Starting phenix.real_space_refine on Sat Feb 24 22:20:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bgl_7097/02_2024/6bgl_7097_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bgl_7097/02_2024/6bgl_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_7097/02_2024/6bgl_7097.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bgl_7097/02_2024/6bgl_7097.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bgl_7097/02_2024/6bgl_7097_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bgl_7097/02_2024/6bgl_7097_neut.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 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. 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: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 24.68, per 1000 atoms: 0.53 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: 18.85 Conformation dependent library (CDL) restraints added in 8.9 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: 5.83 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: 21.25 Time building geometry restraints manager: 19.90 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 16.120 Check model and map are aligned: 0.770 Set scattering table: 0.480 Process input model: 122.700 Find NCS groups from input model: 3.430 Set up NCS constraints: 0.500 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 151.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 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 % Allowed : 5.02 % Favored : 94.08 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP Y 429 HIS 0.005 0.001 HIS U 365 PHE 0.030 0.004 PHE F 68 TYR 0.015 0.002 TYR M 139 ARG 0.004 0.001 ARG M 189 *********************** 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 : 5.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ASN cc_start: 0.6761 (t0) cc_final: 0.6408 (t0) REVERT: D 45 ASN cc_start: 0.7267 (t0) cc_final: 0.6450 (t0) REVERT: D 116 LYS cc_start: 0.8143 (ttpp) cc_final: 0.7709 (tmtt) REVERT: D 163 ILE cc_start: 0.7684 (mt) cc_final: 0.7393 (mt) REVERT: E 45 ASN cc_start: 0.7369 (t0) cc_final: 0.6582 (t0) REVERT: E 109 THR cc_start: 0.8934 (m) cc_final: 0.8714 (t) REVERT: E 147 ILE cc_start: 0.8011 (pt) cc_final: 0.7748 (pt) REVERT: E 209 GLU cc_start: 0.5917 (tt0) cc_final: 0.5666 (tt0) REVERT: F 28 LYS cc_start: 0.8135 (mmtm) cc_final: 0.7909 (mmtp) REVERT: F 45 ASN cc_start: 0.7113 (t0) cc_final: 0.5902 (t0) REVERT: G 116 LYS cc_start: 0.8086 (ttpp) cc_final: 0.7833 (tmtt) REVERT: H 45 ASN cc_start: 0.7006 (t0) cc_final: 0.6765 (t0) REVERT: J 45 ASN cc_start: 0.7086 (t0) cc_final: 0.6790 (t0) REVERT: K 45 ASN cc_start: 0.7316 (t0) cc_final: 0.6891 (t0) REVERT: L 45 ASN cc_start: 0.7425 (t0) cc_final: 0.6870 (t0) REVERT: N 45 ASN cc_start: 0.7108 (t0) cc_final: 0.6859 (t0) REVERT: N 74 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8126 (mt) REVERT: O 45 ASN cc_start: 0.6897 (t0) cc_final: 0.6573 (t0) REVERT: O 147 ILE cc_start: 0.8487 (pt) cc_final: 0.8275 (pt) REVERT: T 390 ASN cc_start: 0.8136 (t0) cc_final: 0.7934 (t0) REVERT: U 390 ASN cc_start: 0.8268 (t0) cc_final: 0.8061 (t0) REVERT: V 390 ASN cc_start: 0.8415 (t0) cc_final: 0.8189 (t0) REVERT: X 379 LYS cc_start: 0.8557 (mttt) cc_final: 0.8049 (mttt) REVERT: X 383 LEU cc_start: 0.8967 (tp) cc_final: 0.8741 (tp) REVERT: X 390 ASN cc_start: 0.7896 (t0) cc_final: 0.7591 (t0) REVERT: X 432 GLU cc_start: 0.8391 (tp30) cc_final: 0.8135 (tp30) REVERT: Y 390 ASN cc_start: 0.7903 (t0) cc_final: 0.7694 (t0) REVERT: Z 432 GLU cc_start: 0.8547 (tp30) cc_final: 0.8292 (tp30) REVERT: a 390 ASN cc_start: 0.8126 (t0) cc_final: 0.7706 (t0) REVERT: b 390 ASN cc_start: 0.8128 (t0) cc_final: 0.7923 (t0) REVERT: c 390 ASN cc_start: 0.8337 (t0) cc_final: 0.8048 (t0) REVERT: j 173 TYR cc_start: 0.7553 (m-80) cc_final: 0.7125 (m-10) outliers start: 42 outliers final: 12 residues processed: 1252 average time/residue: 0.5831 time to fit residues: 1188.8290 Evaluate side-chains 643 residues out of total 4662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 630 time to evaluate : 5.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ARG Chi-restraints excluded: chain C residue 14 ARG Chi-restraints excluded: chain D residue 14 ARG Chi-restraints excluded: chain E residue 14 ARG Chi-restraints excluded: chain H residue 14 ARG Chi-restraints excluded: chain I residue 14 ARG Chi-restraints excluded: chain I residue 74 LEU Chi-restraints excluded: chain J residue 14 ARG Chi-restraints excluded: chain K residue 14 ARG Chi-restraints excluded: chain L residue 14 ARG Chi-restraints excluded: chain M residue 14 ARG Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain O residue 14 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 508 optimal weight: 2.9990 chunk 456 optimal weight: 1.9990 chunk 253 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 307 optimal weight: 0.9990 chunk 243 optimal weight: 6.9990 chunk 471 optimal weight: 4.9990 chunk 182 optimal weight: 4.9990 chunk 286 optimal weight: 9.9990 chunk 351 optimal weight: 3.9990 chunk 546 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN C 80 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: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 47304 Z= 0.246 Angle : 0.640 7.271 64019 Z= 0.344 Chirality : 0.043 0.182 7279 Planarity : 0.004 0.049 8442 Dihedral : 5.246 68.619 6936 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.64 % Allowed : 14.25 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.11), residues: 6062 helix: 2.25 (0.10), residues: 2590 sheet: 0.26 (0.13), residues: 1484 loop : -0.58 (0.13), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP c 429 HIS 0.001 0.000 HIS C 129 PHE 0.036 0.002 PHE K 71 TYR 0.015 0.001 TYR Q 308 ARG 0.006 0.001 ARG O 140 *********************** 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 825 residues out of total 4662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 702 time to evaluate : 5.467 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: A 45 ASN cc_start: 0.7286 (t0) cc_final: 0.5755 (t0) REVERT: C 53 ILE cc_start: 0.9340 (pt) cc_final: 0.9038 (pt) REVERT: C 209 GLU cc_start: 0.6454 (tt0) cc_final: 0.5257 (tt0) REVERT: D 113 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7999 (mm-30) REVERT: D 116 LYS cc_start: 0.8284 (ttpp) cc_final: 0.7836 (tmtt) REVERT: D 141 ILE cc_start: 0.9140 (mp) cc_final: 0.8803 (tt) REVERT: E 45 ASN cc_start: 0.7277 (t0) cc_final: 0.6720 (t0) REVERT: F 167 LEU cc_start: 0.8858 (mt) cc_final: 0.8549 (tp) REVERT: G 167 LEU cc_start: 0.8846 (mt) cc_final: 0.8626 (tp) REVERT: H 45 ASN cc_start: 0.7144 (t0) cc_final: 0.6897 (t0) REVERT: H 163 ILE cc_start: 0.7922 (mt) cc_final: 0.7525 (mt) REVERT: I 147 ILE cc_start: 0.9268 (pt) cc_final: 0.9023 (pt) REVERT: J 45 ASN cc_start: 0.7412 (t0) cc_final: 0.6151 (t0) REVERT: J 167 LEU cc_start: 0.8816 (mt) cc_final: 0.8609 (tp) REVERT: K 52 LYS cc_start: 0.8677 (mtmt) cc_final: 0.8448 (mtpp) REVERT: L 45 ASN cc_start: 0.7284 (t0) cc_final: 0.7049 (t0) REVERT: L 216 ASN cc_start: 0.8840 (t0) cc_final: 0.8554 (t0) REVERT: O 14 ARG cc_start: 0.9239 (OUTLIER) cc_final: 0.8941 (mtm-85) REVERT: O 45 ASN cc_start: 0.7093 (t0) cc_final: 0.6144 (t0) REVERT: O 163 ILE cc_start: 0.7928 (mt) cc_final: 0.7562 (mt) REVERT: R 330 ASP cc_start: 0.8691 (p0) cc_final: 0.8454 (p0) REVERT: T 390 ASN cc_start: 0.8499 (t0) cc_final: 0.8206 (t0) REVERT: U 390 ASN cc_start: 0.8550 (t0) cc_final: 0.8316 (t0) REVERT: V 390 ASN cc_start: 0.8451 (t0) cc_final: 0.8147 (t0) REVERT: Y 390 ASN cc_start: 0.8263 (t0) cc_final: 0.7953 (t0) REVERT: b 390 ASN cc_start: 0.8267 (t0) cc_final: 0.8028 (t0) REVERT: b 430 ASN cc_start: 0.8350 (t0) cc_final: 0.8099 (t0) REVERT: c 390 ASN cc_start: 0.8454 (t0) cc_final: 0.8167 (t0) REVERT: h 173 TYR cc_start: 0.7911 (m-80) cc_final: 0.7486 (m-80) outliers start: 123 outliers final: 61 residues processed: 785 average time/residue: 0.5968 time to fit residues: 762.6540 Evaluate side-chains 641 residues out of total 4662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 579 time to evaluate : 4.