Starting phenix.real_space_refine on Fri Feb 23 22:50:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cg7_30351/02_2024/7cg7_30351.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cg7_30351/02_2024/7cg7_30351.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cg7_30351/02_2024/7cg7_30351.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cg7_30351/02_2024/7cg7_30351.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cg7_30351/02_2024/7cg7_30351.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cg7_30351/02_2024/7cg7_30351.pdb" } resolution = 3.61 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= 0.001 sd= 0.043 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 24548 2.51 5 N 7514 2.21 5 O 8126 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 ASP 271": "OD1" <-> "OD2" Residue "A PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 384": "NH1" <-> "NH2" Residue "B ARG 244": "NH1" <-> "NH2" Residue "B ASP 271": "OD1" <-> "OD2" Residue "B PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 384": "NH1" <-> "NH2" Residue "C ARG 244": "NH1" <-> "NH2" Residue "C ASP 271": "OD1" <-> "OD2" Residue "C PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 384": "NH1" <-> "NH2" Residue "D ARG 244": "NH1" <-> "NH2" Residue "D ASP 271": "OD1" <-> "OD2" Residue "D PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 384": "NH1" <-> "NH2" Residue "E ARG 244": "NH1" <-> "NH2" Residue "E ASP 271": "OD1" <-> "OD2" Residue "E PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 384": "NH1" <-> "NH2" Residue "F ARG 244": "NH1" <-> "NH2" Residue "F ASP 271": "OD1" <-> "OD2" Residue "F PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 384": "NH1" <-> "NH2" Residue "G ARG 244": "NH1" <-> "NH2" Residue "G ASP 271": "OD1" <-> "OD2" Residue "G PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 384": "NH1" <-> "NH2" Residue "H ARG 244": "NH1" <-> "NH2" Residue "H ASP 271": "OD1" <-> "OD2" Residue "H PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 384": "NH1" <-> "NH2" Residue "I ARG 244": "NH1" <-> "NH2" Residue "I ASP 271": "OD1" <-> "OD2" Residue "I PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 384": "NH1" <-> "NH2" Residue "J ARG 244": "NH1" <-> "NH2" Residue "J ASP 271": "OD1" <-> "OD2" Residue "J PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 384": "NH1" <-> "NH2" Residue "K ARG 244": "NH1" <-> "NH2" Residue "K ASP 271": "OD1" <-> "OD2" Residue "K PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 384": "NH1" <-> "NH2" Residue "L ARG 244": "NH1" <-> "NH2" Residue "L ASP 271": "OD1" <-> "OD2" Residue "L PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 384": "NH1" <-> "NH2" Residue "M ARG 244": "NH1" <-> "NH2" Residue "M ASP 271": "OD1" <-> "OD2" Residue "M PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 384": "NH1" <-> "NH2" Residue "N ARG 244": "NH1" <-> "NH2" Residue "N ASP 271": "OD1" <-> "OD2" Residue "N PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 384": "NH1" <-> "NH2" Residue "O ARG 244": "NH1" <-> "NH2" Residue "O ASP 271": "OD1" <-> "OD2" Residue "O PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 384": "NH1" <-> "NH2" Residue "P ARG 244": "NH1" <-> "NH2" Residue "P ASP 271": "OD1" <-> "OD2" Residue "P PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 384": "NH1" <-> "NH2" Residue "Q ARG 244": "NH1" <-> "NH2" Residue "Q ASP 271": "OD1" <-> "OD2" Residue "Q PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 384": "NH1" <-> "NH2" Residue "R ARG 244": "NH1" <-> "NH2" Residue "R ASP 271": "OD1" <-> "OD2" Residue "R PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 384": "NH1" <-> "NH2" Residue "S ARG 244": "NH1" <-> "NH2" Residue "S ASP 271": "OD1" <-> "OD2" Residue "S PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 384": "NH1" <-> "NH2" Residue "T ARG 244": "NH1" <-> "NH2" Residue "T ASP 271": "OD1" <-> "OD2" Residue "T PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 384": "NH1" <-> "NH2" Residue "U ARG 244": "NH1" <-> "NH2" Residue "U ASP 271": "OD1" <-> "OD2" Residue "U PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 384": "NH1" <-> "NH2" Residue "V ARG 244": "NH1" <-> "NH2" Residue "V ASP 271": "OD1" <-> "OD2" Residue "V PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 384": "NH1" <-> "NH2" Residue "W ARG 244": "NH1" <-> "NH2" Residue "W ASP 271": "OD1" <-> "OD2" Residue "W PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 384": "NH1" <-> "NH2" Residue "X ARG 244": "NH1" <-> "NH2" Residue "X ASP 271": "OD1" <-> "OD2" Residue "X PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 384": "NH1" <-> "NH2" Residue "Y ARG 244": "NH1" <-> "NH2" Residue "Y ASP 271": "OD1" <-> "OD2" Residue "Y PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 384": "NH1" <-> "NH2" Residue "Z ARG 244": "NH1" <-> "NH2" Residue "Z ASP 271": "OD1" <-> "OD2" Residue "Z PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 384": "NH1" <-> "NH2" Residue "a ARG 244": "NH1" <-> "NH2" Residue "a ASP 271": "OD1" <-> "OD2" Residue "a PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 384": "NH1" <-> "NH2" Residue "c ARG 244": "NH1" <-> "NH2" Residue "c ASP 271": "OD1" <-> "OD2" Residue "c PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 384": "NH1" <-> "NH2" Residue "b ARG 244": "NH1" <-> "NH2" Residue "b ASP 271": "OD1" <-> "OD2" Residue "b PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 384": "NH1" <-> "NH2" Residue "d ARG 244": "NH1" <-> "NH2" Residue "d ASP 271": "OD1" <-> "OD2" Residue "d PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 384": "NH1" <-> "NH2" Residue "e ARG 244": "NH1" <-> "NH2" Residue "e ASP 271": "OD1" <-> "OD2" Residue "e PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 384": "NH1" <-> "NH2" Residue "f ARG 244": "NH1" <-> "NH2" Residue "f ASP 271": "OD1" <-> "OD2" Residue "f PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 384": "NH1" <-> "NH2" Residue "g ARG 244": "NH1" <-> "NH2" Residue "g ASP 271": "OD1" <-> "OD2" Residue "g PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 384": "NH1" <-> "NH2" Residue "h ARG 244": "NH1" <-> "NH2" Residue "h ASP 271": "OD1" <-> "OD2" Residue "h PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 384": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 40290 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "B" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "C" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "D" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "E" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "F" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "G" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "H" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "I" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "J" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "K" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "L" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "M" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "N" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "O" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "P" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "Q" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "R" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "S" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "T" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "U" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "V" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "W" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "X" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "Y" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "Z" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "a" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "c" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "b" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "d" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "e" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "f" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "g" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "h" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Time building chain proxies: 21.16, per 1000 atoms: 0.53 Number of scatterers: 40290 At special positions: 0 Unit cell: (254.865, 253.558, 100.639, 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 8126 8.00 N 7514 7.00 C 24548 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: 16.86 Conformation dependent library (CDL) restraints added in 7.4 seconds 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9792 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 64 sheets defined 28.7% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.10 Creating SS restraints... Processing helix chain 'A' and resid 233 through 258 Proline residue: A 255 - end of helix Processing helix chain 'A' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLY A 421 " --> pdb=" O ARG A 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 258 Proline residue: B 255 - end of helix Processing helix chain 'B' and resid 405 through 421 removed outlier: 3.778A pdb=" N GLY B 421 " --> pdb=" O ARG B 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 258 Proline residue: C 255 - end of helix Processing helix chain 'C' and resid 405 through 421 removed outlier: 3.778A pdb=" N GLY C 421 " --> pdb=" O ARG C 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 258 Proline residue: D 255 - end of helix Processing helix chain 'D' and resid 405 through 421 removed outlier: 3.778A pdb=" N GLY D 421 " --> pdb=" O ARG D 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 258 Proline residue: E 255 - end of helix Processing helix chain 'E' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLY E 421 " --> pdb=" O ARG E 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 258 Proline residue: F 255 - end of helix Processing helix chain 'F' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLY F 421 " --> pdb=" O ARG F 417 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 258 Proline residue: G 255 - end of helix Processing helix chain 'G' and resid 405 through 421 removed outlier: 3.778A pdb=" N GLY G 421 " --> pdb=" O ARG G 417 " (cutoff:3.500A) Processing helix chain 'H' and resid 233 through 258 Proline residue: H 255 - end of helix Processing helix chain 'H' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLY H 421 " --> pdb=" O ARG H 417 " (cutoff:3.500A) Processing helix chain 'I' and resid 233 through 258 Proline residue: I 255 - end of helix Processing helix chain 'I' and resid 405 through 421 removed outlier: 3.778A pdb=" N GLY I 421 " --> pdb=" O ARG I 417 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 258 Proline residue: J 255 - end of helix Processing helix chain 'J' and resid 405 through 421 removed outlier: 3.778A pdb=" N GLY J 421 " --> pdb=" O ARG J 417 " (cutoff:3.500A) Processing helix chain 'K' and resid 233 through 258 Proline residue: K 255 - end of helix Processing helix chain 'K' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLY K 421 " --> pdb=" O ARG K 417 " (cutoff:3.500A) Processing helix chain 'L' and resid 233 through 258 Proline residue: L 255 - end of helix Processing helix chain 'L' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLY L 421 " --> pdb=" O ARG L 417 " (cutoff:3.500A) Processing helix chain 'M' and resid 233 through 258 Proline residue: M 255 - end of helix Processing helix chain 'M' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLY M 421 " --> pdb=" O ARG M 417 " (cutoff:3.500A) Processing helix chain 'N' and resid 233 through 258 Proline residue: N 255 - end of helix Processing helix chain 'N' and resid 405 through 421 removed outlier: 3.778A pdb=" N GLY N 421 " --> pdb=" O ARG N 417 " (cutoff:3.500A) Processing helix chain 'O' and resid 233 through 258 Proline residue: O 255 - end of helix Processing helix chain 'O' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLY O 421 " --> pdb=" O ARG O 417 " (cutoff:3.500A) Processing helix chain 'P' and resid 233 through 258 Proline residue: P 255 - end of helix Processing helix chain 'P' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLY P 421 " --> pdb=" O ARG P 417 " (cutoff:3.500A) Processing helix chain 'Q' and resid 233 through 258 Proline residue: Q 255 - end of helix Processing helix chain 'Q' and resid 405 through 421 removed outlier: 3.778A pdb=" N GLY Q 421 " --> pdb=" O ARG Q 417 " (cutoff:3.500A) Processing helix chain 'R' and resid 233 through 258 Proline residue: R 255 - end of helix Processing helix chain 'R' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLY R 421 " --> pdb=" O ARG R 417 " (cutoff:3.500A) Processing helix chain 'S' and resid 233 through 258 Proline residue: S 255 - end of helix Processing helix chain 'S' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLY S 421 " --> pdb=" O ARG S 417 " (cutoff:3.500A) Processing helix chain 'T' and resid 233 through 258 Proline residue: T 255 - end of helix Processing helix chain 'T' and resid 405 through 421 removed outlier: 3.778A pdb=" N GLY T 421 " --> pdb=" O ARG T 417 " (cutoff:3.500A) Processing helix chain 'U' and resid 233 through 258 Proline residue: U 255 - end of helix Processing helix chain 'U' and resid 405 through 421 removed outlier: 3.778A pdb=" N GLY U 421 " --> pdb=" O ARG U 417 " (cutoff:3.500A) Processing helix chain 'V' and resid 233 through 258 Proline residue: V 255 - end of helix Processing helix chain 'V' and resid 405 through 421 removed outlier: 3.778A pdb=" N GLY V 421 " --> pdb=" O ARG V 417 " (cutoff:3.500A) Processing helix chain 'W' and resid 233 through 258 Proline residue: W 255 - end of helix Processing helix chain 'W' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLY W 421 " --> pdb=" O ARG W 417 " (cutoff:3.500A) Processing helix chain 'X' and resid 233 through 258 Proline residue: X 255 - end of helix Processing helix chain 'X' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLY X 421 " --> pdb=" O ARG X 417 " (cutoff:3.500A) Processing helix chain 'Y' and resid 233 through 258 Proline residue: Y 255 - end of helix Processing helix chain 'Y' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLY Y 421 " --> pdb=" O ARG Y 417 " (cutoff:3.500A) Processing helix chain 'Z' and resid 233 through 258 Proline residue: Z 255 - end of helix Processing helix chain 'Z' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLY Z 421 " --> pdb=" O ARG Z 417 " (cutoff:3.500A) Processing helix chain 'a' and resid 233 through 258 Proline residue: a 255 - end of helix Processing helix chain 'a' and resid 405 through 421 removed outlier: 3.778A pdb=" N GLY a 421 " --> pdb=" O ARG a 417 " (cutoff:3.500A) Processing helix chain 'c' and resid 233 through 258 Proline residue: c 255 - end of helix Processing helix chain 'c' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLY c 421 " --> pdb=" O ARG c 417 " (cutoff:3.500A) Processing helix chain 'b' and resid 233 through 258 Proline residue: b 255 - end of helix Processing helix chain 'b' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLY b 421 " --> pdb=" O ARG b 417 " (cutoff:3.500A) Processing helix chain 'd' and resid 233 through 258 Proline residue: d 255 - end of helix Processing helix chain 'd' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLY d 421 " --> pdb=" O ARG d 417 " (cutoff:3.500A) Processing helix chain 'e' and resid 233 through 258 Proline residue: e 255 - end of helix Processing helix chain 'e' and resid 405 through 421 removed outlier: 3.778A pdb=" N GLY e 421 " --> pdb=" O ARG e 417 " (cutoff:3.500A) Processing helix chain 'f' and resid 233 through 258 Proline residue: f 255 - end of helix Processing helix chain 'f' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLY f 421 " --> pdb=" O ARG f 417 " (cutoff:3.500A) Processing helix chain 'g' and resid 233 through 258 Proline residue: g 255 - end of helix Processing helix chain 'g' and resid 405 through 421 removed outlier: 3.778A pdb=" N GLY g 421 " --> pdb=" O ARG g 417 " (cutoff:3.500A) Processing helix chain 'h' and resid 233 through 258 Proline residue: h 255 - end of helix Processing helix chain 'h' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLY h 421 " --> pdb=" O ARG h 417 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASP A 271 " --> pdb=" O ILE A 382 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE A 382 " --> pdb=" O ASP A 271 " (cutoff:3.500A) removed outlier: 8.791A pdb=" N THR A 429 " --> pdb=" O GLU A 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU A 385 " --> pdb=" O THR A 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASN A 431 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL A 387 " --> pdb=" O ASN A 431 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL A 433 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL A 389 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 279 through 281 removed outlier: 3.731A pdb=" N ARG A 373 " --> pdb=" O GLU A 279 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 293 through 302 removed outlier: 6.754A pdb=" N ASN A 365 " --> pdb=" O ARG A 294 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARG A 296 " --> pdb=" O THR A 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR A 363 " --> pdb=" O ARG A 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU A 298 " --> pdb=" O ASN A 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN A 361 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ILE A 300 " --> pdb=" O GLN A 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN A 359 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU B 302 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ARG B 294 " --> pdb=" O TYR A 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN B 365 " --> pdb=" O ARG B 294 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARG B 296 " --> pdb=" O THR B 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR B 363 " --> pdb=" O ARG B 296 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU B 298 " --> pdb=" O ASN B 361 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASN B 361 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ILE B 300 " --> pdb=" O GLN B 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN B 359 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU C 302 " --> pdb=" O THR B 358 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ARG C 294 " --> pdb=" O TYR B 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN C 365 " --> pdb=" O ARG C 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG C 296 " --> pdb=" O THR C 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR C 363 " --> pdb=" O ARG C 296 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU C 298 " --> pdb=" O ASN C 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN C 361 " --> pdb=" O LEU C 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE C 300 " --> pdb=" O GLN C 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN C 359 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU D 302 " --> pdb=" O THR C 358 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ARG D 294 " --> pdb=" O TYR C 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN D 365 " --> pdb=" O ARG D 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG D 296 " --> pdb=" O THR D 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR D 363 " --> pdb=" O ARG D 296 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU D 298 " --> pdb=" O ASN D 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN D 361 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE D 300 " --> pdb=" O GLN D 359 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLN D 359 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU E 302 " --> pdb=" O THR D 358 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ARG E 294 " --> pdb=" O TYR D 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN E 365 " --> pdb=" O ARG E 294 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARG E 296 " --> pdb=" O THR E 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR E 363 " --> pdb=" O ARG E 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU E 298 " --> pdb=" O ASN E 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN E 361 " --> pdb=" O LEU E 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE E 300 " --> pdb=" O GLN E 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN E 359 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU F 302 " --> pdb=" O THR E 358 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ARG F 294 " --> pdb=" O TYR E 366 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASN F 365 " --> pdb=" O ARG F 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG F 296 " --> pdb=" O THR F 363 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N THR F 363 " --> pdb=" O ARG F 296 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU F 298 " --> pdb=" O ASN F 361 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASN F 361 " --> pdb=" O LEU F 298 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ILE F 300 " --> pdb=" O GLN F 359 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLN F 359 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU G 302 " --> pdb=" O THR F 358 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU F 362 " --> pdb=" O LEU G 298 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ARG G 294 " --> pdb=" O TYR F 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN G 365 " --> pdb=" O ARG G 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG G 296 " --> pdb=" O THR G 363 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N THR G 363 " --> pdb=" O ARG G 296 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU G 298 " --> pdb=" O ASN G 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN G 361 " --> pdb=" O LEU G 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE G 300 " --> pdb=" O GLN G 359 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLN G 359 " --> pdb=" O ILE G 300 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU H 302 " --> pdb=" O THR G 358 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ARG H 294 " --> pdb=" O TYR G 366 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASN H 365 " --> pdb=" O ARG H 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG H 296 " --> pdb=" O THR H 363 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N THR H 363 " --> pdb=" O ARG H 296 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU H 298 " --> pdb=" O ASN H 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN H 361 " --> pdb=" O LEU H 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE H 300 " --> pdb=" O GLN H 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN H 359 " --> pdb=" O ILE H 300 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU I 302 " --> pdb=" O THR H 358 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ARG I 294 " --> pdb=" O TYR H 366 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ASN I 365 " --> pdb=" O ARG I 294 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARG I 296 " --> pdb=" O THR I 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR I 363 " --> pdb=" O ARG I 296 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU I 298 " --> pdb=" O ASN I 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN I 361 " --> pdb=" O LEU I 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE I 300 " --> pdb=" O GLN I 