delta sigma weight residual 1.237 1.190 0.047 1.13e-02 7.83e+03 1.70e+01 bond pdb=" C ILE E 110 " pdb=" O ILE E 110 " ideal model delta sigma weight residual 1.237 1.190 0.046 1.13e-02 7.83e+03 1.69e+01 bond pdb=" C ILE J 110 " pdb=" O ILE J 110 " ideal model delta sigma weight residual 1.237 1.191 0.046 1.13e-02 7.83e+03 1.68e+01 bond pdb=" C ILE G 110 " pdb=" O ILE G 110 " ideal model delta sigma weight residual 1.237 1.191 0.046 1.13e-02 7.83e+03 1.67e+01 ... (remaining 47299 not shown) Histogram of bond angle deviations from ideal: 100.05 - 106.80: 1085 106.80 - 113.55: 25838 113.55 - 120.30: 17764 120.30 - 127.05: 19108 127.05 - 133.80: 224 Bond angle restraints: 64019 Sorted by residual: angle pdb=" N GLY O 227 " pdb=" CA GLY O 227 " pdb=" C GLY O 227 " ideal model delta sigma weight residual 111.50 123.18 -11.68 1.74e+00 3.30e-01 4.51e+01 angle pdb=" N GLY F 227 " pdb=" CA GLY F 227 " pdb=" C GLY F 227 " ideal model delta sigma weight residual 111.50 123.17 -11.67 1.74e+00 3.30e-01 4.50e+01 angle pdb=" N GLY G 227 " pdb=" CA GLY G 227 " pdb=" C GLY G 227 " ideal model delta sigma weight residual 111.50 123.15 -11.65 1.74e+00 3.30e-01 4.48e+01 angle pdb=" N GLY E 227 " pdb=" CA GLY E 227 " pdb=" C GLY E 227 " ideal model delta sigma weight residual 111.50 123.15 -11.65 1.74e+00 3.30e-01 4.48e+01 angle pdb=" N GLY D 227 " pdb=" CA GLY D 227 " pdb=" C GLY D 227 " ideal model delta sigma weight residual 111.50 123.14 -11.64 1.74e+00 3.30e-01 4.48e+01 ... (remaining 64014 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 26457 17.22 - 34.45: 1486 34.45 - 51.67: 336 51.67 - 68.90: 126 68.90 - 86.12: 56 Dihedral angle restraints: 28461 sinusoidal: 10863 harmonic: 17598 Sorted by residual: dihedral pdb=" CA THR c 321 " pdb=" C THR c 321 " pdb=" N GLN c 322 " pdb=" CA GLN c 322 " ideal model delta harmonic sigma weight residual 180.00 163.51 16.49 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA THR b 321 " pdb=" C THR b 321 " pdb=" N GLN b 322 " pdb=" CA GLN b 322 " ideal model delta harmonic sigma weight residual 180.00 163.52 16.48 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA THR W 321 " pdb=" C THR W 321 " pdb=" N GLN W 322 " pdb=" CA GLN W 322 " ideal model delta harmonic sigma weight residual 180.00 163.54 16.46 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 28458 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 6015 0.067 - 0.135: 1074 0.135 - 0.202: 156 0.202 - 0.269: 20 0.269 - 0.336: 14 Chirality restraints: 7279 Sorted by residual: chirality pdb=" CA GLN I 114 " pdb=" N GLN I 114 " pdb=" C GLN I 114 " pdb=" CB GLN I 114 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CA GLN F 114 " pdb=" N GLN F 114 " pdb=" C GLN F 114 " pdb=" CB GLN F 114 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CA GLN N 114 " pdb=" N GLN N 114 " pdb=" C GLN N 114 " pdb=" CB GLN N 114 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.78e+00 ... (remaining 7276 not shown) Planarity restraints: 8442 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE L 111 " -0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C PHE L 111 " 0.056 2.00e-02 2.50e+03 pdb=" O PHE L 111 " -0.021 2.00e-02 2.50e+03 pdb=" N THR L 112 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE K 111 " -0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C PHE K 111 " 0.056 2.00e-02 2.50e+03 pdb=" O PHE K 111 " -0.021 2.00e-02 2.50e+03 pdb=" N THR K 112 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE G 111 " 0.016 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C PHE G 111 " -0.056 2.00e-02 2.50e+03 pdb=" O PHE G 111 " 0.021 2.00e-02 2.50e+03 pdb=" N THR G 112 " 0.019 2.00e-02 2.50e+03 ... (remaining 8439 not shown) Histogram of nonbonded interaction distances: 1.24 - 1.98: 52 1.98 - 2.71: 1886 2.71 - 3.44: 66129 3.44 - 4.17: 104907 4.17 - 4.90: 191380 Nonbonded interactions: 364354 Sorted by model distance: nonbonded pdb=" NH2 ARG D 135 " pdb=" NH1 ARG E 48 " model vdw 1.244 3.200 nonbonded pdb=" O GLY K 66 " pdb=" O LEU n 174 " model vdw 1.262 3.040 nonbonded pdb=" NH2 ARG E 135 " pdb=" NH1 ARG F 48 " model vdw 1.290 3.200 nonbonded pdb=" O GLY A 66 " pdb=" O LEU l 174 " model vdw 1.361 3.040 nonbonded pdb=" O GLY L 66 " pdb=" O LEU o 174 " model vdw 1.420 3.040 ... (remaining 364349 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 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' } ncs_group { reference = (chain 