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ARG Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain C residue 14 ARG Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain D residue 14 ARG Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain E residue 14 ARG Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 179 ASP Chi-restraints excluded: chain H residue 14 ARG Chi-restraints excluded: chain H residue 58 ASP Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 179 ASP Chi-restraints excluded: chain I residue 14 ARG Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain I residue 179 ASP Chi-restraints excluded: chain J residue 14 ARG Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain K residue 14 ARG Chi-restraints excluded: chain K residue 48 ARG Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 179 ASP Chi-restraints excluded: chain L residue 14 ARG Chi-restraints excluded: chain L residue 72 ASP Chi-restraints excluded: chain L residue 179 ASP Chi-restraints excluded: chain M residue 58 ASP Chi-restraints excluded: chain M residue 72 ASP Chi-restraints excluded: chain M residue 179 ASP Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain N residue 149 ASP Chi-restraints excluded: chain N residue 179 ASP Chi-restraints excluded: chain O residue 14 ARG Chi-restraints excluded: chain O residue 58 ASP Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain O residue 99 LEU Chi-restraints excluded: chain O residue 149 ASP Chi-restraints excluded: chain O residue 179 ASP Chi-restraints excluded: chain P residue 363 LEU Chi-restraints excluded: chain P residue 457 VAL Chi-restraints excluded: chain R residue 363 LEU Chi-restraints excluded: chain R residue 456 GLN Chi-restraints excluded: chain T residue 363 LEU Chi-restraints excluded: chain W residue 457 VAL Chi-restraints excluded: chain Y residue 363 LEU Chi-restraints excluded: chain Y residue 386 MET Chi-restraints excluded: chain Z residue 363 LEU Chi-restraints excluded: chain a residue 363 LEU Chi-restraints excluded: chain a residue 457 VAL Chi-restraints excluded: chain b residue 410 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 303 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 454 optimal weight: 5.9990 chunk 372 optimal weight: 5.9990 chunk 150 optimal weight: 2.9990 chunk 547 optimal weight: 0.9990 chunk 591 optimal weight: 7.9990 chunk 487 optimal weight: 0.9980 chunk 543 optimal weight: 3.9990 chunk 186 optimal weight: 6.9990 chunk 439 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 H 98 GLN ** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 114 GLN N 51 GLN ** 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 R 390 ASN X 390 ASN ** f 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.5505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 47304 Z= 0.226 Angle : 0.618 14.010 64019 Z= 0.322 Chirality : 0.042 0.168 7279 Planarity : 0.004 0.047 8442 Dihedral : 4.738 59.530 6928 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.21 % Allowed : 15.45 % Favored : 82.34 % 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: 1.78 (0.11), residues: 6062 helix: 2.80 (0.10), residues: 2604 sheet: 0.86 (0.14), residues: 1386 loop : -0.75 (0.13), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP S 429 HIS 0.002 0.000 HIS T 365 PHE 0.029 0.002 PHE K 71 TYR 0.015 0.001 TYR l 173 ARG 0.005 0.000 ARG M 14 *********************** 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 748 residues out of total 4662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 645 time to evaluate : 5.589 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: A 45 ASN cc_start: 0.8208 (t0) cc_final: 0.7782 (t0) REVERT: B 172 GLN cc_start: 0.7514 (pt0) cc_final: 0.7202 (pm20) REVERT: C 53 ILE cc_start: 0.9361 (pt) cc_final: 0.9061 (pt) REVERT: D 116 LYS cc_start: 0.8461 (ttpp) cc_final: 0.7680 (ttpp) REVERT: F 167 LEU cc_start: 0.8884 (mt) cc_final: 0.8617 (tp) REVERT: G 45 ASN cc_start: 0.7849 (t0) cc_final: 0.7545 (t0) REVERT: G 116 LYS cc_start: 0.8135 (tmtt) cc_final: 0.6986 (tmtt) REVERT: G 167 LEU cc_start: 0.8810 (mt) cc_final: 0.8577 (tp) REVERT: H 45 ASN cc_start: 0.7943 (t0) cc_final: 0.7537 (t0) REVERT: J 45 ASN cc_start: 0.7821 (t0) cc_final: 0.7467 (t0) REVERT: J 167 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8643 (tp) REVERT: K 45 ASN cc_start: 0.7666 (t0) cc_final: 0.7461 (t0) REVERT: K 141 ILE cc_start: 0.9139 (mp) cc_final: 0.8846 (tt) REVERT: L 45 ASN cc_start: 0.7800 (t0) cc_final: 0.6917 (t0) REVERT: L 216 ASN cc_start: 0.8903 (t0) cc_final: 0.8542 (t0) REVERT: M 45 ASN cc_start: 0.7595 (t0) cc_final: 0.7356 (t0) REVERT: N 167 LEU cc_start: 0.8804 (mt) cc_final: 0.8578 (tp) REVERT: P 325 MET cc_start: 0.8016 (tmm) cc_final: 0.7722 (tmm) REVERT: Q 326 ILE cc_start: 0.9125 (OUTLIER) cc_final: 0.8846 (pt) REVERT: X 410 HIS cc_start: 0.8370 (OUTLIER) cc_final: 0.8022 (t70) REVERT: Y 325 MET cc_start: 0.7718 (tmm) cc_final: 0.7453 (tmm) REVERT: Z 325 MET cc_start: 0.8270 (tmm) cc_final: 0.7901 (tmm) REVERT: b 430 ASN cc_start: 0.8371 (t0) cc_final: 0.8160 (t0) REVERT: i 173 TYR cc_start: 0.7915 (m-80) cc_final: 0.7394 (m-80) outliers start: 103 outliers final: 61 residues processed: 701 average time/residue: 0.6092 time to fit residues: 689.9198 Evaluate side-chains 606 residues out of total 4662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 542 time to evaluate : 4.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ARG Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain C residue 14 ARG Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain D residue 14 ARG Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain E residue 14 ARG Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 179 ASP Chi-restraints excluded: chain H residue 14 ARG Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 179 ASP Chi-restraints excluded: chain I residue 14 ARG Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 179 ASP Chi-restraints excluded: chain J residue 14 ARG Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 179 ASP Chi-restraints excluded: chain K residue 14 ARG Chi-restraints excluded: chain K residue 48 ARG Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 174 ASN Chi-restraints excluded: chain K residue 179 ASP Chi-restraints excluded: chain L residue 14 ARG Chi-restraints excluded: chain L residue 72 ASP Chi-restraints excluded: chain L residue 154 VAL Chi-restraints excluded: chain L residue 179 ASP Chi-restraints excluded: chain M residue 72 ASP Chi-restraints excluded: chain M residue 149 ASP Chi-restraints excluded: chain M residue 179 ASP Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain N residue 149 ASP Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 179 ASP Chi-restraints excluded: chain O residue 14 ARG Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain O residue 103 TYR Chi-restraints excluded: chain O residue 149 ASP Chi-restraints excluded: chain O residue 179 ASP Chi-restraints excluded: chain P residue 363 LEU Chi-restraints excluded: chain Q residue 326 ILE Chi-restraints excluded: chain Q residue 330 ASP Chi-restraints excluded: chain Q residue 447 LYS Chi-restraints excluded: chain R residue 363 LEU Chi-restraints excluded: chain S residue 363 LEU Chi-restraints excluded: chain T residue 363 LEU Chi-restraints excluded: chain U residue 363 LEU Chi-restraints excluded: chain X residue 410 HIS Chi-restraints excluded: chain Y residue 410 HIS Chi-restraints excluded: chain Z residue 363 LEU Chi-restraints excluded: chain a residue 363 LEU 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: 5.9990 chunk 284 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 261 optimal weight: 1.9990 chunk 367 optimal weight: 2.9990 chunk 549 optimal weight: 2.9990 chunk 581 optimal weight: 7.9990 chunk 287 optimal weight: 0.9980 chunk 520 optimal weight: 4.9990 chunk 156 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 GLN C 174 ASN D 174 ASN ** D 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN E 165 ASN ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 114 GLN I 114 GLN ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 114 GLN ** L 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 114 GLN ** N 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 