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN I 359 " --> pdb=" O ILE I 300 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU J 302 " --> pdb=" O THR I 358 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ARG J 294 " --> pdb=" O TYR I 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN J 365 " --> pdb=" O ARG J 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG J 296 " --> pdb=" O THR J 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR J 363 " --> pdb=" O ARG J 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU J 298 " --> pdb=" O ASN J 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN J 361 " --> pdb=" O LEU J 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE J 300 " --> pdb=" O GLN J 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN J 359 " --> pdb=" O ILE J 300 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU K 302 " --> pdb=" O THR J 358 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ARG K 294 " --> pdb=" O TYR J 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN K 365 " --> pdb=" O ARG K 294 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARG K 296 " --> pdb=" O THR K 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR K 363 " --> pdb=" O ARG K 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU K 298 " --> pdb=" O ASN K 361 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASN K 361 " --> pdb=" O LEU K 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE K 300 " --> pdb=" O GLN K 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN K 359 " --> pdb=" O ILE K 300 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU L 302 " --> pdb=" O THR K 358 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ARG L 294 " --> pdb=" O TYR K 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN L 365 " --> pdb=" O ARG L 294 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARG L 296 " --> pdb=" O THR L 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR L 363 " --> pdb=" O ARG L 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU L 298 " --> pdb=" O ASN L 361 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASN L 361 " --> pdb=" O LEU L 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE L 300 " --> pdb=" O GLN L 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN L 359 " --> pdb=" O ILE L 300 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU M 302 " --> pdb=" O THR L 358 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ARG M 294 " --> pdb=" O TYR L 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN M 365 " --> pdb=" O ARG M 294 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARG M 296 " --> pdb=" O THR M 363 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N THR M 363 " --> pdb=" O ARG M 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU M 298 " --> pdb=" O ASN M 361 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASN M 361 " --> pdb=" O LEU M 298 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ILE M 300 " --> pdb=" O GLN M 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN M 359 " --> pdb=" O ILE M 300 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU N 302 " --> pdb=" O THR M 358 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU M 362 " --> pdb=" O LEU N 298 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ARG N 294 " --> pdb=" O TYR M 366 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ASN N 365 " --> pdb=" O ARG N 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG N 296 " --> pdb=" O THR N 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR N 363 " --> pdb=" O ARG N 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU N 298 " --> pdb=" O ASN N 361 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASN N 361 " --> pdb=" O LEU N 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE N 300 " --> pdb=" O GLN N 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN N 359 " --> pdb=" O ILE N 300 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU O 302 " --> pdb=" O THR N 358 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ARG O 294 " --> pdb=" O TYR N 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN O 365 " --> pdb=" O ARG O 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG O 296 " --> pdb=" O THR O 363 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N THR O 363 " --> pdb=" O ARG O 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU O 298 " --> pdb=" O ASN O 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN O 361 " --> pdb=" O LEU O 298 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ILE O 300 " --> pdb=" O GLN O 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN O 359 " --> pdb=" O ILE O 300 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU P 302 " --> pdb=" O THR O 358 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU O 362 " --> pdb=" O LEU P 298 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ARG P 294 " --> pdb=" O TYR O 366 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASN P 365 " --> pdb=" O ARG P 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG P 296 " --> pdb=" O THR P 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR P 363 " --> pdb=" O ARG P 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU P 298 " --> pdb=" O ASN P 361 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASN P 361 " --> pdb=" O LEU P 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE P 300 " --> pdb=" O GLN P 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN P 359 " --> pdb=" O ILE P 300 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU Q 302 " --> pdb=" O THR P 358 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ARG Q 294 " --> pdb=" O TYR P 366 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ASN Q 365 " --> pdb=" O ARG Q 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG Q 296 " --> pdb=" O THR Q 363 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N THR Q 363 " --> pdb=" O ARG Q 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU Q 298 " --> pdb=" O ASN Q 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN Q 361 " --> pdb=" O LEU Q 298 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ILE Q 300 " --> pdb=" O GLN Q 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN Q 359 " --> pdb=" O ILE Q 300 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU R 302 " --> pdb=" O THR Q 358 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU Q 362 " --> pdb=" O LEU R 298 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ARG R 294 " --> pdb=" O TYR Q 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN R 365 " --> pdb=" O ARG R 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG R 296 " --> pdb=" O THR R 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR R 363 " --> pdb=" O ARG R 296 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU R 298 " --> pdb=" O ASN R 361 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASN R 361 " --> pdb=" O LEU R 298 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ILE R 300 " --> pdb=" O GLN R 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN R 359 " --> pdb=" O ILE R 300 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU S 302 " --> pdb=" O THR R 358 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ARG S 294 " --> pdb=" O TYR R 366 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ASN S 365 " --> pdb=" O ARG S 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG S 296 " --> pdb=" O THR S 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR S 363 " --> pdb=" O ARG S 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU S 298 " --> pdb=" O ASN S 361 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASN S 361 " --> pdb=" O LEU S 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE S 300 " --> pdb=" O GLN S 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN S 359 " --> pdb=" O ILE S 300 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU T 302 " --> pdb=" O THR S 358 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU S 362 " --> pdb=" O LEU T 298 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ARG T 294 " --> pdb=" O TYR S 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN T 365 " --> pdb=" O ARG T 294 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARG T 296 " --> pdb=" O THR T 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR T 363 " --> pdb=" O ARG T 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU T 298 " --> pdb=" O ASN T 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN T 361 " --> pdb=" O LEU T 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE T 300 " --> pdb=" O GLN T 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN T 359 " --> pdb=" O ILE T 300 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU U 302 " --> pdb=" O THR T 358 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ARG U 294 " --> pdb=" O TYR T 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN U 365 " --> pdb=" O ARG U 294 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARG U 296 " --> pdb=" O THR U 363 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N THR U 363 " --> pdb=" O ARG U 296 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU U 298 " --> pdb=" O ASN U 361 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASN U 361 " --> pdb=" O LEU U 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE U 300 " --> pdb=" O GLN U 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN U 359 " --> pdb=" O ILE U 300 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU V 302 " --> pdb=" O THR U 358 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU U 362 " --> pdb=" O LEU V 298 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ARG V 294 " --> pdb=" O TYR U 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN V 365 " --> pdb=" O ARG V 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG V 296 " --> pdb=" O THR V 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR V 363 " --> pdb=" O ARG V 296 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU V 298 " --> pdb=" O ASN V 361 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASN V 361 " --> pdb=" O LEU V 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE V 300 " --> pdb=" O GLN V 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN V 359 " --> pdb=" O ILE V 300 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU W 302 " --> pdb=" O THR V 358 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ARG W 294 " --> pdb=" O TYR V 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN W 365 " --> pdb=" O ARG W 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG W 296 " --> pdb=" O THR W 363 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N THR W 363 " --> pdb=" O ARG W 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU W 298 " --> pdb=" O ASN W 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN W 361 " --> pdb=" O LEU W 298 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ILE W 300 " --> pdb=" O GLN W 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN W 359 " --> pdb=" O ILE W 300 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU X 302 " --> pdb=" O THR W 358 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ARG X 294 " --> pdb=" O TYR W 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN X 365 " --> pdb=" O ARG X 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG X 296 " --> pdb=" O THR X 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR X 363 " --> pdb=" O ARG X 296 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU X 298 " --> pdb=" O ASN X 361 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASN X 361 " --> pdb=" O LEU X 298 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ILE X 300 " --> pdb=" O GLN X 359 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLN X 359 " --> pdb=" O ILE X 300 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU Y 302 " --> pdb=" O THR X 358 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ARG Y 294 " --> pdb=" O TYR X 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN Y 365 " --> pdb=" O ARG Y 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG Y 296 " --> pdb=" O THR Y 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR Y 363 " --> pdb=" O ARG Y 296 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU Y 298 " --> pdb=" O ASN Y 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN Y 361 " --> pdb=" O LEU Y 298 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ILE Y 300 " --> pdb=" O GLN Y 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN Y 359 " --> pdb=" O ILE Y 300 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU Z 302 " --> pdb=" O THR Y 358 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ARG Z 294 " --> pdb=" O TYR Y 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN Z 365 " --> pdb=" O ARG Z 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG Z 296 " --> pdb=" O THR Z 363 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N THR Z 363 " --> pdb=" O ARG Z 296 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU Z 298 " --> pdb=" O ASN Z 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN Z 361 " --> pdb=" O LEU Z 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE Z 300 " --> pdb=" O GLN Z 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN Z 359 " --> pdb=" O ILE Z 300 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU a 302 " --> pdb=" O THR Z 358 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU Z 362 " --> pdb=" O LEU a 298 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ARG a 294 " --> pdb=" O TYR Z 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN a 365 " --> pdb=" O ARG a 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG a 296 " --> pdb=" O THR a 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR a 363 " --> pdb=" O ARG a 296 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU a 298 " --> pdb=" O ASN a 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN a 361 " --> pdb=" O LEU a 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE a 300 " --> pdb=" O GLN a 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN a 359 " --> pdb=" O ILE a 300 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU b 302 " --> pdb=" O THR a 358 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ARG b 294 " --> pdb=" O TYR a 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN b 365 " --> pdb=" O ARG b 294 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARG b 296 " --> pdb=" O THR b 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR b 363 " --> pdb=" O ARG b 296 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU b 298 " --> pdb=" O ASN b 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN b 361 " --> pdb=" O LEU b 298 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ILE b 300 " --> pdb=" O GLN b 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN b 359 " --> pdb=" O ILE b 300 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU c 302 " --> pdb=" O THR b 358 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ARG c 294 " --> pdb=" O TYR b 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN c 365 " --> pdb=" O ARG c 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG c 296 " --> pdb=" O THR c 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR c 363 " --> pdb=" O ARG c 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU c 298 " --> pdb=" O ASN c 361 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASN c 361 " --> pdb=" O LEU c 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE c 300 " --> pdb=" O GLN c 359 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLN c 359 " --> pdb=" O ILE c 300 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU d 302 " --> pdb=" O THR c 358 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU c 362 " --> pdb=" O LEU d 298 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ARG d 294 " --> pdb=" O TYR c 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN d 365 " --> pdb=" O ARG d 294 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARG d 296 " --> pdb=" O THR d 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR d 363 " --> pdb=" O ARG d 296 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU d 298 " --> pdb=" O ASN d 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN d 361 " --> pdb=" O LEU d 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE d 300 " --> pdb=" O GLN d 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN d 359 " --> pdb=" O ILE d 300 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU e 302 " --> pdb=" O THR d 358 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ARG e 294 " --> pdb=" O TYR d 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN e 365 " --> pdb=" O ARG e 294 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARG e 296 " --> pdb=" O THR e 363 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N THR e 363 " --> pdb=" O ARG e 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU e 298 " --> pdb=" O ASN e 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN e 361 " --> pdb=" O LEU e 298 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ILE e 300 " --> pdb=" O GLN e 359 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLN e 359 " --> pdb=" O ILE e 300 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU f 302 " --> pdb=" O THR e 358 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ARG f 294 " --> pdb=" O TYR e 366 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASN f 365 " --> pdb=" O ARG f 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG f 296 " --> pdb=" O THR f 363 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N THR f 363 " --> pdb=" O ARG f 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU f 298 " --> pdb=" O ASN f 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN f 361 " --> pdb=" O LEU f 298 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ILE f 300 " --> pdb=" O GLN f 359 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLN f 359 " --> pdb=" O ILE f 300 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU g 302 " --> pdb=" O THR f 358 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU f 362 " --> pdb=" O LEU g 298 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ARG g 294 " --> pdb=" O TYR f 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN g 365 " --> pdb=" O ARG g 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG g 296 " --> pdb=" O THR g 363 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N THR g 363 " --> pdb=" O ARG g 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU g 298 " --> pdb=" O ASN g 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN g 361 " --> pdb=" O LEU g 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE g 300 " --> pdb=" O GLN g 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN g 359 " --> pdb=" O ILE g 300 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU h 302 " --> pdb=" O THR g 358 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU g 362 " --> pdb=" O LEU h 298 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ARG h 294 " --> pdb=" O TYR g 366 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASN h 365 " --> pdb=" O ARG h 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARG h 296 " --> pdb=" O THR h 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THR h 363 " --> pdb=" O ARG h 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEU h 298 " --> pdb=" O ASN h 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN h 361 " --> pdb=" O LEU h 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE h 300 " --> pdb=" O GLN h 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN h 359 " --> pdb=" O ILE h 300 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU A 302 " --> pdb=" O THR h 358 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU h 362 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER h 364 " --> pdb=" O ARG A 296 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ARG A 294 " --> pdb=" O TYR h 366 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 262 through 271 removed outlier: 6.707A pdb=" N ASP B 271 " --> pdb=" O ILE B 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE B 382 " --> pdb=" O ASP B 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR B 429 " --> pdb=" O GLU B 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU B 385 " --> pdb=" O THR B 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASN B 431 " --> pdb=" O LEU B 385 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL B 387 " --> pdb=" O ASN B 431 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL B 433 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL B 389 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 279 through 281 removed outlier: 3.732A pdb=" N ARG B 373 " --> pdb=" O GLU B 279 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASP C 271 " --> pdb=" O ILE C 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE C 382 " --> pdb=" O ASP C 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR C 429 " --> pdb=" O GLU C 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU C 385 " --> pdb=" O THR C 429 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N ASN C 431 " --> pdb=" O LEU C 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL C 387 " --> pdb=" O ASN C 431 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL C 433 " --> pdb=" O VAL C 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL C 389 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 279 through 281 removed outlier: 3.731A pdb=" N ARG C 373 " --> pdb=" O GLU C 279 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASP D 271 " --> pdb=" O ILE D 382 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE D 382 " --> pdb=" O ASP D 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR D 429 " --> pdb=" O GLU D 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU D 385 " --> pdb=" O THR D 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASN D 431 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL D 387 " --> pdb=" O ASN D 431 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL D 433 " --> pdb=" O VAL D 387 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL D 389 " --> pdb=" O VAL D 433 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 279 through 281 removed outlier: 3.731A pdb=" N ARG D 373 " --> pdb=" O GLU D 279 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASP E 271 " --> pdb=" O ILE E 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE E 382 " --> pdb=" O ASP E 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR E 429 " --> pdb=" O GLU E 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU E 385 " --> pdb=" O THR E 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASN E 431 " --> pdb=" O LEU E 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL E 387 " --> pdb=" O ASN E 431 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL E 433 " --> pdb=" O VAL E 387 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL E 389 " --> pdb=" O VAL E 433 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 279 through 281 removed outlier: 3.731A pdb=" N ARG E 373 " --> pdb=" O GLU E 279 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 262 through 271 removed outlier: 6.707A pdb=" N ASP F 271 " --> pdb=" O ILE F 382 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE F 382 " --> pdb=" O ASP F 271 " (cutoff:3.500A) removed outlier: 8.791A pdb=" N THR F 