'P' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'Q' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'R' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'S' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = chain 'T' selection = (chain 'U' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'V' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'W' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'X' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'Y' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'Z' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'a' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'b' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'c' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 29231 2.51 5 N 8260 2.21 5 O 9015 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.020 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: 0.040 Extract box with map and model: 18.010 Check model and map are aligned: 0.690 Convert atoms to be neutral: 0.390 Process input model: 120.930 Find NCS groups from input model: 4.000 Set up NCS constraints: 0.470 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 152.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 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 : 0.007 0.061 47304 Z= 0.449 Angle : 0.980 11.685 64019 Z= 0.610 Chirality : 0.054 0.336 7279 Planarity : 0.006 0.064 8442 Dihedral : 12.922 86.123 17261 Min Nonbonded Distance : 1.244 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer Outliers : 0.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.11), residues: 6062 helix: 0.83 (0.11), residues: 2534 sheet: -0.71 (0.12), residues: 1526 loop : -0.69 (0.14), residues: 2002 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1256 residues out of total 4662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 1214 time to evaluate : 5.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 12 residues processed: 1252 average time/residue: 0.5799 time to fit residues: 1184.5992 Evaluate side-chains 639 residues out of total 4662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 627 time to evaluate : 5.480 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 1.1659 time to fit residues: 25.5468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 508 optimal weight: 1.9990 chunk 456 optimal weight: 1.9990 chunk 253 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 307 optimal weight: 0.9990 chunk 243 optimal weight: 9.9990 chunk 471 optimal weight: 4.9990 chunk 182 optimal weight: 4.9990 chunk 286 optimal weight: 10.0000 chunk 351 optimal weight: 3.9990 chunk 546 optimal weight: 9.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A 231 GLN C 80 GLN D 11 GLN D 80 GLN ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 11 GLN E 80 GLN F 80 GLN F 174 ASN G 80 GLN ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 GLN I 80 GLN J 80 GLN K 80 GLN L 80 GLN M 80 GLN N 80 GLN O 80 GLN O 174 ASN Q 390 ASN ** k 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 172 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 47304 Z= 0.233 Angle : 0.649 7.821 64019 Z= 0.349 Chirality : 0.043 0.178 7279 Planarity : 0.005 0.049 8442 Dihedral : 4.446 69.838 6888 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer Outliers : 2.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.11), residues: 6062 helix: 2.32 (0.10), residues: 2576 sheet: 0.27 (0.13), residues: 1484 loop : -0.65 (0.13), residues: 2002 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 836 residues out of total 4662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 713 time to evaluate : 5.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 123 outliers final: 52 residues processed: 789 average time/residue: 0.5652 time to fit residues: 733.8531 Evaluate side-chains 631 residues out of total 4662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 579 time to evaluate : 5.533 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 0 residues processed: 52 average time/residue: 0.4013 time to fit residues: 46.4954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 303 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 454 optimal weight: 5.9990 chunk 372 optimal weight: 5.9990 chunk 150 optimal weight: 5.9990 chunk 547 optimal weight: 9.9990 chunk 591 optimal weight: 0.0970 chunk 487 optimal weight: 6.9990 chunk 543 optimal weight: 3.9990 chunk 186 optimal weight: 10.0000 chunk 439 optimal weight: 2.