Starting phenix.real_space_refine on Sun Mar 24 00:53:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sd1_10145/03_2024/6sd1_10145.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sd1_10145/03_2024/6sd1_10145.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sd1_10145/03_2024/6sd1_10145.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sd1_10145/03_2024/6sd1_10145.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sd1_10145/03_2024/6sd1_10145.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sd1_10145/03_2024/6sd1_10145.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 99 5.16 5 C 23958 2.51 5 N 7359 2.21 5 O 7953 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 244": "NH1" <-> "NH2" Residue "A TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 383": "OE1" <-> "OE2" Residue "A ARG 384": "NH1" <-> "NH2" Residue "A ASP 414": "OD1" <-> "OD2" Residue "A PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 232": "OD1" <-> "OD2" Residue "B ARG 244": "NH1" <-> "NH2" Residue "B TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 384": "NH1" <-> "NH2" Residue "B PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 244": "NH1" <-> "NH2" Residue "C TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 384": "NH1" <-> "NH2" Residue "C ASP 407": "OD1" <-> "OD2" Residue "C GLU 413": "OE1" <-> "OE2" Residue "C ASP 414": "OD1" <-> "OD2" Residue "C PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 244": "NH1" <-> "NH2" Residue "D TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 384": "NH1" <-> "NH2" Residue "D ASP 407": "OD1" <-> "OD2" Residue "D PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 232": "OD1" <-> "OD2" Residue "E ASP 240": "OD1" <-> "OD2" Residue "E ARG 244": "NH1" <-> "NH2" Residue "E TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 384": "NH1" <-> "NH2" Residue "E PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 232": "OD1" <-> "OD2" Residue "F ARG 244": "NH1" <-> "NH2" Residue "F TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 383": "OE1" <-> "OE2" Residue "F ARG 384": "NH1" <-> "NH2" Residue "F PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 244": "NH1" <-> "NH2" Residue "G TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 384": "NH1" <-> "NH2" Residue "G ASP 407": "OD1" <-> "OD2" Residue "G GLU 413": "OE1" <-> "OE2" Residue "G PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 244": "NH1" <-> "NH2" Residue "H ASP 271": "OD1" <-> "OD2" Residue "H TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 383": "OE1" <-> "OE2" Residue "H ARG 384": "NH1" <-> "NH2" Residue "H PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 232": "OD1" <-> "OD2" Residue "I ARG 244": "NH1" <-> "NH2" Residue "I TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 384": "NH1" <-> "NH2" Residue "I ASP 407": "OD1" <-> "OD2" Residue "I ASP 414": "OD1" <-> "OD2" Residue "I PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 424": "OD1" <-> "OD2" Residue "J ARG 244": "NH1" <-> "NH2" Residue "J ASP 271": "OD1" <-> "OD2" Residue "J TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 384": "NH1" <-> "NH2" Residue "J ASP 407": "OD1" <-> "OD2" Residue "J ASP 414": "OD1" <-> "OD2" Residue "J PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 424": "OD1" <-> "OD2" Residue "K ASP 232": "OD1" <-> "OD2" Residue "K ARG 244": "NH1" <-> "NH2" Residue "K TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 384": "NH1" <-> "NH2" Residue "K ASP 407": "OD1" <-> "OD2" Residue "K PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 232": "OD1" <-> "OD2" Residue "L ARG 244": "NH1" <-> "NH2" Residue "L TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 287": "OD1" <-> "OD2" Residue "L GLU 383": "OE1" <-> "OE2" Residue "L ARG 384": "NH1" <-> "NH2" Residue "L ASP 407": "OD1" <-> "OD2" Residue "L PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 244": "NH1" <-> "NH2" Residue "M TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 287": "OD1" <-> "OD2" Residue "M GLU 383": "OE1" <-> "OE2" Residue "M ARG 384": "NH1" <-> "NH2" Residue "M PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 424": "OD1" <-> "OD2" Residue "N ASP 232": "OD1" <-> "OD2" Residue "N ARG 244": "NH1" <-> "NH2" Residue "N TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 383": "OE1" <-> "OE2" Residue "N ARG 384": "NH1" <-> "NH2" Residue "N ASP 407": "OD1" <-> "OD2" Residue "N PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 424": "OD1" <-> "OD2" Residue "O ASP 232": "OD1" <-> "OD2" Residue "O ARG 244": "NH1" <-> "NH2" Residue "O TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 384": "NH1" <-> "NH2" Residue "O PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 232": "OD1" <-> "OD2" Residue "P ARG 244": "NH1" <-> "NH2" Residue "P TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 384": "NH1" <-> "NH2" Residue "P ASP 407": "OD1" <-> "OD2" Residue "P GLU 413": "OE1" <-> "OE2" Residue "P ASP 414": "OD1" <-> "OD2" Residue "P PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 232": "OD1" <-> "OD2" Residue "Q ARG 244": "NH1" <-> "NH2" Residue "Q TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 383": "OE1" <-> "OE2" Residue "Q ARG 384": "NH1" <-> "NH2" Residue "Q PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 244": "NH1" <-> "NH2" Residue "R ASP 271": "OD1" <-> "OD2" Residue "R TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 383": "OE1" <-> "OE2" Residue "R ARG 384": "NH1" <-> "NH2" Residue "R ASP 407": "OD1" <-> "OD2" Residue "R ASP 414": "OD1" <-> "OD2" Residue "R PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 244": "NH1" <-> "NH2" Residue "S TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 383": "OE1" <-> "OE2" Residue "S ARG 384": "NH1" <-> "NH2" Residue "S PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 424": "OD1" <-> "OD2" Residue "T ARG 244": "NH1" <-> "NH2" Residue "T TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 384": "NH1" <-> "NH2" Residue "T GLU 413": "OE1" <-> "OE2" Residue "T ASP 414": "OD1" <-> "OD2" Residue "T PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 244": "NH1" <-> "NH2" Residue "U TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 383": "OE1" <-> "OE2" Residue "U ARG 384": "NH1" <-> "NH2" Residue "U ASP 407": "OD1" <-> "OD2" Residue "U PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 232": "OD1" <-> "OD2" Residue "V ARG 244": "NH1" <-> "NH2" Residue "V TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 383": "OE1" <-> "OE2" Residue "V ARG 384": "NH1" <-> "NH2" Residue "V ASP 407": "OD1" <-> "OD2" Residue "V GLU 413": "OE1" <-> "OE2" Residue "V PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 232": "OD1" <-> "OD2" Residue "W ARG 244": "NH1" <-> "NH2" Residue "W TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 383": "OE1" <-> "OE2" Residue "W ARG 384": "NH1" <-> "NH2" Residue "W ASP 407": "OD1" <-> "OD2" Residue "W GLU 413": "OE1" <-> "OE2" Residue "W PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 232": "OD1" <-> "OD2" Residue "X ARG 244": "NH1" <-> "NH2" Residue "X TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 302": "OE1" <-> "OE2" Residue "X ARG 384": "NH1" <-> "NH2" Residue "X GLU 413": "OE1" <-> "OE2" Residue "X PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 244": "NH1" <-> "NH2" Residue "Y TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 384": "NH1" <-> "NH2" Residue "Y ASP 407": "OD1" <-> "OD2" Residue "Y ASP 414": "OD1" <-> "OD2" Residue "Y PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 424": "OD1" <-> "OD2" Residue "Z ARG 244": "NH1" <-> "NH2" Residue "Z ASP 271": "OD1" <-> "OD2" Residue "Z TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 383": "OE1" <-> "OE2" Residue "Z ARG 384": "NH1" <-> "NH2" Residue "Z ASP 407": "OD1" <-> "OD2" Residue "Z ASP 414": "OD1" <-> "OD2" Residue "Z PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 244": "NH1" <-> "NH2" Residue "a TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 384": "NH1" <-> "NH2" Residue "a ASP 407": "OD1" <-> "OD2" Residue "a ASP 414": "OD1" <-> "OD2" Residue "a PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 424": "OD1" <-> "OD2" Residue "b ARG 244": "NH1" <-> "NH2" Residue "b ASP 271": "OD1" <-> "OD2" Residue "b TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 384": "NH1" <-> "NH2" Residue "b ASP 414": "OD1" <-> "OD2" Residue "b PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 244": "NH1" <-> "NH2" Residue "c TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 384": "NH1" <-> "NH2" Residue "c GLU 413": "OE1" <-> "OE2" Residue "c ASP 414": "OD1" <-> "OD2" Residue "c PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 244": "NH1" <-> "NH2" Residue "d ASP 271": "OD1" <-> "OD2" Residue "d TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 384": "NH1" <-> "NH2" Residue "d ASP 414": "OD1" <-> "OD2" Residue "d PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 244": "NH1" <-> "NH2" Residue "e ASP 271": "OD1" <-> "OD2" Residue "e GLU 276": "OE1" <-> "OE2" Residue "e TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 383": "OE1" <-> "OE2" Residue "e ARG 384": "NH1" <-> "NH2" Residue "e GLU 413": "OE1" <-> "OE2" Residue "e PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 244": "NH1" <-> "NH2" Residue "f TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 384": "NH1" <-> "NH2" Residue "f ASP 407": "OD1" <-> "OD2" Residue "f ASP 414": "OD1" <-> "OD2" Residue "f PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 232": "OD1" <-> "OD2" Residue "g ARG 244": "NH1" <-> "NH2" Residue "g ASP 271": "OD1" <-> "OD2" Residue "g TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 384": "NH1" <-> "NH2" Residue "g ASP 407": "OD1" <-> "OD2" Residue "g PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 424": "OD1" <-> "OD2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 39369 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "B" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "C" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "D" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "E" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "F" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "G" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "H" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "I" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "J" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "K" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "L" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "M" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "N" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "O" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "P" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "Q" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "R" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "S" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "T" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "U" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "V" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "W" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "X" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "Y" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "Z" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "a" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "b" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "c" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "d" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "e" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "f" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Chain: "g" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1193 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain breaks: 2 Time building chain proxies: 19.12, per 1000 atoms: 0.49 Number of scatterers: 39369 At special positions: 0 Unit cell: (244.134, 244.134, 97.818, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 99 16.00 O 7953 8.00 N 7359 7.00 C 23958 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.49 Conformation dependent library (CDL) restraints added in 6.8 seconds 9570 Ramachandran restraints generated. 4785 Oldfield, 0 Emsley, 4785 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9570 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 99 sheets defined 29.4% alpha, 32.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.43 Creating SS restraints... Processing helix chain 'A' and resid 231 through 253 removed outlier: 3.824A pdb=" N LEU A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 258 Processing helix chain 'A' and resid 405 through 421 removed outlier: 3.699A pdb=" N GLY A 421 " --> pdb=" O ARG A 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 258 removed outlier: 3.540A pdb=" N SER B 254 " --> pdb=" O GLU B 250 " (cutoff:3.500A) Proline residue: B 255 - end of helix Processing helix chain 'B' and resid 405 through 421 removed outlier: 3.670A pdb=" N GLY B 421 " --> pdb=" O ARG B 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 258 removed outlier: 3.502A pdb=" N SER C 254 " --> pdb=" O GLU C 250 " (cutoff:3.500A) Proline residue: C 255 - end of helix Processing helix chain 'C' and resid 405 through 421 removed outlier: 3.667A pdb=" N GLY C 421 " --> pdb=" O ARG C 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 258 removed outlier: 3.538A pdb=" N SER D 254 " --> pdb=" O GLU D 250 " (cutoff:3.500A) Proline residue: D 255 - end of helix Processing helix chain 'D' and resid 405 through 421 removed outlier: 3.627A pdb=" N GLY D 421 " --> pdb=" O ARG D 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 253 Processing helix chain 'E' and resid 253 through 258 Processing helix chain 'E' and resid 405 through 421 removed outlier: 3.630A pdb=" N GLY E 421 " --> pdb=" O ARG E 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 232 through 258 Proline residue: F 255 - end of helix Processing helix chain 'F' and resid 405 through 421 removed outlier: 3.646A pdb=" N GLY F 421 " --> pdb=" O ARG F 417 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 253 Processing helix chain 'G' and resid 253 through 258 Processing helix chain 'G' and resid 405 through 421 removed outlier: 3.633A pdb=" N GLY G 421 " --> pdb=" O ARG G 417 " (cutoff:3.500A) Processing helix chain 'H' and resid 232 through 253 Processing helix chain 'H' and resid 253 through 258 Processing helix chain 'H' and resid 405 through 421 removed outlier: 3.640A pdb=" N GLY H 421 " --> pdb=" O ARG H 417 " (cutoff:3.500A) Processing helix chain 'I' and resid 232 through 258 Proline residue: I 255 - end of helix Processing helix chain 'I' and resid 405 through 421 removed outlier: 3.669A pdb=" N GLY I 421 " --> pdb=" O ARG I 417 " (cutoff:3.500A) Processing helix chain 'J' and resid 232 through 253 Processing helix chain 'J' and resid 253 through 258 Processing helix chain 'J' and resid 405 through 421 removed outlier: 3.698A pdb=" N GLY J 421 " --> pdb=" O ARG J 417 " (cutoff:3.500A) Processing helix chain 'K' and resid 232 through 258 removed outlier: 3.515A pdb=" N SER K 254 " --> pdb=" O GLU K 250 " (cutoff:3.500A) Proline residue: K 255 - end of helix Processing helix chain 'K' and resid 405 through 421 removed outlier: 3.569A pdb=" N GLY K 421 " --> pdb=" O ARG K 417 " (cutoff:3.500A) Processing helix chain 'L' and resid 232 through 258 removed outlier: 3.562A pdb=" N SER L 254 " --> pdb=" O GLU L 250 " (cutoff:3.500A) Proline residue: L 255 - end of helix Processing helix chain 'L' and resid 405 through 421 removed outlier: 3.637A pdb=" N GLY L 421 " --> pdb=" O ARG L 417 " (cutoff:3.500A) Processing helix chain 'M' and resid 232 through 258 Proline residue: M 255 - end of helix Processing helix chain 'M' and resid 405 through 421 removed outlier: 3.605A pdb=" N GLY M 421 " --> pdb=" O ARG M 417 " (cutoff:3.500A) Processing helix chain 'N' and resid 232 through 258 Proline residue: N 255 - end of helix Processing helix chain 'N' and resid 405 through 421 removed outlier: 3.623A pdb=" N GLY N 421 " --> pdb=" O ARG N 417 " (cutoff:3.500A) Processing helix chain 'O' and resid 232 through 253 Processing helix chain 'O' and resid 253 through 258 Processing helix chain 'O' and resid 405 through 421 removed outlier: 3.615A pdb=" N GLY O 421 " --> pdb=" O ARG O 417 " (cutoff:3.500A) Processing helix chain 'P' and resid 232 through 253 Processing helix chain 'P' and resid 253 through 258 Processing helix chain 'P' and resid 405 through 421 removed outlier: 3.695A pdb=" N GLY P 421 " --> pdb=" O ARG P 417 " (cutoff:3.500A) Processing helix chain 'Q' and resid 232 through 253 Processing helix chain 'Q' and resid 253 through 258 Processing helix chain 'Q' and resid 405 through 421 removed outlier: 3.628A pdb=" N LEU Q 415 " --> pdb=" O GLN Q 411 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY Q 421 " --> pdb=" O ARG Q 417 " (cutoff:3.500A) Processing helix chain 'R' and resid 232 through 258 removed outlier: 3.531A pdb=" N SER R 254 " --> pdb=" O GLU R 250 " (cutoff:3.500A) Proline residue: R 255 - end of helix Processing helix chain 'R' and resid 405 through 421 removed outlier: 3.641A pdb=" N GLY R 421 " --> pdb=" O ARG R 417 " (cutoff:3.500A) Processing helix chain 'S' and resid 232 through 253 Processing helix chain 'S' and resid 253 through 258 Processing helix chain 'S' and resid 405 through 421 removed outlier: 3.692A pdb=" N GLY S 421 " --> pdb=" O ARG S 417 " (cutoff:3.500A) Processing helix chain 'T' and