429 " --> pdb=" O GLU F 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU F 385 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASN F 431 " --> pdb=" O LEU F 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL F 387 " --> pdb=" O ASN F 431 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL F 433 " --> pdb=" O VAL F 387 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL F 389 " --> pdb=" O VAL F 433 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 279 through 281 removed outlier: 3.732A pdb=" N ARG F 373 " --> pdb=" O GLU F 279 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASP G 271 " --> pdb=" O ILE G 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE G 382 " --> pdb=" O ASP G 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR G 429 " --> pdb=" O GLU G 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU G 385 " --> pdb=" O THR G 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASN G 431 " --> pdb=" O LEU G 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL G 387 " --> pdb=" O ASN G 431 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL G 433 " --> pdb=" O VAL G 387 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL G 389 " --> pdb=" O VAL G 433 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 279 through 281 removed outlier: 3.732A pdb=" N ARG G 373 " --> pdb=" O GLU G 279 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 262 through 271 removed outlier: 6.707A pdb=" N ASP H 271 " --> pdb=" O ILE H 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE H 382 " --> pdb=" O ASP H 271 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N THR H 429 " --> pdb=" O GLU H 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU H 385 " --> pdb=" O THR H 429 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N ASN H 431 " --> pdb=" O LEU H 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL H 387 " --> pdb=" O ASN H 431 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL H 433 " --> pdb=" O VAL H 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL H 389 " --> pdb=" O VAL H 433 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 279 through 281 removed outlier: 3.731A pdb=" N ARG H 373 " --> pdb=" O GLU H 279 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASP I 271 " --> pdb=" O ILE I 382 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE I 382 " --> pdb=" O ASP I 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR I 429 " --> pdb=" O GLU I 383 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU I 385 " --> pdb=" O THR I 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASN I 431 " --> pdb=" O LEU I 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL I 387 " --> pdb=" O ASN I 431 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL I 433 " --> pdb=" O VAL I 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL I 389 " --> pdb=" O VAL I 433 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 371 through 373 removed outlier: 3.731A pdb=" N ARG I 373 " --> pdb=" O GLU I 279 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE J 372 " --> pdb=" O THR I 278 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG J 373 " --> pdb=" O GLU J 279 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASP J 271 " --> pdb=" O ILE J 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE J 382 " --> pdb=" O ASP J 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR J 429 " --> pdb=" O GLU J 383 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU J 385 " --> pdb=" O THR J 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASN J 431 " --> pdb=" O LEU J 385 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL J 387 " --> pdb=" O ASN J 431 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL J 433 " --> pdb=" O VAL J 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL J 389 " --> pdb=" O VAL J 433 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASP K 271 " --> pdb=" O ILE K 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE K 382 " --> pdb=" O ASP K 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR K 429 " --> pdb=" O GLU K 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU K 385 " --> pdb=" O THR K 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASN K 431 " --> pdb=" O LEU K 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL K 387 " --> pdb=" O ASN K 431 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL K 433 " --> pdb=" O VAL K 387 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL K 389 " --> pdb=" O VAL K 433 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 279 through 281 removed outlier: 3.732A pdb=" N ARG K 373 " --> pdb=" O GLU K 279 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASP L 271 " --> pdb=" O ILE L 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE L 382 " --> pdb=" O ASP L 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR L 429 " --> pdb=" O GLU L 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU L 385 " --> pdb=" O THR L 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASN L 431 " --> pdb=" O LEU L 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL L 387 " --> pdb=" O ASN L 431 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL L 433 " --> pdb=" O VAL L 387 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL L 389 " --> pdb=" O VAL L 433 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 279 through 281 removed outlier: 3.732A pdb=" N ARG L 373 " --> pdb=" O GLU L 279 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASP M 271 " --> pdb=" O ILE M 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE M 382 " --> pdb=" O ASP M 271 " (cutoff:3.500A) removed outlier: 8.791A pdb=" N THR M 429 " --> pdb=" O GLU M 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU M 385 " --> pdb=" O THR M 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASN M 431 " --> pdb=" O LEU M 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL M 387 " --> pdb=" O ASN M 431 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL M 433 " --> pdb=" O VAL M 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL M 389 " --> pdb=" O VAL M 433 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 279 through 281 removed outlier: 3.732A pdb=" N ARG M 373 " --> pdb=" O GLU M 279 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASP N 271 " --> pdb=" O ILE N 382 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE N 382 " --> pdb=" O ASP N 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR N 429 " --> pdb=" O GLU N 383 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU N 385 " --> pdb=" O THR N 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASN N 431 " --> pdb=" O LEU N 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL N 387 " --> pdb=" O ASN N 431 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL N 433 " --> pdb=" O VAL N 387 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL N 389 " --> pdb=" O VAL N 433 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 279 through 281 removed outlier: 3.732A pdb=" N ARG N 373 " --> pdb=" O GLU N 279 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASP O 271 " --> pdb=" O ILE O 382 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE O 382 " --> pdb=" O ASP O 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR O 429 " --> pdb=" O GLU O 383 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU O 385 " --> pdb=" O THR O 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASN O 431 " --> pdb=" O LEU O 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL O 387 " --> pdb=" O ASN O 431 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL O 433 " --> pdb=" O VAL O 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL O 389 " --> pdb=" O VAL O 433 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 371 through 373 removed outlier: 3.732A pdb=" N ARG O 373 " --> pdb=" O GLU O 279 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG P 373 " --> pdb=" O GLU P 279 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE Q 372 " --> pdb=" O THR P 278 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG Q 373 " --> pdb=" O GLU Q 279 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'P' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASP P 271 " --> pdb=" O ILE P 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE P 382 " --> pdb=" O ASP P 271 " (cutoff:3.500A) removed outlier: 8.791A pdb=" N THR P 429 " --> pdb=" O GLU P 383 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU P 385 " --> pdb=" O THR P 429 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N ASN P 431 " --> pdb=" O LEU P 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL P 387 " --> pdb=" O ASN P 431 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL P 433 " --> pdb=" O VAL P 387 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL P 389 " --> pdb=" O VAL P 433 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Q' and resid 262 through 271 removed outlier: 6.707A pdb=" N ASP Q 271 " --> pdb=" O ILE Q 382 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE Q 382 " --> pdb=" O ASP Q 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR Q 429 " --> pdb=" O GLU Q 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU Q 385 " --> pdb=" O THR Q 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASN Q 431 " --> pdb=" O LEU Q 385 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL Q 387 " --> pdb=" O ASN Q 431 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL Q 433 " --> pdb=" O VAL Q 387 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL Q 389 " --> pdb=" O VAL Q 433 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'R' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASP R 271 " --> pdb=" O ILE R 382 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE R 382 " --> pdb=" O ASP R 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR R 429 " --> pdb=" O GLU R 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU R 385 " --> pdb=" O THR R 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASN R 431 " --> pdb=" O LEU R 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL R 387 " --> pdb=" O ASN R 431 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL R 433 " --> pdb=" O VAL R 387 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL R 389 " --> pdb=" O VAL R 433 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'R' and resid 279 through 281 removed outlier: 3.732A pdb=" N ARG R 373 " --> pdb=" O GLU R 279 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'S' and resid 262 through 271 removed outlier: 6.707A pdb=" N ASP S 271 " --> pdb=" O ILE S 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE S 382 " --> pdb=" O ASP S 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR S 429 " --> pdb=" O GLU S 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU S 385 " --> pdb=" O THR S 429 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N ASN S 431 " --> pdb=" O LEU S 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL S 387 " --> pdb=" O ASN S 431 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL S 433 " --> pdb=" O VAL S 387 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL S 389 " --> pdb=" O VAL S 433 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'S' and resid 371 through 373 removed outlier: 3.732A pdb=" N ARG S 373 " --> pdb=" O GLU S 279 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE T 372 " --> pdb=" O THR S 278 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG T 373 " --> pdb=" O GLU T 279 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'T' and resid 262 through 271 removed outlier: 6.707A pdb=" N ASP T 271 " --> pdb=" O ILE T 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE T 382 " --> pdb=" O ASP T 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR T 429 " --> pdb=" O GLU T 383 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU T 385 " --> pdb=" O THR T 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASN T 431 " --> pdb=" O LEU T 385 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL T 387 " --> pdb=" O ASN T 431 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL T 433 " --> pdb=" O VAL T 387 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL T 389 " --> pdb=" O VAL T 433 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'U' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASP U 271 " --> pdb=" O ILE U 382 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE U 382 " --> pdb=" O ASP U 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR U 429 " --> pdb=" O GLU U 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU U 385 " --> pdb=" O THR U 429 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N ASN U 431 " --> pdb=" O LEU U 385 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL U 387 " --> pdb=" O ASN U 431 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL U 433 " --> pdb=" O VAL U 387 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL U 389 " --> pdb=" O VAL U 433 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'U' and resid 279 through 281 removed outlier: 3.732A pdb=" N ARG U 373 " --> pdb=" O GLU U 279 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'V' and resid 262 through 271 removed outlier: 6.707A pdb=" N ASP V 271 " --> pdb=" O ILE V 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE V 382 " --> pdb=" O ASP V 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR V 429 " --> pdb=" O GLU V 383 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU V 385 " --> pdb=" O THR V 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASN V 431 " --> pdb=" O LEU V 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL V 387 " --> pdb=" O ASN V 431 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL V 433 " --> pdb=" O VAL V 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL V 389 " --> pdb=" O VAL V 433 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'V' and resid 279 through 281 removed outlier: 3.731A pdb=" N ARG V 373 " --> pdb=" O GLU V 279 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'W' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASP W 271 " --> pdb=" O ILE W 382 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE W 382 " --> pdb=" O ASP W 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR W 429 " --> pdb=" O GLU W 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU W 385 " --> pdb=" O THR W 429 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N ASN W 431 " --> pdb=" O LEU W 385 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL W 387 " --> pdb=" O ASN W 431 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL W 433 " --> pdb=" O VAL W 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL W 389 " --> pdb=" O VAL W 433 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'W' and resid 279 through 281 removed outlier: 3.731A pdb=" N ARG W 373 " --> pdb=" O GLU W 279 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'X' and resid 262 through 271 removed outlier: 6.707A pdb=" N ASP X 271 " --> pdb=" O ILE X 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE X 382 " --> pdb=" O ASP X 271 " (cutoff:3.500A) removed outlier: 8.791A pdb=" N THR X 429 " --> pdb=" O GLU X 383 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU X 385 " --> pdb=" O THR X 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASN X 431 " --> pdb=" O LEU X 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL X 387 " --> pdb=" O ASN X 431 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL X 433 " --> pdb=" O VAL X 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL X 389 " --> pdb=" O VAL X 433 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'X' and resid 279 through 281 removed outlier: 3.731A pdb=" N ARG X 373 " --> pdb=" O GLU X 279 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Y' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASP Y 271 " --> pdb=" O ILE Y 382 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE Y 382 " --> pdb=" O ASP Y 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR Y 429 " --> pdb=" O GLU Y 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU Y 385 " --> pdb=" O THR Y 429 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N ASN Y 431 " --> pdb=" O LEU Y 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL Y 387 " --> pdb=" O ASN Y 431 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL Y 433 " --> pdb=" O VAL Y 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL Y 389 " --> pdb=" O VAL Y 433 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Y' and resid 279 through 281 removed outlier: 3.732A pdb=" N ARG Y 373 " --> pdb=" O GLU Y 279 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Z' and resid 262 through 271 removed outlier: 6.707A pdb=" N ASP Z 271 " --> pdb=" O ILE Z 382 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE Z 382 " --> pdb=" O ASP Z 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR Z 429 " --> pdb=" O GLU Z 383 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU Z 385 " --> pdb=" O THR Z 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASN Z 431 " --> pdb=" O LEU Z 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL Z 387 " --> pdb=" O ASN Z 431 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL Z 433 " --> pdb=" O VAL Z 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL Z 389 " --> pdb=" O VAL Z 433 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Z' and resid 279 through 281 removed outlier: 3.732A pdb=" N ARG Z 373 " --> pdb=" O GLU Z 279 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'a' and resid 262 through 271 removed outlier: 6.707A pdb=" N ASP a 271 " --> pdb=" O ILE a 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE a 382 " --> pdb=" O ASP a 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR a 429 " --> pdb=" O GLU a 383 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU a 385 " --> pdb=" O THR a 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASN a 431 " --> pdb=" O LEU a 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL a 387 " --> pdb=" O ASN a 431 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL a 433 " --> pdb=" O VAL a 387 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL a 389 " --> pdb=" O VAL a 433 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'a' and resid 279 through 281 removed outlier: 3.732A pdb=" N ARG a 373 " --> pdb=" O GLU a 279 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'c' and resid 262 through 271 removed outlier: 6.707A pdb=" N ASP c 271 " --> pdb=" O ILE c 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE c 382 " --> pdb=" O ASP c 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR c 429 " --> pdb=" O GLU c 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU c 385 " --> pdb=" O THR c 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASN c 431 " --> pdb=" O LEU c 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL c 387 " --> pdb=" O ASN c 431 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL c 433 " --> pdb=" O VAL c 387 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL c 389 " --> pdb=" O VAL c 433 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'c' and resid 279 through 281 removed outlier: 3.731A pdb=" N ARG c 373 " --> pdb=" O GLU c 279 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'b' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASP b 271 " --> pdb=" O ILE b 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE b 382 " --> pdb=" O ASP b 271 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N THR b 429 " --> pdb=" O GLU b 383 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU b 385 " --> pdb=" O THR b 429 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N ASN b 431 " --> pdb=" O LEU b 385 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL b 387 " --> pdb=" O ASN b 431 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL b 433 " --> pdb=" O VAL b 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL b 389 " --> pdb=" O VAL b 433 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'b' and resid 279 through 281 removed outlier: 3.732A pdb=" N ARG b 373 " --> pdb=" O GLU b 279 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'd' and resid 262 through 271 removed outlier: 6.707A pdb=" N ASP d 271 " --> pdb=" O ILE d 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE d 382 " --> pdb=" O ASP d 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR d 429 " --> pdb=" O GLU d 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU d 385 " --> pdb=" O THR d 429 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N ASN d 431 " --> pdb=" O LEU d 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL d 387 " --> pdb=" O ASN d 431 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL d 433 " --> pdb=" O VAL d 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL d 389 " --> pdb=" O VAL d 433 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'd' and resid 279 through 281 removed outlier: 3.732A pdb=" N ARG d 373 " --> pdb=" O GLU d 279 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'e' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASP e 271 " --> pdb=" O ILE e 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE e 382 " --> pdb=" O ASP e 271 " (cutoff:3.500A) removed outlier: 8.791A pdb=" N THR e 429 " --> pdb=" O GLU e 383 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU e 385 " --> pdb=" O THR e 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASN e 431 " --> pdb=" O LEU e 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL e 387 " --> pdb=" O ASN e 431 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL e 433 " --> pdb=" O VAL e 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL e 389 " --> pdb=" O VAL e 433 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'e' and resid 279 through 281 removed outlier: 3.731A pdb=" N ARG e 373 " --> pdb=" O GLU e 279 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'f' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASP f 271 " --> pdb=" O ILE f 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE f 382 " --> pdb=" O ASP f 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR f 429 " --> pdb=" O GLU f 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU f 385 " --> pdb=" O THR f 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASN f 431 " --> pdb=" O LEU f 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL f 387 " --> pdb=" O ASN f 431 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL f 433 " --> pdb=" O VAL f 387 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL f 389 " --> pdb=" O VAL f 433 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'f' and resid 279 through 281 removed outlier: 3.731A pdb=" N ARG f 373 " --> pdb=" O GLU f 279 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'g' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASP g 271 " --> pdb=" O ILE g 382 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE g 382 " --> pdb=" O ASP g 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR g 429 " --> pdb=" O GLU g 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU g 385 " --> pdb=" O THR g 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASN g 431 " --> pdb=" O LEU g 385 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL g 387 " --> pdb=" O ASN g 431 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL g 433 " --> pdb=" O VAL g 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL g 389 " --> pdb=" O VAL g 433 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'g' and resid 371 through 373 removed outlier: 3.732A pdb=" N ARG g 373 " --> pdb=" O GLU g 279 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG h 373 " --> pdb=" O GLU h 279 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'h' and resid 262 through 271 removed outlier: 6.707A pdb=" N ASP h 271 " --> pdb=" O ILE h 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE h 382 " --> pdb=" O ASP h 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THR h 429 " --> pdb=" O GLU h 383 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU h 385 " --> pdb=" O THR h 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASN h 431 " --> pdb=" O LEU h 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL h 387 " --> pdb=" O ASN h 431 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL h 433 " --> pdb=" O VAL h 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL h 389 " --> pdb=" O VAL h 433 " (cutoff:3.500A) 1739 hydrogen bonds defined for protein. 