Starting phenix.real_space_refine on Sun Mar 24 07:30:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sd4_10148/03_2024/6sd4_10148.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sd4_10148/03_2024/6sd4_10148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sd4_10148/03_2024/6sd4_10148.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sd4_10148/03_2024/6sd4_10148.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sd4_10148/03_2024/6sd4_10148.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sd4_10148/03_2024/6sd4_10148.pdb" } resolution = 2.8 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= 0.002 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 102 5.16 5 C 24684 2.51 5 N 7582 2.21 5 O 8194 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 244": "NH1" <-> "NH2" Residue "A TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 384": "NH1" <-> "NH2" Residue "A ASP 407": "OD1" <-> "OD2" Residue "A PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 424": "OD1" <-> "OD2" Residue "B ARG 244": "NH1" <-> "NH2" Residue "B TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 384": "NH1" <-> "NH2" Residue "B ASP 407": "OD1" <-> "OD2" Residue "B PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 424": "OD1" <-> "OD2" Residue "C ARG 244": "NH1" <-> "NH2" Residue "C TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 384": "NH1" <-> "NH2" Residue "C ASP 407": "OD1" <-> "OD2" Residue "C PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 424": "OD1" <-> "OD2" Residue "D ARG 244": "NH1" <-> "NH2" Residue "D TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 384": "NH1" <-> "NH2" Residue "D ASP 407": "OD1" <-> "OD2" Residue "D PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 424": "OD1" <-> "OD2" Residue "E ARG 244": "NH1" <-> "NH2" Residue "E TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 384": "NH1" <-> "NH2" Residue "E ASP 407": "OD1" <-> "OD2" Residue "E PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 424": "OD1" <-> "OD2" Residue "F ARG 244": "NH1" <-> "NH2" Residue "F TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 384": "NH1" <-> "NH2" Residue "F ASP 407": "OD1" <-> "OD2" Residue "F PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 424": "OD1" <-> "OD2" Residue "G ARG 244": "NH1" <-> "NH2" Residue "G TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 384": "NH1" <-> "NH2" Residue "G ASP 407": "OD1" <-> "OD2" Residue "G PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 424": "OD1" <-> "OD2" Residue "H ARG 244": "NH1" <-> "NH2" Residue "H TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 384": "NH1" <-> "NH2" Residue "H ASP 407": "OD1" <-> "OD2" Residue "H PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 424": "OD1" <-> "OD2" Residue "I ARG 244": "NH1" <-> "NH2" Residue "I TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 384": "NH1" <-> "NH2" Residue "I ASP 407": "OD1" <-> "OD2" Residue "I PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 424": "OD1" <-> "OD2" Residue "J ARG 244": "NH1" <-> "NH2" Residue "J TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 384": "NH1" <-> "NH2" Residue "J ASP 407": "OD1" <-> "OD2" Residue "J PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 424": "OD1" <-> "OD2" Residue "K ARG 244": "NH1" <-> "NH2" Residue "K TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 384": "NH1" <-> "NH2" Residue "K ASP 407": "OD1" <-> "OD2" Residue "K PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 424": "OD1" <-> "OD2" Residue "L ARG 244": "NH1" <-> "NH2" Residue "L TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 384": "NH1" <-> "NH2" Residue "L ASP 407": "OD1" <-> "OD2" Residue "L PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 424": "OD1" <-> "OD2" Residue "M ARG 244": "NH1" <-> "NH2" Residue "M TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 384": "NH1" <-> "NH2" Residue "M ASP 407": "OD1" <-> "OD2" Residue "M PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 424": "OD1" <-> "OD2" Residue "N ARG 244": "NH1" <-> "NH2" Residue "N TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 384": "NH1" <-> "NH2" Residue "N ASP 407": "OD1" <-> "OD2" Residue "N PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 424": "OD1" <-> "OD2" Residue "O ARG 244": "NH1" <-> "NH2" Residue "O TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 384": "NH1" <-> "NH2" Residue "O ASP 407": "OD1" <-> "OD2" Residue "O PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 424": "OD1" <-> "OD2" Residue "P ARG 244": "NH1" <-> "NH2" Residue "P TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 384": "NH1" <-> "NH2" Residue "P ASP 407": "OD1" <-> "OD2" Residue "P PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 424": "OD1" <-> "OD2" Residue "Q ARG 244": "NH1" <-> "NH2" Residue "Q TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 384": "NH1" <-> "NH2" Residue "Q ASP 407": "OD1" <-> "OD2" Residue "Q PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 424": "OD1" <-> "OD2" Residue "R ARG 244": "NH1" <-> "NH2" Residue "R TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 384": "NH1" <-> "NH2" Residue "R ASP 407": "OD1" <-> "OD2" Residue "R PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 424": "OD1" <-> "OD2" Residue "S ARG 244": "NH1" <-> "NH2" Residue "S TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 384": "NH1" <-> "NH2" Residue "S ASP 407": "OD1" <-> "OD2" Residue "S PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 424": "OD1" <-> "OD2" Residue "T ARG 244": "NH1" <-> "NH2" Residue "T TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 384": "NH1" <-> "NH2" Residue "T ASP 407": "OD1" <-> "OD2" Residue "T PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 424": "OD1" <-> "OD2" Residue "U ARG 244": "NH1" <-> "NH2" Residue "U TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 384": "NH1" <-> "NH2" Residue "U ASP 407": "OD1" <-> "OD2" Residue "U PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 424": "OD1" <-> "OD2" Residue "V ARG 244": "NH1" <-> "NH2" Residue "V TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 384": "NH1" <-> "NH2" Residue "V ASP 407": "OD1" <-> "OD2" Residue "V PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 424": "OD1" <-> "OD2" Residue "W ARG 244": "NH1" <-> "NH2" Residue "W TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 384": "NH1" <-> "NH2" Residue "W ASP 407": "OD1" <-> "OD2" Residue "W PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 424": "OD1" <-> "OD2" Residue "X ARG 244": "NH1" <-> "NH2" Residue "X TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 384": "NH1" <-> "NH2" Residue "X ASP 407": "OD1" <-> "OD2" Residue "X PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 424": "OD1" <-> "OD2" Residue "Y ARG 244": "NH1" <-> "NH2" Residue "Y TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 384": "NH1" <-> "NH2" Residue "Y ASP 407": "OD1" <-> "OD2" Residue "Y PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 424": "OD1" <-> "OD2" Residue "Z ARG 244": "NH1" <-> "NH2" Residue "Z TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 384": "NH1" <-> "NH2" Residue "Z ASP 407": "OD1" <-> "OD2" Residue "Z PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 424": "OD1" <-> "OD2" Residue "a ARG 244": "NH1" <-> "NH2" Residue "a TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 384": "NH1" <-> "NH2" Residue "a ASP 407": "OD1" <-> "OD2" Residue "a PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 424": "OD1" <-> "OD2" Residue "b ARG 244": "NH1" <-> "NH2" Residue "b TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 384": "NH1" <-> "NH2" Residue "b ASP 407": "OD1" <-> "OD2" Residue "b PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 424": "OD1" <-> "OD2" Residue "c ARG 244": "NH1" <-> "NH2" Residue "c TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 384": "NH1" <-> "NH2" Residue "c ASP 407": "OD1" <-> "OD2" Residue "c PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 424": "OD1" <-> "OD2" Residue "d ARG 244": "NH1" <-> "NH2" Residue "d TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 384": "NH1" <-> "NH2" Residue "d ASP 407": "OD1" <-> "OD2" Residue "d PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 424": "OD1" <-> "OD2" Residue "e ARG 244": "NH1" <-> "NH2" Residue "e TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 384": "NH1" <-> "NH2" Residue "e ASP 407": "OD1" <-> "OD2" Residue "e PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 424": "OD1" <-> "OD2" Residue "f ARG 244": "NH1" <-> "NH2" Residue "f TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 384": "NH1" <-> "NH2" Residue "f ASP 407": "OD1" <-> "OD2" Residue "f PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 424": "OD1" <-> "OD2" Residue "g ARG 244": "NH1" <-> "NH2" Residue "g TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 384": "NH1" <-> "NH2" Residue "g ASP 407": "OD1" <-> "OD2" Residue "g PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 424": "OD1" <-> "OD2" Residue "h ARG 244": "NH1" <-> "NH2" Residue "h TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 384": "NH1" <-> "NH2" Residue "h ASP 407": "OD1" <-> "OD2" Residue "h PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 424": "OD1" <-> "OD2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 40562 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "B" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "C" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "D" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "E" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "F" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "G" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "H" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "I" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "J" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "K" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "L" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "M" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "N" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "O" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "P" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "Q" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "R" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "S" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "T" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "U" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "V" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "W" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "X" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "Y" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "Z" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "a" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "b" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "c" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "d" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "e" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "f" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "g" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "h" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Time building chain proxies: 20.99, per 1000 atoms: 0.52 Number of scatterers: 40562 At special positions: 0 Unit cell: (247.422, 247.422, 97.818, 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 102 16.00 O 8194 8.00 N 7582 7.00 C 24684 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: 13.47 Conformation dependent library (CDL) restraints added in 7.1 seconds 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9860 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 101 sheets defined 31.8% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.27 Creating SS restraints... Processing helix chain 'A' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS A 236 " --> pdb=" O ASP A 232 " (cutoff:3.500A) Proline residue: A 255 - end of helix Processing helix chain 'A' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA A 291 " --> pdb=" O ALA A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE A 412 " --> pdb=" O GLN A 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A 415 " --> pdb=" O GLN A 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS B 236 " --> pdb=" O ASP B 232 " (cutoff:3.500A) Proline residue: B 255 - end of helix Processing helix chain 'B' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA B 291 " --> pdb=" O ALA B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE B 412 " --> pdb=" O GLN B 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU B 415 " --> pdb=" O GLN B 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS C 236 " --> pdb=" O ASP C 232 " (cutoff:3.500A) Proline residue: C 255 - end of helix Processing helix chain 'C' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA C 291 " --> pdb=" O ALA C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 420 removed outlier: 3.841A pdb=" N ILE C 412 " --> pdb=" O GLN C 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU C 415 " --> pdb=" O GLN C 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS D 236 " --> pdb=" O ASP D 232 " (cutoff:3.500A) Proline residue: D 255 - end of helix Processing helix chain 'D' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA D 291 " --> pdb=" O ALA D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE D 412 " --> pdb=" O GLN D 408 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU D 415 " --> pdb=" O GLN D 411 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS E 236 " --> pdb=" O ASP E 232 " (cutoff:3.500A) Proline residue: E 255 - end of helix Processing helix chain 'E' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA E 291 " --> pdb=" O ALA E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE E 412 " --> pdb=" O GLN E 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU E 415 " --> pdb=" O GLN E 411 " (cutoff:3.500A) Processing helix chain 'F' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS F 236 " --> pdb=" O ASP F 232 " (cutoff:3.500A) Proline residue: F 255 - end of helix Processing helix chain 'F' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA F 291 " --> pdb=" O ALA F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE F 412 " --> pdb=" O GLN F 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU F 415 " --> pdb=" O GLN F 411 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS G 236 " --> pdb=" O ASP G 232 " (cutoff:3.500A) Proline residue: G 255 - end of helix Processing helix chain 'G' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA G 291 " --> pdb=" O ALA G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE G 412 " --> pdb=" O GLN G 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU G 415 " --> pdb=" O GLN G 411 " (cutoff:3.500A) Processing helix chain 'H' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS H 236 " --> pdb=" O ASP H 232 " (cutoff:3.500A) Proline residue: H 255 - end of helix Processing helix chain 'H' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA H 291 " --> pdb=" O ALA H 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE H 412 " --> pdb=" O GLN H 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU H 415 " --> pdb=" O GLN H 411 " (cutoff:3.500A) Processing helix chain 'I' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS I 236 " --> pdb=" O ASP I 232 " (cutoff:3.500A) Proline residue: I 255 - end of helix Processing helix chain 'I' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA I 291 " --> pdb=" O ALA I 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE I 412 " --> pdb=" O GLN I 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU I 415 " --> pdb=" O GLN I 411 " (cutoff:3.500A) Processing helix chain 'J' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS J 236 " --> pdb=" O ASP J 232 " (cutoff:3.500A) Proline residue: J 255 - end of helix Processing helix chain 'J' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA J 291 " --> pdb=" O ALA J 288 " (cutoff:3.500A) Processing helix chain 'J' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE J 412 " --> pdb=" O GLN J 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU J 415 " --> pdb=" O GLN J 411 " (cutoff:3.500A) Processing helix chain 'K' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS K 236 " --> pdb=" O ASP K 232 " (cutoff:3.500A) Proline residue: K 255 - end of helix Processing helix chain 'K' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA K 291 " --> pdb=" O ALA K 288 " (cutoff:3.500A) Processing helix chain 'K' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE K 412 " --> pdb=" O GLN K 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU K 415 " --> pdb=" O GLN K 411 " (cutoff:3.500A) Processing helix chain 'L' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS L 236 " --> pdb=" O ASP L 232 " (cutoff:3.500A) Proline residue: L 255 - end of helix Processing helix chain 'L' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA L 291 " --> pdb=" O ALA L 288 " (cutoff:3.500A) Processing helix chain 'L' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE L 412 " --> pdb=" O GLN L 408 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU L 415 " --> pdb=" O GLN L 411 " (cutoff:3.500A) Processing helix chain 'M' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS M 236 " --> pdb=" O ASP M 232 " (cutoff:3.500A) Proline residue: M 255 - end of helix Processing helix chain 'M' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA M 291 " --> pdb=" O ALA M 288 " (cutoff:3.500A) Processing helix chain 'M' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE M 412 " --> pdb=" O GLN M 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU M 415 " --> pdb=" O GLN M 411 " (cutoff:3.500A) Processing helix chain 'N' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS N 236 " --> pdb=" O ASP N 232 " (cutoff:3.500A) Proline