114 GLN P 415 GLN ** Q 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 415 GLN U 415 GLN V 415 GLN W 415 GLN Y 415 GLN ** a 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 415 GLN l 172 GLN ** m 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.6504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 47304 Z= 0.280 Angle : 0.636 13.562 64019 Z= 0.335 Chirality : 0.042 0.145 7279 Planarity : 0.004 0.043 8442 Dihedral : 4.768 59.200 6928 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.25 % Allowed : 16.63 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.11), residues: 6062 helix: 2.95 (0.10), residues: 2562 sheet: 0.98 (0.13), residues: 1386 loop : -0.84 (0.13), residues: 2114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP X 429 HIS 0.002 0.000 HIS H 152 PHE 0.033 0.002 PHE E 71 TYR 0.016 0.001 TYR b 359 ARG 0.004 0.000 ARG D 26 *********************** 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 708 residues out of total 4662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 603 time to evaluate : 5.307 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: A 45 ASN cc_start: 0.8467 (t0) cc_final: 0.7979 (t0) REVERT: A 118 TYR cc_start: 0.9274 (m-80) cc_final: 0.9039 (m-80) REVERT: C 45 ASN cc_start: 0.8532 (t0) cc_final: 0.8321 (t0) REVERT: C 163 ILE cc_start: 0.8732 (mm) cc_final: 0.8404 (mm) REVERT: E 163 ILE cc_start: 0.8699 (mm) cc_final: 0.8468 (mm) REVERT: F 118 TYR cc_start: 0.9142 (m-80) cc_final: 0.8792 (m-80) REVERT: F 216 ASN cc_start: 0.9035 (t0) cc_final: 0.8679 (t0) REVERT: G 45 ASN cc_start: 0.8029 (t0) cc_final: 0.7693 (t0) REVERT: H 45 ASN cc_start: 0.8231 (t0) cc_final: 0.7745 (t0) REVERT: H 167 LEU cc_start: 0.9059 (tt) cc_final: 0.8588 (tp) REVERT: I 45 ASN cc_start: 0.7993 (t0) cc_final: 0.7778 (t0) REVERT: I 163 ILE cc_start: 0.8756 (mm) cc_final: 0.8293 (mm) REVERT: J 45 ASN cc_start: 0.8301 (t0) cc_final: 0.7733 (t0) REVERT: J 167 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8631 (tp) REVERT: K 45 ASN cc_start: 0.7996 (t0) cc_final: 0.7624 (t0) REVERT: L 45 ASN cc_start: 0.8336 (t0) cc_final: 0.7916 (t0) REVERT: L 216 ASN cc_start: 0.9008 (t0) cc_final: 0.8687 (t0) REVERT: M 45 ASN cc_start: 0.8158 (t0) cc_final: 0.7776 (t0) REVERT: M 116 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8873 (ttpp) REVERT: N 45 ASN cc_start: 0.7837 (t0) cc_final: 0.7603 (t0) REVERT: N 167 LEU cc_start: 0.8855 (mt) cc_final: 0.8596 (tp) REVERT: O 45 ASN cc_start: 0.8481 (t0) cc_final: 0.7777 (t0) REVERT: O 163 ILE cc_start: 0.8175 (mp) cc_final: 0.7942 (mm) REVERT: P 325 MET cc_start: 0.8246 (tmm) cc_final: 0.7900 (tmm) REVERT: Q 390 ASN cc_start: 0.8595 (t0) cc_final: 0.8383 (t0) REVERT: S 330 ASP cc_start: 0.9133 (p0) cc_final: 0.8792 (p0) REVERT: T 330 ASP cc_start: 0.9099 (p0) cc_final: 0.8695 (p0) REVERT: U 330 ASP cc_start: 0.9054 (p0) cc_final: 0.8743 (p0) REVERT: W 330 ASP cc_start: 0.9006 (p0) cc_final: 0.8652 (p0) REVERT: X 330 ASP cc_start: 0.8880 (p0) cc_final: 0.8593 (p0) REVERT: X 359 TYR cc_start: 0.8776 (t80) cc_final: 0.8559 (t80) REVERT: X 390 ASN cc_start: 0.8485 (t0) cc_final: 0.8231 (t0) REVERT: Y 325 MET cc_start: 0.8193 (tmm) cc_final: 0.7950 (tmm) REVERT: a 330 ASP cc_start: 0.9100 (p0) cc_final: 0.8710 (p0) REVERT: b 325 MET cc_start: 0.8013 (tmm) cc_final: 0.7812 (tmm) REVERT: b 330 ASP cc_start: 0.9082 (p0) cc_final: 0.8777 (p0) REVERT: i 173 TYR cc_start: 0.7962 (m-80) cc_final: 0.7463 (m-80) REVERT: l 172 GLN cc_start: 0.7628 (OUTLIER) cc_final: 0.7314 (pm20) REVERT: l 173 TYR cc_start: 0.8159 (m-80) cc_final: 0.7775 (m-10) outliers start: 105 outliers final: 74 residues processed: 652 average time/residue: 0.5975 time to fit residues: 629.8491 Evaluate side-chains 621 residues out of total 4662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 544 time to evaluate : 5.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ARG Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain C residue 14 ARG Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain D residue 14 ARG Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain E residue 14 ARG Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 103 TYR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 103 TYR Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 179 ASP Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 179 ASP Chi-restraints excluded: chain I residue 14 ARG Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain I residue 179 ASP Chi-restraints excluded: chain J residue 14 ARG Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 179 ASP Chi-restraints excluded: chain K residue 14 ARG Chi-restraints excluded: chain K residue 48 ARG Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 179 ASP Chi-restraints excluded: chain L residue 14 ARG Chi-restraints excluded: chain L residue 72 ASP Chi-restraints excluded: chain L residue 99 LEU Chi-restraints excluded: chain L residue 103 TYR Chi-restraints excluded: chain L residue 154 VAL Chi-restraints excluded: chain L residue 179 ASP Chi-restraints excluded: chain M residue 72 ASP Chi-restraints excluded: chain M residue 103 TYR Chi-restraints excluded: chain M residue 116 LYS Chi-restraints excluded: chain M residue 179 ASP Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain N residue 103 TYR Chi-restraints excluded: chain N residue 149 ASP Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 179 ASP Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain O residue 103 TYR Chi-restraints excluded: chain O residue 149 ASP Chi-restraints excluded: chain O residue 179 ASP Chi-restraints excluded: chain P residue 372 VAL Chi-restraints excluded: chain Q residue 330 ASP Chi-restraints excluded: chain Q residue 372 VAL Chi-restraints excluded: chain Q residue 447 LYS Chi-restraints excluded: chain R residue 363 LEU Chi-restraints excluded: chain R residue 372 VAL Chi-restraints excluded: chain S residue 363 LEU Chi-restraints excluded: chain T residue 363 LEU Chi-restraints excluded: chain U residue 363 LEU Chi-restraints excluded: chain U residue 372 VAL Chi-restraints excluded: chain V residue 363 LEU Chi-restraints excluded: chain X residue 372 VAL Chi-restraints excluded: chain Y residue 372 VAL Chi-restraints excluded: chain Y residue 522 SER Chi-restraints excluded: chain Z residue 522 SER Chi-restraints excluded: chain a residue 363 LEU Chi-restraints excluded: chain b residue 372 VAL Chi-restraints excluded: chain l residue 172 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 484 optimal weight: 4.9990 chunk 330 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 433 optimal weight: 0.9980 chunk 240 optimal weight: 4.9990 chunk 496 optimal weight: 0.9990 chunk 402 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 297 optimal weight: 4.9990 chunk 522 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 H 114 GLN I 114 GLN J 114 GLN K 114 GLN L 114 GLN M 114 GLN N 114 GLN O 114 GLN ** Q 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 415 GLN ** m 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.6781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 47304 Z= 0.173 Angle : 0.575 10.630 64019 Z= 0.301 Chirality : 0.042 0.151 7279 Planarity : 0.003 0.040 8442 Dihedral : 4.469 59.913 6920 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.17 % Allowed : 17.36 % Favored : 80.48 % 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: 3.09 (0.10), residues: 2576 sheet: 1.19 (0.14), residues: 1386 loop : -0.85 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP S 429 HIS 0.002 0.000 HIS U 365 PHE 0.031 0.001 PHE E 71 TYR 0.022 0.001 TYR l 173 ARG 0.007 0.000 ARG O 48 *********************** 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 706 residues out of total 4662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 605 time to evaluate : 5.310 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: A 45 ASN cc_start: 0.8445 (t0) cc_final: 0.7930 (t0) REVERT: A 118 TYR cc_start: 0.9203 (m-80) cc_final: 0.8910 (m-80) REVERT: C 45 ASN cc_start: 0.8587 (t0) cc_final: 0.8276 (t0) REVERT: C 163 ILE cc_start: 0.8609 (mm) cc_final: 0.8284 (mm) REVERT: C 167 