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 114 GLN ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 GLN ** K 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 390 ASN Q 390 ASN R 390 ASN V 390 ASN Y 390 ASN ** i 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 172 GLN ** m 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.6054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 47304 Z= 0.291 Angle : 0.656 13.787 64019 Z= 0.347 Chirality : 0.043 0.155 7279 Planarity : 0.004 0.048 8442 Dihedral : 4.171 46.175 6888 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer Outliers : 1.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.11), residues: 6062 helix: 2.66 (0.10), residues: 2604 sheet: 0.78 (0.13), residues: 1386 loop : -0.85 (0.13), residues: 2072 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 4662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 661 time to evaluate : 5.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 15 residues processed: 683 average time/residue: 0.5885 time to fit residues: 657.2149 Evaluate side-chains 551 residues out of total 4662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 536 time to evaluate : 5.965 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.4514 time to fit residues: 20.2748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 541 optimal weight: 4.9990 chunk 411 optimal weight: 0.6980 chunk 284 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 261 optimal weight: 1.9990 chunk 367 optimal weight: 6.9990 chunk 549 optimal weight: 0.9980 chunk 581 optimal weight: 6.9990 chunk 287 optimal weight: 5.9990 chunk 520 optimal weight: 0.6980 chunk 156 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 114 GLN C 174 ASN ** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 ASN E 165 ASN ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 114 GLN ** I 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 114 GLN ** L 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 114 GLN N 114 GLN ** N 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 114 GLN P 415 GLN T 415 GLN U 415 GLN V 415 GLN V 456 GLN W 415 GLN Y 415 GLN a 415 GLN c 415 GLN c 456 GLN m 172 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.6510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 47304 Z= 0.186 Angle : 0.602 13.116 64019 Z= 0.312 Chirality : 0.042 0.185 7279 Planarity : 0.003 0.041 8442 Dihedral : 3.994 47.076 6888 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer Outliers : 1.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.11), residues: 6062 helix: 2.91 (0.10), residues: 2604 sheet: 1.08 (0.14), residues: 1386 loop : -0.83 (0.13), residues: 2072 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 4662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 608 time to evaluate : 5.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 51 residues processed: 631 average time/residue: 0.5815 time to fit residues: 600.7380 Evaluate side-chains 586 residues out of total 4662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 535 time to evaluate : 5.491 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 0 residues processed: 51 average time/residue: 0.4053 time to fit residues: 45.3835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 484 optimal weight: 1.9990 chunk 330 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 433 optimal weight: 0.0370 chunk 240 optimal weight: 0.7980 chunk 496 optimal weight: 5.9990 chunk 402 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 297 optimal weight: 4.9990 chunk 522 optimal weight: 0.0980 chunk 146 optimal weight: 0.9990 overall best weight: 0.5660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN C 114 GLN ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 ASN F 114 GLN G 80 GLN G 114 GLN H 114 GLN J 114 GLN K 114 GLN L 114 GLN M 114 GLN N 114 GLN O 114 GLN O 174 ASN ** V 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 415 GLN ** j 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.6691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 47304 Z= 0.149 Angle : 0.579 11.106 64019 Z= 0.298 Chirality : 0.042 0.146 7279 Planarity : 0.003 0.040 8442 Dihedral : 3.810 45.852 6888 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.11), residues: 6062 helix: 2.98 (0.10), residues: 2604 sheet: 1.28 (0.14), residues: 1386 loop : -0.83 (0.13), residues: 2072 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 4662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 611 time to evaluate : 5.