residue: N 255 - end of helix Processing helix chain 'N' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA N 291 " --> pdb=" O ALA N 288 " (cutoff:3.500A) Processing helix chain 'N' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE N 412 " --> pdb=" O GLN N 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU N 415 " --> pdb=" O GLN N 411 " (cutoff:3.500A) Processing helix chain 'O' and resid 232 through 258 removed outlier: 3.756A pdb=" N LYS O 236 " --> pdb=" O ASP O 232 " (cutoff:3.500A) Proline residue: O 255 - end of helix Processing helix chain 'O' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA O 291 " --> pdb=" O ALA O 288 " (cutoff:3.500A) Processing helix chain 'O' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE O 412 " --> pdb=" O GLN O 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU O 415 " --> pdb=" O GLN O 411 " (cutoff:3.500A) Processing helix chain 'P' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS P 236 " --> pdb=" O ASP P 232 " (cutoff:3.500A) Proline residue: P 255 - end of helix Processing helix chain 'P' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA P 291 " --> pdb=" O ALA P 288 " (cutoff:3.500A) Processing helix chain 'P' and resid 405 through 420 removed outlier: 3.841A pdb=" N ILE P 412 " --> pdb=" O GLN P 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU P 415 " --> pdb=" O GLN P 411 " (cutoff:3.500A) Processing helix chain 'Q' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS Q 236 " --> pdb=" O ASP Q 232 " (cutoff:3.500A) Proline residue: Q 255 - end of helix Processing helix chain 'Q' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA Q 291 " --> pdb=" O ALA Q 288 " (cutoff:3.500A) Processing helix chain 'Q' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE Q 412 " --> pdb=" O GLN Q 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU Q 415 " --> pdb=" O GLN Q 411 " (cutoff:3.500A) Processing helix chain 'R' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS R 236 " --> pdb=" O ASP R 232 " (cutoff:3.500A) Proline residue: R 255 - end of helix Processing helix chain 'R' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA R 291 " --> pdb=" O ALA R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 420 removed outlier: 3.841A pdb=" N ILE R 412 " --> pdb=" O GLN R 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU R 415 " --> pdb=" O GLN R 411 " (cutoff:3.500A) Processing helix chain 'S' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS S 236 " --> pdb=" O ASP S 232 " (cutoff:3.500A) Proline residue: S 255 - end of helix Processing helix chain 'S' and resid 287 through 291 removed outlier: 3.591A pdb=" N ALA S 291 " --> pdb=" O ALA S 288 " (cutoff:3.500A) Processing helix chain 'S' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE S 412 " --> pdb=" O GLN S 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU S 415 " --> pdb=" O GLN S 411 " (cutoff:3.500A) Processing helix chain 'T' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS T 236 " --> pdb=" O ASP T 232 " (cutoff:3.500A) Proline residue: T 255 - end of helix Processing helix chain 'T' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA T 291 " --> pdb=" O ALA T 288 " (cutoff:3.500A) Processing helix chain 'T' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE T 412 " --> pdb=" O GLN T 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU T 415 " --> pdb=" O GLN T 411 " (cutoff:3.500A) Processing helix chain 'U' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS U 236 " --> pdb=" O ASP U 232 " (cutoff:3.500A) Proline residue: U 255 - end of helix Processing helix chain 'U' and resid 287 through 291 removed outlier: 3.593A pdb=" N ALA U 291 " --> pdb=" O ALA U 288 " (cutoff:3.500A) Processing helix chain 'U' and resid 405 through 420 removed outlier: 3.841A pdb=" N ILE U 412 " --> pdb=" O GLN U 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU U 415 " --> pdb=" O GLN U 411 " (cutoff:3.500A) Processing helix chain 'V' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS V 236 " --> pdb=" O ASP V 232 " (cutoff:3.500A) Proline residue: V 255 - end of helix Processing helix chain 'V' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA V 291 " --> pdb=" O ALA V 288 " (cutoff:3.500A) Processing helix chain 'V' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE V 412 " --> pdb=" O GLN V 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU V 415 " --> pdb=" O GLN V 411 " (cutoff:3.500A) Processing helix chain 'W' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS W 236 " --> pdb=" O ASP W 232 " (cutoff:3.500A) Proline residue: W 255 - end of helix Processing helix chain 'W' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA W 291 " --> pdb=" O ALA W 288 " (cutoff:3.500A) Processing helix chain 'W' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE W 412 " --> pdb=" O GLN W 408 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU W 415 " --> pdb=" O GLN W 411 " (cutoff:3.500A) Processing helix chain 'X' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS X 236 " --> pdb=" O ASP X 232 " (cutoff:3.500A) Proline residue: X 255 - end of helix Processing helix chain 'X' and resid 287 through 291 removed outlier: 3.593A pdb=" N ALA X 291 " --> pdb=" O ALA X 288 " (cutoff:3.500A) Processing helix chain 'X' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE X 412 " --> pdb=" O GLN X 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU X 415 " --> pdb=" O GLN X 411 " (cutoff:3.500A) Processing helix chain 'Y' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS Y 236 " --> pdb=" O ASP Y 232 " (cutoff:3.500A) Proline residue: Y 255 - end of helix Processing helix chain 'Y' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA Y 291 " --> pdb=" O ALA Y 288 " (cutoff:3.500A) Processing helix chain 'Y' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE Y 412 " --> pdb=" O GLN Y 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU Y 415 " --> pdb=" O GLN Y 411 " (cutoff:3.500A) Processing helix chain 'Z' and resid 232 through 258 removed outlier: 3.756A pdb=" N LYS Z 236 " --> pdb=" O ASP Z 232 " (cutoff:3.500A) Proline residue: Z 255 - end of helix Processing helix chain 'Z' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA Z 291 " --> pdb=" O ALA Z 288 " (cutoff:3.500A) Processing helix chain 'Z' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE Z 412 " --> pdb=" O GLN Z 408 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU Z 415 " --> pdb=" O GLN Z 411 " (cutoff:3.500A) Processing helix chain 'a' and resid 232 through 258 removed outlier: 3.756A pdb=" N LYS a 236 " --> pdb=" O ASP a 232 " (cutoff:3.500A) Proline residue: a 255 - end of helix Processing helix chain 'a' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA a 291 " --> pdb=" O ALA a 288 " (cutoff:3.500A) Processing helix chain 'a' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE a 412 " --> pdb=" O GLN a 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU a 415 " --> pdb=" O GLN a 411 " (cutoff:3.500A) Processing helix chain 'b' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS b 236 " --> pdb=" O ASP b 232 " (cutoff:3.500A) Proline residue: b 255 - end of helix Processing helix chain 'b' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA b 291 " --> pdb=" O ALA b 288 " (cutoff:3.500A) Processing helix chain 'b' and resid 405 through 420 removed outlier: 3.841A pdb=" N ILE b 412 " --> pdb=" O GLN b 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU b 415 " --> pdb=" O GLN b 411 " (cutoff:3.500A) Processing helix chain 'c' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS c 236 " --> pdb=" O ASP c 232 " (cutoff:3.500A) Proline residue: c 255 - end of helix Processing helix chain 'c' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA c 291 " --> pdb=" O ALA c 288 " (cutoff:3.500A) Processing helix chain 'c' and resid 405 through 420 removed outlier: 3.841A pdb=" N ILE c 412 " --> pdb=" O GLN c 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU c 415 " --> pdb=" O GLN c 411 " (cutoff:3.500A) Processing helix chain 'd' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS d 236 " --> pdb=" O ASP d 232 " (cutoff:3.500A) Proline residue: d 255 - end of helix Processing helix chain 'd' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA d 291 " --> pdb=" O ALA d 288 " (cutoff:3.500A) Processing helix chain 'd' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE d 412 " --> pdb=" O GLN d 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU d 415 " --> pdb=" O GLN d 411 " (cutoff:3.500A) Processing helix chain 'e' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS e 236 " --> pdb=" O ASP e 232 " (cutoff:3.500A) Proline residue: e 255 - end of helix Processing helix chain 'e' and resid 287 through 291 removed outlier: 3.593A pdb=" N ALA e 291 " --> pdb=" O ALA e 288 " (cutoff:3.500A) Processing helix chain 'e' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE e 412 " --> pdb=" O GLN e 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU e 415 " --> pdb=" O GLN e 411 " (cutoff:3.500A) Processing helix chain 'f' and resid 232 through 258 removed outlier: 3.756A pdb=" N LYS f 236 " --> pdb=" O ASP f 232 " (cutoff:3.500A) Proline residue: f 255 - end of helix Processing helix chain 'f' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA f 291 " --> pdb=" O ALA f 288 " (cutoff:3.500A) Processing helix chain 'f' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE f 412 " --> pdb=" O GLN f 408 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU f 415 " --> pdb=" O GLN f 411 " (cutoff:3.500A) Processing helix chain 'g' and resid 232 through 258 removed outlier: 3.756A pdb=" N LYS g 236 " --> pdb=" O ASP g 232 " (cutoff:3.500A) Proline residue: g 255 - end of helix Processing helix chain 'g' and resid 287 through 291 removed outlier: 3.592A pdb=" N ALA g 291 " --> pdb=" O ALA g 288 " (cutoff:3.500A) Processing helix chain 'g' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE g 412 " --> pdb=" O GLN g 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU g 415 " --> pdb=" O GLN g 411 " (cutoff:3.500A) Processing helix chain 'h' and resid 232 through 258 removed outlier: 3.757A pdb=" N LYS h 236 " --> pdb=" O ASP h 232 " (cutoff:3.500A) Proline residue: h 255 - end of helix Processing helix chain 'h' and resid 287 through 291 removed outlier: 3.593A pdb=" N ALA h 291 " --> pdb=" O ALA h 288 " (cutoff:3.500A) Processing helix chain 'h' and resid 405 through 420 removed outlier: 3.842A pdb=" N ILE h 412 " --> pdb=" O GLN h 408 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU h 415 " --> pdb=" O GLN h 411 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 271 removed outlier: 6.619A pdb=" N HIS A 263 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL A 389 " --> pdb=" O HIS A 263 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN A 265 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL A 387 " --> pdb=" O GLN A 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR A 267 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU A 385 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLN A 269 " --> pdb=" O GLU A 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP A 381 " --> pdb=" O ASP A 271 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 274 through 276 Processing sheet with id=AA3, first strand: chain 'A' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR A 292 " --> pdb=" O GLU A 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN A 365 " --> pdb=" O ARG A 294 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG A 296 " --> pdb=" O THR A 363 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR A 363 " --> pdb=" O ARG A 296 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 374 through 376 Processing sheet with id=AA5, first strand: chain 'B' and resid 262 through 271 removed outlier: 6.619A pdb=" N HIS B 263 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL B 389 " --> pdb=" O HIS B 263 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN B 265 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL B 387 " --> pdb=" O GLN B 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR B 267 " --> pdb=" O LEU B 385 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU B 385 " --> pdb=" O THR B 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN B 269 " --> pdb=" O GLU B 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP B 381 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR B 292 " --> pdb=" O GLU B 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN B 365 " --> pdb=" O ARG B 294 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG B 296 " --> pdb=" O THR B 363 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR B 363 " --> pdb=" O ARG B 296 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 374 through 376 Processing sheet with id=AA8, first strand: chain 'C' and resid 262 through 271 removed outlier: 6.619A pdb=" N HIS C 263 " --> pdb=" O VAL C 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL C 389 " --> pdb=" O HIS C 263 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN C 265 " --> pdb=" O VAL C 387 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL C 387 " --> pdb=" O GLN C 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR C 267 " --> pdb=" O LEU C 385 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU C 385 " --> pdb=" O THR C 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN C 269 " --> pdb=" O GLU C 383 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP C 381 " --> pdb=" O ASP C 271 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR C 292 " --> pdb=" O GLU C 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN C 365 " --> pdb=" O ARG C 294 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ARG C 296 " --> pdb=" O THR C 363 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N THR C 363 " --> pdb=" O ARG C 296 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 374 through 376 Processing sheet with id=AB2, first strand: chain 'D' and resid 262 through 271 removed outlier: 6.621A pdb=" N HIS D 263 " --> pdb=" O VAL D 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL D 389 " --> pdb=" O HIS D 263 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN D 265 " --> pdb=" O VAL D 387 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL D 387 " --> pdb=" O GLN D 265 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N THR D 267 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU D 385 " --> pdb=" O THR D 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN D 269 " --> pdb=" O GLU D 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP D 381 " --> pdb=" O ASP D 271 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR D 292 " --> pdb=" O GLU D 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN D 365 " --> pdb=" O ARG D 294 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG D 296 " --> pdb=" O THR D 363 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR D 363 " --> pdb=" O ARG D 296 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 374 through 376 Processing sheet with id=AB5, first strand: chain 'E' and resid 262 through 271 removed outlier: 6.620A pdb=" N HIS E 263 " --> pdb=" O VAL E 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL E 389 " --> pdb=" O HIS E 263 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN E 265 " --> pdb=" O VAL E 387 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL E 387 " --> pdb=" O GLN E 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR E 267 " --> pdb=" O LEU E 385 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU E 385 " --> pdb=" O THR E 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN E 269 " --> pdb=" O GLU E 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP E 381 " --> pdb=" O ASP E 271 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR E 292 " --> pdb=" O GLU E 367 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN E 365 " --> pdb=" O ARG E 294 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ARG E 296 " --> pdb=" O THR E 363 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR E 363 " --> pdb=" O ARG E 296 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 374 through 376 Processing sheet with id=AB8, first strand: chain 'F' and resid 262 through 271 removed outlier: 6.620A pdb=" N HIS F 263 " --> pdb=" O VAL F 389 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL F 389 " --> pdb=" O HIS F 263 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN F 265 " --> pdb=" O VAL F 387 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL F 387 " --> pdb=" O GLN F 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR F 267 " --> pdb=" O LEU F 385 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU F 385 " --> pdb=" O THR F 267 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLN F 269 " --> pdb=" O GLU F 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP F 381 " --> pdb=" O ASP F 271 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR F 292 " --> pdb=" O GLU F 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN F 365 " --> pdb=" O ARG F 294 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ARG F 296 " --> pdb=" O THR F 363 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR F 363 " --> pdb=" O ARG F 296 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 374 through 376 Processing sheet with id=AC2, first strand: chain 'G' and resid 262 through 271 removed outlier: 6.619A pdb=" N HIS G 263 " --> pdb=" O VAL G 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL G 389 " --> pdb=" O HIS G 263 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN G 265 " --> pdb=" O VAL G 387 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL G 387 " --> pdb=" O GLN G 265 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N THR G 267 " --> pdb=" O LEU G 385 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU G 385 " --> pdb=" O THR G 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN G 269 " --> pdb=" O GLU G 383 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASP G 381 " --> pdb=" O ASP G 271 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR G 292 " --> pdb=" O GLU G 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN G 365 " --> pdb=" O ARG G 294 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG G 296 " --> pdb=" O THR G 363 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR G 363 " --> pdb=" O ARG G 296 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 374 through 376 Processing sheet with id=AC5, first strand: chain 'H' and resid 262 through 271 removed outlier: 6.621A pdb=" N HIS H 263 " --> pdb=" O VAL H 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL H 389 " --> pdb=" O HIS H 263 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN H 265 " --> pdb=" O VAL H 387 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL H 387 " --> pdb=" O GLN H 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR H 267 " --> pdb=" O LEU H 385 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU H 385 " --> pdb=" O THR H 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN H 269 " --> pdb=" O GLU H 383 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP H 381 " --> pdb=" O ASP H 271 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR H 292 " --> pdb=" O GLU H 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN H 365 " --> pdb=" O ARG H 294 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG H 296 " --> pdb=" O THR H 363 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR H 363 " --> pdb=" O ARG H 296 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 374 through 376 Processing sheet with id=AC8, first strand: chain 'I' and resid 262 through 271 removed outlier: 6.620A pdb=" N HIS I 263 " --> pdb=" O VAL I 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL I 389 " --> pdb=" O HIS I 263 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN I 265 " --> pdb=" O VAL I 387 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL I 387 " --> pdb=" O GLN I 265 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N THR I 267 " --> pdb=" O LEU I 385 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU I 385 " --> pdb=" O THR I 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN I 269 " --> pdb=" O GLU I 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP I 381 " --> pdb=" O ASP I 271 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR I 292 " --> pdb=" O GLU I 367 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASN I 365 " --> pdb=" O ARG I 294 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG I 296 " --> pdb=" O THR I 363 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR I 363 " --> pdb=" O ARG I 296 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 374 through 376 Processing sheet with id=AD2, first strand: chain 'J' and resid 262 through 271 removed outlier: 6.619A pdb=" N HIS J 263 " --> pdb=" O VAL J 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL J 389 " --> pdb=" O HIS J 263 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN J 265 " --> pdb=" O VAL J 387 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL J 387 " --> pdb=" O GLN J 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR J 267 " --> pdb=" O LEU J 385 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU J 385 " --> pdb=" O THR J 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN J 269 " --> pdb=" O GLU J 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP J 381 " --> pdb=" O ASP J 271 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR J 292 " --> pdb=" O GLU J 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN J 365 " --> pdb=" O ARG J 294 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG J 296 " --> pdb=" O THR J 363 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR J 363 " --> pdb=" O ARG J 296 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 374 through 376 Processing sheet with id=AD5, first strand: chain 'K' and resid 262 through 271 removed outlier: 6.619A pdb=" N HIS K 263 " --> pdb=" O VAL K 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL K 389 " --> pdb=" O HIS K 263 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN K 265 " --> pdb=" O VAL K 387 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL K 387 " --> pdb=" O GLN K 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR K 267 " --> pdb=" O LEU K 385 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU K 385 " --> pdb=" O THR K 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN K 269 " --> pdb=" O GLU K 383 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP K 381 " --> pdb=" O ASP K 271 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 292 through 298 removed outlier: 4.218A pdb=" N THR K 292 " --> pdb=" O GLU K 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN K 365 " --> pdb=" O ARG K 294 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ARG K 296 " --> pdb=" O THR K 363 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N THR K 363 " --> pdb=" O ARG K 296 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 374 through 376 Processing sheet with id=AD8, first strand: chain 'L' and resid 262 through 271 removed outlier: 6.620A pdb=" N HIS L 263 " --> pdb=" O VAL L 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL L 389 " --> pdb=" O HIS L 263 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN L 265 " --> pdb=" O VAL L 387 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL L 387 " --> pdb=" O GLN L 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR L 267 " --> pdb=" O LEU L 385 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU L 385 " --> pdb=" O THR L 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN L 269 " --> pdb=" O GLU L 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP L 381 " --> pdb=" O ASP L 271 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR L 292 " --> pdb=" O GLU L 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN L 365 " --> pdb=" O ARG L 294 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ARG L 296 " --> pdb=" O THR L 363 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR L 363 " --> pdb=" O ARG L 296 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 374 through 376 Processing sheet with id=AE2, first strand: chain 'M' and resid 262 through 271 removed outlier: 6.620A pdb=" N HIS M 263 " --> pdb=" O VAL M 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL M 389 " --> pdb=" O HIS M 263 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN M 265 " --> pdb=" O VAL M 387 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL M 387 " --> pdb=" O GLN M 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR M 267 " --> pdb=" O LEU M 385 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU M 385 " --> pdb=" O THR M 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN M 269 " --> pdb=" O GLU M 383 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASP M 381 " --> pdb=" O ASP M 271 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 362 through 367 removed outlier: 6.613A pdb=" N THR M 363 " --> pdb=" O ARG M 296 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG M 296 " --> pdb=" O THR M 363 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN M 365 " --> pdb=" O ARG M 294 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N THR M 292 " --> pdb=" O GLU M 367 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ARG M 294 " --> pdb=" O TYR N 366 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR N 363 " --> pdb=" O ARG N 296 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG N 296 " --> pdb=" O THR N 363 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN N 365 " --> pdb=" O ARG N 294 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N THR N 292 " --> pdb=" O GLU N 367 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 374 through 376 Processing sheet with id=AE5, first strand: chain 'N' and resid 262 through 271 removed outlier: 6.621A pdb=" N HIS N 263 " --> pdb=" O VAL N 389 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL N 389 " --> pdb=" O HIS N 263 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN N 265 " --> pdb=" O VAL N 387 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL N 387 " --> pdb=" O GLN N 265 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N THR N 267 " --> pdb=" O LEU N 385 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU N 385 " --> pdb=" O THR N 267 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLN N 269 " --> pdb=" O GLU N 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP N 381 " --> pdb=" O ASP N 271 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 374 through 376 Processing sheet with id=AE7, first strand: chain 'O' and resid 262 through 271 removed outlier: 6.619A pdb=" N HIS O 263 " --> pdb=" O VAL O 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL O 389 " --> pdb=" O HIS O 263 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN O 265 " --> pdb=" O VAL O 387 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL O 387 " --> pdb=" O GLN O 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR O 267 " --> pdb=" O LEU O 385 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU O 385 " --> pdb=" O THR O 267 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLN O 269 " --> pdb=" O GLU O 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP O 381 " --> pdb=" O ASP O 271 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR O 292 " --> pdb=" O GLU O 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN O 365 " --> pdb=" O ARG O 294 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ARG O 296 " --> pdb=" O THR O 363 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR O 363 " --> pdb=" O ARG O 296 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'O' and resid 374 through 376 Processing sheet with id=AF1, first strand: chain 'P' and resid 262 through 271 removed outlier: 6.619A pdb=" N HIS P 263 " --> pdb=" O VAL P 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL P 389 " --> pdb=" O HIS P 263 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN P 265 " --> pdb=" O VAL P 387 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL P 387 " --> pdb=" O GLN P 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR P 267 " --> pdb=" O LEU P 385 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU P 385 " --> pdb=" O THR P 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN P 269 " --> pdb=" O GLU P 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP P 381 " --> pdb=" O ASP P 271 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'P' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR P 292 " --> pdb=" O GLU P 367 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN P 365 " --> pdb=" O ARG P 294 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG P 296 " --> pdb=" O THR P 363 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR P 363 " --> pdb=" O ARG P 296 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'P' and resid 374 through 376 Processing sheet with id=AF4, first strand: chain 'Q' and resid 262 through 271 removed outlier: 6.620A pdb=" N HIS Q 263 " --> pdb=" O VAL Q 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL Q 389 " --> pdb=" O HIS Q 263 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN Q 265 " --> pdb=" O VAL Q 387 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL Q 387 " --> pdb=" O GLN Q 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR Q 267 " --> pdb=" O LEU Q 385 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU Q 385 " --> pdb=" O THR Q 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN Q 269 " --> pdb=" O GLU Q 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP Q 381 " --> pdb=" O ASP Q 271 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Q' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR Q 292 " --> pdb=" O GLU Q 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN Q 365 " --> pdb=" O ARG Q 294 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG Q 296 " --> pdb=" O THR Q 363 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N THR Q 363 " --> pdb=" O ARG Q 296 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Q' and resid 374 through 376 Processing sheet with id=AF7, first strand: chain 'R' and resid 262 through 271 removed outlier: 6.619A pdb=" N HIS R 263 " --> pdb=" O VAL R 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL R 389 " --> pdb=" O HIS R 263 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN R 265 " --> pdb=" O VAL R 387 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL R 387 " --> pdb=" O GLN R 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR R 267 " --> pdb=" O LEU R 385 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU R 385 " --> pdb=" O THR R 267 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLN R 269 " --> pdb=" O GLU R 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP R 381 " --> pdb=" O ASP R 271 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'R' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR R 292 " --> pdb=" O GLU R 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN R 365 " --> pdb=" O ARG R 294 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG R 296 " --> pdb=" O THR R 363 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR R 363 " --> pdb=" O ARG R 296 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'R' and resid 374 through 376 Processing sheet with id=AG1, first strand: chain 'S' and resid 262 through 271 removed outlier: 6.620A pdb=" N HIS S 263 " --> pdb=" O VAL S 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL S 389 " --> pdb=" O HIS S 263 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN S 265 " --> pdb=" O VAL S 387 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL S 387 " --> pdb=" O GLN S 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR S 267 " --> pdb=" O LEU S 385 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU S 385 " --> pdb=" O THR S 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN S 269 " --> pdb=" O GLU S 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP S 381 " --> pdb=" O ASP S 271 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'S' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR S 292 " --> pdb=" O GLU S 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN S 365 " --> pdb=" O ARG S 294 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ARG S 296 " --> pdb=" O THR S 363 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N THR S 363 " --> pdb=" O ARG S 296 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'S' and resid 374 through 376 Processing sheet with id=AG4, first strand: chain 'T' and resid 262 through 271 removed outlier: 6.620A pdb=" N HIS T 263 " --> pdb=" O VAL T 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL T 389 " --> pdb=" O HIS T 263 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN T 265 " --> pdb=" O VAL T 387 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL T 387 " --> pdb=" O GLN T 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR T 267 " --> pdb=" O LEU T 385 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU T 385 " --> pdb=" O THR T 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN T 269 " --> pdb=" O GLU T 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP T 381 " --> pdb=" O ASP T 271 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'T' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR T 292 " --> pdb=" O GLU T 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN T 365 " --> pdb=" O ARG T 294 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ARG T 296 " --> pdb=" O THR T 363 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR T 363 " --> pdb=" O ARG T 296 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'T' and resid 374 through 376 Processing sheet with id=AG7, first strand: chain 'U' and resid 262 through 271 removed outlier: 6.620A pdb=" N HIS U 263 " --> pdb=" O VAL U 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL U 389 " --> pdb=" O HIS U 263 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN U 265 " --> pdb=" O VAL U 387 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL U 387 " --> pdb=" O GLN U 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR U 267 " --> pdb=" O LEU U 385 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU U 385 " --> pdb=" O THR U 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN U 269 " --> pdb=" O GLU U 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP U 381 " --> pdb=" O ASP U 271 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'U' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR U 292 " --> pdb=" O GLU U 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN U 365 " --> pdb=" O ARG U 294 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG U 296 " --> pdb=" O THR U 363 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR U 363 " --> pdb=" O ARG U 296 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'U' and resid 374 through 376 Processing sheet with id=AH1, first strand: chain 'V' and resid 262 through 271 removed outlier: 6.620A pdb=" N HIS V 263 " --> pdb=" O VAL V 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL V 389 " --> pdb=" O HIS V 263 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN V 265 " --> pdb=" O VAL V 387 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL V 387 " --> pdb=" O GLN V 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR V 267 " --> pdb=" O LEU V 385 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU V 385 " --> pdb=" O THR V 267 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLN V 269 " --> pdb=" O GLU V 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP V 381 " --> pdb=" O ASP V 271 