LEU cc_start: 0.8949 (tp) cc_final: 0.8725 (tp) REVERT: D 118 TYR cc_start: 0.9284 (m-80) cc_final: 0.8793 (m-80) REVERT: E 163 ILE cc_start: 0.8704 (mm) cc_final: 0.8383 (mm) REVERT: E 216 ASN cc_start: 0.9012 (t0) cc_final: 0.8701 (t0) REVERT: F 118 TYR cc_start: 0.9184 (m-80) cc_final: 0.8785 (m-80) REVERT: F 216 ASN cc_start: 0.9039 (t0) cc_final: 0.8707 (t0) REVERT: G 45 ASN cc_start: 0.8130 (t0) cc_final: 0.7759 (t0) REVERT: G 167 LEU cc_start: 0.8857 (mt) cc_final: 0.8591 (tp) REVERT: H 45 ASN cc_start: 0.8310 (t0) cc_final: 0.7734 (t0) REVERT: H 167 LEU cc_start: 0.9073 (tt) cc_final: 0.8640 (tp) REVERT: I 45 ASN cc_start: 0.7963 (t0) cc_final: 0.7580 (t0) REVERT: J 45 ASN cc_start: 0.8251 (t0) cc_final: 0.7711 (t0) REVERT: J 167 LEU cc_start: 0.8883 (mt) cc_final: 0.8600 (tp) REVERT: K 45 ASN cc_start: 0.8002 (t0) cc_final: 0.7641 (t0) REVERT: K 216 ASN cc_start: 0.9115 (t0) cc_final: 0.8759 (t0) REVERT: L 45 ASN cc_start: 0.8362 (t0) cc_final: 0.7956 (t0) REVERT: L 216 ASN cc_start: 0.8941 (t0) cc_final: 0.8595 (t0) REVERT: M 45 ASN cc_start: 0.8171 (t0) cc_final: 0.7825 (t0) REVERT: N 45 ASN cc_start: 0.7879 (t0) cc_final: 0.7572 (t0) REVERT: N 167 LEU cc_start: 0.8853 (mt) cc_final: 0.8595 (tp) REVERT: O 45 ASN cc_start: 0.8561 (t0) cc_final: 0.8020 (t0) REVERT: O 167 LEU cc_start: 0.8913 (tp) cc_final: 0.8682 (tp) REVERT: P 325 MET cc_start: 0.8284 (tmm) cc_final: 0.7998 (tmm) REVERT: Q 390 ASN cc_start: 0.8462 (t0) cc_final: 0.8223 (t0) REVERT: S 330 ASP cc_start: 0.9095 (p0) cc_final: 0.8742 (p0) REVERT: T 330 ASP cc_start: 0.9054 (p0) cc_final: 0.8681 (p0) REVERT: U 330 ASP cc_start: 0.9036 (p0) cc_final: 0.8715 (p0) REVERT: W 330 ASP cc_start: 0.8963 (p0) cc_final: 0.8539 (p0) REVERT: X 330 ASP cc_start: 0.8910 (p0) cc_final: 0.8587 (p0) REVERT: X 359 TYR cc_start: 0.8665 (t80) cc_final: 0.8406 (t80) REVERT: X 390 ASN cc_start: 0.8383 (t0) cc_final: 0.8176 (t0) REVERT: b 330 ASP cc_start: 0.9059 (p0) cc_final: 0.8758 (p0) REVERT: c 324 ASN cc_start: 0.8593 (p0) cc_final: 0.8226 (p0) REVERT: i 173 TYR cc_start: 0.7826 (m-80) cc_final: 0.7491 (m-10) outliers start: 101 outliers final: 76 residues processed: 654 average time/residue: 0.6376 time to fit residues: 681.2299 Evaluate side-chains 629 residues out of total 4662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 553 time to evaluate : 5.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain C residue 14 ARG Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain D residue 14 ARG Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 103 TYR Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 103 TYR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 103 TYR Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 179 ASP Chi-restraints excluded: chain H residue 14 ARG Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 179 ASP Chi-restraints excluded: chain I residue 14 ARG Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain I residue 179 ASP Chi-restraints excluded: chain J residue 14 ARG Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain J residue 103 TYR Chi-restraints excluded: chain J residue 116 LYS Chi-restraints excluded: chain J residue 179 ASP Chi-restraints excluded: chain K residue 14 ARG Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 103 TYR Chi-restraints excluded: chain K residue 179 ASP Chi-restraints excluded: chain L residue 14 ARG Chi-restraints excluded: chain L residue 72 ASP Chi-restraints excluded: chain L residue 103 TYR Chi-restraints excluded: chain L residue 154 VAL Chi-restraints excluded: chain L residue 179 ASP Chi-restraints excluded: chain M residue 72 ASP Chi-restraints excluded: chain M residue 103 TYR Chi-restraints excluded: chain M residue 116 LYS Chi-restraints excluded: chain M residue 149 ASP Chi-restraints excluded: chain M residue 179 ASP Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain N residue 103 TYR Chi-restraints excluded: chain N residue 149 ASP Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 179 ASP Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain O residue 103 TYR Chi-restraints excluded: chain O residue 149 ASP Chi-restraints excluded: chain O residue 179 ASP Chi-restraints excluded: chain Q residue 330 ASP Chi-restraints excluded: chain Q residue 363 LEU Chi-restraints excluded: chain R residue 363 LEU Chi-restraints excluded: chain R residue 372 VAL Chi-restraints excluded: chain S residue 363 LEU Chi-restraints excluded: chain T residue 363 LEU Chi-restraints excluded: chain U residue 363 LEU Chi-restraints excluded: chain V residue 363 LEU Chi-restraints excluded: chain W residue 372 VAL Chi-restraints excluded: chain Y residue 372 VAL Chi-restraints excluded: chain Y residue 410 HIS Chi-restraints excluded: chain Y residue 522 SER Chi-restraints excluded: chain a residue 363 LEU Chi-restraints excluded: chain a residue 504 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 195 optimal weight: 0.8980 chunk 524 optimal weight: 7.9990 chunk 115 optimal weight: 9.9990 chunk 341 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 582 optimal weight: 5.9990 chunk 483 optimal weight: 0.0980 chunk 269 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 192 optimal weight: 6.9990 chunk 305 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 GLN F 114 GLN ** G 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 114 GLN J 114 GLN J 216 ASN K 114 GLN L 114 GLN M 114 GLN M 165 ASN N 114 GLN O 114 GLN ** Q 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.7008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 47304 Z= 0.174 Angle : 0.572 11.473 64019 Z= 0.300 Chirality : 0.042 0.203 7279 Planarity : 0.003 0.040 8442 Dihedral : 4.239 59.189 6912 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.19 % Allowed : 18.28 % Favored : 79.53 % 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: 2.08 (0.11), residues: 6062 helix: 3.11 (0.10), residues: 2576 sheet: 1.27 (0.14), residues: 1386 loop : -0.85 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP Q 429 HIS 0.001 0.000 HIS W 365 PHE 0.033 0.001 PHE F 71 TYR 0.017 0.001 TYR Z 359 ARG 0.008 0.000 ARG E 14 *********************** 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 695 residues out of total 4662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 593 time to evaluate : 5.255 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: A 45 ASN cc_start: 0.8569 (t0) cc_final: 0.8030 (t0) REVERT: A 118 TYR cc_start: 0.9217 (m-80) cc_final: 0.8822 (m-80) REVERT: C 45 ASN cc_start: 0.8505 (t0) cc_final: 0.8198 (t0) REVERT: C 163 ILE cc_start: 0.8591 (mm) cc_final: 0.8252 (mm) REVERT: C 167 LEU cc_start: 0.8892 (tp) cc_final: 0.8678 (tp) REVERT: D 118 TYR cc_start: 0.9290 (m-80) cc_final: 0.8834 (m-80) REVERT: E 163 ILE cc_start: 0.8685 (mm) cc_final: 0.8350 (mm) REVERT: E 216 ASN cc_start: 0.8969 (t0) cc_final: 0.8723 (t0) REVERT: F 67 LYS cc_start: 0.7575 (tppt) cc_final: 0.7019 (tppp) REVERT: F 118 TYR cc_start: 0.9235 (m-80) cc_final: 0.8710 (m-80) REVERT: F 216 ASN cc_start: 0.9078 (t0) cc_final: 0.8732 (t0) REVERT: G 45 ASN cc_start: 0.8187 (t0) cc_final: 0.7807 (t0) REVERT: H 45 ASN cc_start: 0.8271 (t0) cc_final: 0.7670 (t0) REVERT: I 45 ASN cc_start: 0.8040 (t0) cc_final: 0.7608 (t0) REVERT: J 45 ASN cc_start: 0.8341 (t0) cc_final: 0.7796 (t0) REVERT: J 167 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8643 (tp) REVERT: K 45 ASN cc_start: 0.8068 (t0) cc_final: 0.7695 (t0) REVERT: K 216 ASN cc_start: 0.9044 (t0) cc_final: 0.8617 (t0) REVERT: L 45 ASN cc_start: 0.8447 (t0) cc_final: 0.7933 (t0) REVERT: L 216 ASN cc_start: 0.8962 (t0) cc_final: 0.8603 (t0) REVERT: M 45 ASN cc_start: 0.8179 (t0) cc_final: 0.7808 (t0) REVERT: M 216 ASN cc_start: 0.9007 (t0) cc_final: 0.8624 (t0) REVERT: N 45 ASN cc_start: 0.7988 (t0) cc_final: 0.7637 (t0) REVERT: N 167 LEU cc_start: 0.8851 (mt) cc_final: 0.8590 (tp) REVERT: O 45 ASN cc_start: 0.8569 (t0) cc_final: 0.7977 (t0) REVERT: O 67 LYS cc_start: 0.7641 (mmmm) cc_final: 0.7399 (mmmm) REVERT: O 167 LEU cc_start: 0.8872 (tp) cc_final: 0.8644 (tp) REVERT: P 325 MET cc_start: 0.8303 (tmm) cc_final: 0.8067 (tmm) REVERT: P 330 ASP cc_start: 0.8797 (p0) cc_final: 0.8531 (p0) REVERT: Q 390 ASN cc_start: 0.8483 (t0) cc_final: 0.8276 (t0) REVERT: S 330 ASP cc_start: 0.9088 (p0) cc_final: 0.8727 (p0) REVERT: T 330 ASP cc_start: 0.9050 (p0) cc_final: 0.8684 (p0) REVERT: U 330 ASP cc_start: 0.9002 (p0) cc_final: 0.8671 (p0) REVERT: W 330 ASP cc_start: 0.8959 (p0) cc_final: 0.8529 (p0) REVERT: Z 330 ASP cc_start: 0.9082 (p0) cc_final: 0.8721 (p0) REVERT: a 330 ASP cc_start: 0.9074 (p0) cc_final: 0.8734 (p0) REVERT: b 330 ASP cc_start: 0.9049 (p0) cc_final: 0.8744 (p0) REVERT: d 173 TYR cc_start: 0.7000 (OUTLIER) cc_final: 0.6772 (t80) REVERT: i 173 TYR cc_start: 0.7729 (m-80) cc_final: 0.7490 (m-10) outliers start: 102 outliers final: 83 residues processed: 633 average time/residue: 0.5853 time to fit residues: 608.6508 Evaluate side-chains 631 residues out of total 4662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 546 time to evaluate : 5.