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 9 residues processed: 625 average time/residue: 0.5868 time to fit residues: 606.1560 Evaluate side-chains 558 residues out of total 4662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 549 time to evaluate : 5.500 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.4526 time to fit residues: 14.4047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 195 optimal weight: 2.9990 chunk 524 optimal weight: 8.9990 chunk 115 optimal weight: 10.0000 chunk 341 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 582 optimal weight: 0.6980 chunk 483 optimal weight: 8.9990 chunk 269 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 192 optimal weight: 5.9990 chunk 305 optimal weight: 10.0000 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN C 114 GLN C 174 ASN ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 GLN ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 114 GLN ** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 114 GLN ** J 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 114 GLN L 114 GLN ** L 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 114 GLN N 114 GLN O 114 GLN V 390 ASN ** e 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.7306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.042 47304 Z= 0.387 Angle : 0.678 10.490 64019 Z= 0.363 Chirality : 0.043 0.170 7279 Planarity : 0.004 0.043 8442 Dihedral : 4.170 44.272 6888 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.11), residues: 6062 helix: 2.71 (0.10), residues: 2604 sheet: 1.08 (0.14), residues: 1358 loop : -1.00 (0.13), residues: 2100 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 4662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 553 time to evaluate : 6.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 32 residues processed: 572 average time/residue: 0.5836 time to fit residues: 552.7199 Evaluate side-chains 534 residues out of total 4662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 502 time to evaluate : 5.909 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.4529 time to fit residues: 34.6622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 561 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 331 optimal weight: 2.9990 chunk 425 optimal weight: 8.9990 chunk 329 optimal weight: 3.9990 chunk 490 optimal weight: 4.9990 chunk 325 optimal weight: 5.9990 chunk 580 optimal weight: 0.8980 chunk 363 optimal weight: 1.9990 chunk 353 optimal weight: 2.9990 chunk 267 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 114 GLN F 114 GLN ** J 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 114 GLN V 390 ASN ** j 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.7480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 47304 Z= 0.222 Angle : 0.621 10.979 64019 Z= 0.327 Chirality : 0.043 0.190 7279 Planarity : 0.003 0.040 8442 Dihedral : 4.018 46.928 6888 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.11), residues: 6062 helix: 2.77 (0.10), residues: 2604 sheet: 1.21 (0.13), residues: 1386 loop : -0.98 (0.13), residues: 2072 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 4662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 578 time to evaluate : 5.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 579 average time/residue: 0.5905 time to fit residues: 568.8876 Evaluate side-chains 548 residues out of total 4662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 540 time to evaluate : 5.675 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.4319 time to fit residues: 13.9507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 358 optimal weight: 0.0040 chunk 231 optimal weight: 0.0020 chunk 346 optimal weight: 4.9990 chunk 174 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 368 optimal weight: 0.7980 chunk 395 optimal weight: 5.9990 chunk 286 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 456 optimal weight: 2.9990 overall best weight: 1.3604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.7638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 47304 Z= 0.187 Angle : 0.611 14.403 64019 Z= 0.322 Chirality : 0.043 0.191 7279 Planarity : 0.003 0.039 8442 Dihedral : 3.909 45.121 6888 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.11), residues: 6062 helix: 2.77 (0.10), residues: 2604 sheet: 1.32 (0.13), residues: 1386 loop : -0.96 (0.13), residues: 2072 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 4662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 575 time to evaluate : 6.