4911 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: 15.98 Time building geometry restraints manager: 17.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 14450 1.34 - 1.46: 6419 1.46 - 1.57: 19625 1.57 - 1.69: 0 1.69 - 1.80: 204 Bond restraints: 40698 Sorted by residual: bond pdb=" CB LEU T 415 " pdb=" CG LEU T 415 " ideal model delta sigma weight residual 1.530 1.514 0.016 2.00e-02 2.50e+03 6.79e-01 bond pdb=" CB LEU L 415 " pdb=" CG LEU L 415 " ideal model delta sigma weight residual 1.530 1.514 0.016 2.00e-02 2.50e+03 6.66e-01 bond pdb=" N SER V 254 " pdb=" CA SER V 254 " ideal model delta sigma weight residual 1.462 1.455 0.007 8.50e-03 1.38e+04 6.58e-01 bond pdb=" CB LEU K 415 " pdb=" CG LEU K 415 " ideal model delta sigma weight residual 1.530 1.514 0.016 2.00e-02 2.50e+03 6.56e-01 bond pdb=" CB LEU N 415 " pdb=" CG LEU N 415 " ideal model delta sigma weight residual 1.530 1.514 0.016 2.00e-02 2.50e+03 6.55e-01 ... (remaining 40693 not shown) Histogram of bond angle deviations from ideal: 100.52 - 106.69: 850 106.69 - 112.87: 22441 112.87 - 119.05: 10644 119.05 - 125.23: 20669 125.23 - 131.41: 238 Bond angle restraints: 54842 Sorted by residual: angle pdb=" N GLY h 421 " pdb=" CA GLY h 421 " pdb=" C GLY h 421 " ideal model delta sigma weight residual 113.18 107.43 5.75 2.37e+00 1.78e-01 5.88e+00 angle pdb=" N GLY R 421 " pdb=" CA GLY R 421 " pdb=" C GLY R 421 " ideal model delta sigma weight residual 113.18 107.44 5.74 2.37e+00 1.78e-01 5.87e+00 angle pdb=" N GLY e 421 " pdb=" CA GLY e 421 " pdb=" C GLY e 421 " ideal model delta sigma weight residual 113.18 107.44 5.74 2.37e+00 1.78e-01 5.86e+00 angle pdb=" N GLY O 421 " pdb=" CA GLY O 421 " pdb=" C GLY O 421 " ideal model delta sigma weight residual 113.18 107.44 5.74 2.37e+00 1.78e-01 5.86e+00 angle pdb=" N GLY Z 421 " pdb=" CA GLY Z 421 " pdb=" C GLY Z 421 " ideal model delta sigma weight residual 113.18 107.45 5.73 2.37e+00 1.78e-01 5.85e+00 ... (remaining 54837 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.63: 21332 11.63 - 23.26: 2740 23.26 - 34.89: 1012 34.89 - 46.53: 246 46.53 - 58.16: 102 Dihedral angle restraints: 25432 sinusoidal: 10540 harmonic: 14892 Sorted by residual: dihedral pdb=" CA MET E 420 " pdb=" C MET E 420 " pdb=" N GLY E 421 " pdb=" CA GLY E 421 " ideal model delta harmonic sigma weight residual 180.00 -161.43 -18.57 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA MET K 420 " pdb=" C MET K 420 " pdb=" N GLY K 421 " pdb=" CA GLY K 421 " ideal model delta harmonic sigma weight residual -180.00 -161.43 -18.57 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA MET Q 420 " pdb=" C MET Q 420 " pdb=" N GLY Q 421 " pdb=" CA GLY Q 421 " ideal model delta harmonic sigma weight residual 180.00 -161.44 -18.56 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 25429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 2930 0.023 - 0.046: 2139 0.046 - 0.069: 656 0.069 - 0.092: 262 0.092 - 0.115: 303 Chirality restraints: 6290 Sorted by residual: chirality pdb=" CA PRO K 255 " pdb=" N PRO K 255 " pdb=" C PRO K 255 " pdb=" CB PRO K 255 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.11 2.00e-01 2.50e+01 3.31e-01 chirality pdb=" CA PRO L 255 " pdb=" N PRO L 255 " pdb=" C PRO L 255 " pdb=" CB PRO L 255 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.11 2.00e-01 2.50e+01 3.28e-01 chirality pdb=" CA PRO S 255 " pdb=" N PRO S 255 " pdb=" C PRO S 255 " pdb=" CB PRO S 255 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.11 2.00e-01 2.50e+01 3.27e-01 ... (remaining 6287 not shown) Planarity restraints: 7344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER J 435 " -0.016 5.00e-02 4.00e+02 2.35e-02 8.87e-01 pdb=" N PRO J 436 " 0.041 5.00e-02 4.00e+02 pdb=" CA PRO J 436 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO J 436 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER M 435 " -0.016 5.00e-02 4.00e+02 2.35e-02 8.83e-01 pdb=" N PRO M 436 " 0.041 5.00e-02 4.00e+02 pdb=" CA PRO M 436 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO M 436 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER c 435 " 0.015 5.00e-02 4.00e+02 2.35e-02 8.81e-01 pdb=" N PRO c 436 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO c 436 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO c 436 " 0.013 5.00e-02 4.00e+02 ... (remaining 7341 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 577 2.60 - 3.18: 34081 3.18 - 3.75: 54523 3.75 - 4.33: 77579 4.33 - 4.90: 136174 Nonbonded interactions: 302934 Sorted by model distance: nonbonded pdb=" OD2 ASP A 414 " pdb=" ND2 ASN h 431 " model vdw 2.027 2.520 nonbonded pdb=" ND2 ASN g 431 " pdb=" OD2 ASP h 414 " model vdw 2.043 2.520 nonbonded pdb=" ND2 ASN N 431 " pdb=" OD2 ASP O 414 " model vdw 2.047 2.520 nonbonded pdb=" ND2 ASN c 431 " pdb=" OD2 ASP d 414 " model vdw 2.061 2.520 nonbonded pdb=" ND2 ASN Q 431 " pdb=" OD2 ASP R 414 " model vdw 2.063 2.520 ... (remaining 302929 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.500 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: 0.030 Extract box with map and model: 29.150 Check model and map are aligned: 0.600 Set scattering table: 0.340 Process input model: 106.380 Find NCS groups from input model: 3.120 Set up NCS constraints: 0.500 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 148.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 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 : 0.005 0.027 40698 Z= 0.346 Angle : 0.665 5.747 54842 Z= 0.409 Chirality : 0.039 0.115 6290 Planarity : 0.003 0.024 7344 Dihedral : 12.606 58.158 15640 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.26 % Allowed : 5.26 % Favored : 92.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.11), residues: 4896 helix: 0.99 (0.15), residues: 1292 sheet: -2.82 (0.10), residues: 2312 loop : -2.93 (0.11), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS S 374 PHE 0.006 0.001 PHE R 422 TYR 0.011 0.002 TYR B 393 ARG 0.002 0.000 ARG H 248 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1325 residues out of total 4522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 1223 time to evaluate : 5.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 GLN cc_start: 0.7966 (tt0) cc_final: 0.7700 (tt0) REVERT: A 409 MET cc_start: 0.7116 (tmm) cc_final: 0.6673 (tmm) REVERT: A 410 LYS cc_start: 0.8662 (ttpt) cc_final: 0.8275 (ttpt) REVERT: B 290 LYS cc_start: 0.8497 (ptpp) cc_final: 0.8254 (mtmm) REVERT: B 373 ARG cc_start: 0.7842 (mtp85) cc_final: 0.7549 (mtp85) REVERT: B 385 LEU cc_start: 0.9012 (mt) cc_final: 0.8681 (mt) REVERT: B 394 LYS cc_start: 0.7017 (ttpt) cc_final: 0.6763 (ttpp) REVERT: B 410 LYS cc_start: 0.8286 (ttpt) cc_final: 0.8042 (ttpt) REVERT: B 428 ASP cc_start: 0.8511 (m-30) cc_final: 0.8139 (m-30) REVERT: B 431 ASN cc_start: 0.7194 (t0) cc_final: 0.6721 (t0) REVERT: C 385 LEU cc_start: 0.9108 (mt) cc_final: 0.8765 (mt) REVERT: C 413 GLU cc_start: 0.8140 (tt0) cc_final: 0.7807 (tm-30) REVERT: C 428 ASP cc_start: 0.8336 (m-30) cc_final: 0.8106 (m-30) REVERT: C 431 ASN cc_start: 0.6915 (t0) cc_final: 0.6578 (t0) REVERT: D 240 ASP cc_start: 0.7759 (m-30) cc_final: 0.7515 (m-30) REVERT: D 359 GLN cc_start: 0.8142 (tt0) cc_final: 0.7811 (tt0) REVERT: E 367 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8280 (mm-30) REVERT: F 295 SER cc_start: 0.8470 (OUTLIER) cc_final: 0.8070 (t) REVERT: F 418 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7957 (mm-30) REVERT: G 295 SER cc_start: 0.8772 (OUTLIER) cc_final: 0.8420 (t) REVERT: G 409 MET cc_start: 0.6934 (tmm) cc_final: 0.6595 (tmm) REVERT: G 410 LYS cc_start: 0.8373 (ttpt) cc_final: 0.8113 (ttpt) REVERT: G 413 GLU cc_start: 0.7890 (tt0) cc_final: 0.7523 (tm-30) REVERT: G 431 ASN cc_start: 0.7611 (t0) cc_final: 0.7223 (t0) REVERT: H 290 LYS cc_start: 0.8088 (ptpp) cc_final: 0.7882 (mtmm) REVERT: H 410 LYS cc_start: 0.8334 (ttpt) cc_final: 0.8019 (ttpt) REVERT: H 431 ASN cc_start: 0.7235 (t0) cc_final: 0.6950 (t0) REVERT: I 290 LYS cc_start: 0.7769 (ptpp) cc_final: 0.7451 (mtmm) REVERT: I 294 ARG cc_start: 0.8907 (tpp-160) cc_final: 0.8663 (ttm-80) REVERT: I 418 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7685 (mm-30) REVERT: J 383 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8123 (mm-30) REVERT: J 413 GLU cc_start: 0.8121 (tt0) cc_final: 0.7668 (tm-30) REVERT: K 295 SER cc_start: 0.8677 (OUTLIER) cc_final: 0.8304 (t) REVERT: K 431 ASN cc_start: 0.7025 (t0) cc_final: 0.6485 (t0) REVERT: L 410 LYS cc_start: 0.8329 (ttpt) cc_final: 0.8088 (ttpp) REVERT: L 431 ASN cc_start: 0.7177 (t0) cc_final: 0.6666 (t0) REVERT: M 280 GLU cc_start: 0.7986 (tt0) cc_final: 0.7733 (tt0) REVERT: M 359 GLN cc_start: 0.8042 (tt0) cc_final: 0.7735 (tt0) REVERT: M 418 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7754 (mm-30) REVERT: N 280 GLU cc_start: 0.8277 (tt0) cc_final: 0.8041 (tt0) REVERT: N 290 LYS cc_start: 0.8540 (ptpp) cc_final: 0.8254 (mtmm) REVERT: N 295 SER cc_start: 0.8764 (OUTLIER) cc_final: 0.8456 (t) REVERT: N 359 GLN cc_start: 0.8236 (tt0) cc_final: 0.7916 (tt0) REVERT: N 367 GLU cc_start: 0.8609 (mm-30) cc_final: 0.7822 (mm-30) REVERT: N 383 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8268 (mm-30) REVERT: O 303 GLN cc_start: 0.7925 (mt0) cc_final: 0.7530 (mp10) REVERT: P 247 ARG cc_start: 0.7825 (ppt170) cc_final: 0.7582 (ppt170) REVERT: P 252 ILE cc_start: 0.8390 (tp) cc_final: 0.8172 (tt) REVERT: P 359 GLN cc_start: 0.8188 (tt0) cc_final: 0.7901 (mt0) REVERT: P 418 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7783 (mt-10) REVERT: P 431 ASN cc_start: 0.7346 (t0) cc_final: 0.7121 (t0) REVERT: Q 377 MET cc_start: 0.8247 (mmt) cc_final: 0.8022 (mmm) REVERT: Q 410 LYS cc_start: 0.8790 (ttpt) cc_final: 0.8433 (ttpt) REVERT: Q 418 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7669 (mm-30) REVERT: Q 425 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8436 (ttpt) REVERT: R 431 ASN cc_start: 0.7255 (t0) cc_final: 0.6941 (t0) REVERT: S 303 GLN cc_start: 0.8111 (mt0) cc_final: 0.7910 (mp10) REVERT: S 410 LYS cc_start: 0.8225 (ttpt) cc_final: 0.7954 (ttpp) REVERT: S 428 ASP cc_start: 0.8157 (m-30) cc_final: 0.7927 (m-30) REVERT: T 431 ASN cc_start: 0.7093 (t0) cc_final: 0.6278 (t0) REVERT: U 410 LYS cc_start: 0.8475 (ttpt) cc_final: 0.8133 (ttpp) REVERT: U 418 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7572 (mm-30) REVERT: U 425 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8387 (ttpt) REVERT: V 429 THR cc_start: 0.8538 (p) cc_final: 0.8330 (p) REVERT: V 431 ASN cc_start: 0.7221 (t0) cc_final: 0.6743 (t0) REVERT: W 418 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7818 (mm-30) REVERT: W 431 ASN cc_start: 0.7482 (t0) cc_final: 0.6916 (t0) REVERT: X 290 LYS cc_start: 0.8397 (ptpp) cc_final: 0.8141 (mtmm) REVERT: X 409 MET cc_start: 0.7028 (tmm) cc_final: 0.6762 (tmm) REVERT: X 425 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8459 (ttpt) REVERT: X 428 ASP cc_start: 0.8388 (m-30) cc_final: 0.8187 (m-30) REVERT: X 431 ASN cc_start: 0.7322 (t0) cc_final: 0.6824 (t0) REVERT: Z 294 ARG cc_start: 0.8914 (tpp-160) cc_final: 0.8627 (ttm-80) REVERT: Z 295 SER cc_start: 0.8791 (OUTLIER) cc_final: 0.8506 (m) REVERT: Z 410 LYS cc_start: 0.8233 (ttpt) cc_final: 0.7963 (ttpt) REVERT: a 418 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7817 (mm-30) REVERT: a 431 ASN cc_start: 0.6753 (t0) cc_final: 0.6525 (t0) REVERT: c 274 ASN cc_start: 0.7773 (t0) cc_final: 0.7474 (t0) REVERT: c 373 ARG cc_start: 0.7875 (mtp85) cc_final: 0.7510 (ttm110) REVERT: c 409 MET cc_start: 0.6260 (tmm) cc_final: 0.5962 (tmm) REVERT: c 431 ASN cc_start: 0.7451 (t0) cc_final: 0.7137 (t0) REVERT: b 431 ASN cc_start: 0.7435 (t0) cc_final: 0.7002 (t0) REVERT: d 373 ARG cc_start: 0.7783 (mtp85) cc_final: 0.7548 (mtp85) REVERT: d 409 MET cc_start: 0.6608 (tmm) cc_final: 0.6366 (tmm) REVERT: d 425 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8418 (ttpt) REVERT: e 280 GLU cc_start: 0.8083 (tt0) cc_final: 0.7552 (tt0) REVERT: e 290 LYS cc_start: 0.8224 (ptpp) cc_final: 0.8013 (mtmm) REVERT: e 360 ARG cc_start: 0.7662 (ttt-90) cc_final: 0.7451 (ttm-80) REVERT: f 270 LEU cc_start: 0.9453 (mt) cc_final: 0.9247 (mt) REVERT: f 303 GLN cc_start: 0.7796 (mt0) cc_final: 0.7464 (mp10) REVERT: f 407 ASP cc_start: 0.7675 (p0) cc_final: 0.7404 (p0) REVERT: f 410 LYS cc_start: 0.8541 (ttpt) cc_final: 0.8228 (ttpt) REVERT: f 418 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7554 (mm-30) REVERT: g 303 GLN cc_start: 0.7730 (mt0) cc_final: 0.7413 (mp10) REVERT: g 367 GLU cc_start: 0.8578 (mm-30) cc_final: 0.7844 (mm-30) REVERT: g 383 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8064 (mm-30) REVERT: g 431 ASN cc_start: 0.7227 (t0) cc_final: 0.6700 (t0) REVERT: h 418 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7953 (mm-30) REVERT: h 431 ASN cc_start: 0.6870 (t0) cc_final: 0.6426 (t0) outliers start: 102 outliers final: 1 residues processed: 1317 average time/residue: 0.6895 time to fit residues: 1334.2894 Evaluate side-chains 955 residues out of total 4522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 945 time to evaluate : 4.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 295 SER Chi-restraints excluded: chain G residue 295 SER Chi-restraints excluded: chain K residue 295 SER Chi-restraints excluded: chain N residue 295 SER Chi-restraints excluded: chain Q residue 425 LYS Chi-restraints excluded: chain S residue 425 LYS Chi-restraints excluded: chain U residue 425 LYS Chi-restraints excluded: chain X residue 425 LYS Chi-restraints excluded: chain Z residue 295 SER Chi-restraints excluded: chain d residue 425 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 430 optimal weight: 0.5980 chunk 386 optimal weight: 0.0170 chunk 214 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 260 optimal weight: 0.9980 chunk 206 optimal weight: 9.9990 chunk 399 optimal weight: 0.9990 chunk 154 optimal weight: 2.9990 chunk 243 optimal weight: 3.9990 chunk 297 optimal weight: 0.9980 chunk 463 optimal weight: 0.0670 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 GLN B 411 GLN C 361 ASN C 411 GLN D 361 ASN D 411 GLN E 411 GLN F 411 GLN G 265 GLN G 411 GLN H 411 GLN I 411 GLN J 411 GLN K 411 GLN L 411 GLN ** M 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 361 ASN M 411 GLN N 361 ASN N 411 GLN O 265 GLN O 361 ASN O 411 GLN ** O 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 265 GLN P 361 ASN P 411 GLN Q 411 GLN R 411 GLN S 361 ASN S 411 GLN T 361 ASN T 411 GLN U 361 ASN U 411 GLN V 411 GLN W 361 ASN W 411 GLN X 361 ASN X 411 GLN Y 265 GLN Y 411 GLN Y 431 ASN Z 411 GLN a 411 GLN c 361 ASN c 411 GLN b 361 ASN b 411 GLN d 361 ASN d 411 GLN e 261 ASN e 361 ASN e 411 GLN f 361 ASN f 411 GLN g 361 ASN g 411 GLN h 361 ASN h 411 GLN Total number of N/Q/H flips: 58 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 40698 Z= 0.182 Angle : 0.518 7.393 54842 Z= 0.265 Chirality : 0.039 0.117 6290 Planarity : 0.003 0.051 7344 Dihedral : 5.148 59.453 5533 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.02 % Favored : 99.98 % Rotamer: Outliers : 2.68 % Allowed : 14.15 % Favored : 83.17 % 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: -1.26 (0.13), residues: 4896 helix: 2.88 (0.14), residues: 1326 sheet: -2.03 (0.10), residues: 2414 loop : -2.19 (0.14), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS S 374 PHE 0.009 0.001 PHE J 422 TYR 0.007 0.001 TYR d 282 ARG 0.009 0.000 ARG b 417 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1050 residues out of total 4522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 929 time to evaluate : 4.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 MET cc_start: 0.6922 (tmm) cc_final: 0.6561 (tmm) REVERT: A 410 LYS cc_start: 0.8385 (ttpt) cc_final: 0.8060 (ttpt) REVERT: B 290 LYS cc_start: 0.8335 (ptpp) cc_final: 0.8105 (mtmm) REVERT: B 394 LYS cc_start: 0.7023 (ttpt) cc_final: 0.6730 (ttpp) REVERT: C 383 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8207 (mm-30) REVERT: D 240 ASP cc_start: 0.7708 (m-30) cc_final: 0.7419 (m-30) REVERT: D 409 MET cc_start: 0.6918 (tmm) cc_final: 0.6653 (tmm) REVERT: E 383 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8232 (mm-30) REVERT: E 385 LEU cc_start: 0.9054 (mt) cc_final: 0.8853 (mt) REVERT: E 418 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7879 (mm-30) REVERT: F 367 GLU cc_start: 0.8600 (mm-30) cc_final: 0.7767 (mt-10) REVERT: G 410 LYS cc_start: 0.8368 (ttpt) cc_final: 0.8162 (ttpt) REVERT: H 410 LYS cc_start: 0.8251 (ttpt) cc_final: 0.8009 (ttpt) REVERT: I 383 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8159 (mm-30) REVERT: I 418 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7599 (mm-30) REVERT: J 244 ARG cc_start: 0.8101 (ttm170) cc_final: 0.7866 (ttm170) REVERT: J 417 ARG cc_start: 0.8155 (ttp80) cc_final: 0.7775 (ttp80) REVERT: J 418 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7675 (mt-10) REVERT: L 385 LEU cc_start: 0.9057 (mt) cc_final: 0.8856 (mt) REVERT: M 280 GLU cc_start: 0.7839 (tt0) cc_final: 0.7631 (tt0) REVERT: M 414 ASP cc_start: 0.7550 (t0) cc_final: 0.7164 (t0) REVERT: M 418 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7714 (mt-10) REVERT: O 290 LYS cc_start: 0.8473 (ptpp) cc_final: 0.8262 (mtmm) REVERT: P 431 ASN cc_start: 0.6893 (t0) cc_final: 0.6640 (t0) REVERT: Q 377 MET cc_start: 0.8208 (mmt) cc_final: 0.7992 (mmm) REVERT: R 414 ASP cc_start: 0.7073 (t0) cc_final: 0.6738 (t0) REVERT: S 410 LYS cc_start: 0.8122 (ttpt) cc_final: 0.7773 (ttpp) REVERT: T 385 LEU cc_start: 0.8931 (mt) cc_final: 0.8714 (mt) REVERT: T 409 MET cc_start: 0.7598 (tmm) cc_final: 0.7348 (tmm) REVERT: W 269 GLN cc_start: 0.8382 (mm-40) cc_final: 0.8165 (mp10) REVERT: X 385 LEU cc_start: 0.8934 (mt) cc_final: 0.8623 (mt) REVERT: X 409 MET cc_start: 0.6979 (tmm) cc_final: 0.6736 (tmm) REVERT: Z 409 MET cc_start: 0.7086 (tmm) cc_final: 0.6785 (tmm) REVERT: Z 410 LYS cc_start: 0.8121 (ttpt) cc_final: 0.7843 (ttpt) REVERT: b 250 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7945 (tt0) REVERT: d 385 LEU cc_start: 0.9048 (mt) cc_final: 0.8800 (mt) REVERT: e 239 ASN cc_start: 0.8434 (t0) cc_final: 0.8213 (t0) REVERT: e 280 GLU cc_start: 0.8074 (tt0) cc_final: 0.7633 (tt0) REVERT: e 360 ARG cc_start: 0.7560 (ttt-90) cc_final: 0.7351 (ttm-80) REVERT: f 280 GLU cc_start: 0.8240 (tt0) cc_final: 0.8030 (tt0) REVERT: g 269 GLN cc_start: 0.8192 (mm-40) cc_final: 0.7578 (mp10) REVERT: g 367 GLU cc_start: 0.8610 (mm-30) cc_final: 0.7893 (mm-30) REVERT: g 377 MET cc_start: 0.8029 (mmm) cc_final: 0.7619 (mmm) outliers start: 121 outliers final: 96 residues processed: 1008 average time/residue: 0.5942 time to fit residues: 927.6323 Evaluate side-chains 898 residues out of total 4522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 801 time to evaluate : 4.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain C residue 232 ASP Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain D residue 232 ASP Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 423 SER Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain E residue 232 ASP Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain F residue 232 ASP Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain G residue 232 ASP Chi-restraints excluded: chain G residue 279 GLU Chi-restraints excluded: chain G residue 405 THR Chi-restraints excluded: chain G residue 424 ASP Chi-restraints excluded: chain G residue 429 THR Chi-restraints excluded: chain H residue 232 ASP Chi-restraints excluded: chain H residue 405 THR Chi-restraints excluded: chain H residue 424 ASP Chi-restraints excluded: chain I residue 232 ASP Chi-restraints excluded: chain I residue 405 THR Chi-restraints excluded: chain J residue 232 ASP Chi-restraints excluded: chain J residue 279 GLU Chi-restraints excluded: chain J residue 405 THR Chi-restraints excluded: chain K residue 232 ASP Chi-restraints excluded: chain K residue 252 ILE Chi-restraints excluded: chain L residue 232 ASP Chi-restraints excluded: chain L residue 405 THR Chi-restraints excluded: chain L residue 424 ASP Chi-restraints excluded: chain M residue 232 ASP Chi-restraints excluded: chain M residue 405 THR Chi-restraints excluded: chain M residue 424 ASP Chi-restraints excluded: chain N residue 232 ASP Chi-restraints excluded: chain N residue 424 ASP Chi-restraints excluded: chain O residue 232 ASP Chi-restraints excluded: chain O residue 405 THR Chi-restraints excluded: chain O residue 424 ASP Chi-restraints excluded: chain P residue 232 ASP Chi-restraints excluded: chain P residue 250 GLU Chi-restraints excluded: chain P residue 424 ASP Chi-restraints excluded: chain Q residue 232 ASP Chi-restraints excluded: chain R residue 232 ASP Chi-restraints excluded: chain R residue 405 THR Chi-restraints excluded: chain S residue 232 ASP Chi-restraints excluded: chain S residue 405 THR Chi-restraints excluded: chain T residue 232 ASP Chi-restraints excluded: chain T residue 405 THR Chi-restraints excluded: chain U residue 232 ASP Chi-restraints excluded: chain U residue 405 THR Chi-restraints excluded: chain V residue 232 ASP Chi-restraints excluded: chain V residue 275 LYS Chi-restraints excluded: chain V residue 405 THR Chi-restraints excluded: chain W residue 232 ASP Chi-restraints excluded: chain W residue 405 THR Chi-restraints excluded: chain X residue 232 ASP Chi-restraints excluded: chain X residue 405 THR Chi-restraints excluded: chain Y residue 232 ASP Chi-restraints excluded: chain Y residue 405 THR Chi-restraints excluded: chain Y residue 424 ASP Chi-restraints excluded: chain Z residue 232 ASP Chi-restraints excluded: chain Z residue 405 THR Chi-restraints excluded: chain Z residue 424 ASP Chi-restraints excluded: chain a residue 232 ASP Chi-restraints excluded: chain a residue 405 THR Chi-restraints excluded: chain a residue 424 ASP Chi-restraints excluded: chain c residue 232 ASP Chi-restraints excluded: chain c residue 279 GLU Chi-restraints excluded: chain c residue 369 ASP Chi-restraints excluded: chain c residue 405 THR Chi-restraints excluded: chain b residue 232 ASP Chi-restraints excluded: chain b residue 250 GLU Chi-restraints excluded: chain b residue 405 THR Chi-restraints excluded: chain b residue 424 ASP Chi-restraints excluded: chain d residue 232 ASP Chi-restraints excluded: chain d residue 405 THR Chi-restraints excluded: chain e residue 232 ASP Chi-restraints excluded: chain e residue 404 LEU Chi-restraints excluded: chain e residue 405 THR Chi-restraints excluded: chain e residue 424 ASP Chi-restraints excluded: chain e residue 429 THR Chi-restraints excluded: chain f residue 232 ASP Chi-restraints excluded: chain f residue 246 GLN Chi-restraints excluded: chain f residue 424 ASP Chi-restraints excluded: chain g residue 232 ASP Chi-restraints excluded: chain g residue 279 GLU Chi-restraints excluded: chain g residue 405 THR Chi-restraints excluded: chain h residue 232 ASP Chi-restraints excluded: chain h residue 424 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 257 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 385 optimal weight: 1.9990 chunk 315 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 463 optimal weight: 0.8980 chunk 501 optimal weight: 2.9990 chunk 413 optimal weight: 0.7980 chunk 460 optimal weight: 0.9980 chunk 158 optimal weight: 0.9980 chunk 372 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 374 HIS J 365 ASN K 374 HIS O 265 GLN P 265 GLN P 374 HIS ** T 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 431 ASN ** X 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 365 ASN Y 431 ASN d 365 ASN h 374 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 40698 Z= 0.243 Angle : 0.528 6.018 54842 Z= 0.268 Chirality : 0.039 0.122 6290 Planarity : 0.003 0.041 7344 Dihedral : 4.448 17.406 5508 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 3.87 % Allowed : 16.59 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.13), residues: 4896 helix: 3.30 (0.14), residues: 1326 sheet: -1.78 (0.11), residues: 2414 loop : -1.87 (0.15), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS S 374 PHE 0.015 0.001 PHE T 422 TYR 0.010 0.001 TYR B 282 ARG 0.006 0.000 ARG C 417 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1000 residues out of total 4522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 825 time to evaluate : 4.