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain C residue 14 ARG Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain D residue 14 ARG Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 103 TYR Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 103 TYR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 174 ASN Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 103 TYR Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 179 ASP Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 179 ASP Chi-restraints excluded: chain I residue 14 ARG Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain I residue 179 ASP Chi-restraints excluded: chain J residue 14 ARG Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain J residue 103 TYR Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 179 ASP Chi-restraints excluded: chain K residue 14 ARG Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 103 TYR Chi-restraints excluded: chain K residue 179 ASP Chi-restraints excluded: chain L residue 14 ARG Chi-restraints excluded: chain L residue 72 ASP Chi-restraints excluded: chain L residue 99 LEU Chi-restraints excluded: chain L residue 103 TYR Chi-restraints excluded: chain L residue 154 VAL Chi-restraints excluded: chain L residue 179 ASP Chi-restraints excluded: chain M residue 72 ASP Chi-restraints excluded: chain M residue 103 TYR Chi-restraints excluded: chain M residue 149 ASP Chi-restraints excluded: chain M residue 179 ASP Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain N residue 103 TYR Chi-restraints excluded: chain N residue 149 ASP Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 179 ASP Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain O residue 103 TYR Chi-restraints excluded: chain O residue 149 ASP Chi-restraints excluded: chain O residue 179 ASP Chi-restraints excluded: chain P residue 372 VAL Chi-restraints excluded: chain Q residue 330 ASP Chi-restraints excluded: chain Q residue 363 LEU Chi-restraints excluded: chain Q residue 447 LYS Chi-restraints excluded: chain R residue 330 ASP Chi-restraints excluded: chain R residue 363 LEU Chi-restraints excluded: chain T residue 363 LEU Chi-restraints excluded: chain U residue 363 LEU Chi-restraints excluded: chain V residue 330 ASP Chi-restraints excluded: chain V residue 363 LEU Chi-restraints excluded: chain V residue 522 SER Chi-restraints excluded: chain W residue 372 VAL Chi-restraints excluded: chain Y residue 522 SER Chi-restraints excluded: chain Z residue 522 SER Chi-restraints excluded: chain a residue 363 LEU Chi-restraints excluded: chain a residue 504 ASP Chi-restraints excluded: chain b residue 363 LEU Chi-restraints excluded: chain d residue 173 TYR Chi-restraints excluded: chain g residue 173 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 561 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 331 optimal weight: 0.5980 chunk 425 optimal weight: 1.9990 chunk 329 optimal weight: 0.7980 chunk 490 optimal weight: 4.9990 chunk 325 optimal weight: 6.9990 chunk 580 optimal weight: 1.9990 chunk 363 optimal weight: 5.9990 chunk 353 optimal weight: 6.9990 chunk 267 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 114 GLN ** G 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 114 GLN J 216 ASN ** J 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 114 GLN M 165 ASN ** O 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 390 ASN X 390 ASN ** h 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.7274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 47304 Z= 0.195 Angle : 0.580 10.450 64019 Z= 0.306 Chirality : 0.042 0.203 7279 Planarity : 0.003 0.039 8442 Dihedral : 4.195 58.845 6912 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.12 % Allowed : 19.09 % Favored : 78.78 % 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: 2.06 (0.11), residues: 6062 helix: 3.04 (0.10), residues: 2576 sheet: 1.32 (0.14), residues: 1386 loop : -0.84 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP b 429 HIS 0.001 0.000 HIS W 365 PHE 0.036 0.001 PHE E 71 TYR 0.016 0.001 TYR b 359 ARG 0.005 0.000 ARG I 48 *********************** 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 688 residues out of total 4662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 589 time to evaluate : 4.941 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: A 45 ASN cc_start: 0.8509 (t0) cc_final: 0.7990 (t0) REVERT: A 67 LYS cc_start: 0.8220 (ttmm) cc_final: 0.8005 (mmmm) REVERT: A 116 LYS cc_start: 0.8808 (tptp) cc_final: 0.8597 (tmtt) REVERT: C 167 LEU cc_start: 0.8943 (tp) cc_final: 0.8726 (tp) REVERT: D 116 LYS cc_start: 0.9342 (OUTLIER) cc_final: 0.9114 (ptmm) REVERT: D 118 TYR cc_start: 0.9330 (m-80) cc_final: 0.8928 (m-80) REVERT: D 216 ASN cc_start: 0.9063 (t0) cc_final: 0.8758 (t0) REVERT: E 216 ASN cc_start: 0.8969 (t0) cc_final: 0.8712 (t0) REVERT: F 67 LYS cc_start: 0.7993 (tppt) cc_final: 0.7671 (mmmm) REVERT: F 216 ASN cc_start: 0.9014 (t0) cc_final: 0.8656 (t0) REVERT: G 45 ASN cc_start: 0.8182 (t0) cc_final: 0.7863 (t0) REVERT: G 216 ASN cc_start: 0.8991 (t0) cc_final: 0.8586 (t0) REVERT: H 45 ASN cc_start: 0.8361 (t0) cc_final: 0.7803 (t0) REVERT: H 216 ASN cc_start: 0.8895 (t0) cc_final: 0.8609 (t0) REVERT: I 45 ASN cc_start: 0.8137 (t0) cc_final: 0.7660 (t0) REVERT: I 216 ASN cc_start: 0.8904 (t0) cc_final: 0.8574 (t0) REVERT: J 45 ASN cc_start: 0.8405 (t0) cc_final: 0.7889 (t0) REVERT: J 114 GLN cc_start: 0.8065 (tp-100) cc_final: 0.7672 (tm-30) REVERT: J 167 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8636 (tp) REVERT: K 45 ASN cc_start: 0.8239 (t0) cc_final: 0.7862 (t0) REVERT: K 118 TYR cc_start: 0.9260 (m-80) cc_final: 0.8841 (m-80) REVERT: K 216 ASN cc_start: 0.9052 (t0) cc_final: 0.8600 (t0) REVERT: L 45 ASN cc_start: 0.8556 (t0) cc_final: 0.8005 (t0) REVERT: L 216 ASN cc_start: 0.8953 (t0) cc_final: 0.8595 (t0) REVERT: M 45 ASN cc_start: 0.8353 (t0) cc_final: 0.7900 (t0) REVERT: M 118 TYR cc_start: 0.8857 (m-80) cc_final: 0.8649 (m-80) REVERT: M 216 ASN cc_start: 0.8995 (t0) cc_final: 0.8640 (t0) REVERT: N 45 ASN cc_start: 0.8114 (t0) cc_final: 0.7743 (t0) REVERT: N 167 LEU cc_start: 0.8861 (mt) cc_final: 0.8621 (tp) REVERT: O 45 ASN cc_start: 0.8623 (t0) cc_final: 0.8075 (t0) REVERT: O 167 LEU cc_start: 0.8879 (tp) cc_final: 0.8634 (tp) REVERT: P 325 MET cc_start: 0.8299 (tmm) cc_final: 0.8071 (tmm) REVERT: P 330 ASP cc_start: 0.8793 (p0) cc_final: 0.8487 (p0) REVERT: S 330 ASP cc_start: 0.9076 (p0) cc_final: 0.8711 (p0) REVERT: T 330 ASP cc_start: 0.9041 (p0) cc_final: 0.8666 (p0) REVERT: U 330 ASP cc_start: 0.8989 (p0) cc_final: 0.8657 (p0) REVERT: W 330 ASP cc_start: 0.8957 (p0) cc_final: 0.8583 (p0) REVERT: X 330 ASP cc_start: 0.8900 (p0) cc_final: 0.8543 (p0) REVERT: X 390 ASN cc_start: 0.8183 (OUTLIER) cc_final: 0.7975 (t0) REVERT: Z 330 ASP cc_start: 0.9072 (p0) cc_final: 0.8710 (p0) REVERT: a 330 ASP cc_start: 0.9068 (p0) cc_final: 0.8736 (p0) REVERT: b 330 ASP cc_start: 0.9050 (p0) cc_final: 0.8747 (p0) outliers start: 99 outliers final: 80 residues processed: 625 average time/residue: 0.5764 time to fit residues: 591.9117 Evaluate side-chains 623 residues out of total 4662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 540 time to evaluate : 5.