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'V' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR V 292 " --> pdb=" O GLU V 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN V 365 " --> pdb=" O ARG V 294 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG V 296 " --> pdb=" O THR V 363 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR V 363 " --> pdb=" O ARG V 296 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'V' and resid 374 through 376 Processing sheet with id=AH4, first strand: chain 'W' and resid 262 through 271 removed outlier: 6.620A pdb=" N HIS W 263 " --> pdb=" O VAL W 389 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N VAL W 389 " --> pdb=" O HIS W 263 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN W 265 " --> pdb=" O VAL W 387 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL W 387 " --> pdb=" O GLN W 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR W 267 " --> pdb=" O LEU W 385 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU W 385 " --> pdb=" O THR W 267 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLN W 269 " --> pdb=" O GLU W 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP W 381 " --> pdb=" O ASP W 271 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'W' and resid 292 through 298 removed outlier: 4.218A pdb=" N THR W 292 " --> pdb=" O GLU W 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN W 365 " --> pdb=" O ARG W 294 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG W 296 " --> pdb=" O THR W 363 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR W 363 " --> pdb=" O ARG W 296 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'W' and resid 374 through 376 Processing sheet with id=AH7, first strand: chain 'X' and resid 262 through 271 removed outlier: 6.619A pdb=" N HIS X 263 " --> pdb=" O VAL X 389 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL X 389 " --> pdb=" O HIS X 263 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN X 265 " --> pdb=" O VAL X 387 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL X 387 " --> pdb=" O GLN X 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR X 267 " --> pdb=" O LEU X 385 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU X 385 " --> pdb=" O THR X 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN X 269 " --> pdb=" O GLU X 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP X 381 " --> pdb=" O ASP X 271 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'X' and resid 292 through 298 removed outlier: 4.218A pdb=" N THR X 292 " --> pdb=" O GLU X 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN X 365 " --> pdb=" O ARG X 294 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ARG X 296 " --> pdb=" O THR X 363 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR X 363 " --> pdb=" O ARG X 296 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'X' and resid 374 through 376 Processing sheet with id=AI1, first strand: chain 'Y' and resid 262 through 271 removed outlier: 6.620A pdb=" N HIS Y 263 " --> pdb=" O VAL Y 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL Y 389 " --> pdb=" O HIS Y 263 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN Y 265 " --> pdb=" O VAL Y 387 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL Y 387 " --> pdb=" O GLN Y 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR Y 267 " --> pdb=" O LEU Y 385 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU Y 385 " --> pdb=" O THR Y 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN Y 269 " --> pdb=" O GLU Y 383 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASP Y 381 " --> pdb=" O ASP Y 271 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'Y' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR Y 292 " --> pdb=" O GLU Y 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN Y 365 " --> pdb=" O ARG Y 294 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG Y 296 " --> pdb=" O THR Y 363 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR Y 363 " --> pdb=" O ARG Y 296 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'Y' and resid 374 through 376 Processing sheet with id=AI4, first strand: chain 'Z' and resid 262 through 271 removed outlier: 6.620A pdb=" N HIS Z 263 " --> pdb=" O VAL Z 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL Z 389 " --> pdb=" O HIS Z 263 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN Z 265 " --> pdb=" O VAL Z 387 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL Z 387 " --> pdb=" O GLN Z 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR Z 267 " --> pdb=" O LEU Z 385 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU Z 385 " --> pdb=" O THR Z 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN Z 269 " --> pdb=" O GLU Z 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP Z 381 " --> pdb=" O ASP Z 271 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'Z' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR Z 292 " --> pdb=" O GLU Z 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN Z 365 " --> pdb=" O ARG Z 294 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG Z 296 " --> pdb=" O THR Z 363 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR Z 363 " --> pdb=" O ARG Z 296 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'Z' and resid 374 through 376 Processing sheet with id=AI7, first strand: chain 'a' and resid 262 through 271 removed outlier: 6.620A pdb=" N HIS a 263 " --> pdb=" O VAL a 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL a 389 " --> pdb=" O HIS a 263 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN a 265 " --> pdb=" O VAL a 387 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL a 387 " --> pdb=" O GLN a 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR a 267 " --> pdb=" O LEU a 385 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU a 385 " --> pdb=" O THR a 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN a 269 " --> pdb=" O GLU a 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP a 381 " --> pdb=" O ASP a 271 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'a' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR a 292 " --> pdb=" O GLU a 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN a 365 " --> pdb=" O ARG a 294 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG a 296 " --> pdb=" O THR a 363 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR a 363 " --> pdb=" O ARG a 296 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'a' and resid 374 through 376 Processing sheet with id=AJ1, first strand: chain 'b' and resid 262 through 271 removed outlier: 6.620A pdb=" N HIS b 263 " --> pdb=" O VAL b 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL b 389 " --> pdb=" O HIS b 263 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN b 265 " --> pdb=" O VAL b 387 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL b 387 " --> pdb=" O GLN b 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR b 267 " --> pdb=" O LEU b 385 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU b 385 " --> pdb=" O THR b 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN b 269 " --> pdb=" O GLU b 383 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP b 381 " --> pdb=" O ASP b 271 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'b' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR b 292 " --> pdb=" O GLU b 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN b 365 " --> pdb=" O ARG b 294 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG b 296 " --> pdb=" O THR b 363 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR b 363 " --> pdb=" O ARG b 296 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'b' and resid 374 through 376 Processing sheet with id=AJ4, first strand: chain 'c' and resid 262 through 271 removed outlier: 6.620A pdb=" N HIS c 263 " --> pdb=" O VAL c 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL c 389 " --> pdb=" O HIS c 263 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN c 265 " --> pdb=" O VAL c 387 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL c 387 " --> pdb=" O GLN c 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR c 267 " --> pdb=" O LEU c 385 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU c 385 " --> pdb=" O THR c 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN c 269 " --> pdb=" O GLU c 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP c 381 " --> pdb=" O ASP c 271 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'c' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR c 292 " --> pdb=" O GLU c 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN c 365 " --> pdb=" O ARG c 294 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG c 296 " --> pdb=" O THR c 363 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR c 363 " --> pdb=" O ARG c 296 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'c' and resid 374 through 376 Processing sheet with id=AJ7, first strand: chain 'd' and resid 262 through 271 removed outlier: 6.619A pdb=" N HIS d 263 " --> pdb=" O VAL d 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL d 389 " --> pdb=" O HIS d 263 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN d 265 " --> pdb=" O VAL d 387 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL d 387 " --> pdb=" O GLN d 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR d 267 " --> pdb=" O LEU d 385 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU d 385 " --> pdb=" O THR d 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN d 269 " --> pdb=" O GLU d 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP d 381 " --> pdb=" O ASP d 271 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'd' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR d 292 " --> pdb=" O GLU d 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN d 365 " --> pdb=" O ARG d 294 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG d 296 " --> pdb=" O THR d 363 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR d 363 " --> pdb=" O ARG d 296 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'd' and resid 374 through 376 Processing sheet with id=AK1, first strand: chain 'e' and resid 262 through 271 removed outlier: 6.619A pdb=" N HIS e 263 " --> pdb=" O VAL e 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL e 389 " --> pdb=" O HIS e 263 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN e 265 " --> pdb=" O VAL e 387 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL e 387 " --> pdb=" O GLN e 265 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N THR e 267 " --> pdb=" O LEU e 385 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU e 385 " --> pdb=" O THR e 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN e 269 " --> pdb=" O GLU e 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP e 381 " --> pdb=" O ASP e 271 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'e' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR e 292 " --> pdb=" O GLU e 367 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN e 365 " --> pdb=" O ARG e 294 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG e 296 " --> pdb=" O THR e 363 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR e 363 " --> pdb=" O ARG e 296 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'e' and resid 374 through 376 Processing sheet with id=AK4, first strand: chain 'f' and resid 262 through 271 removed outlier: 6.620A pdb=" N HIS f 263 " --> pdb=" O VAL f 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL f 389 " --> pdb=" O HIS f 263 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN f 265 " --> pdb=" O VAL f 387 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL f 387 " --> pdb=" O GLN f 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR f 267 " --> pdb=" O LEU f 385 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU f 385 " --> pdb=" O THR f 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN f 269 " --> pdb=" O GLU f 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP f 381 " --> pdb=" O ASP f 271 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'f' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR f 292 " --> pdb=" O GLU f 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN f 365 " --> pdb=" O ARG f 294 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG f 296 " --> pdb=" O THR f 363 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N THR f 363 " --> pdb=" O ARG f 296 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'f' and resid 374 through 376 Processing sheet with id=AK7, first strand: chain 'g' and resid 262 through 271 removed outlier: 6.620A pdb=" N HIS g 263 " --> pdb=" O VAL g 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL g 389 " --> pdb=" O HIS g 263 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN g 265 " --> pdb=" O VAL g 387 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL g 387 " --> pdb=" O GLN g 265 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR g 267 " --> pdb=" O LEU g 385 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU g 385 " --> pdb=" O THR g 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN g 269 " --> pdb=" O GLU g 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP g 381 " --> pdb=" O ASP g 271 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'g' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR g 292 " --> pdb=" O GLU g 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN g 365 " --> pdb=" O ARG g 294 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG g 296 " --> pdb=" O THR g 363 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR g 363 " --> pdb=" O ARG g 296 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'g' and resid 374 through 376 Processing sheet with id=AL1, first strand: chain 'h' and resid 262 through 271 removed outlier: 6.620A pdb=" N HIS h 263 " --> pdb=" O VAL h 389 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL h 389 " --> pdb=" O HIS h 263 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN h 265 " --> pdb=" O VAL h 387 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL h 387 " --> pdb=" O GLN h 265 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR h 267 " --> pdb=" O LEU h 385 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU h 385 " --> pdb=" O THR h 267 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLN h 269 " --> pdb=" O GLU h 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP h 381 " --> pdb=" O ASP h 271 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'h' and resid 292 through 298 removed outlier: 4.217A pdb=" N THR h 292 " --> pdb=" O GLU h 367 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN h 365 " --> pdb=" O ARG h 294 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG h 296 " --> pdb=" O THR h 363 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR h 363 " --> pdb=" O ARG h 296 " (cutoff:3.500A) 1501 hydrogen bonds defined for protein. 4092 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: 12.76 Time building geometry restraints manager: 14.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 13655 1.33 - 1.45: 3994 1.45 - 1.57: 23117 1.57 - 1.68: 0 1.68 - 1.80: 204 Bond restraints: 40970 Sorted by residual: bond pdb=" C TYR f 282 " pdb=" N SER f 283 " ideal model delta sigma weight residual 1.332 1.287 0.045 1.92e-02 2.71e+03 5.46e+00 bond pdb=" C TYR T 282 " pdb=" N SER T 283 " ideal model delta sigma weight residual 1.332 1.287 0.045 1.92e-02 2.71e+03 5.45e+00 bond pdb=" C TYR E 282 " pdb=" N SER E 283 " ideal model delta sigma weight residual 1.332 1.287 0.045 1.92e-02 2.71e+03 5.39e+00 bond pdb=" C TYR W 282 " pdb=" N SER W 283 " ideal model delta sigma weight residual 1.332 1.287 0.045 1.92e-02 2.71e+03 5.39e+00 bond pdb=" C TYR H 282 " pdb=" N SER H 283 " ideal model delta sigma weight residual 1.332 1.287 0.045 1.92e-02 2.71e+03 5.38e+00 ... (remaining 40965 not shown) Histogram of bond angle deviations from ideal: 100.38 - 106.57: 830 106.57 - 112.76: 22437 112.76 - 118.96: 10572 118.96 - 125.15: 21139 125.15 - 131.35: 238 Bond angle restraints: 55216 Sorted by residual: angle pdb=" N GLY F 421 " pdb=" CA GLY F 421 " pdb=" C GLY F 421 " ideal model delta sigma weight residual 115.08 107.06 8.02 1.64e+00 3.72e-01 2.39e+01 angle pdb=" N GLY V 421 " pdb=" CA GLY V 421 " pdb=" C GLY V 421 " ideal model delta sigma weight residual 115.08 107.06 8.02 1.64e+00 3.72e-01 2.39e+01 angle pdb=" N GLY U 421 " pdb=" CA GLY U 421 " pdb=" C GLY U 421 " ideal model delta sigma weight residual 115.08 107.07 8.01 1.64e+00 3.72e-01 2.39e+01 angle pdb=" N GLY b 421 " pdb=" CA GLY b 421 " pdb=" C GLY b 421 " ideal model delta sigma weight residual 115.08 107.07 8.01 1.64e+00 3.72e-01 2.38e+01 angle pdb=" N GLY a 421 " pdb=" CA GLY a 421 " pdb=" C GLY a 421 " ideal model delta sigma weight residual 115.08 107.08 8.00 1.64e+00 3.72e-01 2.38e+01 ... (remaining 55211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.43: 20546 10.43 - 20.86: 3661 20.86 - 31.28: 1055 31.28 - 41.71: 208 41.71 - 52.14: 132 Dihedral angle restraints: 25602 sinusoidal: 10608 harmonic: 14994 Sorted by residual: dihedral pdb=" CA MET c 420 " pdb=" C MET c 420 " pdb=" N GLY c 421 " pdb=" CA GLY c 421 " ideal model delta harmonic sigma weight residual 180.00 -161.53 -18.47 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA MET O 420 " pdb=" C MET O 420 " pdb=" N GLY O 421 " pdb=" CA GLY O 421 " ideal model delta harmonic sigma weight residual -180.00 -161.56 -18.44 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA MET N 420 " pdb=" C MET N 420 " pdb=" N GLY N 421 " pdb=" CA GLY N 421 " ideal model delta harmonic sigma weight residual -180.00 -161.56 -18.44 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 25599 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 2747 0.023 - 0.045: 1834 0.045 - 0.068: 1120 0.068 - 0.091: 369 0.091 - 0.114: 254 Chirality restraints: 6324 Sorted by residual: chirality pdb=" CA VAL a 432 " pdb=" N VAL a 432 " pdb=" C VAL a 432 " pdb=" CB VAL a 432 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.23e-01 chirality pdb=" CA ILE W 382 " pdb=" N ILE W 382 " pdb=" C ILE W 382 " pdb=" CB ILE W 382 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.14e-01 chirality pdb=" CA VAL e 432 " pdb=" N VAL e 432 " pdb=" C VAL e 432 " pdb=" CB VAL e 432 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.13e-01 ... (remaining 6321 not shown) Planarity restraints: 7412 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER J 254 " 0.022 5.00e-02 4.00e+02 3.36e-02 1.80e+00 pdb=" N PRO J 255 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO J 255 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO J 255 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER H 254 " 0.022 5.00e-02 4.00e+02 3.35e-02 1.80e+00 pdb=" N PRO H 255 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO H 255 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO H 255 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER P 254 " 0.022 5.00e-02 4.00e+02 3.35e-02 1.80e+00 pdb=" N PRO P 255 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO P 255 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO P 255 " 0.019 5.00e-02 4.00e+02 ... (remaining 7409 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 8537 2.77 - 3.30: 35634 3.30 - 3.83: 63593 3.83 - 4.37: 84356 4.37 - 4.90: 145833 Nonbonded interactions: 337953 Sorted by model distance: nonbonded pdb=" O GLU A 250 " pdb=" OG SER A 254 " model vdw 2.235 2.440 nonbonded pdb=" O GLU C 250 " pdb=" OG SER C 254 " model vdw 2.235 2.440 nonbonded pdb=" O GLU G 250 " pdb=" OG SER G 254 " model vdw 2.235 2.440 nonbonded pdb=" O GLU E 250 " pdb=" OG SER E 254 " model vdw 2.235 2.440 nonbonded pdb=" O GLU O 250 " pdb=" OG SER O 254 " model vdw 2.235 2.440 ... (remaining 337948 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 'B' 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' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' } 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: 4.