resid 232 through 258 Proline residue: T 255 - end of helix Processing helix chain 'T' and resid 405 through 421 removed outlier: 3.647A pdb=" N GLY T 421 " --> pdb=" O ARG T 417 " (cutoff:3.500A) Processing helix chain 'U' and resid 232 through 258 Proline residue: U 255 - end of helix Processing helix chain 'U' and resid 405 through 421 removed outlier: 3.590A pdb=" N GLY U 421 " --> pdb=" O ARG U 417 " (cutoff:3.500A) Processing helix chain 'V' and resid 232 through 258 removed outlier: 3.504A pdb=" N SER V 254 " --> pdb=" O GLU V 250 " (cutoff:3.500A) Proline residue: V 255 - end of helix Processing helix chain 'V' and resid 405 through 421 removed outlier: 3.664A pdb=" N GLY V 421 " --> pdb=" O ARG V 417 " (cutoff:3.500A) Processing helix chain 'W' and resid 232 through 253 Processing helix chain 'W' and resid 253 through 258 Processing helix chain 'W' and resid 405 through 421 removed outlier: 3.613A pdb=" N GLY W 421 " --> pdb=" O ARG W 417 " (cutoff:3.500A) Processing helix chain 'X' and resid 232 through 253 Processing helix chain 'X' and resid 253 through 258 Processing helix chain 'X' and resid 405 through 421 removed outlier: 3.724A pdb=" N GLY X 421 " --> pdb=" O ARG X 417 " (cutoff:3.500A) Processing helix chain 'Y' and resid 232 through 253 Processing helix chain 'Y' and resid 253 through 258 Processing helix chain 'Y' and resid 405 through 421 removed outlier: 3.644A pdb=" N GLY Y 421 " --> pdb=" O ARG Y 417 " (cutoff:3.500A) Processing helix chain 'Z' and resid 232 through 258 Proline residue: Z 255 - end of helix Processing helix chain 'Z' and resid 405 through 421 removed outlier: 3.682A pdb=" N GLY Z 421 " --> pdb=" O ARG Z 417 " (cutoff:3.500A) Processing helix chain 'a' and resid 232 through 258 Proline residue: a 255 - end of helix Processing helix chain 'a' and resid 405 through 421 removed outlier: 3.628A pdb=" N GLY a 421 " --> pdb=" O ARG a 417 " (cutoff:3.500A) Processing helix chain 'b' and resid 232 through 258 Proline residue: b 255 - end of helix Processing helix chain 'b' and resid 405 through 421 removed outlier: 3.510A pdb=" N GLU b 418 " --> pdb=" O ASP b 414 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY b 421 " --> pdb=" O ARG b 417 " (cutoff:3.500A) Processing helix chain 'c' and resid 232 through 258 Proline residue: c 255 - end of helix Processing helix chain 'c' and resid 405 through 421 removed outlier: 3.586A pdb=" N GLY c 421 " --> pdb=" O ARG c 417 " (cutoff:3.500A) Processing helix chain 'd' and resid 232 through 258 Proline residue: d 255 - end of helix Processing helix chain 'd' and resid 405 through 421 removed outlier: 3.638A pdb=" N GLY d 421 " --> pdb=" O ARG d 417 " (cutoff:3.500A) Processing helix chain 'e' and resid 232 through 258 Proline residue: e 255 - end of helix Processing helix chain 'e' and resid 405 through 421 removed outlier: 3.634A pdb=" N GLY e 421 " --> pdb=" O ARG e 417 " (cutoff:3.500A) Processing helix chain 'f' and resid 232 through 253 Processing helix chain 'f' and resid 253 through 258 Processing helix chain 'f' and resid 405 through 421 removed outlier: 3.592A pdb=" N GLY f 421 " --> pdb=" O ARG f 417 " (cutoff:3.500A) Processing helix chain 'g' and resid 232 through 258 Proline residue: g 255 - end of helix Processing helix chain 'g' and resid 405 through 421 removed outlier: 3.646A pdb=" N GLY g 421 " --> pdb=" O ARG g 417 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 276 through 278 Processing sheet with id= B, first strand: chain 'A' and resid 429 through 434 removed outlier: 3.544A pdb=" N ASP A 381 " --> pdb=" O ASP A 271 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLN A 269 " --> pdb=" O GLU A 383 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LEU A 385 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N THR A 267 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL A 387 " --> pdb=" O GLN A 265 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLN A 265 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL A 389 " --> pdb=" O HIS A 263 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N HIS A 263 " --> pdb=" O VAL A 389 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 292 through 302 removed outlier: 4.208A pdb=" N THR A 292 " --> pdb=" O GLU A 367 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN A 365 " --> pdb=" O ARG A 294 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARG A 296 " --> pdb=" O THR A 363 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N THR A 363 " --> pdb=" O ARG A 296 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU A 298 " --> pdb=" O ASN A 361 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ASN A 361 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ILE A 300 " --> pdb=" O GLN A 359 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLN A 359 " --> pdb=" O ILE A 300 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 276 through 278 Processing sheet with id= E, first strand: chain 'B' and resid 429 through 434 removed outlier: 3.578A pdb=" N ASP B 381 " --> pdb=" O ASP B 271 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLN B 269 " --> pdb=" O GLU B 383 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU B 385 " --> pdb=" O THR B 267 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR B 267 " --> pdb=" O LEU B 385 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL B 387 " --> pdb=" O GLN B 265 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLN B 265 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N VAL B 389 " --> pdb=" O HIS B 263 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N HIS B 263 " --> pdb=" O VAL B 389 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 292 through 303 removed outlier: 4.193A pdb=" N THR B 292 " --> pdb=" O GLU B 367 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ASN B 365 " --> pdb=" O ARG B 294 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ARG B 296 " --> pdb=" O THR B 363 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR B 363 " --> pdb=" O ARG B 296 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU B 298 " --> pdb=" O ASN B 361 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ASN B 361 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ILE B 300 " --> pdb=" O GLN B 359 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLN B 359 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU B 302 " --> pdb=" O SER B 357 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N SER B 357 " --> pdb=" O GLU B 302 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 276 through 278 Processing sheet with id= H, first strand: chain 'C' and resid 429 through 434 removed outlier: 3.594A pdb=" N ASP C 381 " --> pdb=" O ASP C 271 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLN C 269 " --> pdb=" O GLU C 383 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU C 385 " --> pdb=" O THR C 267 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR C 267 " --> pdb=" O LEU C 385 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL C 387 " --> pdb=" O GLN C 265 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N GLN C 265 " --> pdb=" O VAL C 387 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL C 389 " --> pdb=" O HIS C 263 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N HIS C 263 " --> pdb=" O VAL C 389 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 292 through 303 removed outlier: 4.211A pdb=" N THR C 292 " --> pdb=" O GLU C 367 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ASN C 365 " --> pdb=" O ARG C 294 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ARG C 296 " --> pdb=" O THR C 363 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR C 363 " --> pdb=" O ARG C 296 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU C 298 " --> pdb=" O ASN C 361 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ASN C 361 " --> pdb=" O LEU C 298 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ILE C 300 " --> pdb=" O GLN C 359 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLN C 359 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLU C 302 " --> pdb=" O SER C 357 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N SER C 357 " --> pdb=" O GLU C 302 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 276 through 278 Processing sheet with id= K, first strand: chain 'D' and resid 429 through 434 removed outlier: 3.632A pdb=" N ASP D 381 " --> pdb=" O ASP D 271 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLN D 269 " --> pdb=" O GLU D 383 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU D 385 " --> pdb=" O THR D 267 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THR D 267 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL D 387 " --> pdb=" O GLN D 265 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLN D 265 " --> pdb=" O VAL D 387 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL D 389 " --> pdb=" O HIS D 263 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N HIS D 263 " --> pdb=" O VAL D 389 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 292 through 303 removed outlier: 4.208A pdb=" N THR D 292 " --> pdb=" O GLU D 367 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ASN D 365 " --> pdb=" O ARG D 294 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ARG D 296 " --> pdb=" O THR D 363 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR D 363 " --> pdb=" O ARG D 296 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU D 298 " --> pdb=" O ASN D 361 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ASN D 361 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ILE D 300 " --> pdb=" O GLN D 359 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLN D 359 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU D 302 " --> pdb=" O SER D 357 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N SER D 357 " --> pdb=" O GLU D 302 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 276 through 278 Processing sheet with id= N, first strand: chain 'E' and resid 429 through 434 removed outlier: 3.594A pdb=" N ASP E 381 " --> pdb=" O ASP E 271 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLN E 269 " --> pdb=" O GLU E 383 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU E 385 " --> pdb=" O THR E 267 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N THR E 267 " --> pdb=" O LEU E 385 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL E 387 " --> pdb=" O GLN E 265 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLN E 265 " --> pdb=" O VAL E 387 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL E 389 " --> pdb=" O HIS E 263 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N HIS E 263 " --> pdb=" O VAL E 389 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 293 through 303 removed outlier: 6.634A pdb=" N ASN E 365 " --> pdb=" O ARG E 294 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ARG E 296 " --> pdb=" O THR E 363 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N THR E 363 " --> pdb=" O ARG E 296 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU E 298 " --> pdb=" O ASN E 361 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ASN E 361 " --> pdb=" O LEU E 298 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ILE E 300 " --> pdb=" O GLN E 359 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLN E 359 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU E 302 " --> pdb=" O SER E 357 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N SER E 357 " --> pdb=" O GLU E 302 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 276 through 278 Processing sheet with id= Q, first strand: chain 'F' and resid 429 through 434 removed outlier: 3.590A pdb=" N ASP F 381 " --> pdb=" O ASP F 271 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLN F 269 " --> pdb=" O GLU F 383 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LEU F 385 " --> pdb=" O THR F 267 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR F 267 " --> pdb=" O LEU F 385 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL F 387 " --> pdb=" O GLN F 265 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N GLN F 265 " --> pdb=" O VAL F 387 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL F 389 " --> pdb=" O HIS F 263 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N HIS F 263 " --> pdb=" O VAL F 389 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 292 through 302 removed outlier: 4.202A pdb=" N THR F 292 " --> pdb=" O GLU F 367 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ASN F 365 " --> pdb=" O ARG F 294 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ARG F 296 " --> pdb=" O THR F 363 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THR F 363 " --> pdb=" O ARG F 296 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU F 298 " --> pdb=" O ASN F 361 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASN F 361 " --> pdb=" O LEU F 298 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE F 300 " --> pdb=" O GLN F 359 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLN F 359 " --> pdb=" O ILE F 300 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'G' and resid 276 through 278 Processing sheet with id= T, first strand: chain 'G' and resid 429 through 434 removed outlier: 3.596A pdb=" N ASP G 381 " --> pdb=" O ASP G 271 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLN G 269 " --> pdb=" O GLU G 383 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU G 385 " --> pdb=" O THR G 267 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N THR G 267 " --> pdb=" O LEU G 385 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL G 387 " --> pdb=" O GLN G 265 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLN G 265 " --> pdb=" O VAL G 387 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL G 389 " --> pdb=" O HIS G 263 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N HIS G 263 " --> pdb=" O VAL G 389 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'G' and resid 292 through 302 removed outlier: 4.245A pdb=" N THR G 292 " --> pdb=" O GLU G 367 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN G 365 " --> pdb=" O ARG G 294 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG G 296 " --> pdb=" O THR G 363 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N THR G 363 " --> pdb=" O ARG G 296 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU G 298 " --> pdb=" O ASN G 361 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASN G 361 " --> pdb=" O LEU G 298 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ILE G 300 " --> pdb=" O GLN G 359 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLN G 359 " --> pdb=" O ILE G 300 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'H' and resid 276 through 278 Processing sheet with id= W, first strand: chain 'H' and resid 429 through 434 removed outlier: 3.592A pdb=" N ASP H 381 " --> pdb=" O ASP H 271 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLN H 269 " --> pdb=" O GLU H 383 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU H 385 " --> pdb=" O THR H 267 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N THR H 267 " --> pdb=" O LEU H 385 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL H 387 " --> pdb=" O GLN H 265 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLN H 265 " --> pdb=" O VAL H 387 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N VAL H 389 " --> pdb=" O HIS H 263 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N HIS H 263 " --> pdb=" O VAL H 389 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'H' and resid 292 through 303 removed outlier: 4.211A pdb=" N THR H 292 " --> pdb=" O GLU H 367 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASN H 365 " --> pdb=" O ARG H 294 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ARG H 296 " --> pdb=" O THR H 363 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N THR H 363 " --> pdb=" O ARG H 296 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU H 298 " --> pdb=" O ASN H 361 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ASN H 361 " --> pdb=" O LEU H 298 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ILE H 300 " --> pdb=" O GLN H 359 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLN H 359 " --> pdb=" O ILE H 300 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLU H 302 " --> pdb=" O SER H 357 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N SER H 357 " --> pdb=" O GLU H 302 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'I' and resid 276 through 278 Processing sheet with id= Z, first strand: chain 'I' and resid 429 through 434 removed outlier: 3.559A pdb=" N ASP I 381 " --> pdb=" O ASP I 271 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLN I 269 " --> pdb=" O GLU I 383 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LEU I 385 " --> pdb=" O THR I 267 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N THR I 267 " --> pdb=" O LEU I 385 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL I 387 " --> pdb=" O GLN I 265 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLN I 265 " --> pdb=" O VAL I 387 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL I 389 " --> pdb=" O HIS I 263 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N HIS I 263 " --> pdb=" O VAL I 389 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'I' and resid 292 through 302 removed outlier: 4.204A pdb=" N THR I 292 " --> pdb=" O GLU I 367 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ASN I 365 " --> pdb=" O ARG I 294 