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 103 TYR Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain C residue 14 ARG Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain D residue 14 ARG Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 103 TYR Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 103 TYR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 103 TYR Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 179 ASP Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 179 ASP Chi-restraints excluded: chain I residue 14 ARG Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain I residue 179 ASP Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain J residue 103 TYR Chi-restraints excluded: chain J residue 116 LYS Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 179 ASP Chi-restraints excluded: chain K residue 14 ARG Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 103 TYR Chi-restraints excluded: chain K residue 179 ASP Chi-restraints excluded: chain L residue 14 ARG Chi-restraints excluded: chain L residue 72 ASP Chi-restraints excluded: chain L residue 99 LEU Chi-restraints excluded: chain L residue 103 TYR Chi-restraints excluded: chain L residue 154 VAL Chi-restraints excluded: chain L residue 179 ASP Chi-restraints excluded: chain M residue 72 ASP Chi-restraints excluded: chain M residue 103 TYR Chi-restraints excluded: chain M residue 149 ASP Chi-restraints excluded: chain M residue 179 ASP Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain N residue 103 TYR Chi-restraints excluded: chain N residue 149 ASP Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 179 ASP Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain O residue 103 TYR Chi-restraints excluded: chain O residue 149 ASP Chi-restraints excluded: chain O residue 179 ASP Chi-restraints excluded: chain P residue 372 VAL Chi-restraints excluded: chain Q residue 330 ASP Chi-restraints excluded: chain Q residue 447 LYS Chi-restraints excluded: chain T residue 363 LEU Chi-restraints excluded: chain U residue 363 LEU Chi-restraints excluded: chain U residue 450 MET Chi-restraints excluded: chain V residue 330 ASP Chi-restraints excluded: chain V residue 363 LEU Chi-restraints excluded: chain V residue 522 SER Chi-restraints excluded: chain X residue 390 ASN Chi-restraints excluded: chain Y residue 330 ASP Chi-restraints excluded: chain Y residue 363 LEU Chi-restraints excluded: chain Y residue 522 SER Chi-restraints excluded: chain Z residue 522 SER Chi-restraints excluded: chain a residue 363 LEU Chi-restraints excluded: chain a residue 504 ASP Chi-restraints excluded: chain b residue 363 LEU Chi-restraints excluded: chain b residue 450 MET Chi-restraints excluded: chain g residue 173 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 358 optimal weight: 7.9990 chunk 231 optimal weight: 1.9990 chunk 346 optimal weight: 0.8980 chunk 174 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 112 optimal weight: 4.9990 chunk 368 optimal weight: 1.9990 chunk 395 optimal weight: 1.9990 chunk 286 optimal weight: 9.9990 chunk 54 optimal weight: 0.0970 chunk 456 optimal weight: 1.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 GLN J 216 ASN ** J 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 165 ASN M 165 ASN ** O 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.7444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 47304 Z= 0.170 Angle : 0.598 14.238 64019 Z= 0.311 Chirality : 0.042 0.202 7279 Planarity : 0.003 0.038 8442 Dihedral : 4.096 59.339 6908 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.85 % Allowed : 20.06 % Favored : 78.09 % 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: 2.07 (0.11), residues: 6062 helix: 3.06 (0.10), residues: 2562 sheet: 1.23 (0.13), residues: 1428 loop : -0.78 (0.13), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP T 429 HIS 0.002 0.000 HIS Q 365 PHE 0.034 0.001 PHE H 71 TYR 0.015 0.001 TYR o 173 ARG 0.007 0.000 ARG C 48 *********************** 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 682 residues out of total 4662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 596 time to evaluate : 5.458 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: A 45 ASN cc_start: 0.8451 (t0) cc_final: 0.7965 (t0) REVERT: A 116 LYS cc_start: 0.8773 (tptp) cc_final: 0.8523 (tmtt) REVERT: C 167 LEU cc_start: 0.8931 (tp) cc_final: 0.8699 (tp) REVERT: C 216 ASN cc_start: 0.9050 (t0) cc_final: 0.8774 (t0) REVERT: D 118 TYR cc_start: 0.9355 (m-80) cc_final: 0.9029 (m-80) REVERT: D 216 ASN cc_start: 0.9099 (t0) cc_final: 0.8819 (t0) REVERT: E 216 ASN cc_start: 0.8954 (t0) cc_final: 0.8696 (t0) REVERT: F 67 LYS cc_start: 0.7826 (tppt) cc_final: 0.7567 (mmmm) REVERT: F 216 ASN cc_start: 0.8998 (t0) cc_final: 0.8646 (t0) REVERT: G 45 ASN cc_start: 0.8116 (t0) cc_final: 0.7584 (t0) REVERT: G 216 ASN cc_start: 0.8932 (t0) cc_final: 0.8589 (t0) REVERT: H 45 ASN cc_start: 0.8314 (t0) cc_final: 0.7763 (t0) REVERT: H 216 ASN cc_start: 0.8906 (t0) cc_final: 0.8638 (t0) REVERT: I 45 ASN cc_start: 0.8119 (t0) cc_final: 0.7637 (t0) REVERT: I 118 TYR cc_start: 0.9117 (m-80) cc_final: 0.8880 (m-80) REVERT: I 216 ASN cc_start: 0.8917 (t0) cc_final: 0.8663 (t0) REVERT: J 45 ASN cc_start: 0.8440 (t0) cc_final: 0.7871 (t0) REVERT: J 167 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8679 (tp) REVERT: K 45 ASN cc_start: 0.8205 (t0) cc_final: 0.7837 (t0) REVERT: K 118 TYR cc_start: 0.9270 (m-80) cc_final: 0.8860 (m-80) REVERT: K 216 ASN cc_start: 0.9019 (t0) cc_final: 0.8698 (t0) REVERT: L 45 ASN cc_start: 0.8518 (t0) cc_final: 0.7971 (t0) REVERT: L 216 ASN cc_start: 0.8988 (t0) cc_final: 0.8605 (t0) REVERT: M 45 ASN cc_start: 0.8317 (t0) cc_final: 0.7856 (t0) REVERT: M 216 ASN cc_start: 0.8968 (t0) cc_final: 0.8600 (t0) REVERT: N 45 ASN cc_start: 0.8059 (t0) cc_final: 0.7532 (t0) REVERT: N 167 LEU cc_start: 0.8865 (mt) cc_final: 0.8609 (tp) REVERT: O 45 ASN cc_start: 0.8622 (t0) cc_final: 0.8089 (t0) REVERT: O 167 LEU cc_start: 0.8862 (tp) cc_final: 0.8609 (tp) REVERT: P 330 ASP cc_start: 0.8765 (p0) cc_final: 0.8459 (p0) REVERT: S 330 ASP cc_start: 0.9037 (p0) cc_final: 0.8669 (p0) REVERT: U 330 ASP cc_start: 0.8955 (p0) cc_final: 0.8618 (p0) REVERT: W 330 ASP cc_start: 0.8951 (p0) cc_final: 0.8568 (p0) REVERT: X 330 ASP cc_start: 0.8896 (p0) cc_final: 0.8543 (p0) REVERT: Z 330 ASP cc_start: 0.9040 (p0) cc_final: 0.8671 (p0) REVERT: a 330 ASP cc_start: 0.9050 (p0) cc_final: 0.8628 (p0) REVERT: b 330 ASP cc_start: 0.9025 (p0) cc_final: 0.8719 (p0) REVERT: o 173 TYR cc_start: 0.7793 (m-10) cc_final: 0.7572 (m-10) outliers start: 86 outliers final: 78 residues processed: 627 average time/residue: 0.5726 time to fit residues: 592.5420 Evaluate side-chains 620 residues out of total 4662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 541 time to evaluate : 4.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain C residue 14 ARG Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 103 TYR Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 103 TYR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 174 ASN Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 103 TYR Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 174 ASN Chi-restraints excluded: chain G residue 179 ASP Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 179 ASP Chi-restraints excluded: chain I residue 14 ARG Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 167 LEU Chi-restraints excluded: chain I residue 179 ASP Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain J residue 103 TYR Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 179 ASP Chi-restraints excluded: chain K residue 14 ARG Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 103 TYR Chi-restraints excluded: chain K residue 179 ASP Chi-restraints excluded: chain L residue 14 ARG Chi-restraints excluded: chain L residue 72 ASP Chi-restraints excluded: chain L residue 99 LEU Chi-restraints excluded: chain L residue 103 TYR Chi-restraints excluded: chain L residue 154 VAL Chi-restraints excluded: chain L residue 179 ASP Chi-restraints excluded: chain M residue 72 ASP Chi-restraints excluded: chain M residue 103 TYR