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 19.890 Check model and map are aligned: 0.700 Set scattering table: 0.320 Process input model: 97.360 Find NCS groups from input model: 3.080 Set up NCS constraints: 0.600 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:14.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 140.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 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 : 0.010 0.045 40970 Z= 0.627 Angle : 0.782 8.022 55216 Z= 0.475 Chirality : 0.041 0.114 6324 Planarity : 0.004 0.034 7412 Dihedral : 12.269 52.140 15742 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.69 % Allowed : 9.66 % Favored : 89.66 % Rotamer: Outliers : 0.75 % Allowed : 7.11 % Favored : 92.14 % 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: -4.67 (0.10), residues: 4930 helix: -3.62 (0.09), residues: 1326 sheet: -2.64 (0.10), residues: 2380 loop : -2.46 (0.15), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS b 281 PHE 0.014 0.002 PHE Z 422 TYR 0.022 0.003 TYR P 393 ARG 0.005 0.000 ARG D 426 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1326 residues out of total 4556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 1292 time to evaluate : 4.698 Fit side-chains revert: symmetry clash REVERT: A 408 GLN cc_start: 0.7670 (tt0) cc_final: 0.7423 (tt0) REVERT: C 414 ASP cc_start: 0.7688 (m-30) cc_final: 0.6939 (m-30) REVERT: C 418 GLU cc_start: 0.8841 (mm-30) cc_final: 0.7598 (mp0) REVERT: D 383 GLU cc_start: 0.7850 (tt0) cc_final: 0.7615 (tm-30) REVERT: F 267 THR cc_start: 0.8776 (m) cc_final: 0.8568 (m) REVERT: H 418 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8621 (mm-30) REVERT: I 408 GLN cc_start: 0.7800 (tt0) cc_final: 0.7503 (tm-30) REVERT: I 417 ARG cc_start: 0.7599 (ttm110) cc_final: 0.7329 (mtt90) REVERT: J 367 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8353 (mm-30) REVERT: J 408 GLN cc_start: 0.7589 (tt0) cc_final: 0.7330 (tm-30) REVERT: K 408 GLN cc_start: 0.7667 (tt0) cc_final: 0.7429 (tm-30) REVERT: M 418 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8408 (mp0) REVERT: N 417 ARG cc_start: 0.7894 (ttm110) cc_final: 0.7688 (mtm-85) REVERT: O 367 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8566 (mm-30) REVERT: Q 394 LYS cc_start: 0.7224 (tttt) cc_final: 0.6907 (tttm) REVERT: R 408 GLN cc_start: 0.7574 (tt0) cc_final: 0.7317 (tt0) REVERT: T 414 ASP cc_start: 0.7695 (m-30) cc_final: 0.6791 (m-30) REVERT: T 417 ARG cc_start: 0.7822 (ttm110) cc_final: 0.7621 (ttm-80) REVERT: T 418 GLU cc_start: 0.8814 (mm-30) cc_final: 0.7533 (mp0) REVERT: U 383 GLU cc_start: 0.7809 (tt0) cc_final: 0.7554 (tm-30) REVERT: V 417 ARG cc_start: 0.7843 (ttm110) cc_final: 0.7605 (mtt-85) REVERT: X 296 ARG cc_start: 0.7302 (ttt90) cc_final: 0.7083 (ttm170) REVERT: Y 414 ASP cc_start: 0.7695 (m-30) cc_final: 0.6687 (m-30) REVERT: Y 418 GLU cc_start: 0.8649 (mm-30) cc_final: 0.7432 (mp0) REVERT: a 408 GLN cc_start: 0.7641 (tt0) cc_final: 0.7362 (tm-30) REVERT: a 417 ARG cc_start: 0.7558 (ttm110) cc_final: 0.7354 (mtt90) REVERT: c 276 GLU cc_start: 0.7262 (mt-10) cc_final: 0.7045 (mt-10) REVERT: c 414 ASP cc_start: 0.7628 (m-30) cc_final: 0.6942 (m-30) REVERT: d 429 THR cc_start: 0.8560 (m) cc_final: 0.8353 (p) REVERT: e 417 ARG cc_start: 0.7896 (ttm110) cc_final: 0.7668 (mtm-85) REVERT: e 418 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8129 (mm-30) REVERT: f 367 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8564 (mm-30) REVERT: g 418 GLU cc_start: 0.8744 (mm-30) cc_final: 0.8262 (mm-30) outliers start: 34 outliers final: 26 residues processed: 1320 average time/residue: 1.9669 time to fit residues: 3004.4120 Evaluate side-chains 1187 residues out of total 4556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 1161 time to evaluate : 5.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain H residue 369 ASP Chi-restraints excluded: chain I residue 369 ASP Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain L residue 369 ASP Chi-restraints excluded: chain M residue 369 ASP Chi-restraints excluded: chain N residue 369 ASP Chi-restraints excluded: chain O residue 369 ASP Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain R residue 369 ASP Chi-restraints excluded: chain S residue 369 ASP Chi-restraints excluded: chain T residue 369 ASP Chi-restraints excluded: chain U residue 369 ASP Chi-restraints excluded: chain V residue 369 ASP Chi-restraints excluded: chain X residue 369 ASP Chi-restraints excluded: chain Z residue 369 ASP Chi-restraints excluded: chain a residue 369 ASP Chi-restraints excluded: chain b residue 369 ASP Chi-restraints excluded: chain c residue 369 ASP Chi-restraints excluded: chain d residue 369 ASP Chi-restraints excluded: chain e residue 369 ASP Chi-restraints excluded: chain f residue 369 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 430 optimal weight: 0.6980 chunk 386 optimal weight: 0.0870 chunk 214 optimal weight: 0.9990 chunk 132 optimal weight: 0.9980 chunk 260 optimal weight: 0.7980 chunk 206 optimal weight: 0.0770 chunk 399 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 243 optimal weight: 6.9990 chunk 297 optimal weight: 0.8980 chunk 463 optimal weight: 0.9980 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 HIS ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 HIS B 269 GLN ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 HIS C 281 HIS C 408 GLN ** C 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 HIS D 269 GLN D 365 ASN D 408 GLN ** D 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 HIS ** E 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 263 HIS ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 263 HIS ** G 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 263 HIS H 365 ASN ** H 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 263 HIS I 297 GLN I 299 ASN I 365 ASN ** I 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 263 HIS J 365 ASN ** J 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 263 HIS K 365 ASN ** K 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 263 HIS L 365 ASN ** L 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 263 HIS M 365 ASN ** M 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 263 HIS ** N 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 246 GLN O 263 HIS ** O 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 263 HIS P 269 GLN ** P 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 263 HIS ** Q 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 263 HIS ** R 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 263 HIS S 269 GLN ** S 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 263 HIS ** T 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 263 HIS U 303 GLN U 365 ASN ** U 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 263 HIS ** V 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 263 HIS W 365 ASN ** W 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 263 HIS X 303 GLN X 365 ASN ** X 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 263 HIS Y 269 GLN ** Y 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 263 HIS Z 374 HIS ** Z 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 263 HIS ** a 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 263 HIS b 297 GLN b 299 ASN b 365 ASN ** b 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 263 HIS ** c 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 263 HIS ** d 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 263 HIS ** e 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 246 GLN f 263 HIS f 303 GLN ** f 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 263 HIS g 269 GLN ** g 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 263 HIS h 408 GLN ** h 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 65 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 40970 Z= 0.144 Angle : 0.486 4.893 55216 Z= 0.266 Chirality : 0.039 0.128 6324 Planarity : 0.004 0.027 7412 Dihedral : 5.120 22.204 5594 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.58 % Allowed : 15.72 % Favored : 82.70 % 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: -2.62 (0.12), residues: 4930 helix: -0.63 (0.14), residues: 1326 sheet: -1.82 (0.10), residues: 2380 loop : -2.18 (0.15), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS L 281 PHE 0.011 0.001 PHE d 237 TYR 0.008 0.001 TYR d 393 ARG 0.004 0.000 ARG E 417 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1328 residues out of total 4556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 1256 time to evaluate : 4.229 Fit side-chains REVERT: B 377 MET cc_start: 0.7810 (mpt) cc_final: 0.7523 (mpt) REVERT: B 418 GLU cc_start: 0.8447 (mp0) cc_final: 0.8156 (tp30) REVERT: C 429 THR cc_start: 0.8863 (m) cc_final: 0.8436 (p) REVERT: G 429 THR cc_start: 0.8780 (m) cc_final: 0.8469 (p) REVERT: K 429 THR cc_start: 0.8749 (m) cc_final: 0.8422 (p) REVERT: N 420 MET cc_start: 0.8114 (mtp) cc_final: 0.7901 (mtp) REVERT: O 246 GLN cc_start: 0.8699 (tt0) cc_final: 0.8456 (tt0) REVERT: O 297 GLN cc_start: 0.7383 (tt0) cc_final: 0.7157 (tp40) REVERT: O 367 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8515 (mm-30) REVERT: Q 276 GLU cc_start: 0.7196 (mt-10) cc_final: 0.6977 (mm-30) REVERT: Q 394 LYS cc_start: 0.7300 (tttt) cc_final: 0.6965 (tttm) REVERT: T 377 MET cc_start: 0.8042 (mpt) cc_final: 0.7245 (mpt) REVERT: T 383 GLU cc_start: 0.7493 (tt0) cc_final: 0.7279 (tt0) REVERT: T 429 THR cc_start: 0.8843 (m) cc_final: 0.8627 (p) REVERT: U 275 LYS cc_start: 0.8304 (ttmp) cc_final: 0.8077 (ttmt) REVERT: U 418 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8193 (tp30) REVERT: Y 275 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.8075 (ttmt) REVERT: Y 414 ASP cc_start: 0.7428 (m-30) cc_final: 0.7197 (m-30) REVERT: a 408 GLN cc_start: 0.7720 (tt0) cc_final: 0.7144 (tm-30) REVERT: b 429 THR cc_start: 0.8764 (m) cc_final: 0.8438 (p) REVERT: e 367 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8374 (mm-30) REVERT: f 279 GLU cc_start: 0.7541 (mp0) cc_final: 0.7324 (mp0) REVERT: f 367 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8454 (mm-30) REVERT: f 418 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8312 (tp30) REVERT: g 417 ARG cc_start: 0.7858 (ttm110) cc_final: 0.7515 (mtt90) REVERT: h 276 GLU cc_start: 0.7163 (mt-10) cc_final: 0.6950 (mm-30) outliers start: 72 outliers final: 41 residues processed: 1299 average time/residue: 1.8916 time to fit residues: 2864.6907 Evaluate side-chains 1160 residues out of total 4556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 1117 time to evaluate : 4.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain F residue 275 LYS Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain G residue 369 ASP Chi-restraints excluded: chain H residue 369 ASP Chi-restraints excluded: chain I residue 369 ASP Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain K residue 394 LYS Chi-restraints excluded: chain L residue 369 ASP Chi-restraints excluded: chain M residue 369 ASP Chi-restraints excluded: chain N residue 369 ASP Chi-restraints excluded: chain O residue 369 ASP Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain Q residue 369 ASP Chi-restraints excluded: chain Q residue 412 ILE Chi-restraints excluded: chain R residue 369 ASP Chi-restraints excluded: chain S residue 369 ASP Chi-restraints excluded: chain T residue 369 ASP Chi-restraints excluded: chain U residue 369 ASP Chi-restraints excluded: chain V residue 369 ASP Chi-restraints excluded: chain W residue 369 ASP Chi-restraints excluded: chain X residue 369 ASP Chi-restraints excluded: chain Y residue 275 LYS Chi-restraints excluded: chain Y residue 369 ASP Chi-restraints excluded: chain Z residue 369 ASP Chi-restraints excluded: chain a residue 369 ASP Chi-restraints excluded: chain b residue 369 ASP Chi-restraints excluded: chain b residue 394 LYS Chi-restraints excluded: chain c residue 275 LYS Chi-restraints excluded: chain c residue 369 ASP Chi-restraints excluded: chain d residue 369 ASP Chi-restraints excluded: chain e residue 369 ASP Chi-restraints excluded: chain e residue 383 GLU Chi-restraints excluded: chain f residue 369 ASP Chi-restraints excluded: chain f residue 418 GLU Chi-restraints excluded: chain g residue 369 ASP Chi-restraints excluded: chain h residue 369 ASP Chi-restraints excluded: chain h residue 412 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 257 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 385 optimal weight: 8.9990 chunk 315 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 463 optimal weight: 0.4980 chunk 501 optimal weight: 3.9990 chunk 413 optimal weight: 3.9990 chunk 460 optimal weight: 6.9990 chunk 158 optimal weight: 0.6980 chunk 372 optimal weight: 4.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 ASN B 365 ASN B 434 ASN C 239 ASN C 365 ASN C 434 ASN D 434 ASN E 239 ASN E 365 ASN E 434 ASN F 365 ASN F 434 ASN G 365 ASN G 374 HIS G 434 ASN H 239 ASN H 434 ASN I 299 ASN I 434 ASN ** J 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 434 ASN L 434 ASN M 434 ASN N 365 ASN N 434 ASN O 365 ASN O 434 ASN P 269 GLN P 365 ASN P 434 ASN Q 408 GLN Q 434 ASN ** R 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 434 ASN S 365 ASN S 434 ASN T 239 ASN T 365 ASN T 434 ASN U 434 ASN V 365 ASN V 434 ASN W 434 ASN X 374 HIS X 434 ASN Y 365 ASN Y 411 GLN Y 434 ASN Z 365 ASN Z 434 ASN a 365 ASN ** a 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 434 ASN c 365 ASN c 434 ASN d 365 ASN d 434 ASN e 365 ASN e 434 ASN f 365 ASN f 434 ASN g 269 GLN g 365 ASN g 434 ASN h 434 ASN Total number of N/Q/H flips: 62 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 40970 Z= 0.323 Angle : 0.523 4.517 55216 Z= 0.281 Chirality : 0.041 0.129 6324 Planarity : 0.004 0.029 7412 Dihedral : 5.266 21.555 5594 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.37 % Allowed : 17.91 % Favored : 79.72 % 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: -1.55 (0.12), residues: 4930 helix: 1.17 (0.15), residues: 1326 sheet: -1.57 (0.10), residues: 2380 loop : -1.93 (0.15), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS L 281 PHE 0.013 0.001 PHE N 422 TYR 0.010 0.001 TYR K 393 ARG 0.005 0.001 ARG E 417 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1145 residues out of total 4556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 1037 time to evaluate : 4.520 Fit side-chains revert: symmetry clash REVERT: A 297 GLN cc_start: 0.7465 (OUTLIER) cc_final: 0.7097 (tt0) REVERT: C 377 MET cc_start: 0.7885 (mpt) cc_final: 0.7432 (mpt) REVERT: C 429 THR cc_start: 0.8780 (m) cc_final: 0.8560 (p) REVERT: D 418 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.7251 (mp0) REVERT: D 429 THR cc_start: 0.8745 (m) cc_final: 0.8530 (p) REVERT: F 297 GLN cc_start: 0.7351 (OUTLIER) cc_final: 0.6896 (tt0) REVERT: G 418 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8417 (tp30) REVERT: H 297 GLN cc_start: 0.7463 (OUTLIER) cc_final: 0.6983 (tt0) REVERT: K 276 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.7017 (mp0) REVERT: M 275 LYS cc_start: 0.8321 (ttmp) cc_final: 0.8101 (ttmm) REVERT: M 276 GLU cc_start: 0.6992 (OUTLIER) cc_final: 0.6703 (mt-10) REVERT: N 297 GLN cc_start: 0.7355 (OUTLIER) cc_final: 0.7119 (tt0) REVERT: O 296 ARG cc_start: 0.7427 (OUTLIER) cc_final: 0.6633 (tpp-160) REVERT: O 297 GLN cc_start: 0.7425 (tt0) cc_final: 0.7190 (tp40) REVERT: O 367 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8542 (mm-30) REVERT: O 418 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8080 (tp30) REVERT: P 429 THR cc_start: 0.8782 (m) cc_final: 0.8325 (p) REVERT: Q 276 GLU cc_start: 0.7249 (mt-10) cc_final: 0.6939 (mm-30) REVERT: Q 296 ARG cc_start: 0.7482 (OUTLIER) cc_final: 0.7064 (ttp-170) REVERT: Q 297 GLN cc_start: 0.7458 (OUTLIER) cc_final: 0.7205 (tt0) REVERT: R 408 GLN cc_start: 0.7559 (tt0) cc_final: 0.7286 (tt0) REVERT: T 297 GLN cc_start: 0.7408 (OUTLIER) cc_final: 0.7015 (tt0) REVERT: T 377 MET cc_start: 0.7952 (mpt) cc_final: 0.7442 (mpt) REVERT: T 429 THR cc_start: 0.8798 (m) cc_final: 0.8564 (p) REVERT: U 297 GLN cc_start: 0.7326 (OUTLIER) cc_final: 0.7021 (tt0) REVERT: X 297 GLN cc_start: 0.7352 (OUTLIER) cc_final: 0.7129 (tt0) REVERT: a 297 GLN cc_start: 0.7394 (OUTLIER) cc_final: 0.6932 (tt0) REVERT: c 276 GLU cc_start: 0.7091 (mp0) cc_final: 0.6888 (mp0) REVERT: c 297 GLN cc_start: 0.7400 (OUTLIER) cc_final: 0.7165 (tt0) REVERT: e 297 GLN cc_start: 0.7372 (OUTLIER) cc_final: 0.7156 (tt0) REVERT: e 367 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8455 (mm-30) REVERT: f 279 GLU cc_start: 0.7559 (mp0) cc_final: 0.7309 (mp0) REVERT: f 297 GLN cc_start: 0.7335 (OUTLIER) cc_final: 0.7000 (tt0) REVERT: f 367 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8536 (mm-30) REVERT: f 429 THR cc_start: 0.8782 (m) cc_final: 0.8477 (p) REVERT: g 417 ARG cc_start: 0.7990 (ttm110) cc_final: 0.7635 (mtt90) REVERT: g 429 THR cc_start: 0.8737 (m) cc_final: 0.8496 (p) REVERT: h 276 GLU cc_start: 0.7238 (mt-10) cc_final: 0.6938 (mm-30) REVERT: h 429 THR cc_start: 0.8747 (m) cc_final: 0.8492 (p) outliers start: 108 outliers final: 48 residues processed: 1102 average time/residue: 2.0678 time to fit residues: 2630.7333 Evaluate side-chains 1066 residues out of total 4556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 999 time to evaluate : 4.