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 22 residues processed: 579 average time/residue: 0.5756 time to fit residues: 554.4206 Evaluate side-chains 554 residues out of total 4662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 532 time to evaluate : 5.646 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.4156 time to fit residues: 24.9452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 527 optimal weight: 6.9990 chunk 555 optimal weight: 4.9990 chunk 507 optimal weight: 6.9990 chunk 540 optimal weight: 9.9990 chunk 325 optimal weight: 0.1980 chunk 235 optimal weight: 1.9990 chunk 424 optimal weight: 0.9990 chunk 165 optimal weight: 9.9990 chunk 488 optimal weight: 0.6980 chunk 511 optimal weight: 1.9990 chunk 538 optimal weight: 3.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.7763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 47304 Z= 0.182 Angle : 0.634 14.554 64019 Z= 0.330 Chirality : 0.043 0.201 7279 Planarity : 0.003 0.037 8442 Dihedral : 3.885 46.099 6888 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.11), residues: 6062 helix: 2.72 (0.10), residues: 2604 sheet: 1.37 (0.13), residues: 1386 loop : -0.93 (0.13), residues: 2072 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 4662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 571 time to evaluate : 6.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 9 residues processed: 573 average time/residue: 0.5675 time to fit residues: 542.0322 Evaluate side-chains 541 residues out of total 4662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 532 time to evaluate : 5.493 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.4504 time to fit residues: 14.6753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 355 optimal weight: 5.9990 chunk 571 optimal weight: 5.9990 chunk 348 optimal weight: 5.9990 chunk 271 optimal weight: 1.9990 chunk 397 optimal weight: 0.9980 chunk 599 optimal weight: 0.7980 chunk 551 optimal weight: 0.3980 chunk 477 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 368 optimal weight: 0.2980 chunk 292 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 165 ASN ** O 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.7874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 47304 Z= 0.170 Angle : 0.643 16.167 64019 Z= 0.331 Chirality : 0.043 0.196 7279 Planarity : 0.003 0.037 8442 Dihedral : 3.802 46.541 6888 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.11), residues: 6062 helix: 2.77 (0.10), residues: 2576 sheet: 1.43 (0.14), residues: 1386 loop : -0.88 (0.13), residues: 2100 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12124 Ramachandran restraints generated. 6062 Oldfield, 0 Emsley, 6062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 4662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 580 time to evaluate : 5.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 580 average time/residue: 0.5860 time to fit residues: 568.0924 Evaluate side-chains 547 residues out of total 4662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 544 time to evaluate : 5.813 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3935 time to fit residues: 9.7939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 379 optimal weight: 2.9990 chunk 508 optimal weight: 0.7980 chunk 146 optimal weight: 0.4980 chunk 440 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 132 optimal weight: 0.9980 chunk 478 optimal weight: 0.9990 chunk 200 optimal weight: 2.9990 chunk 491 optimal weight: 0.8980 chunk 60 optimal weight: 8.9990 chunk 88 optimal weight: 7.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 165 ASN ** O 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 456 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.067038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.046061 restraints weight = 159465.967| |-----------------------------------------------------------------------------| r_work (start): 0.2671 rms_B_bonded: 5.18 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.7933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 47304 Z= 0.172 Angle : 0.646 16.290 64019 Z= 0.332 Chirality : 0.043 0.196 7279 Planarity : 0.003 0.036 8442 Dihedral : 3.766 46.726 6888 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.11), residues: 6062 helix: 2.79 (0.10), residues: 2562 sheet: 1.46 (0.14), residues: 1386 loop : -0.92 (0.13), residues: 2114 =============================================================================== Job complete usr+sys time: 10881.97 seconds wall clock time: 195 minutes 23.57 seconds (11723.57 seconds total)