Chi-restraints excluded: chain M residue 149 ASP Chi-restraints excluded: chain M residue 154 VAL Chi-restraints excluded: chain M residue 179 ASP Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain N residue 103 TYR Chi-restraints excluded: chain N residue 149 ASP Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 179 ASP Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain O residue 103 TYR Chi-restraints excluded: chain O residue 149 ASP Chi-restraints excluded: chain O residue 154 VAL Chi-restraints excluded: chain O residue 179 ASP Chi-restraints excluded: chain Q residue 330 ASP Chi-restraints excluded: chain Q residue 363 LEU Chi-restraints excluded: chain R residue 330 ASP Chi-restraints excluded: chain T residue 363 LEU Chi-restraints excluded: chain U residue 363 LEU Chi-restraints excluded: chain U residue 450 MET Chi-restraints excluded: chain V residue 330 ASP Chi-restraints excluded: chain V residue 363 LEU Chi-restraints excluded: chain V residue 522 SER Chi-restraints excluded: chain Y residue 330 ASP Chi-restraints excluded: chain Y residue 363 LEU Chi-restraints excluded: chain Y residue 522 SER Chi-restraints excluded: chain a residue 363 LEU Chi-restraints excluded: chain a residue 504 ASP Chi-restraints excluded: chain b residue 363 LEU Chi-restraints excluded: chain b residue 450 MET Chi-restraints excluded: chain g residue 173 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 527 optimal weight: 4.9990 chunk 555 optimal weight: 4.9990 chunk 507 optimal weight: 4.9990 chunk 540 optimal weight: 8.9990 chunk 325 optimal weight: 9.9990 chunk 235 optimal weight: 0.9980 chunk 424 optimal weight: 0.8980 chunk 165 optimal weight: 5.9990 chunk 488 optimal weight: 0.0770 chunk 511 optimal weight: 3.9990 chunk 538 optimal weight: 7.9990 overall best weight: 2.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 GLN J 114 GLN J 216 ASN ** J 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 165 ASN M 165 ASN ** M 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.7659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 47304 Z= 0.241 Angle : 0.642 12.155 64019 Z= 0.335 Chirality : 0.042 0.186 7279 Planarity : 0.004 0.060 8442 Dihedral : 4.120 59.110 6904 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.89 % Allowed : 20.49 % Favored : 77.62 % 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: 1.96 (0.11), residues: 6062 helix: 2.90 (0.10), residues: 2576 sheet: 1.33 (0.14), residues: 1386 loop : -0.86 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP b 429 HIS 0.001 0.000 HIS U 365 PHE 0.037 0.002 PHE E 71 TYR 0.017 0.001 TYR b 359 ARG 0.014 0.000 ARG E 97 *********************** 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 650 residues out of total 4662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 562 time to evaluate : 5.959 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: A 45 ASN cc_start: 0.8550 (t0) cc_final: 0.8017 (t0) REVERT: D 118 TYR cc_start: 0.9377 (m-80) cc_final: 0.9040 (m-80) REVERT: D 216 ASN cc_start: 0.9137 (t0) cc_final: 0.8788 (t0) REVERT: E 216 ASN cc_start: 0.9002 (t0) cc_final: 0.8735 (t0) REVERT: F 118 TYR cc_start: 0.9335 (m-80) cc_final: 0.9092 (m-80) REVERT: F 216 ASN cc_start: 0.9014 (t0) cc_final: 0.8670 (t0) REVERT: G 45 ASN cc_start: 0.8254 (t0) cc_final: 0.7892 (t0) REVERT: G 118 TYR cc_start: 0.9097 (m-80) cc_final: 0.8780 (m-80) REVERT: G 216 ASN cc_start: 0.9026 (t0) cc_final: 0.8720 (t0) REVERT: H 45 ASN cc_start: 0.8343 (t0) cc_final: 0.7886 (t0) REVERT: H 216 ASN cc_start: 0.9006 (t0) cc_final: 0.8733 (t0) REVERT: I 45 ASN cc_start: 0.8218 (t0) cc_final: 0.7735 (t0) REVERT: I 118 TYR cc_start: 0.9177 (m-80) cc_final: 0.8950 (m-80) REVERT: I 216 ASN cc_start: 0.9006 (t0) cc_final: 0.8674 (t0) REVERT: J 45 ASN cc_start: 0.8474 (t0) cc_final: 0.7969 (t0) REVERT: J 167 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8733 (tp) REVERT: K 45 ASN cc_start: 0.8293 (t0) cc_final: 0.7901 (t0) REVERT: K 118 TYR cc_start: 0.9316 (m-80) cc_final: 0.8918 (m-80) REVERT: K 216 ASN cc_start: 0.9035 (t0) cc_final: 0.8732 (t0) REVERT: L 45 ASN cc_start: 0.8703 (t0) cc_final: 0.8138 (t0) REVERT: L 216 ASN cc_start: 0.8949 (t0) cc_final: 0.8625 (t0) REVERT: M 45 ASN cc_start: 0.8435 (t0) cc_final: 0.7990 (t0) REVERT: M 118 TYR cc_start: 0.8930 (m-80) cc_final: 0.8701 (m-80) REVERT: M 216 ASN cc_start: 0.9018 (t0) cc_final: 0.8652 (t0) REVERT: N 45 ASN cc_start: 0.8201 (t0) cc_final: 0.7851 (t0) REVERT: N 167 LEU cc_start: 0.8860 (mt) cc_final: 0.8585 (tp) REVERT: O 45 ASN cc_start: 0.8712 (t0) cc_final: 0.8246 (t0) REVERT: O 167 LEU cc_start: 0.8947 (tp) cc_final: 0.8702 (tp) REVERT: P 330 ASP cc_start: 0.8801 (p0) cc_final: 0.8459 (p0) REVERT: S 330 ASP cc_start: 0.9058 (p0) cc_final: 0.8688 (p0) REVERT: T 330 ASP cc_start: 0.8973 (p0) cc_final: 0.8543 (p0) REVERT: U 330 ASP cc_start: 0.8997 (p0) cc_final: 0.8662 (p0) REVERT: W 330 ASP cc_start: 0.9003 (p0) cc_final: 0.8567 (p0) REVERT: X 330 ASP cc_start: 0.8900 (p0) cc_final: 0.8537 (p0) REVERT: Z 330 ASP cc_start: 0.9069 (p0) cc_final: 0.8699 (p0) REVERT: a 330 ASP cc_start: 0.9087 (p0) cc_final: 0.8752 (p0) REVERT: b 330 ASP cc_start: 0.9059 (p0) cc_final: 0.8755 (p0) REVERT: o 172 GLN cc_start: 0.8345 (mt0) cc_final: 0.7923 (mp10) outliers start: 88 outliers final: 78 residues processed: 591 average time/residue: 0.5769 time to fit residues: 567.1423 Evaluate side-chains 616 residues out of total 4662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 537 time to evaluate : 5.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 103 TYR Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 103 TYR Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 103 TYR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 174 ASN Chi-restraints excluded: chain E residue 179 ASP Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 103 TYR Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 174 ASN Chi-restraints excluded: chain G residue 179 ASP Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 179 ASP Chi-restraints excluded: chain I residue 14 ARG Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 179 ASP Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain J residue 103 TYR Chi-restraints excluded: chain J residue 116 LYS Chi-restraints excluded: chain J residue 167 LEU Chi-restraints excluded: chain J residue 179 ASP Chi-restraints excluded: chain K residue 14 ARG Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 103 TYR Chi-restraints excluded: chain K residue 179 ASP Chi-restraints excluded: chain L residue 14 ARG Chi-restraints excluded: chain L residue 72 ASP Chi-restraints excluded: chain L residue 99 LEU Chi-restraints excluded: chain L residue 103 TYR Chi-restraints excluded: chain L residue 154 VAL Chi-restraints excluded: chain L residue 179 ASP Chi-restraints excluded: chain M residue 72 ASP Chi-restraints excluded: chain M residue 103 TYR Chi-restraints excluded: chain M residue 149 ASP Chi-restraints excluded: chain M residue 179 ASP Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain N residue 103 TYR Chi-restraints excluded: chain N residue 149 ASP Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 179 ASP Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain O residue 103 TYR Chi-restraints excluded: chain O residue 149 ASP Chi-restraints excluded: chain O residue 154 VAL Chi-restraints excluded: chain O residue 179 ASP Chi-restraints excluded: chain P residue 363 LEU Chi-restraints excluded: chain Q residue 363 LEU Chi-restraints excluded: chain T residue 363 LEU Chi-restraints excluded: chain U residue 363 LEU Chi-restraints excluded: chain U residue 450 MET Chi-restraints excluded: chain V residue 330 ASP Chi-restraints excluded: chain V residue 363 LEU Chi-restraints excluded: chain V residue 450 MET Chi-restraints excluded: chain Y residue 363 LEU Chi-restraints excluded: chain Y residue 522 SER Chi-restraints excluded: chain Z residue 522 SER Chi-restraints excluded: chain a residue 363 LEU Chi-restraints excluded: chain a residue 450 MET Chi-restraints excluded: chain a residue 504 ASP Chi-restraints excluded: chain b residue 450 MET Chi-restraints