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ARG I 296 " --> pdb=" O THR I 363 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THR I 363 " --> pdb=" O ARG I 296 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU I 298 " --> pdb=" O ASN I 361 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ASN I 361 " --> pdb=" O LEU I 298 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ILE I 300 " --> pdb=" O GLN I 359 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLN I 359 " --> pdb=" O ILE I 300 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'J' and resid 276 through 278 Processing sheet with id= AC, first strand: chain 'J' and resid 429 through 434 removed outlier: 3.614A pdb=" N ASP J 381 " --> pdb=" O ASP J 271 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLN J 269 " --> pdb=" O GLU J 383 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU J 385 " --> pdb=" O THR J 267 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N THR J 267 " --> pdb=" O LEU J 385 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL J 387 " --> pdb=" O GLN J 265 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLN J 265 " --> pdb=" O VAL J 387 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL J 389 " --> pdb=" O HIS J 263 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N HIS J 263 " --> pdb=" O VAL J 389 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'J' and resid 293 through 303 removed outlier: 6.653A pdb=" N ASN J 365 " --> pdb=" O ARG J 294 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ARG J 296 " --> pdb=" O THR J 363 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N THR J 363 " --> pdb=" O ARG J 296 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU J 298 " --> pdb=" O ASN J 361 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ASN J 361 " --> pdb=" O LEU J 298 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ILE J 300 " --> pdb=" O GLN J 359 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLN J 359 " --> pdb=" O ILE J 300 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLU J 302 " --> pdb=" O SER J 357 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N SER J 357 " --> pdb=" O GLU J 302 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'K' and resid 276 through 278 Processing sheet with id= AF, first strand: chain 'K' and resid 429 through 434 removed outlier: 3.589A pdb=" N ASP K 381 " --> pdb=" O ASP K 271 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLN K 269 " --> pdb=" O GLU K 383 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU K 385 " --> pdb=" O THR K 267 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N THR K 267 " --> pdb=" O LEU K 385 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL K 387 " --> pdb=" O GLN K 265 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLN K 265 " --> pdb=" O VAL K 387 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N VAL K 389 " --> pdb=" O HIS K 263 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N HIS K 263 " --> pdb=" O VAL K 389 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'K' and resid 292 through 303 removed outlier: 4.223A pdb=" N THR K 292 " --> pdb=" O GLU K 367 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ASN K 365 " --> pdb=" O ARG K 294 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ARG K 296 " --> pdb=" O THR K 363 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N THR K 363 " --> pdb=" O ARG K 296 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LEU K 298 " --> pdb=" O ASN K 361 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ASN K 361 " --> pdb=" O LEU K 298 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ILE K 300 " --> pdb=" O GLN K 359 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLN K 359 " --> pdb=" O ILE K 300 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLU K 302 " --> pdb=" O SER K 357 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N SER K 357 " --> pdb=" O GLU K 302 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'L' and resid 276 through 278 Processing sheet with id= AI, first strand: chain 'L' and resid 429 through 434 removed outlier: 3.588A pdb=" N ASP L 381 " --> pdb=" O ASP L 271 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLN L 269 " --> pdb=" O GLU L 383 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LEU L 385 " --> pdb=" O THR L 267 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N THR L 267 " --> pdb=" O LEU L 385 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL L 387 " --> pdb=" O GLN L 265 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLN L 265 " --> pdb=" O VAL L 387 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL L 389 " --> pdb=" O HIS L 263 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N HIS L 263 " --> pdb=" O VAL L 389 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'L' and resid 292 through 303 removed outlier: 4.214A pdb=" N THR L 292 " --> pdb=" O GLU L 367 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ASN L 365 " --> pdb=" O ARG L 294 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG L 296 " --> pdb=" O THR L 363 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N THR L 363 " --> pdb=" O ARG L 296 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LEU L 298 " --> pdb=" O ASN L 361 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ASN L 361 " --> pdb=" O LEU L 298 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ILE L 300 " --> pdb=" O GLN L 359 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLN L 359 " --> pdb=" O ILE L 300 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLU L 302 " --> pdb=" O SER L 357 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N SER L 357 " --> pdb=" O GLU L 302 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'M' and resid 276 through 278 Processing sheet with id= AL, first strand: chain 'M' and resid 429 through 434 removed outlier: 3.575A pdb=" N ASP M 381 " --> pdb=" O ASP M 271 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLN M 269 " --> pdb=" O GLU M 383 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU M 385 " --> pdb=" O THR M 267 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N THR M 267 " --> pdb=" O LEU M 385 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL M 387 " --> pdb=" O GLN M 265 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLN M 265 " --> pdb=" O VAL M 387 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL M 389 " --> pdb=" O HIS M 263 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N HIS M 263 " --> pdb=" O VAL M 389 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'M' and resid 292 through 303 removed outlier: 4.213A pdb=" N THR M 292 " --> pdb=" O GLU M 367 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ASN M 365 " --> pdb=" O ARG M 294 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ARG M 296 " --> pdb=" O THR M 363 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N THR M 363 " --> pdb=" O ARG M 296 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LEU M 298 " --> pdb=" O ASN M 361 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASN M 361 " --> pdb=" O LEU M 298 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ILE M 300 " --> pdb=" O GLN M 359 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLN M 359 " --> pdb=" O ILE M 300 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLU M 302 " --> pdb=" O SER M 357 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER M 357 " --> pdb=" O GLU M 302 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'N' and resid 276 through 278 Processing sheet with id= AO, first strand: chain 'N' and resid 429 through 434 removed outlier: 3.651A pdb=" N ASP N 381 " --> pdb=" O ASP N 271 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLN N 269 " --> pdb=" O GLU N 383 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU N 385 " --> pdb=" O THR N 267 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR N 267 " --> pdb=" O LEU N 385 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL N 387 " --> pdb=" O GLN N 265 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLN N 265 " --> pdb=" O VAL N 387 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL N 389 " --> pdb=" O HIS N 263 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N HIS N 263 " --> pdb=" O VAL N 389 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'N' and resid 292 through 303 removed outlier: 4.226A pdb=" N THR N 292 " --> pdb=" O GLU N 367 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASN N 365 " --> pdb=" O ARG N 294 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG N 296 " --> pdb=" O THR N 363 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR N 363 " --> pdb=" O ARG N 296 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU N 298 " --> pdb=" O ASN N 361 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASN N 361 " --> pdb=" O LEU N 298 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ILE N 300 " --> pdb=" O GLN N 359 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN N 359 " --> pdb=" O ILE N 300 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLU N 302 " --> pdb=" O SER N 357 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N SER N 357 " --> pdb=" O GLU N 302 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'O' and resid 276 through 278 Processing sheet with id= AR, first strand: chain 'O' and resid 429 through 434 removed outlier: 3.553A pdb=" N ASP O 381 " --> pdb=" O ASP O 271 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLN O 269 " --> pdb=" O GLU O 383 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU O 385 " --> pdb=" O THR O 267 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N THR O 267 " --> pdb=" O LEU O 385 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL O 387 " --> pdb=" O GLN O 265 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLN O 265 " --> pdb=" O VAL O 387 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL O 389 " --> pdb=" O HIS O 263 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N HIS O 263 " --> pdb=" O VAL O 389 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'O' and resid 292 through 302 removed outlier: 4.214A pdb=" N THR O 292 " --> pdb=" O GLU O 367 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ASN O 365 " --> pdb=" O ARG O 294 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ARG O 296 " --> pdb=" O THR O 363 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N THR O 363 " --> pdb=" O ARG O 296 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU O 298 " --> pdb=" O ASN O 361 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ASN O 361 " --> pdb=" O LEU O 298 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ILE O 300 " --> pdb=" O GLN O 359 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLN O 359 " --> pdb=" O ILE O 300 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'P' and resid 276 through 278 Processing sheet with id= AU, first strand: chain 'P' and resid 429 through 434 removed outlier: 3.524A pdb=" N ASP P 381 " --> pdb=" O ASP P 271 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLN P 269 " --> pdb=" O GLU P 383 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU P 385 " --> pdb=" O THR P 267 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N THR P 267 " --> pdb=" O LEU P 385 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL P 387 " --> pdb=" O GLN P 265 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLN P 265 " --> pdb=" O VAL P 387 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL P 389 " --> pdb=" O HIS P 263 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N HIS P 263 " --> pdb=" O VAL P 389 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'P' and resid 292 through 303 removed outlier: 4.207A pdb=" N THR P 292 " --> pdb=" O GLU P 367 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ASN P 365 " --> pdb=" O ARG P 294 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ARG P 296 " --> pdb=" O THR P 363 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N THR P 363 " --> pdb=" O ARG P 296 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU P 298 " --> pdb=" O ASN P 361 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ASN P 361 " --> pdb=" O LEU P 298 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ILE P 300 " --> pdb=" O GLN P 359 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLN P 359 " --> pdb=" O ILE P 300 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLU P 302 " --> pdb=" O SER P 357 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N SER P 357 " --> pdb=" O GLU P 302 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'Q' and resid 276 through 278 Processing sheet with id= AX, first strand: chain 'Q' and resid 429 through 434 removed outlier: 3.593A pdb=" N ASP Q 381 " --> pdb=" O ASP Q 271 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLN Q 269 " --> pdb=" O GLU Q 383 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LEU Q 385 " --> pdb=" O THR Q 267 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR Q 267 " --> pdb=" O LEU Q 385 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL Q 387 " --> pdb=" O GLN Q 265 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLN Q 265 " --> pdb=" O VAL Q 387 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL Q 389 " --> pdb=" O HIS Q 263 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N HIS Q 263 " --> pdb=" O VAL Q 389 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'Q' and resid 292 through 302 removed outlier: 4.221A pdb=" N THR Q 292 " --> pdb=" O GLU Q 367 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ASN Q 365 " --> pdb=" O ARG Q 294 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ARG Q 296 " --> pdb=" O THR Q 363 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR Q 363 " --> pdb=" O ARG Q 296 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU Q 298 " --> pdb=" O ASN Q 361 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASN Q 361 " --> pdb=" O LEU Q 298 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE Q 300 " --> pdb=" O GLN Q 359 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLN Q 359 " --> pdb=" O ILE Q 300 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'R' and resid 276 through 278 Processing sheet with id= BA, first strand: chain 'R' and resid 429 through 434 removed outlier: 3.608A pdb=" N ASP R 381 " --> pdb=" O ASP R 271 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLN R 269 " --> pdb=" O GLU R 383 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU R 385 " --> pdb=" O THR R 267 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR R 267 " --> pdb=" O LEU R 385 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL R 387 " --> pdb=" O GLN R 265 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLN R 265 " --> pdb=" O VAL R 387 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N VAL R 389 " --> pdb=" O HIS R 263 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N HIS R 263 " --> pdb=" O VAL R 389 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'R' and resid 292 through 303 removed outlier: 4.189A pdb=" N THR R 292 " --> pdb=" O GLU R 367 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ASN R 365 " --> pdb=" O ARG R 294 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ARG R 296 " --> pdb=" O THR R 363 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N THR R 363 " --> pdb=" O ARG R 296 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU R 298 " --> pdb=" O ASN R 361 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASN R 361 " --> pdb=" O LEU R 298 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ILE R 300 " --> pdb=" O GLN R 359 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLN R 359 " --> pdb=" O ILE R 300 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU R 302 " --> pdb=" O SER R 357 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N SER R 357 " --> pdb=" O GLU R 302 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'S' and resid 276 through 278 Processing sheet with id= BD, first strand: chain 'S' and resid 429 through 434 removed outlier: 3.624A pdb=" N ASP S 381 " --> pdb=" O ASP S 271 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLN S 269 " --> pdb=" O GLU S 383 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LEU S 385 " --> pdb=" O THR S 267 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR S 267 " --> pdb=" O LEU S 385 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL S 387 " --> pdb=" O GLN S 265 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLN S 265 " --> pdb=" O VAL S 387 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N VAL S 389 " --> pdb=" O HIS S 263 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N HIS S 263 " --> pdb=" O VAL S 389 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'S' and resid 292 through 303 removed outlier: 4.194A pdb=" N THR S 292 " --> pdb=" O GLU S 367 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ASN S 365 " --> pdb=" O ARG S 294 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ARG S 296 " --> pdb=" O THR S 363 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THR S 363 " --> pdb=" O ARG S 296 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU S 298 " --> pdb=" O ASN S 361 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ASN S 361 " --> pdb=" O LEU S 298 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ILE S 300 " --> pdb=" O GLN S 359 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLN S 359 " --> pdb=" O ILE S 300 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLU S 302 " --> pdb=" O SER S 357 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER S 357 " --> pdb=" O GLU S 302 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'T' and resid 276 through 278 Processing sheet with id= BG, first strand: chain 'T' and resid 429 through 434 removed outlier: 3.585A pdb=" N ASP T 381 " --> pdb=" O ASP T 271 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLN T 269 " --> pdb=" O GLU T 383 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LEU T 385 " --> pdb=" O THR T 267 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR T 267 " --> pdb=" O LEU T 385 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL T 387 " --> pdb=" O GLN T 265 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLN T 265 " --> pdb=" O VAL T 387 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N VAL T 389 " --> pdb=" O HIS T 263 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N HIS T 263 " --> pdb=" O VAL T 389 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'T' and resid 292 through 302 removed outlier: 4.232A pdb=" N THR T 292 " --> pdb=" O GLU T 367 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ASN T 365 " --> pdb=" O ARG T 294 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ARG T 296 " --> pdb=" O THR T 363 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR T 363 " --> pdb=" O ARG T 296 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU T 298 " --> pdb=" O ASN T 361 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASN T 361 " --> pdb=" O LEU T 298 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ILE T 300 " --> pdb=" O GLN T 359 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLN T 359 " --> pdb=" O ILE T 300 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'U' and resid 276 through 278 Processing sheet with id= BJ, first strand: chain 'U' and resid 429 through 434 removed outlier: 3.577A pdb=" N ASP U 381 " --> pdb=" O ASP U 271 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLN U 269 " --> pdb=" O GLU U 383 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU U 385 " --> pdb=" O THR U 267 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N THR U 267 " --> pdb=" O LEU U 385 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL U 387 " --> pdb=" O GLN U 265 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLN U 265 " --> pdb=" O VAL U 387 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL U 389 " --> pdb=" O HIS U 263 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N HIS U 263 " --> pdb=" O VAL U 389 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'U' and resid 292 through 303 removed outlier: 4.210A pdb=" N THR U 292 " --> pdb=" O GLU U 367 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASN U 365 " --> pdb=" O ARG U 294 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG U 296 " --> pdb=" O THR U 363 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N THR U 363 " --> pdb=" O ARG U 296 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU U 298 " --> pdb=" O ASN U 361 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASN U 361 " --> pdb=" O LEU U 298 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ILE U 300 " --> pdb=" O GLN U 359 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N GLN U 359 " --> pdb=" O ILE U 300 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLU U 302 " --> pdb=" O SER U 357 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N SER U 357 " --> pdb=" O GLU U 302 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'V' and resid 276 through 278 Processing sheet with id= BM, first strand: chain 'V' and resid 429 through 434 removed outlier: 3.548A pdb=" N ASP V 381 " --> pdb=" O ASP V 271 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLN V 269 " --> pdb=" O GLU V 383 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU V 385 " --> pdb=" O THR V 267 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N THR V 267 " --> pdb=" O LEU V 385 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL V 387 " --> pdb=" O GLN V 265 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLN V 265 " --> pdb=" O VAL V 387 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N VAL V 389 " --> pdb=" O HIS V 263 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N HIS V 263 " --> pdb=" O VAL V 389 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'V' and resid 292 through 303 removed outlier: 4.197A pdb=" N THR V 292 " --> pdb=" O GLU V 367 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN V 365 " --> pdb=" O ARG V 294 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ARG V 296 " --> pdb=" O THR V 363 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N THR V 363 " --> pdb=" O ARG V 296 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LEU V 298 " --> pdb=" O ASN V 361 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ASN V 361 " --> pdb=" O LEU V 298 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ILE V 300 " --> pdb=" O GLN V 359 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLN V 359 " --> pdb=" O ILE V 300 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLU V 302 " --> pdb=" O SER V 357 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N SER V 357 " --> pdb=" O GLU V 302 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'W' and resid 276 through 278 Processing sheet with id= BP, first strand: chain 'W' and resid 429 through 434 removed outlier: 3.535A pdb=" N ASP W 381 " --> pdb=" O ASP W 271 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLN W 269 " --> pdb=" O GLU W 383 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU W 385 " --> pdb=" O THR W 267 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N THR W 267 " --> pdb=" O LEU W 385 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL W 387 " --> pdb=" O GLN W 265 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLN W 265 " --> pdb=" O VAL W 387 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL W 389 " --> pdb=" O HIS W 263 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N HIS W 263 " --> pdb=" O VAL W 389 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'W' and resid 292 through 303 removed outlier: 4.191A pdb=" N THR W 292 " --> pdb=" O GLU W 367 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ASN W 365 " --> pdb=" O ARG W 294 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ARG W 296 " --> pdb=" O THR W 363 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR W 363 " --> pdb=" O ARG W 296 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU W 298 " --> pdb=" O ASN W 361 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASN W 361 " --> pdb=" O LEU W 298 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ILE W 300 " --> pdb=" O GLN W 359 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLN W 359 " --> pdb=" O ILE W 300 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU W 302 " --> pdb=" O SER W 357 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N SER W 357 " --> pdb=" O GLU W 302 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'X' and resid 276 through 278 Processing sheet with id= BS, first strand: chain 'X' and resid 429 through 434 removed outlier: 3.608A pdb=" N ASP X 381 " --> pdb=" O ASP X 271 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLN X 269 " --> pdb=" O GLU X 383 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU X 385 " --> pdb=" O THR X 267 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR X 267 " --> pdb=" O LEU X 385 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL X 387 " --> pdb=" O GLN X 265 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLN X 265 " --> pdb=" O VAL X 387 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N VAL X 389 " --> pdb=" O HIS X 263 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N HIS X 263 " --> pdb=" O VAL X 389 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'X' and resid 292 through 303 removed outlier: 4.194A pdb=" N THR X 292 " --> pdb=" O GLU X 367 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ASN X 365 " --> pdb=" O ARG X 294 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ARG X 296 " --> pdb=" O THR X 363 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N THR X 363 " --> pdb=" O ARG X 296 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU X 298 " --> pdb=" O ASN X 361 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ASN X 361 " --> pdb=" O LEU X 298 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ILE X 300 " --> pdb=" O GLN X 359 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLN X 359 " --> pdb=" O ILE X 300 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLU X 302 " --> pdb=" O SER X 357 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N SER X 357 " --> pdb=" O GLU X 302 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'Y' and resid 276 through 278 Processing sheet with id= BV, first strand: chain 'Y' and resid 429 through 434 removed outlier: 3.543A pdb=" N ASP Y 381 " --> pdb=" O ASP Y 271 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLN Y 269 " --> pdb=" O GLU Y 383 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU Y 385 " --> pdb=" O THR Y 267 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N THR Y 267 " --> pdb=" O LEU Y 385 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL Y 387 " --> pdb=" O GLN Y 265 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLN Y 265 " --> pdb=" O VAL Y 387 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL Y 389 " --> pdb=" O HIS Y 263 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N HIS Y 263 " --> pdb=" O VAL Y 389 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'Y' and resid 292 through 302 removed outlier: 4.205A pdb=" N THR Y 292 " --> pdb=" O GLU Y 367 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ASN Y 365 " --> pdb=" O ARG Y 294 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ARG Y 296 " --> pdb=" O THR Y 363 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N THR Y 363 " --> pdb=" O ARG Y 296 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU Y 298 " --> pdb=" O ASN Y 361 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ASN Y 361 " --> pdb=" O LEU Y 298 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE Y 300 " --> pdb=" O GLN Y 359 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLN Y 359 " --> pdb=" O ILE Y 300 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'Z' and resid 276 through 278 Processing sheet with id= BY, first strand: chain 'Z' and resid 429 through 434 removed outlier: 3.603A pdb=" N ASP Z 381 " --> pdb=" O ASP Z 271 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLN Z 269 " --> pdb=" O GLU Z 383 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU Z 385 " --> pdb=" O THR Z 267 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR Z 267 " --> pdb=" O LEU Z 385 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL Z 387 " --> pdb=" O GLN Z 265 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLN Z 265 " --> pdb=" O VAL Z 387 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL Z 389 " --> pdb=" O HIS Z 263 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N HIS Z 263 " --> pdb=" O VAL Z 389 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'Z' and resid 292 through 303 removed outlier: 4.190A pdb=" N THR Z 292 " --> pdb=" O GLU Z 367 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ASN Z 365 " --> pdb=" O ARG Z 294 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ARG Z 296 " --> pdb=" O THR Z 363 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N THR Z 363 " --> pdb=" O ARG Z 296 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU Z 298 " --> pdb=" O ASN Z 361 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ASN Z 361 " --> pdb=" O LEU Z 298 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ILE Z 300 " --> pdb=" O GLN Z 359 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLN Z 359 " --> pdb=" O ILE Z 300 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLU Z 302 " --> pdb=" O SER Z 357 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N SER Z 357 " --> pdb=" O GLU Z 302 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'a' and resid 276 through 278 Processing sheet with id= CB, first strand: chain 'a' and resid 429 through 434 removed outlier: 3.618A pdb=" N ASP a 381 " --> pdb=" O ASP a 271 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLN a 269 " --> pdb=" O GLU a 383 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LEU a 385 " --> pdb=" O THR a 267 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR a 267 " --> pdb=" O LEU a 385 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL a 387 " --> pdb=" O GLN a 265 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLN a 265 " --> pdb=" O VAL a 387 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL a 389 " --> pdb=" O HIS a 263 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N HIS a 263 " --> pdb=" O VAL a 389 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'a' and resid 292 through 303 removed outlier: 4.214A pdb=" N THR a 292 " --> pdb=" O GLU a 367 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ASN a 365 " --> pdb=" O ARG a 294 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ARG a 296 " --> pdb=" O THR a 363 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N THR a 363 " --> pdb=" O ARG a 296 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU a 298 " --> pdb=" O ASN a 361 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASN a 361 " --> pdb=" O LEU a 298 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ILE a 300 " --> pdb=" O GLN a 359 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLN a 359 " --> pdb=" O ILE a 300 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU a 302 " --> pdb=" O SER a 357 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N SER a 357 " --> pdb=" O GLU a 302 " (cutoff:3.500A) Processing sheet with id= CD, first strand: chain 'b' and resid 276 through 278 Processing sheet with id= CE, first strand: chain 'b' and resid 429 through 434 removed outlier: 3.589A pdb=" N ASP b 381 " --> pdb=" O ASP b 271 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLN b 269 " --> pdb=" O GLU b 383 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU b 385 " --> pdb=" O THR b 267 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N THR b 267 " --> pdb=" O LEU b 385 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL b 387 " --> pdb=" O GLN b 265 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLN b 265 " --> pdb=" O VAL b 387 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL b 389 " --> pdb=" O HIS b 263 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N HIS b 263 " --> pdb=" O VAL b 389 " (cutoff:3.500A) Processing sheet with id= CF, first strand: chain 'b' and resid 292 through 303 removed outlier: 4.201A pdb=" N THR b 292 " --> pdb=" O GLU b 367 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ASN b 365 " --> pdb=" O ARG b 294 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ARG b 296 " --> pdb=" O THR b 363 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N THR b 363 " --> pdb=" O ARG b 296 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU b 298 " --> pdb=" O ASN b 361 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ASN b 361 " --> pdb=" O LEU b 298 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ILE b 300 " --> pdb=" O GLN b 359 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLN b 359 " --> pdb=" O ILE b 300 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLU b 302 " --> pdb=" O SER b 357 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N SER b 357 " --> pdb=" O GLU b 302 " (cutoff:3.500A) Processing sheet with id= CG, first strand: chain 'c' and resid 276 through 278 Processing sheet with id= CH, first strand: chain 'c' and resid 429 through 434 removed outlier: 3.584A pdb=" N ASP c 381 " --> pdb=" O ASP c 271 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLN c 269 " --> pdb=" O GLU c 383 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU c 385 " --> pdb=" O THR c 267 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N THR c 267 " --> pdb=" O LEU c 385 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL c 387 " --> pdb=" O GLN c 265 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLN c 265 " --> pdb=" O VAL c 387 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL c 389 " --> pdb=" O HIS c 263 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N HIS c 263 " --> pdb=" O VAL c 389 " (cutoff:3.500A) Processing sheet with id= CI, first strand: chain 'c' and resid 292 through 303 removed outlier: 4.213A pdb=" N THR c 292 " --> pdb=" O GLU c 367 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ASN c 365 " --> pdb=" O ARG c 294 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ARG c 296 " --> pdb=" O THR c 363 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N THR c 363 " --> pdb=" O ARG c 296 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LEU c 298 " --> pdb=" O ASN c 361 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ASN c 361 " --> pdb=" O LEU c 298 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ILE c 300 " --> pdb=" O GLN c 359 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLN c 359 " --> pdb=" O ILE c 300 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU c 302 " --> pdb=" O SER c 357 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N