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain F residue 297 GLN Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain G residue 369 ASP Chi-restraints excluded: chain G residue 418 GLU Chi-restraints excluded: chain H residue 297 GLN Chi-restraints excluded: chain H residue 369 ASP Chi-restraints excluded: chain I residue 369 ASP Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain K residue 275 LYS Chi-restraints excluded: chain K residue 276 GLU Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain L residue 369 ASP Chi-restraints excluded: chain M residue 276 GLU Chi-restraints excluded: chain M residue 369 ASP Chi-restraints excluded: chain N residue 297 GLN Chi-restraints excluded: chain N residue 369 ASP Chi-restraints excluded: chain O residue 296 ARG Chi-restraints excluded: chain O residue 369 ASP Chi-restraints excluded: chain O residue 418 GLU Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain Q residue 296 ARG Chi-restraints excluded: chain Q residue 297 GLN Chi-restraints excluded: chain Q residue 369 ASP Chi-restraints excluded: chain Q residue 412 ILE Chi-restraints excluded: chain R residue 369 ASP Chi-restraints excluded: chain S residue 369 ASP Chi-restraints excluded: chain T residue 297 GLN Chi-restraints excluded: chain T residue 369 ASP Chi-restraints excluded: chain U residue 297 GLN Chi-restraints excluded: chain U residue 369 ASP Chi-restraints excluded: chain V residue 369 ASP Chi-restraints excluded: chain W residue 243 SER Chi-restraints excluded: chain W residue 369 ASP Chi-restraints excluded: chain X residue 297 GLN Chi-restraints excluded: chain X residue 369 ASP Chi-restraints excluded: chain Y residue 275 LYS Chi-restraints excluded: chain Y residue 369 ASP Chi-restraints excluded: chain Z residue 369 ASP Chi-restraints excluded: chain a residue 297 GLN Chi-restraints excluded: chain a residue 369 ASP Chi-restraints excluded: chain b residue 275 LYS Chi-restraints excluded: chain b residue 290 LYS Chi-restraints excluded: chain b residue 369 ASP Chi-restraints excluded: chain c residue 297 GLN Chi-restraints excluded: chain c residue 369 ASP Chi-restraints excluded: chain d residue 369 ASP Chi-restraints excluded: chain d residue 391 VAL Chi-restraints excluded: chain e residue 297 GLN Chi-restraints excluded: chain e residue 369 ASP Chi-restraints excluded: chain e residue 418 GLU Chi-restraints excluded: chain f residue 297 GLN Chi-restraints excluded: chain f residue 369 ASP Chi-restraints excluded: chain g residue 243 SER Chi-restraints excluded: chain g residue 293 LEU Chi-restraints excluded: chain g residue 369 ASP Chi-restraints excluded: chain h residue 369 ASP Chi-restraints excluded: chain h residue 412 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 458 optimal weight: 1.9990 chunk 348 optimal weight: 2.9990 chunk 240 optimal weight: 0.4980 chunk 51 optimal weight: 5.9990 chunk 221 optimal weight: 8.9990 chunk 311 optimal weight: 1.9990 chunk 465 optimal weight: 0.9990 chunk 492 optimal weight: 3.9990 chunk 243 optimal weight: 10.0000 chunk 441 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 ASN E 239 ASN F 239 ASN G 374 HIS H 239 ASN ** J 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 269 GLN Q 408 GLN S 269 GLN T 239 ASN W 239 ASN X 374 HIS ** a 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 269 GLN g 297 GLN h 408 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 40970 Z= 0.272 Angle : 0.491 6.043 55216 Z= 0.264 Chirality : 0.040 0.129 6324 Planarity : 0.003 0.027 7412 Dihedral : 5.096 20.948 5594 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.85 % Allowed : 18.24 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.13), residues: 4930 helix: 1.82 (0.16), residues: 1326 sheet: -1.22 (0.11), residues: 2380 loop : -1.66 (0.16), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS H 281 PHE 0.012 0.001 PHE G 422 TYR 0.008 0.001 TYR K 393 ARG 0.004 0.000 ARG H 370 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1130 residues out of total 4556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 1000 time to evaluate : 4.826 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 297 GLN cc_start: 0.7422 (OUTLIER) cc_final: 0.6933 (tt0) REVERT: C 377 MET cc_start: 0.7899 (mpt) cc_final: 0.7381 (mpt) REVERT: C 429 THR cc_start: 0.8805 (m) cc_final: 0.8550 (p) REVERT: D 276 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6879 (mp0) REVERT: D 297 GLN cc_start: 0.7311 (OUTLIER) cc_final: 0.6988 (tt0) REVERT: D 418 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8180 (tp30) REVERT: D 429 THR cc_start: 0.8743 (m) cc_final: 0.8459 (p) REVERT: E 276 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6775 (mt-10) REVERT: F 297 GLN cc_start: 0.7315 (OUTLIER) cc_final: 0.6870 (tt0) REVERT: H 297 GLN cc_start: 0.7444 (OUTLIER) cc_final: 0.6961 (tt0) REVERT: J 297 GLN cc_start: 0.7352 (OUTLIER) cc_final: 0.6914 (tt0) REVERT: K 429 THR cc_start: 0.8733 (m) cc_final: 0.8499 (p) REVERT: L 276 GLU cc_start: 0.7048 (OUTLIER) cc_final: 0.6683 (mt-10) REVERT: M 276 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.6671 (mt-10) REVERT: N 297 GLN cc_start: 0.7324 (OUTLIER) cc_final: 0.7085 (tt0) REVERT: O 296 ARG cc_start: 0.7410 (OUTLIER) cc_final: 0.6636 (tpp-160) REVERT: O 367 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8614 (mm-30) REVERT: Q 276 GLU cc_start: 0.7254 (mt-10) cc_final: 0.6909 (mm-30) REVERT: Q 296 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.7041 (ttp-170) REVERT: Q 297 GLN cc_start: 0.7426 (OUTLIER) cc_final: 0.7221 (tp40) REVERT: T 297 GLN cc_start: 0.7415 (OUTLIER) cc_final: 0.6962 (tt0) REVERT: T 377 MET cc_start: 0.7955 (mpt) cc_final: 0.7470 (mpt) REVERT: T 429 THR cc_start: 0.8816 (m) cc_final: 0.8557 (p) REVERT: U 297 GLN cc_start: 0.7274 (OUTLIER) cc_final: 0.6966 (tt0) REVERT: U 429 THR cc_start: 0.8748 (m) cc_final: 0.8477 (p) REVERT: W 297 GLN cc_start: 0.7341 (OUTLIER) cc_final: 0.6986 (tt0) REVERT: X 297 GLN cc_start: 0.7329 (OUTLIER) cc_final: 0.7110 (tt0) REVERT: Y 297 GLN cc_start: 0.7431 (OUTLIER) cc_final: 0.6943 (tt0) REVERT: a 297 GLN cc_start: 0.7353 (OUTLIER) cc_final: 0.6904 (tt0) REVERT: c 297 GLN cc_start: 0.7345 (OUTLIER) cc_final: 0.7133 (tt0) REVERT: f 297 GLN cc_start: 0.7292 (OUTLIER) cc_final: 0.6993 (tt0) REVERT: f 429 THR cc_start: 0.8747 (m) cc_final: 0.8422 (p) REVERT: g 417 ARG cc_start: 0.8012 (ttm110) cc_final: 0.7646 (mtt90) REVERT: g 418 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8272 (tp30) REVERT: g 429 THR cc_start: 0.8773 (m) cc_final: 0.8507 (p) REVERT: h 276 GLU cc_start: 0.7244 (mt-10) cc_final: 0.6918 (mm-30) REVERT: h 297 GLN cc_start: 0.7358 (OUTLIER) cc_final: 0.7131 (tt0) outliers start: 130 outliers final: 61 residues processed: 1083 average time/residue: 2.0246 time to fit residues: 2535.2946 Evaluate side-chains 1022 residues out of total 4556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 937 time to evaluate : 4.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 297 GLN Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 297 GLN Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain E residue 275 LYS Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain F residue 297 GLN Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain G residue 369 ASP Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain H residue 297 GLN Chi-restraints excluded: chain H residue 369 ASP Chi-restraints excluded: chain I residue 243 SER Chi-restraints excluded: chain I residue 369 ASP Chi-restraints excluded: chain J residue 297 GLN Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain K residue 275 LYS Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain K residue 394 LYS Chi-restraints excluded: chain L residue 276 GLU Chi-restraints excluded: chain L residue 369 ASP Chi-restraints excluded: chain M residue 276 GLU Chi-restraints excluded: chain M residue 369 ASP Chi-restraints excluded: chain N residue 275 LYS Chi-restraints excluded: chain N residue 293 LEU Chi-restraints excluded: chain N residue 297 GLN Chi-restraints excluded: chain N residue 369 ASP Chi-restraints excluded: chain O residue 296 ARG Chi-restraints excluded: chain O residue 369 ASP Chi-restraints excluded: chain O residue 433 VAL Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain P residue 412 ILE Chi-restraints excluded: chain Q residue 296 ARG Chi-restraints excluded: chain Q residue 297 GLN Chi-restraints excluded: chain Q residue 369 ASP Chi-restraints excluded: chain Q residue 412 ILE Chi-restraints excluded: chain R residue 243 SER Chi-restraints excluded: chain R residue 369 ASP Chi-restraints excluded: chain S residue 369 ASP Chi-restraints excluded: chain T residue 297 GLN Chi-restraints excluded: chain T residue 369 ASP Chi-restraints excluded: chain U residue 297 GLN Chi-restraints excluded: chain U residue 369 ASP Chi-restraints excluded: chain V residue 369 ASP Chi-restraints excluded: chain W residue 243 SER Chi-restraints excluded: chain W residue 297 GLN Chi-restraints excluded: chain W residue 369 ASP Chi-restraints excluded: chain X residue 297 GLN Chi-restraints excluded: chain X residue 369 ASP Chi-restraints excluded: chain Y residue 275 LYS Chi-restraints excluded: chain Y residue 297 GLN Chi-restraints excluded: chain Y residue 359 GLN Chi-restraints excluded: chain Y residue 369 ASP Chi-restraints excluded: chain Z residue 297 GLN Chi-restraints excluded: chain Z residue 369 ASP Chi-restraints excluded: chain a residue 297 GLN Chi-restraints excluded: chain a residue 369 ASP Chi-restraints excluded: chain b residue 275 LYS Chi-restraints excluded: chain b residue 369 ASP Chi-restraints excluded: chain c residue 297 GLN Chi-restraints excluded: chain c residue 369 ASP Chi-restraints excluded: chain d residue 369 ASP Chi-restraints excluded: chain e residue 275 LYS Chi-restraints excluded: chain e residue 369 ASP Chi-restraints excluded: chain e residue 418 GLU Chi-restraints excluded: chain f residue 297 GLN Chi-restraints excluded: chain f residue 369 ASP Chi-restraints excluded: chain f residue 418 GLU Chi-restraints excluded: chain f residue 433 VAL Chi-restraints excluded: chain g residue 243 SER Chi-restraints excluded: chain g residue 293 LEU Chi-restraints excluded: chain g residue 369 ASP Chi-restraints excluded: chain g residue 418 GLU Chi-restraints excluded: chain h residue 297 GLN Chi-restraints excluded: chain h residue 369 ASP Chi-restraints excluded: chain h residue 412 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 410 optimal weight: 0.6980 chunk 279 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 367 optimal weight: 4.9990 chunk 203 optimal weight: 0.6980 chunk 420 optimal weight: 0.8980 chunk 340 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 251 optimal weight: 10.0000 chunk 442 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 GLN C 239 ASN E 239 ASN F 239 ASN G 239 ASN H 239 ASN ** J 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 269 GLN Q 408 GLN S 269 GLN T 239 ASN V 239 ASN W 239 ASN X 239 ASN Y 239 ASN ** a 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 269 GLN h 408 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 40970 Z= 0.266 Angle : 0.485 6.809 55216 Z= 0.259 Chirality : 0.040 0.125 6324 Planarity : 0.003 0.029 7412 Dihedral : 5.028 21.083 5594 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.96 % Allowed : 18.99 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.13), residues: 4930 helix: 2.15 (0.16), residues: 1326 sheet: -0.97 (0.11), residues: 2380 loop : -1.38 (0.16), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS c 281 PHE 0.013 0.001 PHE G 422 TYR 0.007 0.001 TYR K 393 ARG 0.004 0.000 ARG Q 370 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1076 residues out of total 4556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 941 time to evaluate : 4.834 Fit side-chains revert: symmetry clash REVERT: B 297 GLN cc_start: 0.7430 (OUTLIER) cc_final: 0.6939 (tt0) REVERT: C 296 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.6544 (ttp-170) REVERT: C 377 MET cc_start: 0.7881 (mpt) cc_final: 0.7427 (mpt) REVERT: C 429 THR cc_start: 0.8805 (m) cc_final: 0.8525 (p) REVERT: D 276 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6931 (mp0) REVERT: D 297 GLN cc_start: 0.7312 (OUTLIER) cc_final: 0.6952 (tt0) REVERT: D 418 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8173 (tp30) REVERT: E 276 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6767 (mt-10) REVERT: F 297 GLN cc_start: 0.7277 (OUTLIER) cc_final: 0.6863 (tt0) REVERT: H 297 GLN cc_start: 0.7405 (OUTLIER) cc_final: 0.6916 (tt0) REVERT: I 276 GLU cc_start: 0.7171 (mp0) cc_final: 0.6912 (mp0) REVERT: J 297 GLN cc_start: 0.7340 (OUTLIER) cc_final: 0.6898 (tt0) REVERT: K 429 THR cc_start: 0.8745 (m) cc_final: 0.8408 (p) REVERT: M 276 GLU cc_start: 0.6970 (OUTLIER) cc_final: 0.6666 (mt-10) REVERT: N 296 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.6539 (tpp-160) REVERT: N 297 GLN cc_start: 0.7346 (OUTLIER) cc_final: 0.7095 (tt0) REVERT: O 296 ARG cc_start: 0.7369 (OUTLIER) cc_final: 0.6608 (tpp-160) REVERT: O 367 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8535 (mm-30) REVERT: O 429 THR cc_start: 0.8725 (m) cc_final: 0.8460 (p) REVERT: Q 276 GLU cc_start: 0.7263 (mt-10) cc_final: 0.6912 (mm-30) REVERT: Q 296 ARG cc_start: 0.7446 (OUTLIER) cc_final: 0.7050 (ttp-170) REVERT: Q 297 GLN cc_start: 0.7428 (OUTLIER) cc_final: 0.7176 (tt0) REVERT: S 418 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.7527 (mp0) REVERT: T 297 GLN cc_start: 0.7386 (OUTLIER) cc_final: 0.6925 (tt0) REVERT: T 377 MET cc_start: 0.7935 (mpt) cc_final: 0.7406 (mpt) REVERT: T 429 THR cc_start: 0.8822 (m) cc_final: 0.8546 (p) REVERT: U 297 GLN cc_start: 0.7296 (OUTLIER) cc_final: 0.6983 (tt0) REVERT: W 297 GLN cc_start: 0.7322 (OUTLIER) cc_final: 0.6944 (tt0) REVERT: X 297 GLN cc_start: 0.7330 (OUTLIER) cc_final: 0.7102 (tt0) REVERT: Y 297 GLN cc_start: 0.7466 (OUTLIER) cc_final: 0.6968 (tt0) REVERT: a 297 GLN cc_start: 0.7352 (OUTLIER) cc_final: 0.6915 (tt0) REVERT: b 429 THR cc_start: 0.8728 (m) cc_final: 0.8516 (p) REVERT: c 297 GLN cc_start: 0.7322 (OUTLIER) cc_final: 0.7117 (tt0) REVERT: f 297 GLN cc_start: 0.7308 (OUTLIER) cc_final: 0.6967 (tt0) REVERT: f 367 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8601 (mm-30) REVERT: f 429 THR cc_start: 0.8713 (m) cc_final: 0.8386 (p) REVERT: g 296 ARG cc_start: 0.7246 (ttt90) cc_final: 0.6997 (ttm170) REVERT: g 429 THR cc_start: 0.8750 (m) cc_final: 0.8472 (p) REVERT: h 297 GLN cc_start: 0.7369 (OUTLIER) cc_final: 0.7156 (tt0) outliers start: 135 outliers final: 73 residues processed: 1032 average time/residue: 2.0059 time to fit residues: 2395.0327 Evaluate side-chains 1011 residues out of total 4556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 913 time to evaluate : 4.