excluded: chain g residue 173 TYR 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: 4.9990 chunk 271 optimal weight: 8.9990 chunk 397 optimal weight: 0.9990 chunk 599 optimal weight: 0.9990 chunk 551 optimal weight: 2.9990 chunk 477 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 368 optimal weight: 6.9990 chunk 292 optimal weight: 0.2980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 165 ASN ** M 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 172 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: 0.8703 moved from start: 0.7776 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 : 0.638 17.722 64019 Z= 0.329 Chirality : 0.043 0.201 7279 Planarity : 0.003 0.037 8442 Dihedral : 4.001 59.370 6900 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.69 % Allowed : 20.77 % Favored : 77.54 % 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: 1.95 (0.11), residues: 6062 helix: 2.90 (0.10), residues: 2576 sheet: 1.20 (0.13), residues: 1428 loop : -0.81 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP T 429 HIS 0.001 0.000 HIS R 365 PHE 0.034 0.001 PHE F 71 TYR 0.015 0.001 TYR b 359 ARG 0.004 0.000 ARG I 48 ********************** 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 655 residues out of total 4662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 576 time to evaluate : 5.282 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: A 45 ASN cc_start: 0.8485 (t0) cc_final: 0.7980 (t0) REVERT: C 216 ASN cc_start: 0.9048 (t0) cc_final: 0.8783 (t0) REVERT: D 118 TYR cc_start: 0.9416 (m-80) cc_final: 0.9123 (m-80) REVERT: D 216 ASN cc_start: 0.9048 (t0) cc_final: 0.8773 (t0) REVERT: E 216 ASN cc_start: 0.8952 (t0) cc_final: 0.8672 (t0) REVERT: F 216 ASN cc_start: 0.9029 (t0) cc_final: 0.8693 (t0) REVERT: G 45 ASN cc_start: 0.8190 (t0) cc_final: 0.7863 (t0) REVERT: G 118 TYR cc_start: 0.9096 (m-80) cc_final: 0.8805 (m-80) REVERT: G 216 ASN cc_start: 0.8977 (t0) cc_final: 0.8677 (t0) REVERT: H 45 ASN cc_start: 0.8237 (t0) cc_final: 0.7804 (t0) REVERT: H 216 ASN cc_start: 0.8999 (t0) cc_final: 0.8738 (t0) REVERT: I 45 ASN cc_start: 0.8156 (t0) cc_final: 0.7697 (t0) REVERT: I 118 TYR cc_start: 0.9165 (m-80) cc_final: 0.8955 (m-80) REVERT: I 216 ASN cc_start: 0.9038 (t0) cc_final: 0.8674 (t0) REVERT: J 45 ASN cc_start: 0.8405 (t0) cc_final: 0.7947 (t0) REVERT: J 167 LEU cc_start: 0.8985 (mt) cc_final: 0.8704 (tp) REVERT: K 45 ASN cc_start: 0.8281 (t0) cc_final: 0.7892 (t0) REVERT: K 118 TYR cc_start: 0.9307 (m-80) cc_final: 0.8931 (m-80) REVERT: K 216 ASN cc_start: 0.9040 (t0) cc_final: 0.8739 (t0) REVERT: L 45 ASN cc_start: 0.8657 (t0) cc_final: 0.8030 (t0) REVERT: L 216 ASN cc_start: 0.8984 (t0) cc_final: 0.8719 (t0) REVERT: M 45 ASN cc_start: 0.8367 (t0) cc_final: 0.7931 (t0) REVERT: M 118 TYR cc_start: 0.8889 (m-80) cc_final: 0.8661 (m-80) REVERT: M 216 ASN cc_start: 0.9005 (t0) cc_final: 0.8659 (t0) REVERT: N 45 ASN cc_start: 0.8205 (t0) cc_final: 0.7851 (t0) REVERT: N 167 LEU cc_start: 0.8844 (mt) cc_final: 0.8562 (tp) REVERT: O 45 ASN cc_start: 0.8662 (t0) cc_final: 0.8237 (t0) REVERT: O 167 LEU cc_start: 0.8882 (tp) cc_final: 0.8674 (tp) REVERT: P 330 ASP cc_start: 0.8756 (p0) cc_final: 0.8459 (p0) REVERT: S 330 ASP cc_start: 0.9036 (p0) cc_final: 0.8631 (p0) REVERT: U 330 ASP cc_start: 0.8962 (p0) cc_final: 0.8590 (p0) REVERT: W 330 ASP cc_start: 0.8948 (p0) cc_final: 0.8560 (p0) REVERT: Z 330 ASP cc_start: 0.9037 (p0) cc_final: 0.8672 (p0) REVERT: Z 432 GLU cc_start: 0.8682 (tp30) cc_final: 0.8469 (tp30) REVERT: a 330 ASP cc_start: 0.9072 (p0) cc_final: 0.8654 (p0) REVERT: b 330 ASP cc_start: 0.9016 (p0) cc_final: 0.8701 (p0) outliers start: 79 outliers final: 77 residues processed: 599 average time/residue: 0.5791 time to fit residues: 577.2314 Evaluate side-chains 620 residues out of total 4662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 543 time to evaluate : 5.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 103 TYR Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 103 TYR Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 103 TYR Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 103 TYR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 174 ASN Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 103 TYR Chi-restraints excluded: chain F residue 179 ASP Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 174 ASN Chi-restraints excluded: chain G residue 179 ASP Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 103 TYR Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 179 ASP Chi-restraints excluded: chain I residue 14 ARG Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 179 ASP Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain J residue 103 TYR Chi-restraints excluded: chain J residue 179 ASP Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 103 TYR Chi-restraints excluded: chain K residue 179 ASP Chi-restraints excluded: chain L residue 14 ARG Chi-restraints excluded: chain L residue 72 ASP Chi-restraints excluded: chain L residue 103 TYR Chi-restraints excluded: chain L residue 154 VAL Chi-restraints excluded: chain L residue 179 ASP Chi-restraints excluded: chain M residue 72 ASP Chi-restraints excluded: chain M residue 103 TYR Chi-restraints excluded: chain M residue 149 ASP Chi-restraints excluded: chain M residue 154 VAL Chi-restraints excluded: chain M residue 179 ASP Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain N residue 103 TYR Chi-restraints excluded: chain N residue 149 ASP Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 179 ASP Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain O residue 103 TYR Chi-restraints excluded: chain O residue 149 ASP Chi-restraints excluded: chain O residue 154 VAL Chi-restraints excluded: chain O residue 179 ASP Chi-restraints excluded: chain Q residue 330 ASP Chi-restraints excluded: chain Q residue 363 LEU Chi-restraints excluded: chain T residue 363 LEU Chi-restraints excluded: chain U residue 363 LEU Chi-restraints excluded: chain U residue 450 MET Chi-restraints excluded: chain V residue 330 ASP Chi-restraints excluded: chain V residue 363 LEU Chi-restraints excluded: chain V residue 450 MET Chi-restraints excluded: chain Y residue 330 ASP Chi-restraints excluded: chain Y residue 363 LEU Chi-restraints excluded: chain Y residue 395 MET Chi-restraints excluded: chain Y residue 522 SER Chi-restraints excluded: chain Z residue 522 SER Chi-restraints excluded: chain a residue 363 LEU Chi-restraints excluded: chain a residue 450 MET Chi-restraints excluded: chain a residue 504 ASP Chi-restraints excluded: chain b residue 450 MET Chi-restraints excluded: chain g residue 173 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 379 optimal weight: 0.7980 chunk 508 optimal weight: 0.8980 chunk 146 optimal weight: 6.9990 chunk 440 optimal weight: 7.9990 chunk 70 optimal weight: 0.7980 chunk 132 optimal weight: 0.8980 chunk 478 optimal weight: 0.7980 chunk 200 optimal weight: 8.9990 chunk 491 optimal weight: 0.4980 chunk 60 optimal weight: 0.6980 chunk 88 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 165 ASN ** M 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.066449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.045965 restraints weight = 160091.963| |-----------------------------------------------------------------------------| r_work (start): 0.2673 rms_B_bonded: 5.19 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.7875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 47304 Z= 0.165 Angle : 0.636 20.336 64019 Z= 0.326 Chirality : 0.043 0.192 7279 Planarity : 0.003 0.069 8442 Dihedral : 3.844 59.495 6896 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.57 % Allowed : 21.39 % Favored : 77.04 % 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: 2.81 (0.10), residues: 2590 sheet: 1.24 (0.13), residues: 1428 loop : -0.86 (0.14), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP V 429 HIS 0.002 0.000 HIS R 365 PHE 0.034 0.001 PHE O 71 TYR 0.014 0.001 TYR b 359 ARG 0.013 0.000 ARG L 48 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11384.17 seconds wall clock time: 205 minutes 18.76 seconds (12318.76 seconds total)