SER c 357 " --> pdb=" O GLU c 302 " (cutoff:3.500A) Processing sheet with id= CJ, first strand: chain 'd' and resid 276 through 278 Processing sheet with id= CK, first strand: chain 'd' and resid 429 through 434 removed outlier: 3.596A pdb=" N ASP d 381 " --> pdb=" O ASP d 271 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLN d 269 " --> pdb=" O GLU d 383 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU d 385 " --> pdb=" O THR d 267 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR d 267 " --> pdb=" O LEU d 385 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL d 387 " --> pdb=" O GLN d 265 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLN d 265 " --> pdb=" O VAL d 387 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N VAL d 389 " --> pdb=" O HIS d 263 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N HIS d 263 " --> pdb=" O VAL d 389 " (cutoff:3.500A) Processing sheet with id= CL, first strand: chain 'd' and resid 292 through 302 removed outlier: 4.202A pdb=" N THR d 292 " --> pdb=" O GLU d 367 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASN d 365 " --> pdb=" O ARG d 294 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG d 296 " --> pdb=" O THR d 363 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR d 363 " --> pdb=" O ARG d 296 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU d 298 " --> pdb=" O ASN d 361 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ASN d 361 " --> pdb=" O LEU d 298 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ILE d 300 " --> pdb=" O GLN d 359 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLN d 359 " --> pdb=" O ILE d 300 " (cutoff:3.500A) Processing sheet with id= CM, first strand: chain 'e' and resid 276 through 278 Processing sheet with id= CN, first strand: chain 'e' and resid 429 through 434 removed outlier: 3.559A pdb=" N ASP e 381 " --> pdb=" O ASP e 271 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLN e 269 " --> pdb=" O GLU e 383 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU e 385 " --> pdb=" O THR e 267 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N THR e 267 " --> pdb=" O LEU e 385 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL e 387 " --> pdb=" O GLN e 265 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLN e 265 " --> pdb=" O VAL e 387 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N VAL e 389 " --> pdb=" O HIS e 263 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N HIS e 263 " --> pdb=" O VAL e 389 " (cutoff:3.500A) Processing sheet with id= CO, first strand: chain 'e' and resid 292 through 303 removed outlier: 4.211A pdb=" N THR e 292 " --> pdb=" O GLU e 367 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASN e 365 " --> pdb=" O ARG e 294 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG e 296 " --> pdb=" O THR e 363 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N THR e 363 " --> pdb=" O ARG e 296 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU e 298 " --> pdb=" O ASN e 361 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASN e 361 " --> pdb=" O LEU e 298 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ILE e 300 " --> pdb=" O GLN e 359 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLN e 359 " --> pdb=" O ILE e 300 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU e 302 " --> pdb=" O SER e 357 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N SER e 357 " --> pdb=" O GLU e 302 " (cutoff:3.500A) Processing sheet with id= CP, first strand: chain 'f' and resid 276 through 278 Processing sheet with id= CQ, first strand: chain 'f' and resid 429 through 434 removed outlier: 3.551A pdb=" N ASP f 381 " --> pdb=" O ASP f 271 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLN f 269 " --> pdb=" O GLU f 383 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LEU f 385 " --> pdb=" O THR f 267 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR f 267 " --> pdb=" O LEU f 385 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL f 387 " --> pdb=" O GLN f 265 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLN f 265 " --> pdb=" O VAL f 387 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL f 389 " --> pdb=" O HIS f 263 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N HIS f 263 " --> pdb=" O VAL f 389 " (cutoff:3.500A) Processing sheet with id= CR, first strand: chain 'f' and resid 292 through 303 removed outlier: 4.213A pdb=" N THR f 292 " --> pdb=" O GLU f 367 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASN f 365 " --> pdb=" O ARG f 294 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ARG f 296 " --> pdb=" O THR f 363 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR f 363 " --> pdb=" O ARG f 296 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU f 298 " --> pdb=" O ASN f 361 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ASN f 361 " --> pdb=" O LEU f 298 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ILE f 300 " --> pdb=" O GLN f 359 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLN f 359 " --> pdb=" O ILE f 300 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLU f 302 " --> pdb=" O SER f 357 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N SER f 357 " --> pdb=" O GLU f 302 " (cutoff:3.500A) Processing sheet with id= CS, first strand: chain 'g' and resid 276 through 278 Processing sheet with id= CT, first strand: chain 'g' and resid 429 through 434 removed outlier: 3.557A pdb=" N ASP g 381 " --> pdb=" O ASP g 271 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLN g 269 " --> pdb=" O GLU g 383 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU g 385 " --> pdb=" O THR g 267 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR g 267 " --> pdb=" O LEU g 385 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL g 387 " --> pdb=" O GLN g 265 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLN g 265 " --> pdb=" O VAL g 387 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL g 389 " --> pdb=" O HIS g 263 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N HIS g 263 " --> pdb=" O VAL g 389 " (cutoff:3.500A) Processing sheet with id= CU, first strand: chain 'g' and resid 292 through 303 removed outlier: 4.224A pdb=" N THR g 292 " --> pdb=" O GLU g 367 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ASN g 365 " --> pdb=" O ARG g 294 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ARG g 296 " --> pdb=" O THR g 363 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N THR g 363 " --> pdb=" O ARG g 296 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU g 298 " --> pdb=" O ASN g 361 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ASN g 361 " --> pdb=" O LEU g 298 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ILE g 300 " --> pdb=" O GLN g 359 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLN g 359 " --> pdb=" O ILE g 300 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU g 302 " --> pdb=" O SER g 357 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N SER g 357 " --> pdb=" O GLU g 302 " (cutoff:3.500A) 1441 hydrogen bonds defined for protein. 4224 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.05 Time building geometry restraints manager: 14.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 14157 1.34 - 1.46: 5214 1.46 - 1.57: 20196 1.57 - 1.69: 0 1.69 - 1.80: 198 Bond restraints: 39765 Sorted by residual: bond pdb=" CA GLU O 280 " pdb=" C GLU O 280 " ideal model delta sigma weight residual 1.533 1.523 0.010 9.60e-03 1.09e+04 1.11e+00 bond pdb=" CA GLU P 280 " pdb=" C GLU P 280 " ideal model delta sigma weight residual 1.533 1.524 0.010 9.60e-03 1.09e+04 9.85e-01 bond pdb=" CA GLU d 280 " pdb=" C GLU d 280 " ideal model delta sigma weight residual 1.533 1.524 0.009 9.60e-03 1.09e+04 9.45e-01 bond pdb=" CA GLU H 280 " pdb=" C GLU H 280 " ideal model delta sigma weight residual 1.533 1.524 0.009 9.60e-03 1.09e+04 9.41e-01 bond pdb=" CA GLU g 280 " pdb=" C GLU g 280 " ideal model delta sigma weight residual 1.533 1.524 0.009 9.60e-03 1.09e+04 9.34e-01 ... (remaining 39760 not shown) Histogram of bond angle deviations from ideal: 100.56 - 106.72: 790 106.72 - 112.88: 22034 112.88 - 119.04: 10100 119.04 - 125.21: 20437 125.21 - 131.37: 231 Bond angle restraints: 53592 Sorted by residual: angle pdb=" N GLY Y 421 " pdb=" CA GLY Y 421 " pdb=" C GLY Y 421 " ideal model delta sigma weight residual 113.18 107.89 5.29 2.37e+00 1.78e-01 4.97e+00 angle pdb=" N GLY F 421 " pdb=" CA GLY F 421 " pdb=" C GLY F 421 " ideal model delta sigma weight residual 113.18 107.95 5.23 2.37e+00 1.78e-01 4.87e+00 angle pdb=" N GLY g 421 " pdb=" CA GLY g 421 " pdb=" C GLY g 421 " ideal model delta sigma weight residual 113.18 107.99 5.19 2.37e+00 1.78e-01 4.79e+00 angle pdb=" N GLY W 421 " pdb=" CA GLY W 421 " pdb=" C GLY W 421 " ideal model delta sigma weight residual 113.18 108.01 5.17 2.37e+00 1.78e-01 4.76e+00 angle pdb=" C TYR R 282 " pdb=" N SER R 283 " pdb=" CA SER R 283 " ideal model delta sigma weight residual 120.67 117.75 2.92 1.34e+00 5.57e-01 4.74e+00 ... (remaining 53587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 23053 18.00 - 36.00: 1526 36.00 - 54.00: 225 54.00 - 72.00: 20 72.00 - 90.00: 25 Dihedral angle restraints: 24849 sinusoidal: 10296 harmonic: 14553 Sorted by residual: dihedral pdb=" CA MET F 420 " pdb=" C MET F 420 " pdb=" N GLY F 421 " pdb=" CA GLY F 421 " ideal model delta harmonic sigma weight residual -180.00 -161.64 -18.36 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA MET Y 420 " pdb=" C MET Y 420 " pdb=" N GLY Y 421 " pdb=" CA GLY Y 421 " ideal model delta harmonic sigma weight residual -180.00 -161.75 -18.25 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA MET B 420 " pdb=" C MET B 420 " pdb=" N GLY B 421 " pdb=" CA GLY B 421 " ideal model delta harmonic sigma weight residual -180.00 -161.77 -18.23 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 24846 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 3436 0.024 - 0.048: 1714 0.048 - 0.073: 504 0.073 - 0.097: 328 0.097 - 0.121: 156 Chirality restraints: 6138 Sorted by residual: chirality pdb=" CA ILE f 382 " pdb=" N ILE f 382 " pdb=" C ILE f 382 " pdb=" CB ILE f 382 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.67e-01 chirality pdb=" CA ILE e 382 " pdb=" N ILE e 382 " pdb=" C ILE e 382 " pdb=" CB ILE e 382 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.41e-01 chirality pdb=" CA ILE F 382 " pdb=" N ILE F 382 " pdb=" C ILE F 382 " pdb=" CB ILE F 382 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.37e-01 ... (remaining 6135 not shown) Planarity restraints: 7194 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 254 " 0.025 5.00e-02 4.00e+02 3.71e-02 2.20e+00 pdb=" N PRO B 255 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 255 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 255 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER Y 254 " 0.024 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO Y 255 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO Y 255 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO Y 255 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER H 254 " 0.023 5.00e-02 4.00e+02 3.54e-02 2.01e+00 pdb=" N PRO H 255 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO H 255 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO H 255 " 0.020 5.00e-02 4.00e+02 ... (remaining 7191 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 716 2.70 - 3.25: 36682 3.25 - 3.80: 60514 3.80 - 4.35: 89093 4.35 - 4.90: 142063 Nonbonded interactions: 329068 Sorted by model distance: nonbonded pdb=" O GLU B 250 " pdb=" OG SER B 254 " model vdw 2.149 2.440 nonbonded pdb=" O GLU T 250 " pdb=" OG SER T 254 " model vdw 2.156 2.440 nonbonded pdb=" O GLU L 250 " pdb=" OG SER L 254 " model vdw 2.179 2.440 nonbonded pdb=" O GLU I 250 " pdb=" OG SER I 254 " model vdw 2.182 2.440 nonbonded pdb=" O GLU U 250 " pdb=" OG SER U 254 " model vdw 2.183 2.440 ... (remaining 329063 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.540 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: 19.390 Check model and map are aligned: 0.560 Set scattering table: 0.340 Process input model: 90.350 Find NCS groups from input model: 2.690 Set up NCS constraints: 0.440 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:13.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 131.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 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 : 0.003 0.021 39765 Z= 0.215 Angle : 0.528 5.286 53592 Z= 0.322 Chirality : 0.037 0.121 6138 Planarity : 0.003 0.037 7194 Dihedral : 12.417 89.998 15279 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % 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: -2.90 (0.11), residues: 4785 helix: -3.82 (0.07), residues: 1320 sheet: -0.64 (0.11), residues: 2442 loop : -1.66 (0.17), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 281 PHE 0.011 0.001 PHE g 422 TYR 0.020 0.002 TYR Z 393 ARG 0.002 0.000 ARG V 248 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9570 Ramachandran restraints generated. 4785 Oldfield, 0 Emsley, 4785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9570 Ramachandran restraints generated. 4785 Oldfield, 0 Emsley, 4785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1388 residues out of total 4422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1388 time to evaluate : 4.629 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: A 246 GLN cc_start: 0.8626 (tt0) cc_final: 0.8359 (tt0) REVERT: A 275 LYS cc_start: 0.8138 (ttmt) cc_final: 0.7923 (tttt) REVERT: A 376 LYS cc_start: 0.7888 (tttt) cc_final: 0.7515 (mttp) REVERT: B 287 ASP cc_start: 0.7575 (t0) cc_final: 0.7365 (t70) REVERT: C 376 LYS cc_start: 0.7948 (tttt) cc_final: 0.7522 (mttp) REVERT: C 425 LYS cc_start: 0.8874 (mtmt) cc_final: 0.8627 (mtmm) REVERT: D 246 GLN cc_start: 0.8538 (tt0) cc_final: 0.8312 (tt0) REVERT: D 297 GLN cc_start: 0.7557 (tt0) cc_final: 0.7355 (tp-100) REVERT: D 376 LYS cc_start: 0.7949 (tttt) cc_final: 0.7692 (mttp) REVERT: E 302 GLU cc_start: 0.6889 (tt0) cc_final: 0.6661 (tt0) REVERT: E 376 LYS cc_start: 0.7828 (tttt) cc_final: 0.7432 (mttp) REVERT: F 376 LYS cc_start: 0.7949 (tttt) cc_final: 0.7556 (mttp) REVERT: G 297 GLN cc_start: 0.7491 (tt0) cc_final: 0.7290 (tp-100) REVERT: G 376 LYS cc_start: 0.7946 (tttt) cc_final: 0.7557 (mttp) REVERT: H 297 GLN cc_start: 0.7572 (tt0) cc_final: 0.7316 (tp40) REVERT: H 376 LYS cc_start: 0.8027 (tttt) cc_final: 0.7622 (mttp) REVERT: H 410 LYS cc_start: 0.8391 (tmmt) cc_final: 0.8144 (tmmt) REVERT: I 376 LYS cc_start: 0.8056 (tttt) cc_final: 0.7637 (mttp) REVERT: J 235 LEU cc_start: 0.9192 (mt) cc_final: 0.8928 (mp) REVERT: J 246 GLN cc_start: 0.8534 (tt0) cc_final: 0.8228 (tt0) REVERT: J 376 LYS cc_start: 0.7890 (tttt) cc_final: 0.7476 (mttp) REVERT: J 383 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7579 (mt-10) REVERT: K 236 LYS cc_start: 0.8142 (mtmt) cc_final: 0.7435 (mttm) REVERT: K 246 GLN cc_start: 0.8571 (tt0) cc_final: 0.8306 (tt0) REVERT: K 275 LYS cc_start: 0.8230 (ttmt) cc_final: 0.8020 (tttp) REVERT: K 376 LYS cc_start: 0.8027 (tttt) cc_final: 0.7668 (mttp) REVERT: L 246 GLN cc_start: 0.8606 (tt0) cc_final: 0.8405 (tt0) REVERT: L 297 GLN cc_start: 0.7539 (tt0) cc_final: 0.7327 (tp-100) REVERT: L 360 ARG cc_start: 0.7829 (ttt-90) cc_final: 0.7515 (ttt-90) REVERT: M 297 GLN cc_start: 0.7526 (tt0) cc_final: 0.7286 (tp-100) REVERT: M 376 LYS cc_start: 0.7938 (tttt) cc_final: 0.7526 (mttp) REVERT: N 297 GLN cc_start: 0.7625 (tt0) cc_final: 0.7421 (tp40) REVERT: N 376 LYS cc_start: 0.7989 (tttt) cc_final: 0.7677 (mttp) REVERT: N 383 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7559 (mt-10) REVERT: O 246 GLN cc_start: 0.8609 (tt0) cc_final: 0.8402 (tt0) REVERT: O 376 LYS cc_start: 0.7991 (tttt) cc_final: 0.7650 (mttp) REVERT: P 376 LYS cc_start: 0.8036 (tttt) cc_final: 0.7714 (mttp) REVERT: Q 297 GLN cc_start: 0.7583 (tt0) cc_final: 0.7368 (tp40) REVERT: Q 376 LYS cc_start: 0.7877 (tttt) cc_final: 0.7404 (mttp) REVERT: R 246 GLN cc_start: 0.8583 (tt0) cc_final: 0.8244 (tt0) REVERT: R 376 LYS cc_start: 0.7785 (tttt) cc_final: 0.7463 (mttp) REVERT: S 297 GLN cc_start: 0.7494 (tt0) cc_final: 0.7288 (tp-100) REVERT: S 376 LYS cc_start: 0.7943 (tttt) cc_final: 0.7549 (mttp) REVERT: T 246 GLN cc_start: 0.8576 (tt0) cc_final: 0.8313 (tt0) REVERT: T 297 GLN cc_start: 0.7527 (tt0) cc_final: 0.7286 (tp-100) REVERT: T 376 LYS cc_start: 0.7870 (tttt) cc_final: 0.7512 (mttp) REVERT: U 246 GLN cc_start: 0.8578 (tt0) cc_final: 0.8366 (tt0) REVERT: U 376 LYS cc_start: 0.7885 (tttt) cc_final: 0.7672 (ttmp) REVERT: V 297 GLN cc_start: 0.7646 (tt0) cc_final: 0.7445 (tp40) REVERT: W 376 LYS cc_start: 0.8011 (tttt) cc_final: 0.7584 (mttp) REVERT: X 370 ARG cc_start: 0.7963 (ttp-170) cc_final: 0.7751 (ttm170) REVERT: X 376 LYS cc_start: 0.7995 (tttt) cc_final: 0.7542 (mttp) REVERT: Y 246 GLN cc_start: 0.8547 (tt0) cc_final: 0.8312 (tt0) REVERT: Y 297 GLN cc_start: 0.7557 (tt0) cc_final: 0.7347 (tp-100) REVERT: Z 246 GLN cc_start: 0.8570 (tt0) cc_final: 0.8289 (tt0) REVERT: Z 376 LYS cc_start: 0.7967 (tttt) cc_final: 0.7621 (mttp) REVERT: a 246 GLN cc_start: 0.8632 (tt0) cc_final: 0.8412 (tt0) REVERT: a 275 LYS cc_start: 0.8193 (ttmt) cc_final: 0.7980 (tttt) REVERT: a 376 LYS cc_start: 0.7811 (tttt) cc_final: 0.7434 (mttp) REVERT: b 246 GLN cc_start: 0.8629 (tt0) cc_final: 0.8316 (tt0) REVERT: b 275 LYS cc_start: 0.8206 (ttmt) cc_final: 0.7949 (tttp) REVERT: b 297 GLN cc_start: 0.7481 (tt0) cc_final: 0.7243 (tp-100) REVERT: b 376 LYS cc_start: 0.7827 (tttt) cc_final: 0.7466 (mttp) REVERT: b 425 LYS cc_start: 0.8897 (mtmt) cc_final: 0.8651 (mtmm) REVERT: c 297 GLN cc_start: 0.7575 (tt0) cc_final: 0.7368 (tp40) REVERT: c 376 LYS cc_start: 0.7949 (tttt) cc_final: 0.7609 (mttp) REVERT: d 376 LYS cc_start: 0.8008 (tttt) cc_final: 0.7689 (mttp) REVERT: e 276 GLU cc_start: 0.7342 (mt-10) cc_final: 0.6979 (mt-10) REVERT: e 297 GLN cc_start: 0.7557 (tt0) cc_final: 0.7355 (tp-100) REVERT: e 376 LYS cc_start: 0.7911 (tttt) cc_final: 0.7657 (mttp) REVERT: f 376 LYS cc_start: 0.8021 (tttt) cc_final: 0.7698 (mttp) REVERT: g 246 GLN cc_start: 0.8562 (tt0) cc_final: 0.8240 (tt0) REVERT: g 376 LYS cc_start: 0.8030 (tttt) cc_final: 0.7639 (mttp) outliers start: 0 outliers final: 0 residues processed: 1388 average time/residue: 1.8991 time to fit residues: 3062.7944 Evaluate side-chains 1232 residues out of total 4422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1232 time to evaluate : 4.