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 MET cc_start: 0.6867 (tmm) cc_final: 0.6520 (tmm) REVERT: A 431 ASN cc_start: 0.6609 (m110) cc_final: 0.6386 (m-40) REVERT: B 414 ASP cc_start: 0.7571 (t0) cc_final: 0.7229 (t0) REVERT: C 383 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8205 (mm-30) REVERT: D 240 ASP cc_start: 0.7722 (m-30) cc_final: 0.7342 (m-30) REVERT: F 367 GLU cc_start: 0.8634 (mm-30) cc_final: 0.7857 (mt-10) REVERT: G 283 SER cc_start: 0.9309 (m) cc_final: 0.8961 (p) REVERT: I 243 SER cc_start: 0.9444 (OUTLIER) cc_final: 0.9099 (p) REVERT: I 367 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8148 (mt-10) REVERT: K 243 SER cc_start: 0.9350 (OUTLIER) cc_final: 0.9060 (p) REVERT: M 280 GLU cc_start: 0.7666 (tt0) cc_final: 0.7443 (tt0) REVERT: M 418 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7771 (mm-30) REVERT: P 418 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7587 (mt-10) REVERT: S 410 LYS cc_start: 0.8115 (ttpt) cc_final: 0.7891 (ttpp) REVERT: V 299 ASN cc_start: 0.7857 (OUTLIER) cc_final: 0.7274 (m-40) REVERT: W 290 LYS cc_start: 0.8090 (mtmm) cc_final: 0.7813 (mtmm) REVERT: W 417 ARG cc_start: 0.8218 (ttp-110) cc_final: 0.7933 (ttp-170) REVERT: X 269 GLN cc_start: 0.8170 (mm-40) cc_final: 0.7457 (mp10) REVERT: X 409 MET cc_start: 0.6979 (tmm) cc_final: 0.6728 (tmm) REVERT: Z 409 MET cc_start: 0.7119 (tmm) cc_final: 0.6797 (tmm) REVERT: Z 410 LYS cc_start: 0.8162 (ttpt) cc_final: 0.7887 (ttpt) REVERT: c 269 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.8057 (mp10) REVERT: b 250 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7927 (tt0) REVERT: b 299 ASN cc_start: 0.7648 (OUTLIER) cc_final: 0.7073 (m-40) REVERT: b 385 LEU cc_start: 0.8793 (mt) cc_final: 0.8587 (mt) REVERT: d 409 MET cc_start: 0.7019 (tmm) cc_final: 0.6693 (tmm) REVERT: e 280 GLU cc_start: 0.8078 (tt0) cc_final: 0.7646 (tt0) REVERT: g 269 GLN cc_start: 0.8187 (mm-40) cc_final: 0.7602 (mp10) REVERT: g 367 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8070 (mm-30) REVERT: g 377 MET cc_start: 0.8051 (mmm) cc_final: 0.7620 (mmm) outliers start: 175 outliers final: 127 residues processed: 947 average time/residue: 0.5856 time to fit residues: 862.8993 Evaluate side-chains 895 residues out of total 4522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 762 time to evaluate : 4.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain C residue 232 ASP Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain D residue 232 ASP Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 423 SER Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain E residue 232 ASP Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain F residue 232 ASP Chi-restraints excluded: chain F residue 250 GLU Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain G residue 232 ASP Chi-restraints excluded: chain G residue 279 GLU Chi-restraints excluded: chain G residue 405 THR Chi-restraints excluded: chain G residue 424 ASP Chi-restraints excluded: chain H residue 232 ASP Chi-restraints excluded: chain H residue 405 THR Chi-restraints excluded: chain H residue 424 ASP Chi-restraints excluded: chain I residue 232 ASP Chi-restraints excluded: chain I residue 243 SER Chi-restraints excluded: chain I residue 266 VAL Chi-restraints excluded: chain I residue 405 THR Chi-restraints excluded: chain J residue 232 ASP Chi-restraints excluded: chain J residue 266 VAL Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain J residue 405 THR Chi-restraints excluded: chain J residue 429 THR Chi-restraints excluded: chain K residue 232 ASP Chi-restraints excluded: chain K residue 243 SER Chi-restraints excluded: chain K residue 252 ILE Chi-restraints excluded: chain L residue 232 ASP Chi-restraints excluded: chain L residue 405 THR Chi-restraints excluded: chain M residue 232 ASP Chi-restraints excluded: chain M residue 405 THR Chi-restraints excluded: chain M residue 424 ASP Chi-restraints excluded: chain N residue 232 ASP Chi-restraints excluded: chain N residue 299 ASN Chi-restraints excluded: chain N residue 370 ARG Chi-restraints excluded: chain O residue 232 ASP Chi-restraints excluded: chain O residue 299 ASN Chi-restraints excluded: chain O residue 405 THR Chi-restraints excluded: chain O residue 415 LEU Chi-restraints excluded: chain O residue 424 ASP Chi-restraints excluded: chain P residue 232 ASP Chi-restraints excluded: chain P residue 250 GLU Chi-restraints excluded: chain P residue 266 VAL Chi-restraints excluded: chain P residue 299 ASN Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain P residue 424 ASP Chi-restraints excluded: chain P residue 429 THR Chi-restraints excluded: chain Q residue 232 ASP Chi-restraints excluded: chain Q residue 252 ILE Chi-restraints excluded: chain Q residue 369 ASP Chi-restraints excluded: chain R residue 232 ASP Chi-restraints excluded: chain R residue 405 THR Chi-restraints excluded: chain S residue 232 ASP Chi-restraints excluded: chain S residue 267 THR Chi-restraints excluded: chain S residue 405 THR Chi-restraints excluded: chain S residue 424 ASP Chi-restraints excluded: chain T residue 232 ASP Chi-restraints excluded: chain T residue 266 VAL Chi-restraints excluded: chain T residue 279 GLU Chi-restraints excluded: chain T residue 369 ASP Chi-restraints excluded: chain T residue 405 THR Chi-restraints excluded: chain U residue 232 ASP Chi-restraints excluded: chain U residue 405 THR Chi-restraints excluded: chain V residue 232 ASP Chi-restraints excluded: chain V residue 275 LYS Chi-restraints excluded: chain V residue 299 ASN Chi-restraints excluded: chain V residue 405 THR Chi-restraints excluded: chain W residue 232 ASP Chi-restraints excluded: chain W residue 405 THR Chi-restraints excluded: chain W residue 424 ASP Chi-restraints excluded: chain X residue 232 ASP Chi-restraints excluded: chain X residue 405 THR Chi-restraints excluded: chain X residue 424 ASP Chi-restraints excluded: chain Y residue 232 ASP Chi-restraints excluded: chain Y residue 252 ILE Chi-restraints excluded: chain Y residue 405 THR Chi-restraints excluded: chain Y residue 424 ASP Chi-restraints excluded: chain Z residue 232 ASP Chi-restraints excluded: chain Z residue 252 ILE Chi-restraints excluded: chain Z residue 266 VAL Chi-restraints excluded: chain Z residue 405 THR Chi-restraints excluded: chain Z residue 424 ASP Chi-restraints excluded: chain a residue 232 ASP Chi-restraints excluded: chain a residue 266 VAL Chi-restraints excluded: chain a residue 405 THR Chi-restraints excluded: chain a residue 424 ASP Chi-restraints excluded: chain a residue 429 THR Chi-restraints excluded: chain c residue 232 ASP Chi-restraints excluded: chain c residue 269 GLN Chi-restraints excluded: chain c residue 369 ASP Chi-restraints excluded: chain c residue 405 THR Chi-restraints excluded: chain b residue 232 ASP Chi-restraints excluded: chain b residue 250 GLU Chi-restraints excluded: chain b residue 299 ASN Chi-restraints excluded: chain b residue 405 THR Chi-restraints excluded: chain b residue 424 ASP Chi-restraints excluded: chain d residue 232 ASP Chi-restraints excluded: chain d residue 299 ASN Chi-restraints excluded: chain d residue 405 THR Chi-restraints excluded: chain e residue 232 ASP Chi-restraints excluded: chain e residue 358 THR Chi-restraints excluded: chain e residue 405 THR Chi-restraints excluded: chain e residue 424 ASP Chi-restraints excluded: chain f residue 232 ASP Chi-restraints excluded: chain f residue 424 ASP Chi-restraints excluded: chain g residue 232 ASP Chi-restraints excluded: chain g residue 279 GLU Chi-restraints excluded: chain g residue 405 THR Chi-restraints excluded: chain g residue 424 ASP Chi-restraints excluded: chain h residue 232 ASP Chi-restraints excluded: chain h residue 266 VAL Chi-restraints excluded: chain h residue 299 ASN Chi-restraints excluded: chain h residue 369 ASP Chi-restraints excluded: chain h residue 424 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 458 optimal weight: 0.7980 chunk 348 optimal weight: 0.2980 chunk 240 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 221 optimal weight: 0.0060 chunk 311 optimal weight: 0.0870 chunk 465 optimal weight: 1.9990 chunk 492 optimal weight: 0.9990 chunk 243 optimal weight: 1.9990 chunk 441 optimal weight: 2.9990 chunk 132 optimal weight: 0.5980 overall best weight: 0.3574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 361 ASN ** X 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 40698 Z= 0.154 Angle : 0.491 7.283 54842 Z= 0.248 Chirality : 0.038 0.121 6290 Planarity : 0.002 0.024 7344 Dihedral : 4.089 15.556 5508 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Rotamer: Outliers : 3.49 % Allowed : 17.71 % Favored : 78.79 % 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: -0.14 (0.13), residues: 4896 helix: 3.85 (0.13), residues: 1326 sheet: -1.40 (0.11), residues: 2414 loop : -1.63 (0.16), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS S 374 PHE 0.030 0.001 PHE D 422 TYR 0.006 0.001 TYR B 282 ARG 0.004 0.000 ARG C 417 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1014 residues out of total 4522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 856 time to evaluate : 5.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 MET cc_start: 0.6874 (tmm) cc_final: 0.6567 (tmm) REVERT: B 240 ASP cc_start: 0.7664 (m-30) cc_final: 0.7332 (m-30) REVERT: B 414 ASP cc_start: 0.7729 (t0) cc_final: 0.6591 (t0) REVERT: D 383 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7979 (mm-30) REVERT: E 236 LYS cc_start: 0.8244 (mptt) cc_final: 0.7900 (mptt) REVERT: E 418 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7905 (mm-30) REVERT: F 367 GLU cc_start: 0.8646 (mm-30) cc_final: 0.7926 (mt-10) REVERT: F 383 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8266 (mm-30) REVERT: G 283 SER cc_start: 0.9362 (m) cc_final: 0.8907 (p) REVERT: G 410 LYS cc_start: 0.8469 (ttpp) cc_final: 0.8135 (ttpt) REVERT: H 418 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7313 (mt-10) REVERT: I 367 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8114 (mt-10) REVERT: I 424 ASP cc_start: 0.7899 (m-30) cc_final: 0.7642 (m-30) REVERT: J 383 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8224 (mm-30) REVERT: K 420 MET cc_start: 0.8458 (ttp) cc_final: 0.8238 (ttp) REVERT: L 418 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7729 (mt-10) REVERT: M 299 ASN cc_start: 0.7727 (OUTLIER) cc_final: 0.7337 (m-40) REVERT: M 418 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7630 (mt-10) REVERT: N 383 GLU cc_start: 0.8741 (mm-30) cc_final: 0.8408 (mm-30) REVERT: O 290 LYS cc_start: 0.7793 (mtmm) cc_final: 0.7591 (mtmm) REVERT: P 418 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7667 (mt-10) REVERT: Q 424 ASP cc_start: 0.7943 (m-30) cc_final: 0.7730 (m-30) REVERT: R 280 GLU cc_start: 0.7970 (tt0) cc_final: 0.7607 (tt0) REVERT: R 299 ASN cc_start: 0.7981 (OUTLIER) cc_final: 0.7397 (m-40) REVERT: T 409 MET cc_start: 0.7569 (tmm) cc_final: 0.7249 (tmm) REVERT: U 422 PHE cc_start: 0.8586 (t80) cc_final: 0.8342 (t80) REVERT: V 275 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.7998 (mtmm) REVERT: V 418 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7849 (mm-30) REVERT: X 269 GLN cc_start: 0.8133 (mm-40) cc_final: 0.7465 (mp10) REVERT: X 409 MET cc_start: 0.7056 (tmm) cc_final: 0.6842 (tmm) REVERT: Z 409 MET cc_start: 0.7060 (tmm) cc_final: 0.6737 (tmm) REVERT: Z 410 LYS cc_start: 0.8148 (ttpt) cc_final: 0.7854 (ttpt) REVERT: a 299 ASN cc_start: 0.8123 (OUTLIER) cc_final: 0.7656 (m-40) REVERT: c 269 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.8019 (mp10) REVERT: b 250 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7914 (tt0) REVERT: d 409 MET cc_start: 0.7065 (tmm) cc_final: 0.6674 (tmm) REVERT: e 280 GLU cc_start: 0.7932 (tt0) cc_final: 0.7480 (tt0) REVERT: f 269 GLN cc_start: 0.8211 (mm-40) cc_final: 0.7778 (mp10) REVERT: g 269 GLN cc_start: 0.8261 (mm-40) cc_final: 0.7818 (mp10) REVERT: g 377 MET cc_start: 0.8089 (mmm) cc_final: 0.7622 (mmm) outliers start: 158 outliers final: 123 residues processed: 964 average time/residue: 0.5965 time to fit residues: 897.8918 Evaluate side-chains 905 residues out of total 4522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 776 time to evaluate : 4.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain C residue 232 ASP Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain D residue 232 ASP Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 283 SER Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain E residue 232 ASP Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain F residue 232 ASP Chi-restraints excluded: chain F residue 250 GLU Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 385 LEU Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 428 ASP Chi-restraints excluded: chain G residue 232 ASP Chi-restraints excluded: chain G residue 266 VAL Chi-restraints excluded: chain G residue 405 THR Chi-restraints excluded: chain G residue 424 ASP Chi-restraints excluded: chain H residue 232 ASP Chi-restraints excluded: chain H residue 266 VAL Chi-restraints excluded: chain H residue 405 THR Chi-restraints excluded: chain H residue 424 ASP Chi-restraints excluded: chain I residue 232 ASP Chi-restraints excluded: chain I residue 405 THR Chi-restraints excluded: chain J residue 232 ASP Chi-restraints excluded: chain J residue 279 GLU Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain J residue 405 THR Chi-restraints excluded: chain K residue 232 ASP Chi-restraints excluded: chain K residue 266 VAL Chi-restraints excluded: chain L residue 232 ASP Chi-restraints excluded: chain L residue 266 VAL Chi-restraints excluded: chain L residue 405 THR Chi-restraints excluded: chain L residue 424 ASP Chi-restraints excluded: chain M residue 232 ASP Chi-restraints excluded: chain M residue 299 ASN Chi-restraints excluded: chain M residue 405 THR Chi-restraints excluded: chain M residue 424 ASP Chi-restraints excluded: chain N residue 232 ASP Chi-restraints excluded: chain N residue 266 VAL Chi-restraints excluded: chain N residue 299 ASN Chi-restraints excluded: chain N residue 424 ASP Chi-restraints excluded: chain O residue 232 ASP Chi-restraints excluded: chain O residue 299 ASN Chi-restraints excluded: chain O residue 405 THR Chi-restraints excluded: chain O residue 424 ASP Chi-restraints excluded: chain P residue 232 ASP Chi-restraints excluded: chain P residue 250 GLU Chi-restraints excluded: chain P residue 266 VAL Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain P residue 424 ASP Chi-restraints excluded: chain Q residue 232 ASP Chi-restraints excluded: chain Q residue 266 VAL Chi-restraints excluded: chain Q residue 369 ASP Chi-restraints excluded: chain R residue 232 ASP Chi-restraints excluded: chain R residue 299 ASN Chi-restraints excluded: chain R residue 405 THR Chi-restraints excluded: chain S residue 232 ASP Chi-restraints excluded: chain S residue 266 VAL Chi-restraints excluded: chain S residue 267 THR Chi-restraints excluded: chain S residue 405 THR Chi-restraints excluded: chain S residue 424 ASP Chi-restraints excluded: chain T residue 232 ASP Chi-restraints excluded: chain T residue 266 VAL Chi-restraints excluded: chain T residue 369 ASP Chi-restraints excluded: chain T residue 405 THR Chi-restraints excluded: chain U residue 232 ASP Chi-restraints excluded: chain U residue 405 THR Chi-restraints excluded: chain V residue 232 ASP Chi-restraints excluded: chain V residue 275 LYS Chi-restraints excluded: chain V residue 405 THR Chi-restraints excluded: chain W residue 232 ASP Chi-restraints excluded: chain W residue 405 THR Chi-restraints excluded: chain W residue 424 ASP Chi-restraints excluded: chain X residue 232 ASP Chi-restraints excluded: chain X residue 266 VAL Chi-restraints excluded: chain X residue 405 THR Chi-restraints excluded: chain X residue 424 ASP Chi-restraints excluded: chain X residue 429 THR Chi-restraints excluded: chain Y residue 232 ASP Chi-restraints excluded: chain Y residue 266 VAL Chi-restraints excluded: chain Y residue 405 THR Chi-restraints excluded: chain Y residue 424 ASP Chi-restraints excluded: chain Z residue 232 ASP Chi-restraints excluded: chain Z residue 405 THR Chi-restraints excluded: chain Z residue 424 ASP Chi-restraints excluded: chain a residue 232 ASP Chi-restraints excluded: chain a residue 299 ASN Chi-restraints excluded: chain a residue 405 THR Chi-restraints excluded: chain a residue 424 ASP Chi-restraints excluded: chain c residue 232 ASP Chi-restraints excluded: chain c residue 269 GLN Chi-restraints excluded: chain c residue 369 ASP Chi-restraints excluded: chain c residue 405 THR Chi-restraints excluded: chain b residue 232 ASP Chi-restraints excluded: chain b residue 250 GLU Chi-restraints excluded: chain b residue 266 VAL Chi-restraints excluded: chain b residue 405 THR Chi-restraints excluded: chain b residue 424 ASP Chi-restraints excluded: chain d residue 232 ASP Chi-restraints excluded: chain d residue 405 THR Chi-restraints excluded: chain e residue 232 ASP Chi-restraints excluded: chain e residue 266 VAL Chi-restraints excluded: chain e residue 358 THR Chi-restraints excluded: chain e residue 405 THR Chi-restraints excluded: chain e residue 424 ASP Chi-restraints excluded: chain e residue 429 THR Chi-restraints excluded: chain f residue 232 ASP Chi-restraints excluded: chain f residue 266 VAL Chi-restraints excluded: chain f residue 424 ASP Chi-restraints excluded: chain g residue 232 ASP Chi-restraints excluded: chain g residue 405 THR Chi-restraints excluded: chain g residue 424 ASP Chi-restraints excluded: chain h residue 232 ASP Chi-restraints excluded: chain h residue 369 ASP Chi-restraints excluded: chain h residue 424 ASP Chi-restraints excluded: chain h residue 429 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 410 optimal weight: 3.9990 chunk 279 optimal weight: 0.0170 chunk 7 optimal weight: 3.9990 chunk 367 optimal weight: 3.9990 chunk 203 optimal weight: 0.9990 chunk 420 optimal weight: 2.9990 chunk 340 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 251 optimal weight: 7.9990 chunk 442 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 overall best weight: 0.9622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 374 HIS F 365 ASN H 365 ASN K 365 ASN N 365 ASN O 365 ASN R 365 ASN V 365 ASN X 365 ASN ** X 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 431 ASN Z 431 ASN d 374 HIS f 365 ASN f 374 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 40698 Z= 0.266 Angle : 0.539 7.066 54842 Z= 0.274 Chirality : 0.039 0.128 6290 Planarity : 0.003 0.028 7344 Dihedral : 4.312 17.764 5508 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.38 % Allowed : 18.55 % Favored : 77.07 % 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: -0.25 (0.13), residues: 4896 helix: 3.62 (0.13), residues: 1326 sheet: -1.43 (0.11), residues: 2414 loop : -1.57 (0.16), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS c 374 PHE 0.027 0.001 PHE Y 422 TYR 0.012 0.002 TYR B 282 ARG 0.006 0.000 ARG C 417 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 984 residues out of total 4522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 786 time to evaluate : 4.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 ARG cc_start: 0.7993 (ppt170) cc_final: 0.7780 (ppt170) REVERT: A 409 MET cc_start: 0.6951 (tmm) cc_final: 0.6632 (tmm) REVERT: B 418 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7250 (tt0) REVERT: F 367 GLU cc_start: 0.8695 (mm-30) cc_final: 0.7989 (mt-10) REVERT: F 383 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8312 (mm-30) REVERT: G 410 LYS cc_start: 0.8444 (ttpp) cc_final: 0.8155 (ttpt) REVERT: I 367 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8126 (mt-10) REVERT: I 424 ASP cc_start: 0.7952 (m-30) cc_final: 0.7688 (m-30) REVERT: J 267 THR cc_start: 0.8585 (OUTLIER) cc_final: 0.8264 (p) REVERT: J 383 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8288 (mm-30) REVERT: L 279 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7544 (mp0) REVERT: M 280 GLU cc_start: 0.7706 (tt0) cc_final: 0.7461 (tt0) REVERT: M 299 ASN cc_start: 0.7765 (OUTLIER) cc_final: 0.7417 (m-40) REVERT: N 383 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8484 (mm-30) REVERT: P 418 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7663 (mt-10) REVERT: Q 393 TYR cc_start: 0.7738 (OUTLIER) cc_final: 0.5644 (m-80) REVERT: Q 424 ASP cc_start: 0.7997 (m-30) cc_final: 0.7767 (m-30) REVERT: R 280 GLU cc_start: 0.8063 (tt0) cc_final: 0.7715 (tt0) REVERT: R 299 ASN cc_start: 0.8014 (OUTLIER) cc_final: 0.7463 (m-40) REVERT: S 412 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7927 (mm) REVERT: T 393 TYR cc_start: 0.8261 (OUTLIER) cc_final: 0.6803 (m-80) REVERT: U 422 PHE cc_start: 0.8660 (t80) cc_final: 0.8424 (t80) REVERT: V 299 ASN cc_start: 0.7769 (OUTLIER) cc_final: 0.7160 (m-40) REVERT: W 253 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7785 (mt) REVERT: W 420 MET cc_start: 0.8607 (ttm) cc_final: 0.8402 (ttp) REVERT: X 269 GLN cc_start: 0.8190 (mm-40) cc_final: 0.7480 (mp10) REVERT: X 367 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8069 (mm-30) REVERT: X 409 MET cc_start: 0.6982 (tmm) cc_final: 0.6736 (tmm) REVERT: Z 409 MET cc_start: 0.7091 (tmm) cc_final: 0.6728 (tmm) REVERT: Z 410 LYS cc_start: 0.8216 (ttpt) cc_final: 0.7892 (ttpt) REVERT: a 299 ASN cc_start: 0.8122 (OUTLIER) cc_final: 0.7721 (m-40) REVERT: a 393 TYR cc_start: 0.8049 (OUTLIER) cc_final: 0.7538 (m-80) REVERT: c 269 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.7759 (mp10) REVERT: b 250 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7916 (tt0) REVERT: b 269 GLN cc_start: 0.8197 (mp10) cc_final: 0.7906 (mp10) REVERT: e 280 GLU cc_start: 0.8050 (tt0) cc_final: 0.7635 (tt0) REVERT: f 393 TYR cc_start: 0.7662 (OUTLIER) cc_final: 0.7193 (m-80) REVERT: g 269 GLN cc_start: 0.8365 (mm-40) cc_final: 0.7828 (mp10) REVERT: g 367 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8074 (mm-30) outliers start: 198 outliers final: 160 residues processed: 927 average time/residue: 0.5836 time to fit residues: 843.2088 Evaluate side-chains 929 residues out of total 4522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 755 time to evaluate : 4.