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 297 GLN Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 296 ARG Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 297 GLN Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain E residue 275 LYS Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain F residue 297 GLN Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain G residue 243 SER Chi-restraints excluded: chain G residue 369 ASP Chi-restraints excluded: chain H residue 297 GLN Chi-restraints excluded: chain H residue 369 ASP Chi-restraints excluded: chain I residue 243 SER Chi-restraints excluded: chain I residue 369 ASP Chi-restraints excluded: chain J residue 297 GLN Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain K residue 275 LYS Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain K residue 433 VAL Chi-restraints excluded: chain L residue 369 ASP Chi-restraints excluded: chain M residue 276 GLU Chi-restraints excluded: chain M residue 369 ASP Chi-restraints excluded: chain N residue 275 LYS Chi-restraints excluded: chain N residue 293 LEU Chi-restraints excluded: chain N residue 296 ARG Chi-restraints excluded: chain N residue 297 GLN Chi-restraints excluded: chain N residue 369 ASP Chi-restraints excluded: chain O residue 296 ARG Chi-restraints excluded: chain O residue 369 ASP Chi-restraints excluded: chain O residue 433 VAL Chi-restraints excluded: chain P residue 243 SER Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain Q residue 296 ARG Chi-restraints excluded: chain Q residue 297 GLN Chi-restraints excluded: chain Q residue 369 ASP Chi-restraints excluded: chain Q residue 433 VAL Chi-restraints excluded: chain R residue 243 SER Chi-restraints excluded: chain R residue 369 ASP Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain S residue 369 ASP Chi-restraints excluded: chain S residue 418 GLU Chi-restraints excluded: chain S residue 433 VAL Chi-restraints excluded: chain T residue 297 GLN Chi-restraints excluded: chain T residue 369 ASP Chi-restraints excluded: chain T residue 433 VAL Chi-restraints excluded: chain U residue 297 GLN Chi-restraints excluded: chain U residue 369 ASP Chi-restraints excluded: chain U residue 394 LYS Chi-restraints excluded: chain U residue 433 VAL Chi-restraints excluded: chain V residue 369 ASP Chi-restraints excluded: chain V residue 433 VAL Chi-restraints excluded: chain W residue 243 SER Chi-restraints excluded: chain W residue 297 GLN Chi-restraints excluded: chain W residue 369 ASP Chi-restraints excluded: chain X residue 297 GLN Chi-restraints excluded: chain X residue 369 ASP Chi-restraints excluded: chain X residue 433 VAL Chi-restraints excluded: chain Y residue 275 LYS Chi-restraints excluded: chain Y residue 297 GLN Chi-restraints excluded: chain Y residue 359 GLN Chi-restraints excluded: chain Y residue 369 ASP Chi-restraints excluded: chain Z residue 297 GLN Chi-restraints excluded: chain Z residue 369 ASP Chi-restraints excluded: chain a residue 297 GLN Chi-restraints excluded: chain a residue 369 ASP Chi-restraints excluded: chain b residue 275 LYS Chi-restraints excluded: chain b residue 369 ASP Chi-restraints excluded: chain b residue 433 VAL Chi-restraints excluded: chain c residue 297 GLN Chi-restraints excluded: chain c residue 369 ASP Chi-restraints excluded: chain d residue 369 ASP Chi-restraints excluded: chain d residue 391 VAL Chi-restraints excluded: chain e residue 275 LYS Chi-restraints excluded: chain e residue 369 ASP Chi-restraints excluded: chain e residue 418 GLU Chi-restraints excluded: chain f residue 297 GLN Chi-restraints excluded: chain f residue 369 ASP Chi-restraints excluded: chain g residue 243 SER Chi-restraints excluded: chain g residue 293 LEU Chi-restraints excluded: chain g residue 369 ASP Chi-restraints excluded: chain h residue 297 GLN Chi-restraints excluded: chain h residue 369 ASP Chi-restraints excluded: chain h residue 412 ILE Chi-restraints excluded: chain h residue 433 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 165 optimal weight: 0.7980 chunk 443 optimal weight: 0.0770 chunk 97 optimal weight: 0.0870 chunk 289 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 493 optimal weight: 0.9990 chunk 409 optimal weight: 0.5980 chunk 228 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 chunk 163 optimal weight: 3.9990 chunk 259 optimal weight: 1.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 ASN E 239 ASN F 239 ASN G 239 ASN H 239 ASN I 297 GLN ** J 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 269 GLN Q 408 GLN S 269 GLN T 239 ASN V 239 ASN W 239 ASN X 239 ASN Y 239 ASN ** a 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 269 GLN g 297 GLN h 408 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 40970 Z= 0.125 Angle : 0.432 6.949 55216 Z= 0.231 Chirality : 0.038 0.128 6324 Planarity : 0.002 0.023 7412 Dihedral : 4.512 20.313 5594 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Rotamer: Outliers : 1.60 % Allowed : 21.40 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.13), residues: 4930 helix: 2.65 (0.16), residues: 1326 sheet: -0.51 (0.11), residues: 2380 loop : -1.07 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS L 281 PHE 0.011 0.001 PHE G 422 TYR 0.006 0.001 TYR R 393 ARG 0.005 0.000 ARG P 370 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1026 residues out of total 4556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 953 time to evaluate : 4.881 Fit side-chains REVERT: C 377 MET cc_start: 0.7941 (mpt) cc_final: 0.7396 (mpt) REVERT: E 429 THR cc_start: 0.8795 (m) cc_final: 0.8575 (p) REVERT: F 381 ASP cc_start: 0.7658 (m-30) cc_final: 0.6998 (m-30) REVERT: I 276 GLU cc_start: 0.7066 (mp0) cc_final: 0.6732 (mp0) REVERT: K 429 THR cc_start: 0.8675 (m) cc_final: 0.8417 (p) REVERT: N 296 ARG cc_start: 0.7259 (OUTLIER) cc_final: 0.6571 (tpp-160) REVERT: O 367 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8536 (mm-30) REVERT: R 303 GLN cc_start: 0.7531 (mp10) cc_final: 0.6564 (mp10) REVERT: T 377 MET cc_start: 0.7960 (mpt) cc_final: 0.7345 (mpt) REVERT: Y 429 THR cc_start: 0.8695 (m) cc_final: 0.8487 (p) REVERT: Z 276 GLU cc_start: 0.7118 (mp0) cc_final: 0.6780 (mp0) REVERT: Z 417 ARG cc_start: 0.7817 (mtp85) cc_final: 0.7489 (mtp85) REVERT: f 367 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8513 (mm-30) REVERT: f 418 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8128 (tp30) REVERT: f 429 THR cc_start: 0.8707 (m) cc_final: 0.8438 (p) REVERT: g 429 THR cc_start: 0.8734 (m) cc_final: 0.8305 (p) outliers start: 73 outliers final: 47 residues processed: 1002 average time/residue: 1.9599 time to fit residues: 2281.9682 Evaluate side-chains 920 residues out of total 4556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 871 time to evaluate : 3.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain G residue 369 ASP Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain H residue 369 ASP Chi-restraints excluded: chain H residue 433 VAL Chi-restraints excluded: chain I residue 369 ASP Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain K residue 394 LYS Chi-restraints excluded: chain K residue 433 VAL Chi-restraints excluded: chain L residue 369 ASP Chi-restraints excluded: chain M residue 369 ASP Chi-restraints excluded: chain N residue 296 ARG Chi-restraints excluded: chain N residue 369 ASP Chi-restraints excluded: chain N residue 394 LYS Chi-restraints excluded: chain O residue 369 ASP Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain Q residue 369 ASP Chi-restraints excluded: chain R residue 369 ASP Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain S residue 369 ASP Chi-restraints excluded: chain T residue 369 ASP Chi-restraints excluded: chain T residue 433 VAL Chi-restraints excluded: chain U residue 369 ASP Chi-restraints excluded: chain U residue 433 VAL Chi-restraints excluded: chain V residue 369 ASP Chi-restraints excluded: chain W residue 369 ASP Chi-restraints excluded: chain X residue 369 ASP Chi-restraints excluded: chain X residue 433 VAL Chi-restraints excluded: chain Y residue 359 GLN Chi-restraints excluded: chain Y residue 369 ASP Chi-restraints excluded: chain Y residue 394 LYS Chi-restraints excluded: chain Z residue 369 ASP Chi-restraints excluded: chain a residue 369 ASP Chi-restraints excluded: chain b residue 369 ASP Chi-restraints excluded: chain c residue 369 ASP Chi-restraints excluded: chain d residue 369 ASP Chi-restraints excluded: chain e residue 369 ASP Chi-restraints excluded: chain e residue 394 LYS Chi-restraints excluded: chain f residue 369 ASP Chi-restraints excluded: chain f residue 418 GLU Chi-restraints excluded: chain f residue 433 VAL Chi-restraints excluded: chain g residue 369 ASP Chi-restraints excluded: chain h residue 369 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 475 optimal weight: 8.9990 chunk 55 optimal weight: 8.9990 chunk 281 optimal weight: 9.9990 chunk 360 optimal weight: 3.9990 chunk 279 optimal weight: 3.9990 chunk 415 optimal weight: 7.9990 chunk 275 optimal weight: 0.7980 chunk 491 optimal weight: 10.0000 chunk 307 optimal weight: 5.9990 chunk 299 optimal weight: 10.0000 chunk 226 optimal weight: 1.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN B 269 GLN C 239 ASN E 239 ASN E 411 GLN F 239 ASN G 239 ASN H 239 ASN H 411 GLN I 239 ASN I 411 GLN J 434 ASN K 239 ASN M 281 HIS N 281 HIS N 411 GLN R 239 ASN S 269 GLN T 239 ASN V 239 ASN V 411 GLN W 239 ASN X 239 ASN Y 239 ASN Z 239 ASN a 434 ASN b 299 ASN e 281 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.042 40970 Z= 0.498 Angle : 0.590 6.634 55216 Z= 0.312 Chirality : 0.044 0.130 6324 Planarity : 0.004 0.042 7412 Dihedral : 5.272 21.351 5594 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.18 % Allowed : 21.86 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.13), residues: 4930 helix: 2.21 (0.15), residues: 1326 sheet: -0.81 (0.11), residues: 2380 loop : -1.02 (0.16), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS C 281 PHE 0.016 0.001 PHE P 422 TYR 0.014 0.001 TYR R 393 ARG 0.005 0.001 ARG I 370 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1093 residues out of total 4556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 948 time to evaluate : 4.739 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 303 GLN cc_start: 0.7810 (mp10) cc_final: 0.6843 (mp10) REVERT: A 408 GLN cc_start: 0.7539 (tt0) cc_final: 0.7283 (tt0) REVERT: B 296 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.6783 (ttp-170) REVERT: B 297 GLN cc_start: 0.7471 (OUTLIER) cc_final: 0.6992 (tt0) REVERT: C 296 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.6674 (ttp-170) REVERT: D 297 GLN cc_start: 0.7395 (OUTLIER) cc_final: 0.7022 (tt0) REVERT: E 276 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6816 (mt-10) REVERT: F 297 GLN cc_start: 0.7355 (OUTLIER) cc_final: 0.6874 (tt0) REVERT: H 297 GLN cc_start: 0.7472 (OUTLIER) cc_final: 0.6961 (tt0) REVERT: I 276 GLU cc_start: 0.7212 (mp0) cc_final: 0.6942 (mp0) REVERT: J 297 GLN cc_start: 0.7431 (OUTLIER) cc_final: 0.6959 (tt0) REVERT: M 296 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.6874 (ttt180) REVERT: N 296 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.6704 (tpp-160) REVERT: N 297 GLN cc_start: 0.7398 (OUTLIER) cc_final: 0.7128 (tt0) REVERT: N 429 THR cc_start: 0.8740 (m) cc_final: 0.8437 (p) REVERT: O 367 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8598 (mm-30) REVERT: P 418 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8209 (tp30) REVERT: Q 296 ARG cc_start: 0.7518 (OUTLIER) cc_final: 0.7070 (ttp-170) REVERT: Q 409 MET cc_start: 0.8416 (mmm) cc_final: 0.8124 (mmm) REVERT: R 297 GLN cc_start: 0.7432 (OUTLIER) cc_final: 0.7001 (tt0) REVERT: R 408 GLN cc_start: 0.7545 (tt0) cc_final: 0.7282 (tt0) REVERT: T 297 GLN cc_start: 0.7414 (OUTLIER) cc_final: 0.6949 (tt0) REVERT: U 297 GLN cc_start: 0.7311 (OUTLIER) cc_final: 0.6997 (tt0) REVERT: V 276 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6785 (mt-10) REVERT: W 296 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.6965 (ttt180) REVERT: W 297 GLN cc_start: 0.7381 (OUTLIER) cc_final: 0.6989 (tt0) REVERT: Y 297 GLN cc_start: 0.7464 (OUTLIER) cc_final: 0.6960 (tt0) REVERT: Z 276 GLU cc_start: 0.7309 (mp0) cc_final: 0.7061 (mp0) REVERT: c 297 GLN cc_start: 0.7371 (OUTLIER) cc_final: 0.7163 (tt0) REVERT: c 303 GLN cc_start: 0.7680 (mp10) cc_final: 0.6888 (mp10) REVERT: e 297 GLN cc_start: 0.7422 (OUTLIER) cc_final: 0.7116 (tt0) REVERT: e 418 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.7340 (mp0) REVERT: f 297 GLN cc_start: 0.7373 (OUTLIER) cc_final: 0.7016 (tt0) REVERT: f 367 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8602 (mm-30) REVERT: g 417 ARG cc_start: 0.8135 (ttm-80) cc_final: 0.7652 (mtt90) REVERT: g 429 THR cc_start: 0.8762 (m) cc_final: 0.8385 (p) REVERT: h 297 GLN cc_start: 0.7404 (OUTLIER) cc_final: 0.7174 (tt0) outliers start: 145 outliers final: 77 residues processed: 1056 average time/residue: 2.0694 time to fit residues: 2522.5018 Evaluate side-chains 1037 residues out of total 4556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 935 time to evaluate : 4.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 296 ARG Chi-restraints excluded: chain B residue 297 GLN Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 296 ARG Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain D residue 297 GLN Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain E residue 275 LYS Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain F residue 297 GLN Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain G residue 243 SER Chi-restraints excluded: chain G residue 369 ASP Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain H residue 297 GLN Chi-restraints excluded: chain H residue 369 ASP Chi-restraints excluded: chain H residue 433 VAL Chi-restraints excluded: chain I residue 243 SER Chi-restraints excluded: chain I residue 369 ASP Chi-restraints excluded: chain I residue 412 ILE Chi-restraints excluded: chain J residue 297 GLN Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain K residue 433 VAL Chi-restraints excluded: chain L residue 369 ASP Chi-restraints excluded: chain L residue 433 VAL Chi-restraints excluded: chain M residue 296 ARG Chi-restraints excluded: chain M residue 369 ASP Chi-restraints excluded: chain N residue 243 SER Chi-restraints excluded: chain N residue 293 LEU Chi-restraints excluded: chain N residue 296 ARG Chi-restraints excluded: chain N residue 297 GLN Chi-restraints excluded: chain N residue 369 ASP Chi-restraints excluded: chain O residue 369 ASP Chi-restraints excluded: chain O residue 433 VAL Chi-restraints excluded: chain P residue 243 SER Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain P residue 418 GLU Chi-restraints excluded: chain Q residue 296 ARG Chi-restraints excluded: chain Q residue 369 ASP Chi-restraints excluded: chain Q residue 433 VAL Chi-restraints excluded: chain R residue 243 SER Chi-restraints excluded: chain R residue 297 GLN Chi-restraints excluded: chain R residue 369 ASP Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain S residue 369 ASP Chi-restraints excluded: chain S residue 433 VAL Chi-restraints excluded: chain T residue 297 GLN Chi-restraints excluded: chain T residue 369 ASP Chi-restraints excluded: chain T residue 433 VAL Chi-restraints excluded: chain U residue 297 GLN Chi-restraints excluded: chain U residue 369 ASP Chi-restraints excluded: chain V residue 276 GLU Chi-restraints excluded: chain V residue 293 LEU Chi-restraints excluded: chain V residue 369 ASP Chi-restraints excluded: chain V residue 433 VAL Chi-restraints excluded: chain W residue 243 SER Chi-restraints excluded: chain W residue 296 ARG Chi-restraints excluded: chain W residue 297 GLN Chi-restraints excluded: chain W residue 369 ASP Chi-restraints excluded: chain W residue 433 VAL Chi-restraints excluded: chain X residue 369 ASP Chi-restraints excluded: chain X residue 433 VAL Chi-restraints excluded: chain Y residue 297 GLN Chi-restraints excluded: chain Y residue 369 ASP Chi-restraints excluded: chain Y residue 433 VAL Chi-restraints excluded: chain Z residue 297 GLN Chi-restraints excluded: chain Z residue 369 ASP Chi-restraints excluded: chain Z residue 433 VAL Chi-restraints excluded: chain a residue 369 ASP Chi-restraints excluded: chain b residue 369 ASP Chi-restraints excluded: chain b residue 433 VAL Chi-restraints excluded: chain c residue 297 GLN Chi-restraints excluded: chain c residue 369 ASP Chi-restraints excluded: chain c residue 433 VAL Chi-restraints excluded: chain d residue 369 ASP Chi-restraints excluded: chain e residue 297 GLN Chi-restraints excluded: chain e residue 369 ASP Chi-restraints excluded: chain e residue 418 GLU Chi-restraints excluded: chain f residue 297 GLN Chi-restraints excluded: chain f residue 369 ASP Chi-restraints excluded: chain f residue 418 GLU Chi-restraints excluded: chain f residue 433 VAL Chi-restraints excluded: chain g residue 243 SER Chi-restraints excluded: chain g residue 275 LYS Chi-restraints excluded: chain g residue 293 LEU Chi-restraints excluded: chain g residue 369 ASP Chi-restraints excluded: chain g residue 418 GLU Chi-restraints excluded: chain h residue 297 GLN Chi-restraints excluded: chain h residue 369 ASP Chi-restraints excluded: chain h residue 433 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 304 optimal weight: 2.9990 chunk 196 optimal weight: 3.9990 chunk 293 optimal weight: 0.7980 chunk 148 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 312 optimal weight: 0.9980 chunk 334 optimal weight: 0.5980 chunk 243 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 386 optimal weight: 9.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 ASN E 239 ASN F 239 ASN G 239 ASN H 239 ASN I 297 GLN N 411 GLN P 269 GLN Q 408 GLN S 269 GLN T 239 ASN V 239 ASN W 239 ASN X 239 ASN Y 239 ASN h 374 HIS h 408 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 40970 Z= 0.166 Angle : 0.460 8.302 55216 Z= 0.245 Chirality : 0.039 0.134 6324 Planarity : 0.003 0.023 7412 Dihedral : 4.684 20.961 5594 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Rotamer: Outliers : 1.78 % Allowed : 23.81 % Favored : 74.41 % 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: 0.38 (0.13), residues: 4930 helix: 2.64 (0.16), residues: 1326 sheet: -0.42 (0.11), residues: 2380 loop : -0.80 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS H 281 PHE 0.012 0.001 PHE O 422 TYR 0.009 0.001 TYR A 393 ARG 0.004 0.000 ARG H 247 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 964 residues out of total 4556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 883 time to evaluate : 3.712 Fit side-chains revert: symmetry clash REVERT: A 303 GLN cc_start: 0.7717 (mp10) cc_final: 0.6825 (mp10) REVERT: B 302 GLU cc_start: 0.6699 (OUTLIER) cc_final: 0.6496 (tp30) REVERT: C 296 ARG cc_start: 0.7297 (OUTLIER) cc_final: 0.6487 (ttp-170) REVERT: E 276 GLU cc_start: 0.6979 (OUTLIER) cc_final: 0.6749 (mt-10) REVERT: I 276 GLU cc_start: 0.7094 (mp0) cc_final: 0.6757 (mp0) REVERT: M 296 ARG cc_start: 0.7198 (OUTLIER) cc_final: 0.6682 (ttt180) REVERT: N 296 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.6516 (tpp-160) REVERT: O 367 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8524 (mm-30) REVERT: P 418 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8117 (tp30) REVERT: Q 409 MET cc_start: 0.8426 (mmm) cc_final: 0.8095 (mmm) REVERT: W 296 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.6745 (ttt180) REVERT: X 276 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6780 (mp0) REVERT: Z 276 GLU cc_start: 0.7180 (mp0) cc_final: 0.6887 (mp0) REVERT: Z 417 ARG cc_start: 0.7795 (mtp85) cc_final: 0.7484 (mtp85) REVERT: f 418 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8132 (tp30) REVERT: g 429 THR cc_start: 0.8727 (m) cc_final: 0.8230 (p) outliers start: 81 outliers final: 56 residues processed: 943 average time/residue: 2.0384 time to fit residues: 2222.7888 Evaluate side-chains 909 residues out of total 4556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 844 time to evaluate : 4.