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 417 optimal weight: 2.9990 chunk 375 optimal weight: 0.5980 chunk 208 optimal weight: 5.9990 chunk 128 optimal weight: 0.6980 chunk 253 optimal weight: 5.9990 chunk 200 optimal weight: 2.9990 chunk 387 optimal weight: 0.8980 chunk 150 optimal weight: 0.0770 chunk 235 optimal weight: 4.9990 chunk 288 optimal weight: 9.9990 chunk 449 optimal weight: 2.9990 overall best weight: 1.0540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN A 263 HIS A 297 GLN A 434 ASN B 246 GLN B 261 ASN B 263 HIS B 297 GLN B 374 HIS ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN C 261 ASN C 263 HIS C 297 GLN ** C 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 HIS D 365 ASN ** D 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN E 261 ASN E 263 HIS ** E 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 246 GLN F 261 ASN F 263 HIS F 434 ASN G 246 GLN G 261 ASN G 263 HIS G 269 GLN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 365 ASN ** G 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 231 ASN H 246 GLN H 261 ASN ** H 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 231 ASN I 246 GLN I 261 ASN I 263 HIS I 434 ASN J 261 ASN J 434 ASN K 263 HIS ** K 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 261 ASN L 263 HIS L 365 ASN L 434 ASN M 246 GLN M 261 ASN M 263 HIS M 277 GLN M 365 ASN ** M 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 246 GLN N 261 ASN N 263 HIS ** N 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 365 ASN ** N 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 261 ASN O 263 HIS O 365 ASN ** O 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 246 GLN P 261 ASN P 263 HIS P 365 ASN ** P 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 246 GLN Q 261 ASN Q 263 HIS Q 365 ASN ** Q 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 261 ASN R 263 HIS R 365 ASN R 431 ASN R 434 ASN S 246 GLN S 261 ASN S 263 HIS S 274 ASN S 365 ASN ** S 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 261 ASN T 263 HIS ** T 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 261 ASN U 263 HIS U 434 ASN V 246 GLN V 261 ASN V 263 HIS V 365 ASN ** V 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 239 ASN W 246 GLN W 261 ASN W 263 HIS W 365 ASN ** W 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 239 ASN X 246 GLN X 261 ASN X 263 HIS X 269 GLN X 365 ASN ** X 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 261 ASN Y 263 HIS ** Y 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 263 HIS Z 365 ASN Z 431 ASN Z 434 ASN a 261 ASN a 263 HIS ** a 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 261 ASN b 263 HIS b 365 ASN b 434 ASN c 246 GLN c 261 ASN c 263 HIS c 365 ASN c 434 ASN d 246 GLN d 261 ASN d 263 HIS ** d 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 231 ASN e 246 GLN e 261 ASN e 263 HIS e 269 GLN e 434 ASN f 246 GLN f 261 ASN f 263 HIS f 297 GLN ** f 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 231 ASN g 261 ASN g 263 HIS g 365 ASN ** g 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 39765 Z= 0.206 Angle : 0.478 5.017 53592 Z= 0.258 Chirality : 0.039 0.126 6138 Planarity : 0.003 0.034 7194 Dihedral : 4.659 17.636 5379 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.79 % Allowed : 13.21 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.13), residues: 4785 helix: 0.34 (0.13), residues: 1320 sheet: -0.12 (0.11), residues: 2475 loop : -0.86 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS T 281 PHE 0.009 0.001 PHE R 422 TYR 0.012 0.001 TYR e 393 ARG 0.007 0.000 ARG C 356 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9570 Ramachandran restraints generated. 4785 Oldfield, 0 Emsley, 4785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9570 Ramachandran restraints generated. 4785 Oldfield, 0 Emsley, 4785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1254 residues out of total 4422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 1219 time to evaluate : 4.370 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: A 246 GLN cc_start: 0.8514 (tt0) cc_final: 0.8241 (tt0) REVERT: A 376 LYS cc_start: 0.7892 (tttt) cc_final: 0.7546 (mttp) REVERT: B 287 ASP cc_start: 0.7564 (t0) cc_final: 0.7356 (t0) REVERT: B 297 GLN cc_start: 0.7550 (OUTLIER) cc_final: 0.7047 (tt0) REVERT: B 376 LYS cc_start: 0.7820 (tttt) cc_final: 0.7362 (mttp) REVERT: C 269 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7599 (mp10) REVERT: C 297 GLN cc_start: 0.7445 (OUTLIER) cc_final: 0.6911 (tt0) REVERT: C 376 LYS cc_start: 0.7887 (tttt) cc_final: 0.7519 (mttp) REVERT: C 418 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8210 (mm-30) REVERT: D 376 LYS cc_start: 0.7764 (tttt) cc_final: 0.7417 (mttp) REVERT: E 302 GLU cc_start: 0.6843 (tt0) cc_final: 0.6586 (tt0) REVERT: E 376 LYS cc_start: 0.7839 (tttt) cc_final: 0.7424 (mttp) REVERT: F 276 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7079 (mt-10) REVERT: F 376 LYS cc_start: 0.7974 (tttt) cc_final: 0.7567 (mttp) REVERT: G 376 LYS cc_start: 0.7872 (tttt) cc_final: 0.7389 (mttp) REVERT: G 409 MET cc_start: 0.8251 (mmm) cc_final: 0.7864 (mmm) REVERT: H 376 LYS cc_start: 0.8001 (tttt) cc_final: 0.7533 (mttp) REVERT: I 376 LYS cc_start: 0.8030 (tttt) cc_final: 0.7632 (mttp) REVERT: J 246 GLN cc_start: 0.8581 (tt0) cc_final: 0.8209 (tt0) REVERT: J 269 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7595 (mp10) REVERT: J 276 GLU cc_start: 0.7353 (mt-10) cc_final: 0.7144 (mt-10) REVERT: J 302 GLU cc_start: 0.6902 (tt0) cc_final: 0.6578 (tt0) REVERT: J 376 LYS cc_start: 0.7884 (tttt) cc_final: 0.7461 (mttp) REVERT: J 383 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7640 (mt-10) REVERT: K 246 GLN cc_start: 0.8450 (tt0) cc_final: 0.8176 (tt0) REVERT: K 269 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7552 (mp10) REVERT: K 376 LYS cc_start: 0.7993 (tttt) cc_final: 0.7646 (mttp) REVERT: L 246 GLN cc_start: 0.8537 (tt0) cc_final: 0.8309 (tt0) REVERT: L 297 GLN cc_start: 0.7603 (tt0) cc_final: 0.7367 (tp-100) REVERT: L 376 LYS cc_start: 0.7872 (tttt) cc_final: 0.7562 (ttmp) REVERT: M 276 GLU cc_start: 0.7330 (mt-10) cc_final: 0.6911 (mt-10) REVERT: M 297 GLN cc_start: 0.7553 (tt0) cc_final: 0.7322 (tp-100) REVERT: M 376 LYS cc_start: 0.7885 (tttt) cc_final: 0.7470 (mttp) REVERT: N 246 GLN cc_start: 0.8408 (tt0) cc_final: 0.8190 (tt0) REVERT: N 276 GLU cc_start: 0.7394 (mt-10) cc_final: 0.7146 (mt-10) REVERT: N 376 LYS cc_start: 0.7885 (tttt) cc_final: 0.7484 (mttp) REVERT: N 377 MET cc_start: 0.8013 (mpt) cc_final: 0.7740 (mpt) REVERT: O 376 LYS cc_start: 0.7984 (tttt) cc_final: 0.7604 (mttp) REVERT: P 376 LYS cc_start: 0.8035 (tttt) cc_final: 0.7632 (mttp) REVERT: Q 235 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8582 (mp) REVERT: Q 297 GLN cc_start: 0.7560 (tt0) cc_final: 0.7355 (tp40) REVERT: Q 376 LYS cc_start: 0.7877 (tttt) cc_final: 0.7357 (mttp) REVERT: Q 409 MET cc_start: 0.8145 (mmm) cc_final: 0.7866 (mmm) REVERT: R 246 GLN cc_start: 0.8511 (tt0) cc_final: 0.8128 (tt0) REVERT: R 376 LYS cc_start: 0.7873 (tttt) cc_final: 0.7482 (mttp) REVERT: S 297 GLN cc_start: 0.7497 (tt0) cc_final: 0.7274 (tp-100) REVERT: S 376 LYS cc_start: 0.7893 (tttt) cc_final: 0.7495 (mttp) REVERT: S 410 LYS cc_start: 0.8297 (tmmt) cc_final: 0.8040 (tttt) REVERT: T 246 GLN cc_start: 0.8537 (tt0) cc_final: 0.8265 (tt0) REVERT: T 297 GLN cc_start: 0.7586 (tt0) cc_final: 0.7340 (tp-100) REVERT: T 376 LYS cc_start: 0.7830 (tttt) cc_final: 0.7493 (mttp) REVERT: U 275 LYS cc_start: 0.8141 (ttmt) cc_final: 0.7933 (tttp) REVERT: U 376 LYS cc_start: 0.7869 (tttt) cc_final: 0.7481 (mttp) REVERT: V 297 GLN cc_start: 0.7653 (tt0) cc_final: 0.7437 (tp40) REVERT: V 376 LYS cc_start: 0.7948 (tttt) cc_final: 0.7675 (ttmp) REVERT: W 276 GLU cc_start: 0.7317 (mt-10) cc_final: 0.6978 (mt-10) REVERT: W 376 LYS cc_start: 0.8012 (tttt) cc_final: 0.7520 (mttp) REVERT: X 275 LYS cc_start: 0.8213 (ttmt) cc_final: 0.8011 (tttt) REVERT: X 376 LYS cc_start: 0.8007 (tttt) cc_final: 0.7534 (mttp) REVERT: Y 246 GLN cc_start: 0.8486 (tt0) cc_final: 0.8089 (tt0) REVERT: Y 275 LYS cc_start: 0.8205 (ttmt) cc_final: 0.7974 (tttt) REVERT: Y 276 GLU cc_start: 0.7171 (mp0) cc_final: 0.6938 (mp0) REVERT: Y 297 GLN cc_start: 0.7575 (tt0) cc_final: 0.7343 (tp-100) REVERT: Z 246 GLN cc_start: 0.8505 (tt0) cc_final: 0.8204 (tt0) REVERT: Z 376 LYS cc_start: 0.7992 (tttt) cc_final: 0.7611 (mttp) REVERT: a 235 LEU cc_start: 0.8966 (mt) cc_final: 0.8687 (mp) REVERT: a 246 GLN cc_start: 0.8485 (tt0) cc_final: 0.8204 (tt0) REVERT: a 275 LYS cc_start: 0.8150 (ttmt) cc_final: 0.7948 (tttt) REVERT: a 376 LYS cc_start: 0.7805 (tttt) cc_final: 0.7423 (mttp) REVERT: b 246 GLN cc_start: 0.8534 (tt0) cc_final: 0.8093 (tt0) REVERT: b 297 GLN cc_start: 0.7509 (tt0) cc_final: 0.7257 (tp-100) REVERT: b 376 LYS cc_start: 0.7728 (tttt) cc_final: 0.7380 (mttp) REVERT: b 377 MET cc_start: 0.7988 (mpt) cc_final: 0.7691 (mpt) REVERT: c 297 GLN cc_start: 0.7594 (tt0) cc_final: 0.7382 (tp40) REVERT: c 376 LYS cc_start: 0.7895 (tttt) cc_final: 0.7556 (mttp) REVERT: d 376 LYS cc_start: 0.7927 (tttt) cc_final: 0.7549 (mttp) REVERT: e 297 GLN cc_start: 0.7561 (tt0) cc_final: 0.7335 (tp-100) REVERT: e 376 LYS cc_start: 0.7895 (tttt) cc_final: 0.7559 (mttp) REVERT: f 297 GLN cc_start: 0.7592 (OUTLIER) cc_final: 0.7086 (tt0) REVERT: f 376 LYS cc_start: 0.7970 (tttt) cc_final: 0.7600 (mttp) REVERT: g 246 GLN cc_start: 0.8524 (tt0) cc_final: 0.8153 (tt0) REVERT: g 376 LYS cc_start: 0.8011 (tttt) cc_final: 0.7586 (mttp) outliers start: 35 outliers final: 9 residues processed: 1229 average time/residue: 1.7410 time to fit residues: 2511.3017 Evaluate side-chains 1204 residues out of total 4422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 1188 time to evaluate : 4.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 297 GLN Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain C residue 297 GLN Chi-restraints excluded: chain J residue 269 GLN Chi-restraints excluded: chain K residue 269 GLN Chi-restraints excluded: chain K residue 435 SER Chi-restraints excluded: chain P residue 363 THR Chi-restraints excluded: chain Q residue 235 LEU Chi-restraints excluded: chain Q residue 363 THR Chi-restraints excluded: chain a residue 435 SER Chi-restraints excluded: chain b residue 412 ILE Chi-restraints excluded: chain f residue 297 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 249 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 374 optimal weight: 9.9990 chunk 306 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 450 optimal weight: 0.9990 chunk 486 optimal weight: 2.9990 chunk 401 optimal weight: 6.9990 chunk 446 optimal weight: 0.8980 chunk 153 optimal weight: 9.9990 chunk 361 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 246 GLN B 297 GLN ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN C 297 GLN C 434 ASN D 246 GLN ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 434 ASN E 246 GLN E 434 ASN F 246 GLN G 246 GLN G 269 GLN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 297 GLN G 434 ASN H 231 ASN H 246 GLN H 263 HIS H 297 GLN ** H 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 246 GLN K 434 ASN M 246 GLN M 434 ASN ** N 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 297 GLN N 434 ASN O 246 GLN ** O 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 246 GLN P 269 GLN P 434 ASN Q 246 GLN Q 261 ASN Q 434 ASN S 246 GLN S 434 ASN T 269 GLN ** T 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 246 GLN V 246 GLN V 269 GLN ** V 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 297 GLN W 434 ASN X 239 ASN X 246 GLN X 269 GLN X 434 ASN ** Y 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 434 ASN c 246 GLN d 246 GLN d 434 ASN e 231 ASN e 246 GLN e 269 GLN f 246 GLN f 297 GLN f 434 ASN g 231 ASN ** g 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 39765 Z= 0.212 Angle : 0.460 4.896 53592 Z= 0.247 Chirality : 0.038 0.128 6138 Planarity : 0.003 0.043 7194 Dihedral : 4.575 16.792 5379 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Rotamer: Outliers : 1.42 % Allowed : 14.68 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.13), residues: 4785 helix: 1.96 (0.14), residues: 1320 sheet: 0.18 (0.11), residues: 2475 loop : -0.68 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS X 281 PHE 0.010 0.001 PHE S 422 TYR 0.011 0.001 TYR e 393 ARG 0.006 0.000 ARG R 370 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9570 Ramachandran restraints generated. 4785 Oldfield, 0 Emsley, 4785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9570 Ramachandran restraints generated. 4785 Oldfield, 0 Emsley, 4785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1256 residues out of total 4422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 1193 time to evaluate : 4.527 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: A 246 GLN cc_start: 0.8512 (tt0) cc_final: 0.8199 (tt0) REVERT: A 376 LYS cc_start: 0.7911 (tttt) cc_final: 0.7559 (mttp) REVERT: A 377 MET cc_start: 0.7775 (mpt) cc_final: 0.7319 (mpt) REVERT: B 297 GLN cc_start: 0.7447 (OUTLIER) cc_final: 0.7222 (tp-100) REVERT: B 376 LYS cc_start: 0.7846 (tttt) cc_final: 0.7363 (mttp) REVERT: C 269 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7572 (mp10) REVERT: C 376 LYS cc_start: 0.7898 (tttt) cc_final: 0.7596 (mttp) REVERT: C 418 GLU cc_start: 0.8335 (mm-30) cc_final: 0.8127 (mm-30) REVERT: D 246 GLN cc_start: 0.8491 (tt0) cc_final: 0.8240 (tt0) REVERT: D 376 LYS cc_start: 0.7774 (tttt) cc_final: 0.7426 (mttp) REVERT: E 376 LYS cc_start: 0.7882 (tttt) cc_final: 0.7456 (mttp) REVERT: F 376 LYS cc_start: 0.7956 (tttt) cc_final: 0.7542 (mttp) REVERT: G 235 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8799 (mp) REVERT: G 303 GLN cc_start: 0.7276 (OUTLIER) cc_final: 0.7027 (mp10) REVERT: G 376 LYS cc_start: 0.7860 (tttt) cc_final: 0.7399 (mttp) REVERT: G 409 MET cc_start: 0.8204 (mmm) cc_final: 0.7880 (mmm) REVERT: H 296 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.7016 (ttp-170) REVERT: H 297 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.7020 (tt0) REVERT: H 376 LYS cc_start: 0.8010 (tttt) cc_final: 0.7534 (mttp) REVERT: I 376 LYS cc_start: 0.8022 (tttt) cc_final: 0.7626 (mttp) REVERT: I 383 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7627 (mt-10) REVERT: J 246 GLN cc_start: 0.8561 (tt0) cc_final: 0.8160 (tt0) REVERT: J 269 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7569 (mp10) REVERT: J 376 LYS cc_start: 0.7886 (tttt) cc_final: 0.7476 (mttp) REVERT: J 383 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7633 (mt-10) REVERT: K 246 GLN cc_start: 0.8371 (tt0) cc_final: 0.8094 (tt0) REVERT: K 269 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7554 (mp10) REVERT: K 376 LYS cc_start: 0.7971 (tttt) cc_final: 0.7617 (mttp) REVERT: L 246 GLN cc_start: 0.8570 (tt0) cc_final: 0.8346 (tt0) REVERT: L 297 GLN cc_start: 0.7583 (tt0) cc_final: 0.7373 (tp-100) REVERT: M 276 GLU cc_start: 0.7271 (mt-10) cc_final: 0.6866 (mt-10) REVERT: M 297 GLN cc_start: 0.7553 (tt0) cc_final: 0.7296 (tp40) REVERT: M 376 LYS cc_start: 0.7876 (tttt) cc_final: 0.7470 (mttp) REVERT: N 246 GLN cc_start: 0.8443 (tt0) cc_final: 0.8204 (tt0) REVERT: N 376 LYS cc_start: 0.7883 (tttt) cc_final: 0.7511 (mttp) REVERT: N 377 MET cc_start: 0.7976 (mpt) cc_final: 0.7681 (mpt) REVERT: O 246 GLN cc_start: 0.8552 (tt0) cc_final: 0.8219 (tt0) REVERT: O 296 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.7218 (ttp-170) REVERT: O 376 LYS cc_start: 0.7986 (tttt) cc_final: 0.7607 (mttp) REVERT: P 376 LYS cc_start: 0.8027 (tttt) cc_final: 0.7622 (mttp) REVERT: P 435 SER cc_start: 0.8346 (t) cc_final: 0.8140 (t) REVERT: Q 235 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8561 (mp) REVERT: Q 297 GLN cc_start: 0.7555 (tt0) cc_final: 0.7345 (tp40) REVERT: Q 376 LYS cc_start: 0.7882 (tttt) cc_final: 0.7362 (mttp) REVERT: Q 409 MET cc_start: 0.8045 (mmm) cc_final: 0.7842 (mmm) REVERT: R 246 GLN cc_start: 0.8525 (tt0) cc_final: 0.8149 (tt0) REVERT: R 376 LYS cc_start: 0.7851 (tttt) cc_final: 0.7473 (mttp) REVERT: S 276 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7081 (tp30) REVERT: S 297 GLN cc_start: 0.7474 (tt0) cc_final: 0.7250 (tp-100) REVERT: S 376 LYS cc_start: 0.7892 (tttt) cc_final: 0.7481 (mttp) REVERT: T 246 GLN cc_start: 0.8527 (tt0) cc_final: 0.8275 (tt0) REVERT: T 297 GLN cc_start: 0.7582 (tt0) cc_final: 0.7349 (tp-100) REVERT: T 376 LYS cc_start: 0.7826 (tttt) cc_final: 0.7487 (mttp) REVERT: U 376 LYS cc_start: 0.7886 (tttt) cc_final: 0.7497 (mttp) REVERT: V 297 GLN cc_start: 0.7658 (tt0) cc_final: 0.7435 (tp40) REVERT: V 376 LYS cc_start: 0.7959 (tttt) cc_final: 0.7677 (ttmp) REVERT: W 276 GLU cc_start: 0.7316 (mt-10) cc_final: 0.6989 (mt-10) REVERT: W 376 LYS cc_start: 0.8025 (tttt) cc_final: 0.7540 (mttp) REVERT: X 376 LYS cc_start: 0.8009 (tttt) cc_final: 0.7521 (mttp) REVERT: Y 246 GLN cc_start: 0.8461 (tt0) cc_final: 0.8064 (tt0) REVERT: Y 275 LYS cc_start: 0.8190 (ttmt) cc_final: 0.7952 (tttt) REVERT: Y 297 GLN cc_start: 0.7560 (tt0) cc_final: 0.7332 (tp-100) REVERT: Y 376 LYS cc_start: 0.7971 (tttt) cc_final: 0.7613 (mttp) REVERT: Y 420 MET cc_start: 0.8197 (ptm) cc_final: 0.7865 (ptm) REVERT: Z 246 GLN cc_start: 0.8560 (tt0) cc_final: 0.8242 (tt0) REVERT: Z 303 GLN cc_start: 0.7291 (OUTLIER) cc_final: 0.6929 (mp10) REVERT: Z 376 LYS cc_start: 0.7959 (tttt) cc_final: 0.7572 (mttp) REVERT: a 235 LEU cc_start: 0.8972 (mt) cc_final: 0.8702 (mp) REVERT: a 246 GLN cc_start: 0.8436 (tt0) cc_final: 0.8143 (tt0) REVERT: a 376 LYS cc_start: 0.7826 (tttt) cc_final: 0.7432 (mttp) REVERT: b 246 GLN cc_start: 0.8494 (tt0) cc_final: 0.8058 (tt0) REVERT: b 297 GLN cc_start: 0.7498 (tt0) cc_final: 0.7287 (tp40) REVERT: b 376 LYS cc_start: 0.7773 (tttt) cc_final: 0.7393 (mttp) REVERT: b 409 MET cc_start: 0.8271 (mmm) cc_final: 0.8000 (mmm) REVERT: c 297 GLN cc_start: 0.7610 (tt0) cc_final: 0.7387 (tp40) REVERT: c 376 LYS cc_start: 0.7897 (tttt) cc_final: 0.7514 (mttp) REVERT: d 279 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7149 (mp0) REVERT: d 356 ARG cc_start: 0.6339 (mpp-170) cc_final: 0.6090 (mpp-170) REVERT: d 376 LYS cc_start: 0.7891 (tttt) cc_final: 0.7502 (mttp) REVERT: d 425 LYS cc_start: 0.8936 (mtmt) cc_final: 0.8736 (mtmm) REVERT: e 297 GLN cc_start: 0.7574 (tt0) cc_final: 0.7341 (tp-100) REVERT: e 376 LYS cc_start: 0.7875 (tttt) cc_final: 0.7533 (mttp) REVERT: f 297 GLN cc_start: 0.7509 (OUTLIER) cc_final: 0.7271 (tp-100) REVERT: f 376 LYS cc_start: 0.7956 (tttt) cc_final: 0.7604 (mttp) REVERT: f 409 MET cc_start: 0.8252 (mmm) cc_final: 0.7906 (mmm) REVERT: g 246 GLN cc_start: 0.8498 (tt0) cc_final: 0.8127 (tt0) REVERT: g 376 LYS cc_start: 0.8002 (tttt) cc_final: 0.7590 (mttp) outliers start: 63 outliers final: 21 residues processed: 1215 average time/residue: 1.7585 time to fit residues: 2505.9593 Evaluate side-chains 1203 residues out of total 4422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 1168 time to evaluate : 4.