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain C residue 232 ASP Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain D residue 232 ASP Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 283 SER Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain E residue 232 ASP Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain E residue 429 THR Chi-restraints excluded: chain F residue 232 ASP Chi-restraints excluded: chain F residue 250 GLU Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 267 THR Chi-restraints excluded: chain F residue 385 LEU Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 428 ASP Chi-restraints excluded: chain G residue 232 ASP Chi-restraints excluded: chain G residue 240 ASP Chi-restraints excluded: chain G residue 266 VAL Chi-restraints excluded: chain G residue 299 ASN Chi-restraints excluded: chain G residue 405 THR Chi-restraints excluded: chain G residue 424 ASP Chi-restraints excluded: chain H residue 232 ASP Chi-restraints excluded: chain H residue 266 VAL Chi-restraints excluded: chain H residue 267 THR Chi-restraints excluded: chain H residue 405 THR Chi-restraints excluded: chain H residue 424 ASP Chi-restraints excluded: chain I residue 232 ASP Chi-restraints excluded: chain I residue 405 THR Chi-restraints excluded: chain J residue 232 ASP Chi-restraints excluded: chain J residue 266 VAL Chi-restraints excluded: chain J residue 267 THR Chi-restraints excluded: chain J residue 279 GLU Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain J residue 405 THR Chi-restraints excluded: chain K residue 232 ASP Chi-restraints excluded: chain K residue 252 ILE Chi-restraints excluded: chain K residue 266 VAL Chi-restraints excluded: chain L residue 232 ASP Chi-restraints excluded: chain L residue 266 VAL Chi-restraints excluded: chain L residue 267 THR Chi-restraints excluded: chain L residue 279 GLU Chi-restraints excluded: chain L residue 405 THR Chi-restraints excluded: chain L residue 424 ASP Chi-restraints excluded: chain M residue 232 ASP Chi-restraints excluded: chain M residue 299 ASN Chi-restraints excluded: chain M residue 405 THR Chi-restraints excluded: chain M residue 424 ASP Chi-restraints excluded: chain N residue 232 ASP Chi-restraints excluded: chain N residue 266 VAL Chi-restraints excluded: chain N residue 299 ASN Chi-restraints excluded: chain N residue 424 ASP Chi-restraints excluded: chain O residue 232 ASP Chi-restraints excluded: chain O residue 299 ASN Chi-restraints excluded: chain O residue 405 THR Chi-restraints excluded: chain O residue 415 LEU Chi-restraints excluded: chain O residue 424 ASP Chi-restraints excluded: chain P residue 232 ASP Chi-restraints excluded: chain P residue 250 GLU Chi-restraints excluded: chain P residue 266 VAL Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain P residue 424 ASP Chi-restraints excluded: chain P residue 429 THR Chi-restraints excluded: chain Q residue 232 ASP Chi-restraints excluded: chain Q residue 252 ILE Chi-restraints excluded: chain Q residue 266 VAL Chi-restraints excluded: chain Q residue 369 ASP Chi-restraints excluded: chain Q residue 393 TYR Chi-restraints excluded: chain R residue 232 ASP Chi-restraints excluded: chain R residue 266 VAL Chi-restraints excluded: chain R residue 299 ASN Chi-restraints excluded: chain R residue 405 THR Chi-restraints excluded: chain R residue 420 MET Chi-restraints excluded: chain S residue 232 ASP Chi-restraints excluded: chain S residue 266 VAL Chi-restraints excluded: chain S residue 267 THR Chi-restraints excluded: chain S residue 293 LEU Chi-restraints excluded: chain S residue 405 THR Chi-restraints excluded: chain S residue 412 ILE Chi-restraints excluded: chain S residue 424 ASP Chi-restraints excluded: chain T residue 232 ASP Chi-restraints excluded: chain T residue 279 GLU Chi-restraints excluded: chain T residue 369 ASP Chi-restraints excluded: chain T residue 393 TYR Chi-restraints excluded: chain T residue 405 THR Chi-restraints excluded: chain T residue 424 ASP Chi-restraints excluded: chain U residue 232 ASP Chi-restraints excluded: chain U residue 390 VAL Chi-restraints excluded: chain U residue 405 THR Chi-restraints excluded: chain V residue 232 ASP Chi-restraints excluded: chain V residue 246 GLN Chi-restraints excluded: chain V residue 267 THR Chi-restraints excluded: chain V residue 275 LYS Chi-restraints excluded: chain V residue 279 GLU Chi-restraints excluded: chain V residue 299 ASN Chi-restraints excluded: chain V residue 405 THR Chi-restraints excluded: chain W residue 232 ASP Chi-restraints excluded: chain W residue 253 LEU Chi-restraints excluded: chain W residue 405 THR Chi-restraints excluded: chain W residue 424 ASP Chi-restraints excluded: chain X residue 232 ASP Chi-restraints excluded: chain X residue 266 VAL Chi-restraints excluded: chain X residue 405 THR Chi-restraints excluded: chain X residue 424 ASP Chi-restraints excluded: chain Y residue 232 ASP Chi-restraints excluded: chain Y residue 252 ILE Chi-restraints excluded: chain Y residue 266 VAL Chi-restraints excluded: chain Y residue 405 THR Chi-restraints excluded: chain Y residue 424 ASP Chi-restraints excluded: chain Z residue 232 ASP Chi-restraints excluded: chain Z residue 252 ILE Chi-restraints excluded: chain Z residue 266 VAL Chi-restraints excluded: chain Z residue 267 THR Chi-restraints excluded: chain Z residue 405 THR Chi-restraints excluded: chain Z residue 424 ASP Chi-restraints excluded: chain Z residue 428 ASP Chi-restraints excluded: chain a residue 232 ASP Chi-restraints excluded: chain a residue 266 VAL Chi-restraints excluded: chain a residue 299 ASN Chi-restraints excluded: chain a residue 393 TYR Chi-restraints excluded: chain a residue 405 THR Chi-restraints excluded: chain a residue 424 ASP Chi-restraints excluded: chain a residue 429 THR Chi-restraints excluded: chain c residue 232 ASP Chi-restraints excluded: chain c residue 269 GLN Chi-restraints excluded: chain c residue 279 GLU Chi-restraints excluded: chain c residue 369 ASP Chi-restraints excluded: chain c residue 405 THR Chi-restraints excluded: chain b residue 232 ASP Chi-restraints excluded: chain b residue 250 GLU Chi-restraints excluded: chain b residue 266 VAL Chi-restraints excluded: chain b residue 405 THR Chi-restraints excluded: chain b residue 411 GLN Chi-restraints excluded: chain b residue 424 ASP Chi-restraints excluded: chain d residue 232 ASP Chi-restraints excluded: chain d residue 405 THR Chi-restraints excluded: chain e residue 232 ASP Chi-restraints excluded: chain e residue 266 VAL Chi-restraints excluded: chain e residue 358 THR Chi-restraints excluded: chain e residue 404 LEU Chi-restraints excluded: chain e residue 405 THR Chi-restraints excluded: chain e residue 424 ASP Chi-restraints excluded: chain e residue 429 THR Chi-restraints excluded: chain f residue 232 ASP Chi-restraints excluded: chain f residue 266 VAL Chi-restraints excluded: chain f residue 393 TYR Chi-restraints excluded: chain f residue 424 ASP Chi-restraints excluded: chain g residue 232 ASP Chi-restraints excluded: chain g residue 405 THR Chi-restraints excluded: chain g residue 424 ASP Chi-restraints excluded: chain h residue 232 ASP Chi-restraints excluded: chain h residue 266 VAL Chi-restraints excluded: chain h residue 299 ASN Chi-restraints excluded: chain h residue 369 ASP Chi-restraints excluded: chain h residue 385 LEU Chi-restraints excluded: chain h residue 424 ASP Chi-restraints excluded: chain h residue 429 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 165 optimal weight: 0.9980 chunk 443 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 289 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 chunk 493 optimal weight: 2.9990 chunk 409 optimal weight: 0.8980 chunk 228 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 163 optimal weight: 0.0060 chunk 259 optimal weight: 0.6980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 265 GLN O 265 GLN O 378 ASN ** X 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 40698 Z= 0.188 Angle : 0.506 8.018 54842 Z= 0.255 Chirality : 0.038 0.125 6290 Planarity : 0.002 0.027 7344 Dihedral : 4.098 15.853 5508 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Rotamer: Outliers : 4.38 % Allowed : 19.55 % Favored : 76.07 % 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: 0.04 (0.13), residues: 4896 helix: 3.91 (0.13), residues: 1326 sheet: -1.26 (0.11), residues: 2414 loop : -1.50 (0.16), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS c 374 PHE 0.021 0.001 PHE Y 422 TYR 0.012 0.001 TYR e 393 ARG 0.005 0.000 ARG C 417 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 988 residues out of total 4522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 790 time to evaluate : 5.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 ARG cc_start: 0.7889 (ppt170) cc_final: 0.7668 (ppt170) REVERT: A 409 MET cc_start: 0.6849 (tmm) cc_final: 0.6533 (tmm) REVERT: F 269 GLN cc_start: 0.8479 (mp10) cc_final: 0.7677 (mp10) REVERT: F 367 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8000 (mt-10) REVERT: F 383 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8260 (mm-30) REVERT: G 283 SER cc_start: 0.9362 (m) cc_final: 0.8991 (p) REVERT: G 410 LYS cc_start: 0.8413 (ttpp) cc_final: 0.8130 (ttpt) REVERT: I 367 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8125 (mt-10) REVERT: I 424 ASP cc_start: 0.7957 (m-30) cc_final: 0.7681 (m-30) REVERT: J 267 THR cc_start: 0.8549 (OUTLIER) cc_final: 0.8277 (p) REVERT: J 383 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8253 (mm-30) REVERT: J 393 TYR cc_start: 0.8260 (OUTLIER) cc_final: 0.7493 (m-80) REVERT: L 279 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7592 (mp0) REVERT: M 299 ASN cc_start: 0.7742 (OUTLIER) cc_final: 0.7378 (m-40) REVERT: N 383 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8533 (mm-30) REVERT: P 418 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7655 (mt-10) REVERT: Q 424 ASP cc_start: 0.7974 (m-30) cc_final: 0.7748 (m-30) REVERT: R 280 GLU cc_start: 0.7982 (tt0) cc_final: 0.7591 (tt0) REVERT: R 299 ASN cc_start: 0.7991 (OUTLIER) cc_final: 0.7421 (m-40) REVERT: T 393 TYR cc_start: 0.8206 (OUTLIER) cc_final: 0.6831 (m-80) REVERT: T 409 MET cc_start: 0.7575 (tmm) cc_final: 0.7279 (tmm) REVERT: U 356 ARG cc_start: 0.7228 (ptp-170) cc_final: 0.6983 (ptp-170) REVERT: V 299 ASN cc_start: 0.7701 (OUTLIER) cc_final: 0.7106 (m-40) REVERT: V 393 TYR cc_start: 0.7718 (OUTLIER) cc_final: 0.6398 (m-80) REVERT: W 253 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7652 (mt) REVERT: X 269 GLN cc_start: 0.8165 (mm-40) cc_final: 0.7512 (mp10) REVERT: X 409 MET cc_start: 0.6978 (tmm) cc_final: 0.6731 (tmm) REVERT: Z 409 MET cc_start: 0.7045 (tmm) cc_final: 0.6677 (tmm) REVERT: Z 410 LYS cc_start: 0.8275 (ttpt) cc_final: 0.7964 (ttpt) REVERT: a 299 ASN cc_start: 0.8101 (OUTLIER) cc_final: 0.7644 (m-40) REVERT: c 269 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.7949 (mp10) REVERT: b 250 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7943 (tt0) REVERT: b 269 GLN cc_start: 0.8153 (mp10) cc_final: 0.7845 (mp10) REVERT: d 409 MET cc_start: 0.6777 (tmm) cc_final: 0.6475 (tmm) REVERT: e 280 GLU cc_start: 0.7914 (tt0) cc_final: 0.7700 (tt0) REVERT: g 269 GLN cc_start: 0.8329 (mm-40) cc_final: 0.7885 (mp10) REVERT: g 367 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8102 (mm-30) outliers start: 198 outliers final: 168 residues processed: 933 average time/residue: 0.5845 time to fit residues: 850.5757 Evaluate side-chains 940 residues out of total 4522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 760 time to evaluate : 4.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain C residue 232 ASP Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain D residue 232 ASP Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 283 SER Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain E residue 232 ASP Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain E residue 429 THR Chi-restraints excluded: chain F residue 232 ASP Chi-restraints excluded: chain F residue 250 GLU Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 428 ASP Chi-restraints excluded: chain G residue 232 ASP Chi-restraints excluded: chain G residue 266 VAL Chi-restraints excluded: chain G residue 299 ASN Chi-restraints excluded: chain G residue 405 THR Chi-restraints excluded: chain G residue 424 ASP Chi-restraints excluded: chain H residue 232 ASP Chi-restraints excluded: chain H residue 266 VAL Chi-restraints excluded: chain H residue 405 THR Chi-restraints excluded: chain H residue 411 GLN Chi-restraints excluded: chain H residue 424 ASP Chi-restraints excluded: chain I residue 232 ASP Chi-restraints excluded: chain I residue 405 THR Chi-restraints excluded: chain J residue 232 ASP Chi-restraints excluded: chain J residue 266 VAL Chi-restraints excluded: chain J residue 267 THR Chi-restraints excluded: chain J residue 279 GLU Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain J residue 393 TYR Chi-restraints excluded: chain J residue 405 THR Chi-restraints excluded: chain K residue 232 ASP Chi-restraints excluded: chain K residue 252 ILE Chi-restraints excluded: chain K residue 266 VAL Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain K residue 411 GLN Chi-restraints excluded: chain L residue 232 ASP Chi-restraints excluded: chain L residue 266 VAL Chi-restraints excluded: chain L residue 279 GLU Chi-restraints excluded: chain L residue 405 THR Chi-restraints excluded: chain L residue 424 ASP Chi-restraints excluded: chain M residue 232 ASP Chi-restraints excluded: chain M residue 253 LEU Chi-restraints excluded: chain M residue 299 ASN Chi-restraints excluded: chain M residue 405 THR Chi-restraints excluded: chain M residue 424 ASP Chi-restraints excluded: chain N residue 232 ASP Chi-restraints excluded: chain N residue 266 VAL Chi-restraints excluded: chain N residue 299 ASN Chi-restraints excluded: chain N residue 411 GLN Chi-restraints excluded: chain N residue 424 ASP Chi-restraints excluded: chain O residue 232 ASP Chi-restraints excluded: chain O residue 299 ASN Chi-restraints excluded: chain O residue 405 THR Chi-restraints excluded: chain O residue 415 LEU Chi-restraints excluded: chain O residue 424 ASP Chi-restraints excluded: chain P residue 232 ASP Chi-restraints excluded: chain P residue 250 GLU Chi-restraints excluded: chain P residue 266 VAL Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain P residue 424 ASP Chi-restraints excluded: chain P residue 429 THR Chi-restraints excluded: chain Q residue 232 ASP Chi-restraints excluded: chain Q residue 266 VAL Chi-restraints excluded: chain Q residue 369 ASP Chi-restraints excluded: chain R residue 232 ASP Chi-restraints excluded: chain R residue 266 VAL Chi-restraints excluded: chain R residue 299 ASN Chi-restraints excluded: chain R residue 405 THR Chi-restraints excluded: chain S residue 232 ASP Chi-restraints excluded: chain S residue 266 VAL Chi-restraints excluded: chain S residue 267 THR Chi-restraints excluded: chain S residue 293 LEU Chi-restraints excluded: chain S residue 369 ASP Chi-restraints excluded: chain S residue 405 THR Chi-restraints excluded: chain S residue 424 ASP Chi-restraints excluded: chain T residue 232 ASP Chi-restraints excluded: chain T residue 266 VAL Chi-restraints excluded: chain T residue 279 GLU Chi-restraints excluded: chain T residue 369 ASP Chi-restraints excluded: chain T residue 393 TYR Chi-restraints excluded: chain T residue 405 THR Chi-restraints excluded: chain T residue 411 GLN Chi-restraints excluded: chain T residue 424 ASP Chi-restraints excluded: chain T residue 429 THR Chi-restraints excluded: chain T residue 430 LEU Chi-restraints excluded: chain U residue 232 ASP Chi-restraints excluded: chain U residue 266 VAL Chi-restraints excluded: chain U residue 390 VAL Chi-restraints excluded: chain U residue 405 THR Chi-restraints excluded: chain V residue 232 ASP Chi-restraints excluded: chain V residue 246 GLN Chi-restraints excluded: chain V residue 275 LYS Chi-restraints excluded: chain V residue 299 ASN Chi-restraints excluded: chain V residue 393 TYR Chi-restraints excluded: chain V residue 405 THR Chi-restraints excluded: chain W residue 232 ASP Chi-restraints excluded: chain W residue 253 LEU Chi-restraints excluded: chain W residue 405 THR Chi-restraints excluded: chain W residue 424 ASP Chi-restraints excluded: chain X residue 232 ASP Chi-restraints excluded: chain X residue 266 VAL Chi-restraints excluded: chain X residue 405 THR Chi-restraints excluded: chain X residue 424 ASP Chi-restraints excluded: chain X residue 429 THR Chi-restraints excluded: chain Y residue 232 ASP Chi-restraints excluded: chain Y residue 246 GLN Chi-restraints excluded: chain Y residue 266 VAL Chi-restraints excluded: chain Y residue 405 THR Chi-restraints excluded: chain Y residue 424 ASP Chi-restraints excluded: chain Z residue 232 ASP Chi-restraints excluded: chain Z residue 252 ILE Chi-restraints excluded: chain Z residue 266 VAL Chi-restraints excluded: chain Z residue 369 ASP Chi-restraints excluded: chain Z residue 405 THR Chi-restraints excluded: chain Z residue 424 ASP Chi-restraints excluded: chain a residue 232 ASP Chi-restraints excluded: chain a residue 266 VAL Chi-restraints excluded: chain a residue 299 ASN Chi-restraints excluded: chain a residue 405 THR Chi-restraints excluded: chain a residue 411 GLN Chi-restraints excluded: chain a residue 424 ASP Chi-restraints excluded: chain a residue 429 THR Chi-restraints excluded: chain c residue 232 ASP Chi-restraints excluded: chain c residue 269 GLN Chi-restraints excluded: chain c residue 279 GLU Chi-restraints excluded: chain c residue 369 ASP Chi-restraints excluded: chain c residue 405 THR Chi-restraints excluded: chain b residue 232 ASP Chi-restraints excluded: chain b residue 250 GLU Chi-restraints excluded: chain b residue 266 VAL Chi-restraints excluded: chain b residue 405 THR Chi-restraints excluded: chain b residue 424 ASP Chi-restraints excluded: chain d residue 232 ASP Chi-restraints excluded: chain d residue 299 ASN Chi-restraints excluded: chain d residue 405 THR Chi-restraints excluded: chain e residue 232 ASP Chi-restraints excluded: chain e residue 266 VAL Chi-restraints excluded: chain e residue 358 THR Chi-restraints excluded: chain e residue 405 THR Chi-restraints excluded: chain e residue 411 GLN Chi-restraints excluded: chain e residue 424 ASP Chi-restraints excluded: chain e residue 429 THR Chi-restraints excluded: chain f residue 232 ASP Chi-restraints excluded: chain f residue 266 VAL Chi-restraints excluded: chain f residue 424 ASP Chi-restraints excluded: chain g residue 232 ASP Chi-restraints excluded: chain g residue 405 THR Chi-restraints excluded: chain g residue 424 ASP Chi-restraints excluded: chain h residue 232 ASP Chi-restraints excluded: chain h residue 266 VAL Chi-restraints excluded: chain h residue 293 LEU Chi-restraints excluded: chain h residue 299 ASN Chi-restraints excluded: chain h residue 369 ASP Chi-restraints excluded: chain h residue 385 LEU Chi-restraints excluded: chain h residue 411 GLN Chi-restraints excluded: chain h residue 424 ASP Chi-restraints excluded: chain h residue 429 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 475 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 281 optimal weight: 0.9980 chunk 360 optimal weight: 1.9990 chunk 279 optimal weight: 0.7980 chunk 415 optimal weight: 0.5980 chunk 275 optimal weight: 0.2980 chunk 491 optimal weight: 0.0270 chunk 307 optimal weight: 0.5980 chunk 299 optimal weight: 3.9990 chunk 226 optimal weight: 0.5980 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN G 265 GLN ** X 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 431 ASN a 361 ASN ** b 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 378 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 40698 Z= 0.169 Angle : 0.499 8.951 54842 Z= 0.250 Chirality : 0.038 0.122 6290 Planarity : 0.002 0.062 7344 Dihedral : 3.909 15.203 5508 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 4.22 % Allowed : 20.10 % Favored : 75.67 % 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: 0.25 (0.13), residues: 4896 helix: 4.04 (0.13), residues: 1326 sheet: -1.10 (0.11), residues: 2414 loop : -1.44 (0.16), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS c 374 PHE 0.031 0.001 PHE U 422 TYR 0.010 0.001 TYR e 393 ARG 0.017 0.000 ARG a 417 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 985 residues out of total 4522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 794 time to evaluate : 4.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 MET cc_start: 0.6880 (tmm) cc_final: 0.6621 (tmm) REVERT: B 418 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7403 (mm-30) REVERT: F 269 GLN cc_start: 0.8556 (mp10) cc_final: 0.7915 (mp10) REVERT: F 383 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8229 (mm-30) REVERT: G 283 SER cc_start: 0.9360 (m) cc_final: 0.8892 (p) REVERT: G 410 LYS cc_start: 0.8406 (ttpp) cc_final: 0.8122 (ttpt) REVERT: I 424 ASP cc_start: 0.7981 (m-30) cc_final: 0.7684 (m-30) REVERT: J 267 THR cc_start: 0.8532 (OUTLIER) cc_final: 0.8265 (p) REVERT: J 383 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8206 (mm-30) REVERT: J 393 TYR cc_start: 0.8202 (OUTLIER) cc_final: 0.7410 (m-80) REVERT: M 280 GLU cc_start: 0.7661 (tt0) cc_final: 0.7397 (tt0) REVERT: N 269 GLN cc_start: 0.8392 (mm-40) cc_final: 0.8009 (mp10) REVERT: N 383 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8558 (mm-30) REVERT: N 418 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7794 (mm-30) REVERT: O 290 LYS cc_start: 0.8049 (mtmm) cc_final: 0.7483 (mppt) REVERT: P 418 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7529 (mt-10) REVERT: Q 393 TYR cc_start: 0.7616 (OUTLIER) cc_final: 0.5468 (m-80) REVERT: Q 424 ASP cc_start: 0.7987 (m-30) cc_final: 0.7780 (m-30) REVERT: R 280 GLU cc_start: 0.8037 (tt0) cc_final: 0.7582 (tt0) REVERT: T 393 TYR cc_start: 0.8153 (OUTLIER) cc_final: 0.6885 (m-80) REVERT: T 409 MET cc_start: 0.7566 (tmm) cc_final: 0.7238 (tmm) REVERT: U 356 ARG cc_start: 0.7196 (ptp-170) cc_final: 0.6900 (ptp-170) REVERT: V 269 GLN cc_start: 0.8206 (mm-40) cc_final: 0.7505 (mp10) REVERT: V 275 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7990 (mtmm) REVERT: V 299 ASN cc_start: 0.7690 (OUTLIER) cc_final: 0.7063 (m-40) REVERT: V 393 TYR cc_start: 0.7665 (OUTLIER) cc_final: 0.6336 (m-80) REVERT: W 282 TYR cc_start: 0.9025 (m-80) cc_final: 0.8691 (m-10) REVERT: X 269 GLN cc_start: 0.8133 (mm-40) cc_final: 0.7566 (mp10) REVERT: X 409 MET cc_start: 0.6759 (tmm) cc_final: 0.6513 (tmm) REVERT: Z 409 MET cc_start: 0.7030 (tmm) cc_final: 0.6687 (tmm) REVERT: Z 410 LYS cc_start: 0.8227 (ttpt) cc_final: 0.7900 (ttpt) REVERT: a 299 ASN cc_start: 0.8103 (OUTLIER) cc_final: 0.7662 (m-40) REVERT: a 393 TYR cc_start: 0.8019 (OUTLIER) cc_final: 0.7480 (m-80) REVERT: c 269 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.7899 (mp10) REVERT: b 250 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7901 (tt0) REVERT: b 269 GLN cc_start: 0.8118 (mp10) cc_final: 0.7824 (mp10) REVERT: d 409 MET cc_start: 0.6676 (tmm) cc_final: 0.6375 (tmm) REVERT: e 280 GLU cc_start: 0.7852 (tt0) cc_final: 0.7335 (tt0) REVERT: e 282 TYR cc_start: 0.8526 (m-10) cc_final: 0.7972 (m-10) REVERT: g 269 GLN cc_start: 0.8266 (mm-40) cc_final: 0.7926 (mp10) REVERT: g 290 LYS cc_start: 0.8484 (mtmm) cc_final: 0.8255 (pttm) REVERT: g 367 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8061 (mm-30) REVERT: g 377 MET cc_start: 0.8224 (mmm) cc_final: 0.7754 (mmm) outliers start: 191 outliers final: 157 residues processed: 938 average time/residue: 0.5786 time to fit residues: 846.6959 Evaluate side-chains 933 residues out of total 4522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 765 time to evaluate : 4.