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 302 GLU Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain C residue 296 ARG Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain G residue 369 ASP Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain H residue 369 ASP Chi-restraints excluded: chain H residue 433 VAL Chi-restraints excluded: chain I residue 369 ASP Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain K residue 433 VAL Chi-restraints excluded: chain L residue 369 ASP Chi-restraints excluded: chain L residue 433 VAL Chi-restraints excluded: chain M residue 296 ARG Chi-restraints excluded: chain M residue 369 ASP Chi-restraints excluded: chain N residue 293 LEU Chi-restraints excluded: chain N residue 296 ARG Chi-restraints excluded: chain N residue 369 ASP Chi-restraints excluded: chain N residue 394 LYS Chi-restraints excluded: chain O residue 369 ASP Chi-restraints excluded: chain O residue 433 VAL Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain P residue 418 GLU Chi-restraints excluded: chain Q residue 243 SER Chi-restraints excluded: chain Q residue 369 ASP Chi-restraints excluded: chain Q residue 433 VAL Chi-restraints excluded: chain R residue 243 SER Chi-restraints excluded: chain R residue 369 ASP Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain S residue 369 ASP Chi-restraints excluded: chain T residue 369 ASP Chi-restraints excluded: chain T residue 433 VAL Chi-restraints excluded: chain U residue 369 ASP Chi-restraints excluded: chain V residue 369 ASP Chi-restraints excluded: chain W residue 296 ARG Chi-restraints excluded: chain W residue 369 ASP Chi-restraints excluded: chain X residue 276 GLU Chi-restraints excluded: chain X residue 369 ASP Chi-restraints excluded: chain X residue 433 VAL Chi-restraints excluded: chain Y residue 369 ASP Chi-restraints excluded: chain Z residue 369 ASP Chi-restraints excluded: chain a residue 369 ASP Chi-restraints excluded: chain b residue 369 ASP Chi-restraints excluded: chain b residue 433 VAL Chi-restraints excluded: chain c residue 369 ASP Chi-restraints excluded: chain c residue 433 VAL Chi-restraints excluded: chain d residue 369 ASP Chi-restraints excluded: chain d residue 391 VAL Chi-restraints excluded: chain e residue 369 ASP Chi-restraints excluded: chain e residue 394 LYS Chi-restraints excluded: chain e residue 433 VAL Chi-restraints excluded: chain f residue 369 ASP Chi-restraints excluded: chain f residue 418 GLU Chi-restraints excluded: chain f residue 433 VAL Chi-restraints excluded: chain g residue 369 ASP Chi-restraints excluded: chain h residue 433 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 447 optimal weight: 3.9990 chunk 470 optimal weight: 1.9990 chunk 429 optimal weight: 4.9990 chunk 458 optimal weight: 0.5980 chunk 275 optimal weight: 2.9990 chunk 199 optimal weight: 1.9990 chunk 359 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 413 optimal weight: 4.9990 chunk 433 optimal weight: 5.9990 chunk 456 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN B 269 GLN B 359 GLN C 239 ASN E 239 ASN F 239 ASN G 239 ASN H 239 ASN I 239 ASN K 239 ASN N 281 HIS N 411 GLN R 239 ASN S 269 GLN S 359 GLN T 239 ASN V 239 ASN W 239 ASN X 239 ASN Y 239 ASN Z 239 ASN b 239 ASN e 281 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 40970 Z= 0.275 Angle : 0.500 7.574 55216 Z= 0.265 Chirality : 0.040 0.180 6324 Planarity : 0.003 0.029 7412 Dihedral : 4.889 21.302 5594 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.09 % Allowed : 24.10 % Favored : 73.81 % 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: 0.43 (0.13), residues: 4930 helix: 2.61 (0.16), residues: 1326 sheet: -0.40 (0.11), residues: 2380 loop : -0.66 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS c 281 PHE 0.013 0.001 PHE H 422 TYR 0.013 0.001 TYR A 393 ARG 0.006 0.000 ARG M 370 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 987 residues out of total 4556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 892 time to evaluate : 4.687 Fit side-chains revert: symmetry clash REVERT: A 276 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6848 (mp0) REVERT: A 303 GLN cc_start: 0.7751 (mp10) cc_final: 0.6816 (mp10) REVERT: B 418 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8154 (mp0) REVERT: C 296 ARG cc_start: 0.7359 (OUTLIER) cc_final: 0.6598 (ttp-170) REVERT: C 429 THR cc_start: 0.8785 (m) cc_final: 0.8500 (p) REVERT: D 297 GLN cc_start: 0.7303 (OUTLIER) cc_final: 0.6921 (tt0) REVERT: E 276 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.6786 (mt-10) REVERT: F 297 GLN cc_start: 0.7259 (OUTLIER) cc_final: 0.6814 (tt0) REVERT: G 276 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6810 (mp0) REVERT: H 394 LYS cc_start: 0.7293 (ttpt) cc_final: 0.7058 (ttpp) REVERT: I 276 GLU cc_start: 0.7101 (mp0) cc_final: 0.6748 (mp0) REVERT: J 297 GLN cc_start: 0.7342 (OUTLIER) cc_final: 0.6891 (tt0) REVERT: K 394 LYS cc_start: 0.7159 (ttpt) cc_final: 0.6822 (ttpt) REVERT: M 296 ARG cc_start: 0.7247 (OUTLIER) cc_final: 0.6744 (ttt180) REVERT: N 296 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.6570 (tpp-160) REVERT: O 367 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8560 (mm-30) REVERT: P 418 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8106 (tp30) REVERT: Q 409 MET cc_start: 0.8448 (mmm) cc_final: 0.8033 (mmm) REVERT: S 276 GLU cc_start: 0.7211 (mp0) cc_final: 0.6981 (mp0) REVERT: T 429 THR cc_start: 0.8775 (m) cc_final: 0.8496 (p) REVERT: U 297 GLN cc_start: 0.7229 (OUTLIER) cc_final: 0.6921 (tt0) REVERT: W 296 ARG cc_start: 0.7268 (OUTLIER) cc_final: 0.6779 (ttt180) REVERT: W 297 GLN cc_start: 0.7267 (OUTLIER) cc_final: 0.6879 (tt0) REVERT: X 276 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6816 (mp0) REVERT: Z 276 GLU cc_start: 0.7235 (mp0) cc_final: 0.6911 (mp0) REVERT: f 367 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8566 (mm-30) REVERT: g 429 THR cc_start: 0.8750 (m) cc_final: 0.8429 (p) REVERT: h 297 GLN cc_start: 0.7385 (OUTLIER) cc_final: 0.7158 (tt0) REVERT: h 429 THR cc_start: 0.8738 (m) cc_final: 0.8508 (p) outliers start: 95 outliers final: 62 residues processed: 965 average time/residue: 1.9895 time to fit residues: 2222.6144 Evaluate side-chains 950 residues out of total 4556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 872 time to evaluate : 4.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain C residue 296 ARG Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain D residue 297 GLN Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain E residue 276 GLU Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain E residue 412 ILE Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain F residue 297 GLN Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain G residue 276 GLU Chi-restraints excluded: chain G residue 369 ASP Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain H residue 369 ASP Chi-restraints excluded: chain H residue 433 VAL Chi-restraints excluded: chain I residue 369 ASP Chi-restraints excluded: chain J residue 297 GLN Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain K residue 433 VAL Chi-restraints excluded: chain L residue 369 ASP Chi-restraints excluded: chain L residue 433 VAL Chi-restraints excluded: chain M residue 296 ARG Chi-restraints excluded: chain M residue 369 ASP Chi-restraints excluded: chain N residue 293 LEU Chi-restraints excluded: chain N residue 296 ARG Chi-restraints excluded: chain N residue 369 ASP Chi-restraints excluded: chain O residue 369 ASP Chi-restraints excluded: chain O residue 433 VAL Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain P residue 418 GLU Chi-restraints excluded: chain Q residue 243 SER Chi-restraints excluded: chain Q residue 369 ASP Chi-restraints excluded: chain Q residue 433 VAL Chi-restraints excluded: chain R residue 243 SER Chi-restraints excluded: chain R residue 369 ASP Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain S residue 369 ASP Chi-restraints excluded: chain T residue 369 ASP Chi-restraints excluded: chain T residue 433 VAL Chi-restraints excluded: chain U residue 297 GLN Chi-restraints excluded: chain U residue 369 ASP Chi-restraints excluded: chain V residue 369 ASP Chi-restraints excluded: chain W residue 243 SER Chi-restraints excluded: chain W residue 296 ARG Chi-restraints excluded: chain W residue 297 GLN Chi-restraints excluded: chain W residue 369 ASP Chi-restraints excluded: chain W residue 433 VAL Chi-restraints excluded: chain X residue 276 GLU Chi-restraints excluded: chain X residue 369 ASP Chi-restraints excluded: chain X residue 433 VAL Chi-restraints excluded: chain Y residue 369 ASP Chi-restraints excluded: chain Y residue 433 VAL Chi-restraints excluded: chain Z residue 369 ASP Chi-restraints excluded: chain a residue 369 ASP Chi-restraints excluded: chain b residue 369 ASP Chi-restraints excluded: chain b residue 433 VAL Chi-restraints excluded: chain c residue 369 ASP Chi-restraints excluded: chain c residue 433 VAL Chi-restraints excluded: chain d residue 369 ASP Chi-restraints excluded: chain d residue 391 VAL Chi-restraints excluded: chain e residue 369 ASP Chi-restraints excluded: chain e residue 433 VAL Chi-restraints excluded: chain f residue 369 ASP Chi-restraints excluded: chain f residue 418 GLU Chi-restraints excluded: chain f residue 433 VAL Chi-restraints excluded: chain g residue 293 LEU Chi-restraints excluded: chain g residue 369 ASP Chi-restraints excluded: chain h residue 297 GLN Chi-restraints excluded: chain h residue 433 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 300 optimal weight: 0.8980 chunk 484 optimal weight: 3.9990 chunk 295 optimal weight: 5.9990 chunk 229 optimal weight: 0.4980 chunk 336 optimal weight: 2.9990 chunk 508 optimal weight: 3.9990 chunk 467 optimal weight: 0.7980 chunk 404 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 312 optimal weight: 0.8980 chunk 248 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN B 359 GLN C 239 ASN E 239 ASN E 411 GLN F 239 ASN F 361 ASN G 239 ASN H 239 ASN H 411 GLN I 239 ASN I 297 GLN J 359 GLN N 411 GLN R 239 ASN S 269 GLN S 359 GLN T 234 GLN T 239 ASN V 239 ASN V 411 GLN W 239 ASN X 239 ASN Y 239 ASN Z 239 ASN a 359 GLN b 239 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 40970 Z= 0.150 Angle : 0.452 7.319 55216 Z= 0.240 Chirality : 0.038 0.130 6324 Planarity : 0.002 0.024 7412 Dihedral : 4.518 21.913 5594 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.51 % Allowed : 24.52 % Favored : 73.97 % 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: 0.85 (0.13), residues: 4930 helix: 2.82 (0.16), residues: 1326 sheet: -0.06 (0.11), residues: 2380 loop : -0.51 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS c 281 PHE 0.013 0.001 PHE N 422 TYR 0.008 0.001 TYR A 393 ARG 0.005 0.000 ARG d 370 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9860 Ramachandran restraints generated. 4930 Oldfield, 0 Emsley, 4930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 949 residues out of total 4556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 880 time to evaluate : 4.687 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 303 GLN cc_start: 0.7686 (mp10) cc_final: 0.6755 (mp10) REVERT: B 276 GLU cc_start: 0.7074 (mp0) cc_final: 0.6826 (mp0) REVERT: C 296 ARG cc_start: 0.7248 (OUTLIER) cc_final: 0.6424 (ttp-170) REVERT: C 429 THR cc_start: 0.8725 (m) cc_final: 0.8496 (p) REVERT: F 381 ASP cc_start: 0.7577 (m-30) cc_final: 0.6958 (m-30) REVERT: H 394 LYS cc_start: 0.7216 (ttpt) cc_final: 0.6972 (ttpp) REVERT: H 429 THR cc_start: 0.8861 (t) cc_final: 0.8498 (p) REVERT: M 296 ARG cc_start: 0.7205 (OUTLIER) cc_final: 0.6677 (ttt180) REVERT: N 296 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.6557 (tpp-160) REVERT: O 367 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8536 (mm-30) REVERT: O 429 THR cc_start: 0.8645 (m) cc_final: 0.8358 (p) REVERT: Q 409 MET cc_start: 0.8432 (mmm) cc_final: 0.8076 (mmm) REVERT: S 276 GLU cc_start: 0.7129 (mp0) cc_final: 0.6896 (mp0) REVERT: T 429 THR cc_start: 0.8734 (m) cc_final: 0.8518 (p) REVERT: W 296 ARG cc_start: 0.7194 (OUTLIER) cc_final: 0.6654 (ttt180) REVERT: Y 429 THR cc_start: 0.8685 (m) cc_final: 0.8463 (p) REVERT: Z 276 GLU cc_start: 0.7173 (mp0) cc_final: 0.6793 (mp0) REVERT: e 402 LEU cc_start: 0.7632 (mt) cc_final: 0.7424 (mm) REVERT: f 418 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8096 (tp30) REVERT: f 429 THR cc_start: 0.8723 (m) cc_final: 0.8514 (p) REVERT: g 429 THR cc_start: 0.8744 (m) cc_final: 0.8289 (p) outliers start: 69 outliers final: 59 residues processed: 938 average time/residue: 1.9433 time to fit residues: 2119.4379 Evaluate side-chains 917 residues out of total 4556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 853 time to evaluate : 4.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 296 ARG Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain D residue 369 ASP Chi-restraints excluded: chain E residue 369 ASP Chi-restraints excluded: chain E residue 412 ILE Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain G residue 369 ASP Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain H residue 369 ASP Chi-restraints excluded: chain H residue 433 VAL Chi-restraints excluded: chain I residue 369 ASP Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain K residue 433 VAL Chi-restraints excluded: chain L residue 369 ASP Chi-restraints excluded: chain L residue 433 VAL Chi-restraints excluded: chain M residue 296 ARG Chi-restraints excluded: chain M residue 369 ASP Chi-restraints excluded: chain N residue 296 ARG Chi-restraints excluded: chain N residue 369 ASP Chi-restraints excluded: chain O residue 369 ASP Chi-restraints excluded: chain O residue 433 VAL Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain Q residue 243 SER Chi-restraints excluded: chain Q residue 369 ASP Chi-restraints excluded: chain Q residue 433 VAL Chi-restraints excluded: chain R residue 243 SER Chi-restraints excluded: chain R residue 369 ASP Chi-restraints excluded: chain R residue 433 VAL Chi-restraints excluded: chain S residue 369 ASP Chi-restraints excluded: chain T residue 369 ASP Chi-restraints excluded: chain T residue 394 LYS Chi-restraints excluded: chain T residue 433 VAL Chi-restraints excluded: chain U residue 369 ASP Chi-restraints excluded: chain V residue 369 ASP Chi-restraints excluded: chain W residue 243 SER Chi-restraints excluded: chain W residue 296 ARG Chi-restraints excluded: chain W residue 369 ASP Chi-restraints excluded: chain X residue 369 ASP Chi-restraints excluded: chain X residue 433 VAL Chi-restraints excluded: chain Y residue 369 ASP Chi-restraints excluded: chain Z residue 297 GLN Chi-restraints excluded: chain Z residue 369 ASP Chi-restraints excluded: chain a residue 369 ASP Chi-restraints excluded: chain b residue 369 ASP Chi-restraints excluded: chain b residue 433 VAL Chi-restraints excluded: chain c residue 369 ASP Chi-restraints excluded: chain c residue 433 VAL Chi-restraints excluded: chain d residue 369 ASP Chi-restraints excluded: chain e residue 369 ASP Chi-restraints excluded: chain e residue 433 VAL Chi-restraints excluded: chain f residue 369 ASP Chi-restraints excluded: chain f residue 418 GLU Chi-restraints excluded: chain f residue 433 VAL Chi-restraints excluded: chain g residue 293 LEU Chi-restraints excluded: chain g residue 369 ASP Chi-restraints excluded: chain h residue 369 ASP Chi-restraints excluded: chain h residue 433 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 321 optimal weight: 3.9990 chunk 430 optimal weight: 6.9990 chunk 123 optimal weight: 10.0000 chunk 373 optimal weight: 0.6980 chunk 59 optimal weight: 8.9990 chunk 112 optimal weight: 0.0270 chunk 405 optimal weight: 0.9980 chunk 169 optimal weight: 2.9990 chunk 416 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 74 optimal weight: 0.6980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN B 359 GLN C 239 ASN E 239 ASN F 239 ASN G 239 ASN H 239 ASN I 239 ASN I 411 GLN K 239 ASN R 239 ASN S 269 GLN S 359 GLN T 239 ASN V 239 ASN W 239 ASN X 239 ASN Y 239 ASN Z 239 ASN b 239 ASN e 297 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.153344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.122914 restraints weight = 44451.753| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.66 r_work: 0.3452 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 40970 Z= 0.138 Angle : 0.442 6.992 55216 Z= 0.234 Chirality : 0.038 0.123 6324 Planarity : 0.002 0.023 7412 Dihedral : 4.368 21.340 5594 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.54 % Allowed : 24.67 % Favored : 73.79 % 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: 1.18 (0.13), residues: 4930 helix: 2.96 (0.16), residues: 1326 sheet: 0.20 (0.11), residues: 2380 loop : -0.31 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS M 281 PHE 0.012 0.001 PHE O 422 TYR 0.008 0.001 TYR A 393 ARG 0.005 0.000 ARG M 370 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 29650.85 seconds wall clock time: 516 minutes 17.26 seconds (30977.26 seconds total)