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 297 GLN Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 303 GLN Chi-restraints excluded: chain H residue 296 ARG Chi-restraints excluded: chain H residue 297 GLN Chi-restraints excluded: chain J residue 269 GLN Chi-restraints excluded: chain J residue 435 SER Chi-restraints excluded: chain K residue 269 GLN Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain O residue 235 LEU Chi-restraints excluded: chain O residue 296 ARG Chi-restraints excluded: chain O residue 429 THR Chi-restraints excluded: chain Q residue 235 LEU Chi-restraints excluded: chain Q residue 363 THR Chi-restraints excluded: chain S residue 276 GLU Chi-restraints excluded: chain U residue 363 THR Chi-restraints excluded: chain V residue 363 THR Chi-restraints excluded: chain V residue 435 SER Chi-restraints excluded: chain Z residue 303 GLN Chi-restraints excluded: chain Z residue 363 THR Chi-restraints excluded: chain a residue 435 SER Chi-restraints excluded: chain c residue 235 LEU Chi-restraints excluded: chain d residue 279 GLU Chi-restraints excluded: chain d residue 363 THR Chi-restraints excluded: chain d residue 383 GLU Chi-restraints excluded: chain d residue 402 LEU Chi-restraints excluded: chain f residue 297 GLN Chi-restraints excluded: chain f residue 435 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 444 optimal weight: 0.8980 chunk 338 optimal weight: 2.9990 chunk 233 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 214 optimal weight: 4.9990 chunk 302 optimal weight: 3.9990 chunk 451 optimal weight: 0.9990 chunk 478 optimal weight: 0.0020 chunk 236 optimal weight: 9.9990 chunk 428 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 246 GLN B 297 GLN ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN D 261 ASN E 246 GLN F 269 GLN G 246 GLN G 269 GLN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 231 ASN H 246 GLN H 297 GLN ** H 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 246 GLN J 411 GLN M 246 GLN N 269 GLN ** N 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 297 GLN O 297 GLN O 299 ASN ** O 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 269 GLN Q 246 GLN S 246 GLN T 269 GLN ** T 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 246 GLN V 246 GLN V 269 GLN ** V 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 297 GLN X 246 GLN ** Y 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 261 ASN c 246 GLN d 246 GLN e 231 ASN e 269 GLN f 246 GLN f 297 GLN g 231 ASN g 374 HIS ** g 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 39765 Z= 0.146 Angle : 0.423 4.827 53592 Z= 0.227 Chirality : 0.038 0.126 6138 Planarity : 0.002 0.030 7194 Dihedral : 4.329 16.469 5379 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.72 % Allowed : 15.08 % Favored : 83.20 % 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: 1.32 (0.13), residues: 4785 helix: 2.80 (0.15), residues: 1320 sheet: 0.45 (0.11), residues: 2475 loop : -0.51 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS X 281 PHE 0.009 0.001 PHE S 422 TYR 0.007 0.001 TYR e 393 ARG 0.004 0.000 ARG C 356 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9570 Ramachandran restraints generated. 4785 Oldfield, 0 Emsley, 4785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9570 Ramachandran restraints generated. 4785 Oldfield, 0 Emsley, 4785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1277 residues out of total 4422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 1201 time to evaluate : 4.617 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: A 246 GLN cc_start: 0.8468 (tt0) cc_final: 0.8134 (tt0) REVERT: A 376 LYS cc_start: 0.7887 (tttt) cc_final: 0.7594 (mttp) REVERT: B 376 LYS cc_start: 0.7803 (tttt) cc_final: 0.7328 (mttp) REVERT: B 409 MET cc_start: 0.8301 (mmm) cc_final: 0.7870 (mmm) REVERT: C 269 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7507 (mp10) REVERT: C 376 LYS cc_start: 0.7863 (tttt) cc_final: 0.7586 (mttp) REVERT: D 246 GLN cc_start: 0.8443 (tt0) cc_final: 0.8176 (tt0) REVERT: D 376 LYS cc_start: 0.7774 (tttt) cc_final: 0.7443 (mttp) REVERT: E 279 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.7078 (mp0) REVERT: E 376 LYS cc_start: 0.7879 (tttt) cc_final: 0.7482 (mttp) REVERT: F 376 LYS cc_start: 0.7951 (tttt) cc_final: 0.7535 (mttp) REVERT: G 235 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8727 (mp) REVERT: G 376 LYS cc_start: 0.7851 (tttt) cc_final: 0.7384 (mttp) REVERT: G 409 MET cc_start: 0.8183 (mmm) cc_final: 0.7880 (mmm) REVERT: H 296 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.7023 (ttp-170) REVERT: H 376 LYS cc_start: 0.7955 (tttt) cc_final: 0.7515 (mttp) REVERT: I 246 GLN cc_start: 0.8324 (tt0) cc_final: 0.8101 (tt0) REVERT: I 376 LYS cc_start: 0.8005 (tttt) cc_final: 0.7691 (mttp) REVERT: J 246 GLN cc_start: 0.8532 (tt0) cc_final: 0.8112 (tt0) REVERT: J 269 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7538 (mp10) REVERT: J 376 LYS cc_start: 0.7867 (tttt) cc_final: 0.7458 (mttp) REVERT: J 383 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7599 (mt-10) REVERT: K 246 GLN cc_start: 0.8357 (tt0) cc_final: 0.8030 (tt0) REVERT: K 269 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7520 (mp10) REVERT: K 296 ARG cc_start: 0.7710 (OUTLIER) cc_final: 0.6697 (ttp-170) REVERT: K 376 LYS cc_start: 0.7939 (tttt) cc_final: 0.7626 (mttp) REVERT: K 383 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7668 (mt-10) REVERT: L 246 GLN cc_start: 0.8484 (tt0) cc_final: 0.8258 (tt0) REVERT: L 297 GLN cc_start: 0.7589 (tt0) cc_final: 0.7372 (tp-100) REVERT: L 376 LYS cc_start: 0.7862 (tttt) cc_final: 0.7433 (mttp) REVERT: M 246 GLN cc_start: 0.8415 (tt0) cc_final: 0.8164 (tt0) REVERT: M 296 ARG cc_start: 0.7644 (OUTLIER) cc_final: 0.6728 (ttp-170) REVERT: M 297 GLN cc_start: 0.7535 (tt0) cc_final: 0.7333 (tp40) REVERT: M 376 LYS cc_start: 0.7835 (tttt) cc_final: 0.7492 (mttp) REVERT: M 377 MET cc_start: 0.7848 (mpt) cc_final: 0.7415 (mpt) REVERT: N 246 GLN cc_start: 0.8447 (tt0) cc_final: 0.8140 (tt0) REVERT: N 376 LYS cc_start: 0.7856 (tttt) cc_final: 0.7481 (mttp) REVERT: N 377 MET cc_start: 0.7946 (mpt) cc_final: 0.7645 (mpt) REVERT: O 376 LYS cc_start: 0.7977 (tttt) cc_final: 0.7614 (mttp) REVERT: P 376 LYS cc_start: 0.8016 (tttt) cc_final: 0.7622 (mttp) REVERT: P 435 SER cc_start: 0.8345 (t) cc_final: 0.8118 (t) REVERT: Q 235 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8498 (mp) REVERT: Q 297 GLN cc_start: 0.7557 (tt0) cc_final: 0.7348 (tp40) REVERT: Q 376 LYS cc_start: 0.7865 (tttt) cc_final: 0.7389 (mttp) REVERT: R 246 GLN cc_start: 0.8473 (tt0) cc_final: 0.8095 (tt0) REVERT: R 376 LYS cc_start: 0.7839 (tttt) cc_final: 0.7459 (mttp) REVERT: S 276 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6990 (tp30) REVERT: S 297 GLN cc_start: 0.7474 (tt0) cc_final: 0.7254 (tp-100) REVERT: S 376 LYS cc_start: 0.7848 (tttt) cc_final: 0.7463 (mttp) REVERT: T 246 GLN cc_start: 0.8492 (tt0) cc_final: 0.8205 (tt0) REVERT: T 297 GLN cc_start: 0.7563 (tt0) cc_final: 0.7323 (tp-100) REVERT: T 376 LYS cc_start: 0.7798 (tttt) cc_final: 0.7450 (mttp) REVERT: U 246 GLN cc_start: 0.8479 (tt0) cc_final: 0.7995 (tt0) REVERT: U 376 LYS cc_start: 0.7843 (tttt) cc_final: 0.7465 (mttp) REVERT: V 297 GLN cc_start: 0.7676 (tt0) cc_final: 0.7454 (tp40) REVERT: W 231 ASN cc_start: 0.4654 (OUTLIER) cc_final: 0.4297 (p0) REVERT: W 276 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6864 (mt-10) REVERT: W 376 LYS cc_start: 0.7989 (tttt) cc_final: 0.7492 (mttp) REVERT: X 269 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7696 (mp10) REVERT: X 376 LYS cc_start: 0.7989 (tttt) cc_final: 0.7520 (mttp) REVERT: Y 246 GLN cc_start: 0.8427 (tt0) cc_final: 0.8085 (tt0) REVERT: Y 275 LYS cc_start: 0.8157 (ttmt) cc_final: 0.7940 (tttt) REVERT: Y 297 GLN cc_start: 0.7534 (tt0) cc_final: 0.7318 (tp-100) REVERT: Y 376 LYS cc_start: 0.7906 (tttt) cc_final: 0.7573 (mttp) REVERT: Y 420 MET cc_start: 0.8186 (ptm) cc_final: 0.7916 (ptm) REVERT: Z 246 GLN cc_start: 0.8545 (tt0) cc_final: 0.8198 (tt0) REVERT: Z 296 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.6778 (ttp-170) REVERT: Z 376 LYS cc_start: 0.7962 (tttt) cc_final: 0.7610 (mttp) REVERT: a 246 GLN cc_start: 0.8421 (tt0) cc_final: 0.8125 (tt0) REVERT: a 376 LYS cc_start: 0.7792 (tttt) cc_final: 0.7407 (mttp) REVERT: b 246 GLN cc_start: 0.8524 (tt0) cc_final: 0.8050 (tt0) REVERT: b 297 GLN cc_start: 0.7488 (tt0) cc_final: 0.7272 (tp40) REVERT: b 376 LYS cc_start: 0.7722 (tttt) cc_final: 0.7339 (mttp) REVERT: c 297 GLN cc_start: 0.7594 (tt0) cc_final: 0.7380 (tp40) REVERT: c 376 LYS cc_start: 0.7861 (tttt) cc_final: 0.7541 (mttp) REVERT: d 276 GLU cc_start: 0.7297 (mt-10) cc_final: 0.7091 (tt0) REVERT: d 376 LYS cc_start: 0.7800 (tttt) cc_final: 0.7450 (mttp) REVERT: e 297 GLN cc_start: 0.7558 (tt0) cc_final: 0.7340 (tp-100) REVERT: e 376 LYS cc_start: 0.7842 (tttt) cc_final: 0.7531 (mttp) REVERT: f 296 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.7119 (tpp-160) REVERT: f 376 LYS cc_start: 0.7935 (tttt) cc_final: 0.7583 (mttp) REVERT: f 409 MET cc_start: 0.8227 (mmm) cc_final: 0.7967 (mmm) REVERT: g 246 GLN cc_start: 0.8470 (tt0) cc_final: 0.8076 (tt0) REVERT: g 376 LYS cc_start: 0.7975 (tttt) cc_final: 0.7550 (mttp) REVERT: g 383 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7621 (mt-10) outliers start: 76 outliers final: 26 residues processed: 1232 average time/residue: 1.7709 time to fit residues: 2563.1932 Evaluate side-chains 1227 residues out of total 4422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 1186 time to evaluate : 4.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain F residue 412 ILE Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain H residue 296 ARG Chi-restraints excluded: chain J residue 269 GLN Chi-restraints excluded: chain J residue 435 SER Chi-restraints excluded: chain K residue 269 GLN Chi-restraints excluded: chain K residue 296 ARG Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain M residue 296 ARG Chi-restraints excluded: chain N residue 363 THR Chi-restraints excluded: chain P residue 363 THR Chi-restraints excluded: chain Q residue 235 LEU Chi-restraints excluded: chain Q residue 363 THR Chi-restraints excluded: chain Q residue 433 VAL Chi-restraints excluded: chain S residue 276 GLU Chi-restraints excluded: chain S residue 429 THR Chi-restraints excluded: chain U residue 429 THR Chi-restraints excluded: chain V residue 363 THR Chi-restraints excluded: chain V residue 429 THR Chi-restraints excluded: chain V residue 435 SER Chi-restraints excluded: chain W residue 231 ASN Chi-restraints excluded: chain X residue 269 GLN Chi-restraints excluded: chain X residue 394 LYS Chi-restraints excluded: chain Z residue 235 LEU Chi-restraints excluded: chain Z residue 296 ARG Chi-restraints excluded: chain Z residue 363 THR Chi-restraints excluded: chain Z residue 433 VAL Chi-restraints excluded: chain c residue 235 LEU Chi-restraints excluded: chain d residue 363 THR Chi-restraints excluded: chain d residue 402 LEU Chi-restraints excluded: chain d residue 435 SER Chi-restraints excluded: chain e residue 363 THR Chi-restraints excluded: chain e residue 433 VAL Chi-restraints excluded: chain f residue 296 ARG Chi-restraints excluded: chain f residue 429 THR Chi-restraints excluded: chain g residue 383 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 398 optimal weight: 0.5980 chunk 271 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 356 optimal weight: 10.0000 chunk 197 optimal weight: 3.9990 chunk 408 optimal weight: 5.9990 chunk 330 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 244 optimal weight: 0.8980 chunk 429 optimal weight: 0.8980 chunk 120 optimal weight: 0.0040 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 GLN A 411 GLN B 246 GLN B 297 GLN ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN C 297 GLN E 246 GLN F 246 GLN F 269 GLN G 246 GLN G 269 GLN G 277 GLN H 231 ASN H 246 GLN H 297 GLN ** H 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 269 GLN N 277 GLN N 297 GLN O 246 GLN O 297 GLN O 299 ASN ** O 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 246 GLN P 269 GLN Q 246 GLN S 246 GLN T 269 GLN T 434 ASN V 246 GLN V 269 GLN V 434 ASN W 246 GLN W 297 GLN W 411 GLN X 246 GLN Y 434 ASN Z 411 GLN c 246 GLN d 246 GLN e 231 ASN e 269 GLN f 246 GLN g 231 ASN ** g 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 39765 Z= 0.139 Angle : 0.413 4.716 53592 Z= 0.221 Chirality : 0.038 0.124 6138 Planarity : 0.002 0.023 7194 Dihedral : 4.205 16.127 5379 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.81 % Allowed : 16.15 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.13), residues: 4785 helix: 3.13 (0.15), residues: 1320 sheet: 0.74 (0.12), residues: 2442 loop : -0.46 (0.19), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS X 281 PHE 0.009 0.001 PHE R 422 TYR 0.007 0.001 TYR e 393 ARG 0.004 0.000 ARG C 356 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9570 Ramachandran restraints generated. 4785 Oldfield, 0 Emsley, 4785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9570 Ramachandran restraints generated. 4785 Oldfield, 0 Emsley, 4785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1291 residues out of total 4422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 1211 time to evaluate : 4.