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain C residue 232 ASP Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain D residue 232 ASP Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 283 SER Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain E residue 232 ASP Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain E residue 429 THR Chi-restraints excluded: chain F residue 232 ASP Chi-restraints excluded: chain F residue 250 GLU Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 428 ASP Chi-restraints excluded: chain G residue 232 ASP Chi-restraints excluded: chain G residue 266 VAL Chi-restraints excluded: chain G residue 405 THR Chi-restraints excluded: chain G residue 424 ASP Chi-restraints excluded: chain H residue 232 ASP Chi-restraints excluded: chain H residue 266 VAL Chi-restraints excluded: chain H residue 405 THR Chi-restraints excluded: chain H residue 411 GLN Chi-restraints excluded: chain H residue 424 ASP Chi-restraints excluded: chain I residue 232 ASP Chi-restraints excluded: chain I residue 266 VAL Chi-restraints excluded: chain I residue 369 ASP Chi-restraints excluded: chain I residue 405 THR Chi-restraints excluded: chain J residue 232 ASP Chi-restraints excluded: chain J residue 266 VAL Chi-restraints excluded: chain J residue 267 THR Chi-restraints excluded: chain J residue 279 GLU Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain J residue 393 TYR Chi-restraints excluded: chain J residue 405 THR Chi-restraints excluded: chain K residue 232 ASP Chi-restraints excluded: chain K residue 252 ILE Chi-restraints excluded: chain K residue 266 VAL Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain K residue 411 GLN Chi-restraints excluded: chain L residue 232 ASP Chi-restraints excluded: chain L residue 405 THR Chi-restraints excluded: chain L residue 424 ASP Chi-restraints excluded: chain M residue 232 ASP Chi-restraints excluded: chain M residue 253 LEU Chi-restraints excluded: chain M residue 405 THR Chi-restraints excluded: chain M residue 424 ASP Chi-restraints excluded: chain N residue 232 ASP Chi-restraints excluded: chain N residue 266 VAL Chi-restraints excluded: chain N residue 299 ASN Chi-restraints excluded: chain N residue 411 GLN Chi-restraints excluded: chain N residue 424 ASP Chi-restraints excluded: chain O residue 232 ASP Chi-restraints excluded: chain O residue 405 THR Chi-restraints excluded: chain O residue 415 LEU Chi-restraints excluded: chain O residue 424 ASP Chi-restraints excluded: chain P residue 232 ASP Chi-restraints excluded: chain P residue 250 GLU Chi-restraints excluded: chain P residue 266 VAL Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain P residue 424 ASP Chi-restraints excluded: chain P residue 429 THR Chi-restraints excluded: chain Q residue 232 ASP Chi-restraints excluded: chain Q residue 266 VAL Chi-restraints excluded: chain Q residue 369 ASP Chi-restraints excluded: chain Q residue 393 TYR Chi-restraints excluded: chain R residue 232 ASP Chi-restraints excluded: chain R residue 266 VAL Chi-restraints excluded: chain R residue 405 THR Chi-restraints excluded: chain S residue 232 ASP Chi-restraints excluded: chain S residue 266 VAL Chi-restraints excluded: chain S residue 267 THR Chi-restraints excluded: chain S residue 293 LEU Chi-restraints excluded: chain S residue 369 ASP Chi-restraints excluded: chain S residue 405 THR Chi-restraints excluded: chain S residue 424 ASP Chi-restraints excluded: chain T residue 232 ASP Chi-restraints excluded: chain T residue 266 VAL Chi-restraints excluded: chain T residue 369 ASP Chi-restraints excluded: chain T residue 393 TYR Chi-restraints excluded: chain T residue 405 THR Chi-restraints excluded: chain T residue 411 GLN Chi-restraints excluded: chain T residue 430 LEU Chi-restraints excluded: chain U residue 232 ASP Chi-restraints excluded: chain U residue 266 VAL Chi-restraints excluded: chain U residue 390 VAL Chi-restraints excluded: chain U residue 405 THR Chi-restraints excluded: chain V residue 232 ASP Chi-restraints excluded: chain V residue 246 GLN Chi-restraints excluded: chain V residue 275 LYS Chi-restraints excluded: chain V residue 299 ASN Chi-restraints excluded: chain V residue 393 TYR Chi-restraints excluded: chain V residue 405 THR Chi-restraints excluded: chain W residue 232 ASP Chi-restraints excluded: chain W residue 405 THR Chi-restraints excluded: chain W residue 424 ASP Chi-restraints excluded: chain X residue 232 ASP Chi-restraints excluded: chain X residue 266 VAL Chi-restraints excluded: chain X residue 405 THR Chi-restraints excluded: chain X residue 424 ASP Chi-restraints excluded: chain Y residue 232 ASP Chi-restraints excluded: chain Y residue 246 GLN Chi-restraints excluded: chain Y residue 266 VAL Chi-restraints excluded: chain Y residue 405 THR Chi-restraints excluded: chain Y residue 424 ASP Chi-restraints excluded: chain Z residue 232 ASP Chi-restraints excluded: chain Z residue 266 VAL Chi-restraints excluded: chain Z residue 369 ASP Chi-restraints excluded: chain Z residue 405 THR Chi-restraints excluded: chain Z residue 424 ASP Chi-restraints excluded: chain Z residue 428 ASP Chi-restraints excluded: chain a residue 232 ASP Chi-restraints excluded: chain a residue 266 VAL Chi-restraints excluded: chain a residue 299 ASN Chi-restraints excluded: chain a residue 393 TYR Chi-restraints excluded: chain a residue 405 THR Chi-restraints excluded: chain a residue 411 GLN Chi-restraints excluded: chain a residue 424 ASP Chi-restraints excluded: chain a residue 429 THR Chi-restraints excluded: chain c residue 232 ASP Chi-restraints excluded: chain c residue 269 GLN Chi-restraints excluded: chain c residue 279 GLU Chi-restraints excluded: chain c residue 369 ASP Chi-restraints excluded: chain c residue 405 THR Chi-restraints excluded: chain b residue 232 ASP Chi-restraints excluded: chain b residue 250 GLU Chi-restraints excluded: chain b residue 266 VAL Chi-restraints excluded: chain b residue 405 THR Chi-restraints excluded: chain b residue 424 ASP Chi-restraints excluded: chain d residue 232 ASP Chi-restraints excluded: chain d residue 299 ASN Chi-restraints excluded: chain d residue 405 THR Chi-restraints excluded: chain e residue 232 ASP Chi-restraints excluded: chain e residue 266 VAL Chi-restraints excluded: chain e residue 358 THR Chi-restraints excluded: chain e residue 405 THR Chi-restraints excluded: chain e residue 411 GLN Chi-restraints excluded: chain e residue 424 ASP Chi-restraints excluded: chain e residue 429 THR Chi-restraints excluded: chain f residue 232 ASP Chi-restraints excluded: chain f residue 266 VAL Chi-restraints excluded: chain f residue 424 ASP Chi-restraints excluded: chain g residue 232 ASP Chi-restraints excluded: chain g residue 405 THR Chi-restraints excluded: chain g residue 424 ASP Chi-restraints excluded: chain h residue 232 ASP Chi-restraints excluded: chain h residue 266 VAL Chi-restraints excluded: chain h residue 293 LEU Chi-restraints excluded: chain h residue 299 ASN Chi-restraints excluded: chain h residue 369 ASP Chi-restraints excluded: chain h residue 429 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 304 optimal weight: 0.8980 chunk 196 optimal weight: 1.9990 chunk 293 optimal weight: 0.9980 chunk 148 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 95 optimal weight: 0.1980 chunk 312 optimal weight: 0.7980 chunk 334 optimal weight: 0.9980 chunk 243 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 386 optimal weight: 0.0070 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 265 GLN I 265 GLN I 365 ASN O 265 GLN Q 365 ASN ** X 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 361 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 40698 Z= 0.185 Angle : 0.516 8.927 54842 Z= 0.258 Chirality : 0.038 0.127 6290 Planarity : 0.002 0.049 7344 Dihedral : 3.910 15.236 5508 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Rotamer: Outliers : 4.51 % Allowed : 20.50 % Favored : 74.99 % 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: 0.31 (0.13), residues: 4896 helix: 3.99 (0.13), residues: 1326 sheet: -1.03 (0.11), residues: 2414 loop : -1.37 (0.16), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS c 374 PHE 0.025 0.001 PHE U 422 TYR 0.011 0.001 TYR e 393 ARG 0.012 0.000 ARG a 417 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 985 residues out of total 4522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 781 time to evaluate : 5.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 MET cc_start: 0.6886 (tmm) cc_final: 0.6615 (tmm) REVERT: F 269 GLN cc_start: 0.8528 (mp10) cc_final: 0.7795 (mp10) REVERT: F 383 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8201 (mm-30) REVERT: G 283 SER cc_start: 0.9362 (m) cc_final: 0.8982 (p) REVERT: G 410 LYS cc_start: 0.8403 (ttpp) cc_final: 0.8132 (ttpt) REVERT: I 424 ASP cc_start: 0.7992 (m-30) cc_final: 0.7701 (m-30) REVERT: J 267 THR cc_start: 0.8516 (OUTLIER) cc_final: 0.8266 (p) REVERT: J 383 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8260 (mm-30) REVERT: J 393 TYR cc_start: 0.8214 (OUTLIER) cc_final: 0.7535 (m-80) REVERT: M 280 GLU cc_start: 0.7690 (tt0) cc_final: 0.7405 (tt0) REVERT: M 428 ASP cc_start: 0.8330 (t70) cc_final: 0.8072 (t70) REVERT: N 269 GLN cc_start: 0.8399 (mm-40) cc_final: 0.8033 (mp10) REVERT: N 383 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8560 (mm-30) REVERT: N 418 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7765 (mm-30) REVERT: P 418 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7520 (mt-10) REVERT: Q 393 TYR cc_start: 0.7623 (OUTLIER) cc_final: 0.5409 (m-80) REVERT: R 280 GLU cc_start: 0.8124 (tt0) cc_final: 0.7672 (tt0) REVERT: S 409 MET cc_start: 0.6689 (tmm) cc_final: 0.6480 (tmm) REVERT: T 393 TYR cc_start: 0.8127 (OUTLIER) cc_final: 0.6843 (m-80) REVERT: T 409 MET cc_start: 0.7581 (tmm) cc_final: 0.7256 (tmm) REVERT: U 356 ARG cc_start: 0.7221 (ptp-170) cc_final: 0.6933 (ptp-170) REVERT: V 269 GLN cc_start: 0.8231 (mm-40) cc_final: 0.7529 (mp10) REVERT: V 299 ASN cc_start: 0.7638 (OUTLIER) cc_final: 0.7002 (m-40) REVERT: V 393 TYR cc_start: 0.7668 (OUTLIER) cc_final: 0.6338 (m-80) REVERT: V 418 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7628 (mm-30) REVERT: W 282 TYR cc_start: 0.9025 (m-80) cc_final: 0.8731 (m-10) REVERT: W 290 LYS cc_start: 0.8232 (mtmm) cc_final: 0.7914 (mppt) REVERT: X 269 GLN cc_start: 0.8141 (mm-40) cc_final: 0.7576 (mp10) REVERT: X 409 MET cc_start: 0.6980 (tmm) cc_final: 0.6721 (tmm) REVERT: Z 409 MET cc_start: 0.7032 (tmm) cc_final: 0.6689 (tmm) REVERT: Z 410 LYS cc_start: 0.8235 (ttpt) cc_final: 0.7893 (ttpt) REVERT: a 299 ASN cc_start: 0.8107 (OUTLIER) cc_final: 0.7665 (m-40) REVERT: a 393 TYR cc_start: 0.8076 (OUTLIER) cc_final: 0.7557 (m-80) REVERT: c 269 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.7829 (mp10) REVERT: c 420 MET cc_start: 0.8469 (ttp) cc_final: 0.8257 (ttp) REVERT: b 250 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7877 (tt0) REVERT: b 269 GLN cc_start: 0.8155 (mp10) cc_final: 0.7857 (mp10) REVERT: d 409 MET cc_start: 0.6699 (tmm) cc_final: 0.6369 (tmm) REVERT: e 280 GLU cc_start: 0.7851 (tt0) cc_final: 0.7361 (tt0) REVERT: e 282 TYR cc_start: 0.8546 (m-10) cc_final: 0.8034 (m-10) REVERT: f 393 TYR cc_start: 0.7714 (OUTLIER) cc_final: 0.7295 (m-80) REVERT: g 269 GLN cc_start: 0.8317 (mm-40) cc_final: 0.7985 (mp10) REVERT: g 367 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8071 (mm-30) REVERT: g 377 MET cc_start: 0.8287 (mmm) cc_final: 0.7816 (mmm) outliers start: 204 outliers final: 173 residues processed: 936 average time/residue: 0.5985 time to fit residues: 874.7734 Evaluate side-chains 953 residues out of total 4522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 769 time to evaluate : 4.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain C residue 232 ASP Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain D residue 232 ASP Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 283 SER Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain E residue 232 ASP Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 411 GLN Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain E residue 429 THR Chi-restraints excluded: chain F residue 232 ASP Chi-restraints excluded: chain F residue 250 GLU Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 428 ASP Chi-restraints excluded: chain G residue 232 ASP Chi-restraints excluded: chain G residue 266 VAL Chi-restraints excluded: chain G residue 405 THR Chi-restraints excluded: chain G residue 424 ASP Chi-restraints excluded: chain H residue 232 ASP Chi-restraints excluded: chain H residue 266 VAL Chi-restraints excluded: chain H residue 369 ASP Chi-restraints excluded: chain H residue 405 THR Chi-restraints excluded: chain H residue 411 GLN Chi-restraints excluded: chain H residue 424 ASP Chi-restraints excluded: chain I residue 232 ASP Chi-restraints excluded: chain I residue 266 VAL Chi-restraints excluded: chain I residue 369 ASP Chi-restraints excluded: chain I residue 405 THR Chi-restraints excluded: chain J residue 232 ASP Chi-restraints excluded: chain J residue 266 VAL Chi-restraints excluded: chain J residue 267 THR Chi-restraints excluded: chain J residue 279 GLU Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain J residue 393 TYR Chi-restraints excluded: chain J residue 405 THR Chi-restraints excluded: chain K residue 232 ASP Chi-restraints excluded: chain K residue 252 ILE Chi-restraints excluded: chain K residue 266 VAL Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain K residue 411 GLN Chi-restraints excluded: chain L residue 232 ASP Chi-restraints excluded: chain L residue 266 VAL Chi-restraints excluded: chain L residue 369 ASP Chi-restraints excluded: chain L residue 405 THR Chi-restraints excluded: chain M residue 232 ASP Chi-restraints excluded: chain M residue 253 LEU Chi-restraints excluded: chain M residue 405 THR Chi-restraints excluded: chain M residue 424 ASP Chi-restraints excluded: chain N residue 232 ASP Chi-restraints excluded: chain N residue 266 VAL Chi-restraints excluded: chain N residue 299 ASN Chi-restraints excluded: chain N residue 411 GLN Chi-restraints excluded: chain N residue 424 ASP Chi-restraints excluded: chain O residue 232 ASP Chi-restraints excluded: chain O residue 266 VAL Chi-restraints excluded: chain O residue 267 THR Chi-restraints excluded: chain O residue 369 ASP Chi-restraints excluded: chain O residue 405 THR Chi-restraints excluded: chain O residue 415 LEU Chi-restraints excluded: chain O residue 424 ASP Chi-restraints excluded: chain P residue 232 ASP Chi-restraints excluded: chain P residue 250 GLU Chi-restraints excluded: chain P residue 266 VAL Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain P residue 424 ASP Chi-restraints excluded: chain P residue 429 THR Chi-restraints excluded: chain Q residue 232 ASP Chi-restraints excluded: chain Q residue 266 VAL Chi-restraints excluded: chain Q residue 369 ASP Chi-restraints excluded: chain Q residue 393 TYR Chi-restraints excluded: chain R residue 232 ASP Chi-restraints excluded: chain R residue 266 VAL Chi-restraints excluded: chain R residue 405 THR Chi-restraints excluded: chain R residue 430 LEU Chi-restraints excluded: chain S residue 232 ASP Chi-restraints excluded: chain S residue 266 VAL Chi-restraints excluded: chain S residue 267 THR Chi-restraints excluded: chain S residue 293 LEU Chi-restraints excluded: chain S residue 369 ASP Chi-restraints excluded: chain S residue 405 THR Chi-restraints excluded: chain S residue 424 ASP Chi-restraints excluded: chain T residue 232 ASP Chi-restraints excluded: chain T residue 266 VAL Chi-restraints excluded: chain T residue 369 ASP Chi-restraints excluded: chain T residue 393 TYR Chi-restraints excluded: chain T residue 405 THR Chi-restraints excluded: chain T residue 411 GLN Chi-restraints excluded: chain T residue 430 LEU Chi-restraints excluded: chain U residue 232 ASP Chi-restraints excluded: chain U residue 266 VAL Chi-restraints excluded: chain U residue 369 ASP Chi-restraints excluded: chain U residue 390 VAL Chi-restraints excluded: chain U residue 405 THR Chi-restraints excluded: chain V residue 232 ASP Chi-restraints excluded: chain V residue 246 GLN Chi-restraints excluded: chain V residue 275 LYS Chi-restraints excluded: chain V residue 299 ASN Chi-restraints excluded: chain V residue 393 TYR Chi-restraints excluded: chain V residue 405 THR Chi-restraints excluded: chain W residue 232 ASP Chi-restraints excluded: chain W residue 405 THR Chi-restraints excluded: chain W residue 424 ASP Chi-restraints excluded: chain X residue 232 ASP Chi-restraints excluded: chain X residue 266 VAL Chi-restraints excluded: chain X residue 405 THR Chi-restraints excluded: chain X residue 424 ASP Chi-restraints excluded: chain Y residue 232 ASP Chi-restraints excluded: chain Y residue 246 GLN Chi-restraints excluded: chain Y residue 266 VAL Chi-restraints excluded: chain Y residue 405 THR Chi-restraints excluded: chain Y residue 424 ASP Chi-restraints excluded: chain Z residue 232 ASP Chi-restraints excluded: chain Z residue 266 VAL Chi-restraints excluded: chain Z residue 369 ASP Chi-restraints excluded: chain Z residue 405 THR Chi-restraints excluded: chain Z residue 424 ASP Chi-restraints excluded: chain Z residue 428 ASP Chi-restraints excluded: chain a residue 232 ASP Chi-restraints excluded: chain a residue 266 VAL Chi-restraints excluded: chain a residue 299 ASN Chi-restraints excluded: chain a residue 393 TYR Chi-restraints excluded: chain a residue 405 THR Chi-restraints excluded: chain a residue 411 GLN Chi-restraints excluded: chain a residue 424 ASP Chi-restraints excluded: chain a residue 429 THR Chi-restraints excluded: chain c residue 232 ASP Chi-restraints excluded: chain c residue 269 GLN Chi-restraints excluded: chain c residue 279 GLU Chi-restraints excluded: chain c residue 369 ASP Chi-restraints excluded: chain c residue 405 THR Chi-restraints excluded: chain b residue 232 ASP Chi-restraints excluded: chain b residue 250 GLU Chi-restraints excluded: chain b residue 266 VAL Chi-restraints excluded: chain b residue 369 ASP Chi-restraints excluded: chain b residue 405 THR Chi-restraints excluded: chain b residue 411 GLN Chi-restraints excluded: chain b residue 424 ASP Chi-restraints excluded: chain d residue 232 ASP Chi-restraints excluded: chain d residue 299 ASN Chi-restraints excluded: chain d residue 405 THR Chi-restraints excluded: chain d residue 410 LYS Chi-restraints excluded: chain e residue 232 ASP Chi-restraints excluded: chain e residue 266 VAL Chi-restraints excluded: chain e residue 358 THR Chi-restraints excluded: chain e residue 405 THR Chi-restraints excluded: chain e residue 411 GLN Chi-restraints excluded: chain e residue 424 ASP Chi-restraints excluded: chain e residue 429 THR Chi-restraints excluded: chain f residue 232 ASP Chi-restraints excluded: chain f residue 266 VAL Chi-restraints excluded: chain f residue 369 ASP Chi-restraints excluded: chain f residue 393 TYR Chi-restraints excluded: chain f residue 424 ASP Chi-restraints excluded: chain g residue 232 ASP Chi-restraints excluded: chain g residue 405 THR Chi-restraints excluded: chain g residue 424 ASP Chi-restraints excluded: chain h residue 232 ASP Chi-restraints excluded: chain h residue 266 VAL Chi-restraints excluded: chain h residue 293 LEU Chi-restraints excluded: chain h residue 299 ASN Chi-restraints excluded: chain h residue 369 ASP Chi-restraints excluded: chain h residue 385 LEU Chi-restraints excluded: chain h residue 411 GLN Chi-restraints excluded: chain h residue 429 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 447 optimal weight: 1.9990 chunk 470 optimal weight: 0.9980 chunk 429 optimal weight: 0.9980 chunk 458 optimal weight: 0.7980 chunk 275 optimal weight: 0.4980 chunk 199 optimal weight: 1.9990 chunk 359 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 413 optimal weight: 0.8980 chunk 433 optimal weight: 2.9990 chunk 456 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 265 GLN ** X 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 40698 Z= 0.239 Angle : 0.547 9.386 54842 Z= 0.274 Chirality : 0.039 0.127 6290 Planarity : 0.003 0.059 7344 Dihedral : 4.084 15.717 5508 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 4.53 % Allowed : 20.77 % Favored : 74.70 % 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: 0.15 (0.13), residues: 4896 helix: 3.78 (0.13), residues: 1326 sheet: -1.10 (0.11), residues: 2414 loop : -1.38 (0.16), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS h 374 PHE 0.027 0.001 PHE L 422 TYR 0.015 0.002 TYR C 393 ARG 0.014 0.000 ARG C 417 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 991 residues out of total 4522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 786 time to evaluate : 4.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 MET cc_start: 0.6882 (tmm) cc_final: 0.6601 (tmm) REVERT: F 269 GLN cc_start: 0.8462 (mp10) cc_final: 0.7668 (mp10) REVERT: F 367 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8070 (mt-10) REVERT: F 383 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8226 (mm-30) REVERT: G 283 SER cc_start: 0.9367 (m) cc_final: 0.8986 (p) REVERT: G 393 TYR cc_start: 0.7863 (OUTLIER) cc_final: 0.5713 (m-80) REVERT: G 410 LYS cc_start: 0.8423 (ttpp) cc_final: 0.8155 (ttpt) REVERT: I 424 ASP cc_start: 0.7965 (m-30) cc_final: 0.7679 (m-30) REVERT: J 267 THR cc_start: 0.8642 (OUTLIER) cc_final: 0.8360 (p) REVERT: J 393 TYR cc_start: 0.8283 (OUTLIER) cc_final: 0.7616 (m-80) REVERT: N 383 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8514 (mm-30) REVERT: N 418 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7771 (mm-30) REVERT: P 418 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7530 (mt-10) REVERT: Q 393 TYR cc_start: 0.7680 (OUTLIER) cc_final: 0.5406 (m-80) REVERT: R 280 GLU cc_start: 0.8124 (tt0) cc_final: 0.7722 (tt0) REVERT: S 428 ASP cc_start: 0.8316 (t0) cc_final: 0.8098 (t70) REVERT: T 393 TYR cc_start: 0.8201 (OUTLIER) cc_final: 0.6944 (m-80) REVERT: T 409 MET cc_start: 0.7582 (tmm) cc_final: 0.7226 (tmm) REVERT: V 299 ASN cc_start: 0.7738 (OUTLIER) cc_final: 0.7131 (m-40) REVERT: V 393 TYR cc_start: 0.7768 (OUTLIER) cc_final: 0.6481 (m-80) REVERT: V 418 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7660 (mm-30) REVERT: X 269 GLN cc_start: 0.8205 (mm-40) cc_final: 0.7583 (mp10) REVERT: X 409 MET cc_start: 0.6967 (tmm) cc_final: 0.6705 (tmm) REVERT: Z 409 MET cc_start: 0.7054 (tmm) cc_final: 0.6655 (tmm) REVERT: Z 410 LYS cc_start: 0.8262 (ttpt) cc_final: 0.7880 (ttpt) REVERT: a 299 ASN cc_start: 0.8131 (OUTLIER) cc_final: 0.7687 (m-40) REVERT: a 393 TYR cc_start: 0.8104 (OUTLIER) cc_final: 0.7585 (m-80) REVERT: c 269 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7880 (mp10) REVERT: b 250 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7922 (tt0) REVERT: d 409 MET cc_start: 0.6776 (tmm) cc_final: 0.6399 (tmm) REVERT: e 280 GLU cc_start: 0.7979 (tt0) cc_final: 0.7762 (tt0) REVERT: f 393 TYR cc_start: 0.7846 (OUTLIER) cc_final: 0.7451 (m-80) REVERT: g 269 GLN cc_start: 0.8284 (mm-40) cc_final: 0.7949 (mp10) REVERT: g 367 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8085 (mm-30) outliers start: 205 outliers final: 180 residues processed: 942 average time/residue: 0.5909 time to fit residues: 866.0967 Evaluate side-chains 965 residues out of total 4522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 773 time to evaluate : 4.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain C residue 232 ASP Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain D residue 232 ASP Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain E residue 232 ASP Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 411 GLN Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain E residue 429 THR Chi-restraints excluded: chain F residue 232 ASP Chi-restraints excluded: chain F residue 250 GLU Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 428 ASP Chi-restraints excluded: chain G residue 232 ASP Chi-restraints excluded: chain G residue 266 VAL Chi-restraints excluded: chain G residue 393 TYR Chi-restraints excluded: chain G residue 405 THR Chi-restraints excluded: chain G residue 424 ASP Chi-restraints excluded: chain H residue 232 ASP Chi-restraints excluded: chain H residue 266 VAL Chi-restraints excluded: chain H residue 369 ASP Chi-restraints excluded: chain H residue 405 THR Chi-restraints excluded: chain H residue 411 GLN Chi-restraints excluded: chain H residue 424 ASP Chi-restraints excluded: chain I residue 232 ASP Chi-restraints excluded: chain I residue 266 VAL Chi-restraints excluded: chain I residue 405 THR Chi-restraints excluded: chain J residue 232 ASP Chi-restraints excluded: chain J residue 266 VAL Chi-restraints excluded: chain J residue 267 THR Chi-restraints excluded: chain J residue 279 GLU Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain J residue 393 TYR Chi-restraints excluded: chain J residue 405 THR Chi-restraints excluded: chain K residue 232 ASP Chi-restraints excluded: chain K residue 252 ILE Chi-restraints excluded: chain K residue 266 VAL Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain K residue 411 GLN Chi-restraints excluded: chain L residue 232 ASP Chi-restraints excluded: chain L residue 266 VAL Chi-restraints excluded: chain L residue 267 THR Chi-restraints excluded: chain L residue 369 ASP Chi-restraints excluded: chain L residue 405 THR Chi-restraints excluded: chain M residue 232 ASP Chi-restraints excluded: chain M residue 253 LEU Chi-restraints excluded: chain M residue 405 THR Chi-restraints excluded: chain M residue 424 ASP Chi-restraints excluded: chain N residue 232 ASP Chi-restraints excluded: chain N residue 266 VAL Chi-restraints excluded: chain N residue 299 ASN Chi-restraints excluded: chain N residue 411 GLN Chi-restraints excluded: chain N residue 424 ASP Chi-restraints excluded: chain O residue 232 ASP Chi-restraints excluded: chain O residue 266 VAL Chi-restraints excluded: chain O residue 267 THR Chi-restraints excluded: chain O residue 369 ASP Chi-restraints excluded: chain O residue 405 THR Chi-restraints excluded: chain O residue 415 LEU Chi-restraints excluded: chain O residue 424 ASP Chi-restraints excluded: chain P residue 232 ASP Chi-restraints excluded: chain P residue 250 GLU Chi-restraints excluded: chain P residue 266 VAL Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain P residue 424 ASP Chi-restraints excluded: chain Q residue 232 ASP Chi-restraints excluded: chain Q residue 252 ILE Chi-restraints excluded: chain Q residue 266 VAL Chi-restraints excluded: chain Q residue 369 ASP Chi-restraints excluded: chain Q residue 393 TYR Chi-restraints excluded: chain R residue 232 ASP Chi-restraints excluded: chain R residue 266 VAL Chi-restraints excluded: chain R residue 405 THR Chi-restraints excluded: chain R residue 430 LEU Chi-restraints excluded: chain S residue 232 ASP Chi-restraints excluded: chain S residue 266 VAL Chi-restraints excluded: chain S residue 267 THR Chi-restraints excluded: chain S residue 293 LEU Chi-restraints excluded: chain S residue 369 ASP Chi-restraints excluded: chain S residue 405 THR Chi-restraints excluded: chain S residue 424 ASP Chi-restraints excluded: chain T residue 232 ASP Chi-restraints excluded: chain T residue 266 VAL Chi-restraints excluded: chain T residue 369 ASP Chi-restraints excluded: chain T residue 393 TYR Chi-restraints excluded: chain T residue 405 THR Chi-restraints excluded: chain T residue 411 GLN Chi-restraints excluded: chain T residue 430 LEU Chi-restraints excluded: chain U residue 232 ASP Chi-restraints excluded: chain U residue 266 VAL Chi-restraints excluded: chain U residue 369 ASP Chi-restraints excluded: chain U residue 390 VAL Chi-restraints excluded: chain U residue 405 THR Chi-restraints excluded: chain V residue 232 ASP Chi-restraints excluded: chain V residue 246 GLN Chi-restraints excluded: chain V residue 267 THR Chi-restraints excluded: chain V residue 275 LYS Chi-restraints excluded: chain V residue 299 ASN Chi-restraints excluded: chain V residue 393 TYR Chi-restraints excluded: chain V residue 405 THR Chi-restraints excluded: chain W residue 232 ASP Chi-restraints excluded: chain W residue 267 THR Chi-restraints excluded: chain W residue 405 THR Chi-restraints excluded: chain W residue 424 ASP Chi-restraints excluded: chain X residue 232 ASP Chi-restraints excluded: chain X residue 266 VAL Chi-restraints excluded: chain X residue 405 THR Chi-restraints excluded: chain X residue 424 ASP Chi-restraints excluded: chain X residue 429 THR Chi-restraints excluded: chain Y residue 232 ASP Chi-restraints excluded: chain Y residue 246 GLN Chi-restraints excluded: chain Y residue 266 VAL Chi-restraints excluded: chain Y residue 405 THR Chi-restraints excluded: chain Y residue 411 GLN Chi-restraints excluded: chain Y residue 424 ASP Chi-restraints excluded: chain Z residue 232 ASP Chi-restraints excluded: chain Z residue 266 VAL Chi-restraints excluded: chain Z residue 369 ASP Chi-restraints excluded: chain Z residue 405 THR Chi-restraints excluded: chain Z residue 424 ASP Chi-restraints excluded: chain Z residue 428 ASP Chi-restraints excluded: chain a residue 232 ASP Chi-restraints excluded: chain a residue 266 VAL Chi-restraints excluded: chain a residue 299 ASN Chi-restraints excluded: chain a residue 393 TYR Chi-restraints excluded: chain a residue 405 THR Chi-restraints excluded: chain a residue 411 GLN Chi-restraints excluded: chain a residue 424 ASP Chi-restraints excluded: chain a residue 429 THR Chi-restraints excluded: chain c residue 232 ASP Chi-restraints excluded: chain c residue 269 GLN Chi-restraints excluded: chain c residue 279 GLU Chi-restraints excluded: chain c residue 369 ASP Chi-restraints excluded: chain c residue 405 THR Chi-restraints excluded: chain c residue 411 GLN Chi-restraints excluded: chain b residue 232 ASP Chi-restraints excluded: chain b residue 250 GLU Chi-restraints excluded: chain b residue 266 VAL Chi-restraints excluded: chain b residue 369 ASP Chi-restraints excluded: chain b residue 405 THR Chi-restraints excluded: chain b residue 411 GLN Chi-restraints excluded: chain b residue 424 ASP Chi-restraints excluded: chain d residue 232 ASP Chi-restraints excluded: chain d residue 299 ASN Chi-restraints excluded: chain d residue 405 THR Chi-restraints excluded: chain d residue 410 LYS Chi-restraints excluded: chain e residue 232 ASP Chi-restraints excluded: chain e residue 266 VAL Chi-restraints excluded: chain e residue 358 THR Chi-restraints excluded: chain e residue 405 THR Chi-restraints excluded: chain e residue 411 GLN Chi-restraints excluded: chain e residue 424 ASP Chi-restraints excluded: chain e residue 429 THR Chi-restraints excluded: chain f residue 232 ASP Chi-restraints excluded: chain f residue 266 VAL Chi-restraints excluded: chain f residue 369 ASP Chi-restraints excluded: chain f residue 393 TYR Chi-restraints excluded: chain f residue 424 ASP Chi-restraints excluded: chain g residue 232 ASP Chi-restraints excluded: chain g residue 405 THR Chi-restraints excluded: chain g residue 424 ASP Chi-restraints excluded: chain h residue 232 ASP Chi-restraints excluded: chain h residue 266 VAL Chi-restraints excluded: chain h residue 279 GLU Chi-restraints excluded: chain h residue 293 LEU Chi-restraints excluded: chain h residue 299 ASN Chi-restraints excluded: chain h residue 369 ASP Chi-restraints excluded: chain h residue 411 GLN Chi-restraints excluded: chain h residue 429 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 300 optimal weight: 0.7980 chunk 484 optimal weight: 0.9990 chunk 295 optimal weight: 0.9980 chunk 229 optimal weight: 1.9990 chunk 336 optimal weight: 1.9990 chunk 508 optimal weight: 0.8980 chunk 467 optimal weight: 0.5980 chunk 404 optimal weight: 0.0170 chunk 42 optimal weight: 2.9990 chunk 312 optimal weight: 0.0060 chunk 248 optimal weight: 0.9990 overall best weight: 0.4634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 265 GLN H 361 ASN ** X 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 378 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 40698 Z= 0.179 Angle : 0.530 9.642 54842 Z= 0.266 Chirality : 0.039 0.120 6290 Planarity : 0.002 0.058 7344 Dihedral : 3.926 15.086 5508 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 4.18 % Allowed : 21.32 % Favored : 74.50 % 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: 0.35 (0.13), residues: 4896 helix: 3.98 (0.13), residues: 1326 sheet: -0.99 (0.11), residues: 2414 loop : -1.32 (0.16), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS c 374 PHE 0.028 0.001 PHE L 422 TYR 0.010 0.001 TYR D 393 ARG 0.014 0.000 ARG C 417 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9792 Ramachandran restraints generated. 4896 Oldfield, 0 Emsley, 4896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 985 residues out of total 4522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 796 time to evaluate : 5.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 409 MET cc_start: 0.6925 (tmm) cc_final: 0.6672 (tmm) REVERT: F 269 GLN cc_start: 0.8484 (mp10) cc_final: 0.7882 (mp10) REVERT: F 383 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8220 (mm-30) REVERT: G 283 SER cc_start: 0.9358 (m) cc_final: 0.8888 (p) REVERT: I 424 ASP cc_start: 0.7956 (m-30) cc_final: 0.7678 (m-30) REVERT: J 267 THR cc_start: 0.8638 (OUTLIER) cc_final: 0.8368 (p) REVERT: J 383 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8336 (mm-30) REVERT: J 393 TYR cc_start: 0.8231 (OUTLIER) cc_final: 0.7550 (m-80) REVERT: N 383 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8538 (mm-30) REVERT: N 418 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7801 (mm-30) REVERT: P 418 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7509 (mt-10) REVERT: Q 393 TYR cc_start: 0.7669 (OUTLIER) cc_final: 0.5356 (m-80) REVERT: R 280 GLU cc_start: 0.7975 (tt0) cc_final: 0.7542 (tt0) REVERT: T 393 TYR cc_start: 0.8150 (OUTLIER) cc_final: 0.6841 (m-80) REVERT: U 269 GLN cc_start: 0.8211 (mp10) cc_final: 0.7944 (mp10) REVERT: U 290 LYS cc_start: 0.7754 (mtmm) cc_final: 0.7350 (mppt) REVERT: U 356 ARG cc_start: 0.7132 (ptp-170) cc_final: 0.6883 (ptp-170) REVERT: V 299 ASN cc_start: 0.7716 (OUTLIER) cc_final: 0.7109 (m-40) REVERT: V 393 TYR cc_start: 0.7683 (OUTLIER) cc_final: 0.6363 (m-80) REVERT: V 418 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7624 (mm-30) REVERT: W 282 TYR cc_start: 0.8896 (m-80) cc_final: 0.8561 (m-10) REVERT: X 269 GLN cc_start: 0.8177 (mm-40) cc_final: 0.7606 (mp10) REVERT: X 409 MET cc_start: 0.6929 (tmm) cc_final: 0.6687 (tmm) REVERT: Z 409 MET cc_start: 0.7000 (tmm) cc_final: 0.6636 (tmm) REVERT: Z 410 LYS cc_start: 0.8231 (ttpt) cc_final: 0.7871 (ttpt) REVERT: a 299 ASN cc_start: 0.8112 (OUTLIER) cc_final: 0.7661 (m-40) REVERT: a 393 TYR cc_start: 0.7974 (OUTLIER) cc_final: 0.7423 (m-80) REVERT: c 236 LYS cc_start: 0.7875 (mptt) cc_final: 0.7661 (mptt) REVERT: c 269 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.7851 (mp10) REVERT: b 250 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7862 (tt0) REVERT: b 269 GLN cc_start: 0.8161 (mp10) cc_final: 0.7866 (mp10) REVERT: d 409 MET cc_start: 0.6718 (tmm) cc_final: 0.6354 (tmm) REVERT: e 280 GLU cc_start: 0.7869 (tt0) cc_final: 0.7416 (tt0) REVERT: e 282 TYR cc_start: 0.8523 (m-10) cc_final: 0.8069 (m-10) REVERT: e 360 ARG cc_start: 0.7419 (ttt-90) cc_final: 0.7193 (ttm-80) REVERT: f 393 TYR cc_start: 0.7852 (OUTLIER) cc_final: 0.7471 (m-80) REVERT: g 269 GLN cc_start: 0.8256 (mm-40) cc_final: 0.7969 (mp10) REVERT: g 367 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8103 (mm-30) REVERT: g 377 MET cc_start: 0.8287 (mmm) cc_final: 0.7817 (mmm) outliers start: 189 outliers final: 172 residues processed: 943 average time/residue: 0.5947 time to fit residues: 872.8260 Evaluate side-chains 965 residues out of total 4522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 782 time to evaluate : 5.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 ASP Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 369 ASP Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 424 ASP Chi-restraints excluded: chain C residue 232 ASP Chi-restraints excluded: chain C residue 369 ASP Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain D residue 232 ASP Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 424 ASP Chi-restraints excluded: chain E residue 232 ASP Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 411 GLN Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain F residue 232 ASP Chi-restraints excluded: chain F residue 250 GLU Chi-restraints excluded: chain F residue 252 ILE Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain F residue 428 ASP Chi-restraints excluded: chain G residue 232 ASP Chi-restraints excluded: chain G residue 266 VAL Chi-restraints excluded: chain G residue 405 THR Chi-restraints excluded: chain G residue 424 ASP Chi-restraints excluded: chain H residue 232 ASP Chi-restraints excluded: chain H residue 266 VAL Chi-restraints excluded: chain H residue 369 ASP Chi-restraints excluded: chain H residue 405 THR Chi-restraints excluded: chain H residue 411 GLN Chi-restraints excluded: chain H residue 424 ASP Chi-restraints excluded: chain I residue 232 ASP Chi-restraints excluded: chain I residue 266 VAL Chi-restraints excluded: chain I residue 405 THR Chi-restraints excluded: chain J residue 232 ASP Chi-restraints excluded: chain J residue 266 VAL Chi-restraints excluded: chain J residue 267 THR Chi-restraints excluded: chain J residue 279 GLU Chi-restraints excluded: chain J residue 369 ASP Chi-restraints excluded: chain J residue 393 TYR Chi-restraints excluded: chain J residue 405 THR Chi-restraints excluded: chain K residue 232 ASP Chi-restraints excluded: chain K residue 252 ILE Chi-restraints excluded: chain K residue 266 VAL Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain K residue 411 GLN Chi-restraints excluded: chain K residue 415 LEU Chi-restraints excluded: chain L residue 232 ASP Chi-restraints excluded: chain L residue 266 VAL Chi-restraints excluded: chain L residue 405 THR Chi-restraints excluded: chain M residue 232 ASP Chi-restraints excluded: chain M residue 253 LEU Chi-restraints excluded: chain M residue 405 THR Chi-restraints excluded: chain M residue 424 ASP Chi-restraints excluded: chain N residue 232 ASP Chi-restraints excluded: chain N residue 266 VAL Chi-restraints excluded: chain N residue 299 ASN Chi-restraints excluded: chain N residue 369 ASP Chi-restraints excluded: chain N residue 411 GLN Chi-restraints excluded: chain N residue 424 ASP Chi-restraints excluded: chain O residue 232 ASP Chi-restraints excluded: chain O residue 266 VAL Chi-restraints excluded: chain O residue 267 THR Chi-restraints excluded: chain O residue 369 ASP Chi-restraints excluded: chain O residue 405 THR Chi-restraints excluded: chain O residue 415 LEU Chi-restraints excluded: chain O residue 424 ASP Chi-restraints excluded: chain P residue 232 ASP Chi-restraints excluded: chain P residue 250 GLU Chi-restraints excluded: chain P residue 266 VAL Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain P residue 424 ASP Chi-restraints excluded: chain Q residue 232 ASP Chi-restraints excluded: chain Q residue 266 VAL Chi-restraints excluded: chain Q residue 369 ASP Chi-restraints excluded: chain Q residue 393 TYR Chi-restraints excluded: chain R residue 232 ASP Chi-restraints excluded: chain R residue 266 VAL Chi-restraints excluded: chain R residue 405 THR Chi-restraints excluded: chain R residue 430 LEU Chi-restraints excluded: chain S residue 232 ASP Chi-restraints excluded: chain S residue 266 VAL Chi-restraints excluded: chain S residue 267 THR Chi-restraints excluded: chain S residue 293 LEU Chi-restraints excluded: chain S residue 369 ASP Chi-restraints excluded: chain S residue 405 THR Chi-restraints excluded: chain S residue 424 ASP Chi-restraints excluded: chain T residue 232 ASP Chi-restraints excluded: chain T residue 266 VAL Chi-restraints excluded: chain T residue 369 ASP Chi-restraints excluded: chain T residue 393 TYR Chi-restraints excluded: chain T residue 405 THR Chi-restraints excluded: chain T residue 411 GLN Chi-restraints excluded: chain T residue 430 LEU Chi-restraints excluded: chain U residue 232 ASP Chi-restraints excluded: chain U residue 266 VAL Chi-restraints excluded: chain U residue 369 ASP Chi-restraints excluded: chain U residue 390 VAL Chi-restraints excluded: chain U residue 405 THR Chi-restraints excluded: chain V residue 232 ASP Chi-restraints excluded: chain V residue 246 GLN Chi-restraints excluded: chain V residue 267 THR Chi-restraints excluded: chain V residue 275 LYS Chi-restraints excluded: chain V residue 299 ASN Chi-restraints excluded: chain V residue 393 TYR Chi-restraints excluded: chain V residue 405 THR Chi-restraints excluded: chain W residue 232 ASP Chi-restraints excluded: chain W residue 405 THR Chi-restraints excluded: chain W residue 424 ASP Chi-restraints excluded: chain X residue 232 ASP Chi-restraints excluded: chain X residue 266 VAL Chi-restraints excluded: chain X residue 405 THR Chi-restraints excluded: chain X residue 424 ASP Chi-restraints excluded: chain Y residue 232 ASP Chi-restraints excluded: chain Y residue 246 GLN Chi-restraints excluded: chain Y residue 266 VAL Chi-restraints excluded: chain Y residue 405 THR Chi-restraints excluded: chain Y residue 411 GLN Chi-restraints excluded: chain Z residue 232 ASP Chi-restraints excluded: chain Z residue 266 VAL Chi-restraints excluded: chain Z residue 369 ASP Chi-restraints excluded: chain Z residue 405 THR Chi-restraints excluded: chain Z residue 424 ASP Chi-restraints excluded: chain Z residue 428 ASP Chi-restraints excluded: chain a residue 232 ASP Chi-restraints excluded: chain a residue 266 VAL Chi-restraints excluded: chain a residue 299 ASN Chi-restraints excluded: chain a residue 393 TYR Chi-restraints excluded: chain a residue 405 THR Chi-restraints excluded: chain a residue 411 GLN Chi-restraints excluded: chain a residue 424 ASP Chi-restraints excluded: chain a residue 429 THR Chi-restraints excluded: chain c residue 232 ASP Chi-restraints excluded: chain c residue 269 GLN Chi-restraints excluded: chain c residue 279 GLU Chi-restraints excluded: chain c residue 369 ASP Chi-restraints excluded: chain c residue 405 THR Chi-restraints excluded: chain c residue 411 GLN Chi-restraints excluded: chain b residue 232 ASP Chi-restraints excluded: chain b residue 250 GLU Chi-restraints excluded: chain b residue 266 VAL Chi-restraints excluded: chain b residue 369 ASP Chi-restraints excluded: chain b residue 405 THR Chi-restraints excluded: chain b residue 411 GLN Chi-restraints excluded: chain b residue 424 ASP Chi-restraints excluded: chain d residue 232 ASP Chi-restraints excluded: chain d residue 369 ASP Chi-restraints excluded: chain d residue 405 THR Chi-restraints excluded: chain e residue 232 ASP Chi-restraints excluded: chain e residue 266 VAL Chi-restraints excluded: chain e residue 358 THR Chi-restraints excluded: chain e residue 405 THR Chi-restraints excluded: chain e residue 411 GLN Chi-restraints excluded: chain e residue 424 ASP Chi-restraints excluded: chain e residue 429 THR Chi-restraints excluded: chain f residue 232 ASP Chi-restraints excluded: chain f residue 266 VAL Chi-restraints excluded: chain f residue 369 ASP Chi-restraints excluded: chain f residue 393 TYR Chi-restraints excluded: chain f residue 424 ASP Chi-restraints excluded: chain g residue 232 ASP Chi-restraints excluded: chain g residue 405 THR Chi-restraints excluded: chain g residue 424 ASP Chi-restraints excluded: chain h residue 232 ASP Chi-restraints excluded: chain h residue 266 VAL Chi-restraints excluded: chain h residue 279 GLU Chi-restraints excluded: chain h residue 293 LEU Chi-restraints excluded: chain h residue 299 ASN Chi-restraints excluded: chain h residue 369 ASP Chi-restraints excluded: chain h residue 411 GLN Chi-restraints excluded: chain h residue 429 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 321 optimal weight: 0.5980 chunk 430 optimal weight: 0.9980 chunk 123 optimal weight: 0.9980 chunk 373 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 112 optimal weight: 3.9990 chunk 405 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 416 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 265 GLN ** X 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.132812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.117669 restraints weight = 67573.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.120877 restraints weight = 33850.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.123156 restraints weight = 20510.361| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 40698 Z= 0.241 Angle : 0.563 9.844 54842 Z= 0.283 Chirality : 0.039 0.125 6290 Planarity : 0.003 0.067 7344 Dihedral : 4.079 15.822 5508 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 4.51 % Allowed : 21.45 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.13), residues: 4896 helix: 3.75 (0.13), residues: 1326 sheet: -1.08 (0.11), residues: 2414 loop : -1.35 (0.16), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS h 374 PHE 0.027 0.001 PHE L 422 TYR 0.014 0.002 TYR R 393 ARG 0.018 0.000 ARG b 417 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13009.04 seconds wall clock time: 233 minutes 21.70 seconds (14001.70 seconds total)