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 GLN cc_start: 0.8488 (tt0) cc_final: 0.8126 (tt0) REVERT: A 376 LYS cc_start: 0.7874 (tttt) cc_final: 0.7552 (mttp) REVERT: A 409 MET cc_start: 0.8104 (mmm) cc_final: 0.7829 (mmm) REVERT: B 297 GLN cc_start: 0.7449 (OUTLIER) cc_final: 0.7127 (tp-100) REVERT: B 376 LYS cc_start: 0.7791 (tttt) cc_final: 0.7340 (mttp) REVERT: B 409 MET cc_start: 0.8310 (mmm) cc_final: 0.7871 (mmm) REVERT: C 269 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7499 (mp10) REVERT: C 297 GLN cc_start: 0.7372 (OUTLIER) cc_final: 0.6924 (tt0) REVERT: C 376 LYS cc_start: 0.7847 (tttt) cc_final: 0.7589 (mttp) REVERT: D 246 GLN cc_start: 0.8437 (tt0) cc_final: 0.8217 (tt0) REVERT: D 376 LYS cc_start: 0.7788 (tttt) cc_final: 0.7457 (mttp) REVERT: E 376 LYS cc_start: 0.7914 (tttt) cc_final: 0.7533 (mttp) REVERT: F 246 GLN cc_start: 0.8509 (tt0) cc_final: 0.8024 (tt0) REVERT: F 376 LYS cc_start: 0.7931 (tttt) cc_final: 0.7538 (mttp) REVERT: F 435 SER cc_start: 0.8328 (t) cc_final: 0.8121 (t) REVERT: G 235 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8730 (mp) REVERT: G 376 LYS cc_start: 0.7844 (tttt) cc_final: 0.7385 (mttp) REVERT: G 409 MET cc_start: 0.8167 (mmm) cc_final: 0.7915 (mmm) REVERT: H 296 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.6970 (ttp-170) REVERT: H 376 LYS cc_start: 0.7946 (tttt) cc_final: 0.7483 (mttp) REVERT: I 376 LYS cc_start: 0.7996 (tttt) cc_final: 0.7646 (mttp) REVERT: J 246 GLN cc_start: 0.8522 (tt0) cc_final: 0.8101 (tt0) REVERT: J 269 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7526 (mp10) REVERT: J 376 LYS cc_start: 0.7842 (tttt) cc_final: 0.7401 (mttp) REVERT: K 235 LEU cc_start: 0.8970 (mt) cc_final: 0.8511 (mp) REVERT: K 246 GLN cc_start: 0.8366 (tt0) cc_final: 0.8049 (tt0) REVERT: K 269 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7542 (mp10) REVERT: K 296 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.6670 (ttp-170) REVERT: K 376 LYS cc_start: 0.7939 (tttt) cc_final: 0.7639 (mttp) REVERT: L 246 GLN cc_start: 0.8480 (tt0) cc_final: 0.8271 (tt0) REVERT: L 297 GLN cc_start: 0.7585 (tt0) cc_final: 0.7376 (tp-100) REVERT: L 376 LYS cc_start: 0.7842 (tttt) cc_final: 0.7423 (mttp) REVERT: M 376 LYS cc_start: 0.7801 (tttt) cc_final: 0.7437 (mttp) REVERT: N 246 GLN cc_start: 0.8433 (tt0) cc_final: 0.8083 (tt0) REVERT: N 376 LYS cc_start: 0.7836 (tttt) cc_final: 0.7491 (mttp) REVERT: N 377 MET cc_start: 0.7938 (mpt) cc_final: 0.7631 (mpt) REVERT: O 246 GLN cc_start: 0.8491 (tt0) cc_final: 0.8182 (tt0) REVERT: O 376 LYS cc_start: 0.7970 (tttt) cc_final: 0.7619 (mttp) REVERT: P 376 LYS cc_start: 0.8004 (tttt) cc_final: 0.7587 (mttp) REVERT: P 435 SER cc_start: 0.8328 (t) cc_final: 0.8100 (t) REVERT: Q 235 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8484 (mp) REVERT: Q 297 GLN cc_start: 0.7546 (tt0) cc_final: 0.7334 (tp40) REVERT: Q 376 LYS cc_start: 0.7857 (tttt) cc_final: 0.7387 (mttp) REVERT: R 246 GLN cc_start: 0.8442 (tt0) cc_final: 0.8133 (tt0) REVERT: R 376 LYS cc_start: 0.7846 (tttt) cc_final: 0.7440 (mttp) REVERT: S 276 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6979 (tp30) REVERT: S 297 GLN cc_start: 0.7467 (tt0) cc_final: 0.7254 (tp-100) REVERT: S 376 LYS cc_start: 0.7830 (tttt) cc_final: 0.7443 (mttp) REVERT: T 246 GLN cc_start: 0.8470 (tt0) cc_final: 0.8150 (tt0) REVERT: T 297 GLN cc_start: 0.7582 (tt0) cc_final: 0.7366 (tp-100) REVERT: T 376 LYS cc_start: 0.7755 (tttt) cc_final: 0.7385 (mttp) REVERT: U 376 LYS cc_start: 0.7822 (tttt) cc_final: 0.7431 (mttp) REVERT: V 246 GLN cc_start: 0.8496 (tt0) cc_final: 0.8016 (tt0) REVERT: V 297 GLN cc_start: 0.7684 (tt0) cc_final: 0.7468 (tp40) REVERT: V 376 LYS cc_start: 0.7906 (tttt) cc_final: 0.7507 (mttp) REVERT: W 231 ASN cc_start: 0.4772 (OUTLIER) cc_final: 0.4410 (p0) REVERT: W 269 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7828 (mp10) REVERT: W 376 LYS cc_start: 0.7964 (tttt) cc_final: 0.7469 (mttp) REVERT: X 269 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7732 (mp10) REVERT: X 279 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.7064 (mp0) REVERT: X 376 LYS cc_start: 0.7971 (tttt) cc_final: 0.7510 (mttp) REVERT: Y 246 GLN cc_start: 0.8441 (tt0) cc_final: 0.8039 (tt0) REVERT: Y 297 GLN cc_start: 0.7550 (tt0) cc_final: 0.7333 (tp-100) REVERT: Y 376 LYS cc_start: 0.7902 (tttt) cc_final: 0.7578 (mttp) REVERT: Y 420 MET cc_start: 0.8254 (ptm) cc_final: 0.7952 (ptm) REVERT: Z 246 GLN cc_start: 0.8535 (tt0) cc_final: 0.8165 (tt0) REVERT: Z 296 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.6698 (ttp-170) REVERT: Z 376 LYS cc_start: 0.7904 (tttt) cc_final: 0.7571 (mttp) REVERT: a 235 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8605 (mp) REVERT: a 246 GLN cc_start: 0.8479 (tt0) cc_final: 0.8054 (tt0) REVERT: a 376 LYS cc_start: 0.7769 (tttt) cc_final: 0.7362 (mttp) REVERT: b 246 GLN cc_start: 0.8509 (tt0) cc_final: 0.8107 (tt0) REVERT: b 297 GLN cc_start: 0.7482 (tt0) cc_final: 0.7274 (tp40) REVERT: b 376 LYS cc_start: 0.7686 (tttt) cc_final: 0.7332 (mttp) REVERT: b 425 LYS cc_start: 0.8888 (mtmt) cc_final: 0.8687 (mtmm) REVERT: c 279 GLU cc_start: 0.7362 (mt-10) cc_final: 0.7055 (mp0) REVERT: c 376 LYS cc_start: 0.7856 (tttt) cc_final: 0.7539 (mttp) REVERT: d 276 GLU cc_start: 0.7257 (mt-10) cc_final: 0.7055 (tt0) REVERT: d 279 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.7010 (mp0) REVERT: d 376 LYS cc_start: 0.7768 (tttt) cc_final: 0.7417 (mttp) REVERT: e 297 GLN cc_start: 0.7557 (tt0) cc_final: 0.7340 (tp-100) REVERT: e 376 LYS cc_start: 0.7823 (tttt) cc_final: 0.7547 (mttp) REVERT: f 296 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.6894 (tpp-160) REVERT: f 376 LYS cc_start: 0.7932 (tttt) cc_final: 0.7611 (mttp) REVERT: f 409 MET cc_start: 0.8249 (mmm) cc_final: 0.7984 (mmm) REVERT: g 246 GLN cc_start: 0.8449 (tt0) cc_final: 0.8029 (tt0) REVERT: g 376 LYS cc_start: 0.7948 (tttt) cc_final: 0.7531 (mttp) REVERT: g 383 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7555 (mt-10) outliers start: 80 outliers final: 32 residues processed: 1238 average time/residue: 1.7335 time to fit residues: 2525.5178 Evaluate side-chains 1245 residues out of total 4422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 1194 time to evaluate : 5.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 297 GLN Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain C residue 297 GLN Chi-restraints excluded: chain F residue 412 ILE Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain H residue 296 ARG Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain J residue 269 GLN Chi-restraints excluded: chain J residue 435 SER Chi-restraints excluded: chain K residue 269 GLN Chi-restraints excluded: chain K residue 296 ARG Chi-restraints excluded: chain N residue 363 THR Chi-restraints excluded: chain O residue 429 THR Chi-restraints excluded: chain P residue 363 THR Chi-restraints excluded: chain Q residue 235 LEU Chi-restraints excluded: chain Q residue 363 THR Chi-restraints excluded: chain Q residue 433 VAL Chi-restraints excluded: chain S residue 276 GLU Chi-restraints excluded: chain S residue 429 THR Chi-restraints excluded: chain U residue 363 THR Chi-restraints excluded: chain U residue 429 THR Chi-restraints excluded: chain V residue 363 THR Chi-restraints excluded: chain V residue 429 THR Chi-restraints excluded: chain V residue 435 SER Chi-restraints excluded: chain W residue 231 ASN Chi-restraints excluded: chain W residue 269 GLN Chi-restraints excluded: chain X residue 269 GLN Chi-restraints excluded: chain X residue 276 GLU Chi-restraints excluded: chain X residue 279 GLU Chi-restraints excluded: chain X residue 394 LYS Chi-restraints excluded: chain X residue 429 THR Chi-restraints excluded: chain Z residue 235 LEU Chi-restraints excluded: chain Z residue 296 ARG Chi-restraints excluded: chain Z residue 363 THR Chi-restraints excluded: chain Z residue 429 THR Chi-restraints excluded: chain a residue 235 LEU Chi-restraints excluded: chain b residue 276 GLU Chi-restraints excluded: chain b residue 363 THR Chi-restraints excluded: chain c residue 235 LEU Chi-restraints excluded: chain d residue 279 GLU Chi-restraints excluded: chain d residue 363 THR Chi-restraints excluded: chain d residue 402 LEU Chi-restraints excluded: chain d residue 433 VAL Chi-restraints excluded: chain e residue 363 THR Chi-restraints excluded: chain f residue 296 ARG Chi-restraints excluded: chain f residue 429 THR Chi-restraints excluded: chain f residue 435 SER Chi-restraints excluded: chain g residue 383 GLU Chi-restraints excluded: chain g residue 435 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 160 optimal weight: 9.9990 chunk 430 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 280 optimal weight: 8.9990 chunk 118 optimal weight: 0.8980 chunk 478 optimal weight: 0.7980 chunk 397 optimal weight: 3.9990 chunk 221 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 158 optimal weight: 4.9990 chunk 251 optimal weight: 5.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 ASN B 246 GLN B 434 ASN C 246 GLN C 297 GLN C 365 ASN E 246 GLN E 365 ASN F 269 GLN F 365 ASN G 246 GLN G 269 GLN H 231 ASN H 246 GLN H 297 GLN H 434 ASN I 246 GLN J 263 HIS K 365 ASN M 246 GLN M 297 GLN N 231 ASN N 269 GLN N 297 GLN O 434 ASN Q 246 GLN S 246 GLN T 269 GLN U 246 GLN V 269 GLN W 297 GLN X 246 GLN a 365 ASN c 246 GLN c 297 GLN d 246 GLN e 231 ASN e 269 GLN f 246 GLN f 297 GLN g 231 ASN g 434 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 39765 Z= 0.278 Angle : 0.474 4.995 53592 Z= 0.254 Chirality : 0.039 0.129 6138 Planarity : 0.002 0.033 7194 Dihedral : 4.576 17.009 5379 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 2.26 % Allowed : 16.30 % Favored : 81.43 % 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: 1.66 (0.13), residues: 4785 helix: 2.93 (0.15), residues: 1320 sheet: 0.81 (0.12), residues: 2442 loop : -0.56 (0.18), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS X 281 PHE 0.011 0.001 PHE Y 422 TYR 0.010 0.001 TYR f 393 ARG 0.005 0.000 ARG J 373 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9570 Ramachandran restraints generated. 4785 Oldfield, 0 Emsley, 4785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9570 Ramachandran restraints generated. 4785 Oldfield, 0 Emsley, 4785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1312 residues out of total 4422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 1212 time to evaluate : 4.508 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: A 246 GLN cc_start: 0.8579 (tt0) cc_final: 0.8276 (tt0) REVERT: A 376 LYS cc_start: 0.7906 (tttt) cc_final: 0.7614 (mttp) REVERT: B 376 LYS cc_start: 0.7853 (tttt) cc_final: 0.7379 (mttp) REVERT: B 409 MET cc_start: 0.8298 (mmm) cc_final: 0.7855 (mmm) REVERT: C 269 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7652 (mp10) REVERT: C 376 LYS cc_start: 0.7939 (tttt) cc_final: 0.7646 (mttp) REVERT: D 246 GLN cc_start: 0.8566 (tt0) cc_final: 0.8361 (tt0) REVERT: D 376 LYS cc_start: 0.7836 (tttt) cc_final: 0.7481 (mttp) REVERT: E 376 LYS cc_start: 0.7870 (tttt) cc_final: 0.7448 (mttp) REVERT: F 376 LYS cc_start: 0.7988 (tttt) cc_final: 0.7560 (mttp) REVERT: G 235 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8831 (mp) REVERT: G 376 LYS cc_start: 0.7902 (tttt) cc_final: 0.7442 (mttp) REVERT: G 409 MET cc_start: 0.8191 (mmm) cc_final: 0.7880 (mmm) REVERT: H 296 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7081 (ttp-170) REVERT: H 297 GLN cc_start: 0.7451 (OUTLIER) cc_final: 0.6926 (tt0) REVERT: H 376 LYS cc_start: 0.8005 (tttt) cc_final: 0.7524 (mttp) REVERT: I 246 GLN cc_start: 0.8530 (tt0) cc_final: 0.8260 (tt0) REVERT: I 376 LYS cc_start: 0.8008 (tttt) cc_final: 0.7606 (mttp) REVERT: J 246 GLN cc_start: 0.8601 (tt0) cc_final: 0.8181 (tt0) REVERT: J 269 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7595 (mp10) REVERT: J 376 LYS cc_start: 0.7890 (tttt) cc_final: 0.7431 (mttp) REVERT: K 235 LEU cc_start: 0.9027 (mt) cc_final: 0.8550 (mp) REVERT: K 246 GLN cc_start: 0.8455 (tt0) cc_final: 0.8090 (tt0) REVERT: K 269 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7556 (mp10) REVERT: K 376 LYS cc_start: 0.7993 (tttt) cc_final: 0.7664 (mttp) REVERT: L 246 GLN cc_start: 0.8600 (tt0) cc_final: 0.8372 (tt0) REVERT: L 297 GLN cc_start: 0.7616 (tt0) cc_final: 0.7390 (tp-100) REVERT: L 376 LYS cc_start: 0.7890 (tttt) cc_final: 0.7471 (mttp) REVERT: M 297 GLN cc_start: 0.7598 (OUTLIER) cc_final: 0.7140 (tt0) REVERT: M 376 LYS cc_start: 0.7889 (tttt) cc_final: 0.7467 (mttp) REVERT: N 246 GLN cc_start: 0.8498 (tt0) cc_final: 0.8205 (tt0) REVERT: N 376 LYS cc_start: 0.7889 (tttt) cc_final: 0.7515 (mttp) REVERT: O 376 LYS cc_start: 0.8005 (tttt) cc_final: 0.7640 (mttp) REVERT: P 376 LYS cc_start: 0.8047 (tttt) cc_final: 0.7646 (mttp) REVERT: P 435 SER cc_start: 0.8366 (t) cc_final: 0.8161 (t) REVERT: Q 235 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8600 (mp) REVERT: Q 297 GLN cc_start: 0.7558 (tt0) cc_final: 0.7325 (tp40) REVERT: Q 376 LYS cc_start: 0.7898 (tttt) cc_final: 0.7383 (mttp) REVERT: R 246 GLN cc_start: 0.8592 (tt0) cc_final: 0.8201 (tt0) REVERT: R 376 LYS cc_start: 0.7893 (tttt) cc_final: 0.7493 (mttp) REVERT: S 376 LYS cc_start: 0.7921 (tttt) cc_final: 0.7584 (mttp) REVERT: T 246 GLN cc_start: 0.8578 (tt0) cc_final: 0.8284 (tt0) REVERT: T 297 GLN cc_start: 0.7596 (tt0) cc_final: 0.7384 (tp-100) REVERT: T 376 LYS cc_start: 0.7868 (tttt) cc_final: 0.7491 (mttp) REVERT: U 246 GLN cc_start: 0.8511 (tt0) cc_final: 0.8014 (tt0) REVERT: U 376 LYS cc_start: 0.7904 (tttt) cc_final: 0.7513 (mttp) REVERT: V 235 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8718 (mp) REVERT: V 297 GLN cc_start: 0.7695 (tt0) cc_final: 0.7477 (tp40) REVERT: V 376 LYS cc_start: 0.7964 (tttt) cc_final: 0.7559 (mttp) REVERT: W 231 ASN cc_start: 0.4788 (OUTLIER) cc_final: 0.4488 (p0) REVERT: W 269 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7866 (mp10) REVERT: W 287 ASP cc_start: 0.7505 (t0) cc_final: 0.7239 (t70) REVERT: W 376 LYS cc_start: 0.8028 (tttt) cc_final: 0.7544 (mttp) REVERT: X 269 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7716 (mp10) REVERT: X 279 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.7121 (mp0) REVERT: X 376 LYS cc_start: 0.8017 (tttt) cc_final: 0.7541 (mttp) REVERT: Y 246 GLN cc_start: 0.8514 (tt0) cc_final: 0.8122 (tt0) REVERT: Y 297 GLN cc_start: 0.7574 (tt0) cc_final: 0.7340 (tp40) REVERT: Y 376 LYS cc_start: 0.7983 (tttt) cc_final: 0.7624 (mttp) REVERT: Y 420 MET cc_start: 0.8454 (ptm) cc_final: 0.8030 (ptm) REVERT: Z 246 GLN cc_start: 0.8544 (tt0) cc_final: 0.8209 (tt0) REVERT: Z 303 GLN cc_start: 0.7283 (OUTLIER) cc_final: 0.7028 (mp10) REVERT: Z 376 LYS cc_start: 0.7948 (tttt) cc_final: 0.7629 (mttp) REVERT: a 246 GLN cc_start: 0.8482 (tt0) cc_final: 0.8178 (tt0) REVERT: a 376 LYS cc_start: 0.7803 (tttt) cc_final: 0.7415 (mttp) REVERT: b 246 GLN cc_start: 0.8554 (tt0) cc_final: 0.8117 (tt0) REVERT: b 376 LYS cc_start: 0.7783 (tttt) cc_final: 0.7430 (mttp) REVERT: c 279 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.7088 (mp0) REVERT: c 297 GLN cc_start: 0.7591 (OUTLIER) cc_final: 0.6919 (tt0) REVERT: c 376 LYS cc_start: 0.7909 (tttt) cc_final: 0.7518 (mttp) REVERT: d 276 GLU cc_start: 0.7303 (mt-10) cc_final: 0.7084 (tt0) REVERT: d 279 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7193 (mp0) REVERT: d 376 LYS cc_start: 0.7863 (tttt) cc_final: 0.7505 (mttp) REVERT: e 297 GLN cc_start: 0.7590 (tt0) cc_final: 0.7370 (tp-100) REVERT: e 376 LYS cc_start: 0.7892 (tttt) cc_final: 0.7555 (mttp) REVERT: f 296 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.7154 (tpp-160) REVERT: f 297 GLN cc_start: 0.7548 (OUTLIER) cc_final: 0.7155 (tt0) REVERT: f 376 LYS cc_start: 0.7925 (tttt) cc_final: 0.7579 (mttp) REVERT: f 409 MET cc_start: 0.8228 (mmm) cc_final: 0.7897 (mmm) REVERT: g 246 GLN cc_start: 0.8536 (tt0) cc_final: 0.8146 (tt0) REVERT: g 297 GLN cc_start: 0.7515 (OUTLIER) cc_final: 0.6731 (tp-100) REVERT: g 376 LYS cc_start: 0.8018 (tttt) cc_final: 0.7612 (mttp) REVERT: g 383 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7492 (mt-10) outliers start: 100 outliers final: 48 residues processed: 1244 average time/residue: 1.7258 time to fit residues: 2523.2860 Evaluate side-chains 1260 residues out of total 4422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 1191 time to evaluate : 4.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain H residue 296 ARG Chi-restraints excluded: chain H residue 297 GLN Chi-restraints excluded: chain I residue 276 GLU Chi-restraints excluded: chain I residue 405 THR Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain J residue 269 GLN Chi-restraints excluded: chain J residue 435 SER Chi-restraints excluded: chain K residue 269 GLN Chi-restraints excluded: chain K residue 429 THR Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain M residue 297 GLN Chi-restraints excluded: chain N residue 231 ASN Chi-restraints excluded: chain N residue 235 LEU Chi-restraints excluded: chain N residue 363 THR Chi-restraints excluded: chain O residue 235 LEU Chi-restraints excluded: chain O residue 429 THR Chi-restraints excluded: chain P residue 363 THR Chi-restraints excluded: chain Q residue 235 LEU Chi-restraints excluded: chain Q residue 363 THR Chi-restraints excluded: chain Q residue 433 VAL Chi-restraints excluded: chain S residue 276 GLU Chi-restraints excluded: chain S residue 429 THR Chi-restraints excluded: chain U residue 363 THR Chi-restraints excluded: chain U residue 405 THR Chi-restraints excluded: chain U residue 429 THR Chi-restraints excluded: chain V residue 235 LEU Chi-restraints excluded: chain V residue 429 THR Chi-restraints excluded: chain V residue 435 SER Chi-restraints excluded: chain W residue 231 ASN Chi-restraints excluded: chain W residue 269 GLN Chi-restraints excluded: chain W residue 435 SER Chi-restraints excluded: chain X residue 269 GLN Chi-restraints excluded: chain X residue 276 GLU Chi-restraints excluded: chain X residue 279 GLU Chi-restraints excluded: chain X residue 429 THR Chi-restraints excluded: chain Y residue 429 THR Chi-restraints excluded: chain Z residue 235 LEU Chi-restraints excluded: chain Z residue 303 GLN Chi-restraints excluded: chain Z residue 363 THR Chi-restraints excluded: chain Z residue 405 THR Chi-restraints excluded: chain Z residue 429 THR Chi-restraints excluded: chain Z residue 433 VAL Chi-restraints excluded: chain a residue 429 THR Chi-restraints excluded: chain c residue 235 LEU Chi-restraints excluded: chain c residue 279 GLU Chi-restraints excluded: chain c residue 297 GLN Chi-restraints excluded: chain c residue 405 THR Chi-restraints excluded: chain d residue 279 GLU Chi-restraints excluded: chain d residue 363 THR Chi-restraints excluded: chain d residue 402 LEU Chi-restraints excluded: chain e residue 412 ILE Chi-restraints excluded: chain e residue 433 VAL Chi-restraints excluded: chain f residue 296 ARG Chi-restraints excluded: chain f residue 297 GLN Chi-restraints excluded: chain f residue 405 THR Chi-restraints excluded: chain f residue 429 THR Chi-restraints excluded: chain f residue 435 SER Chi-restraints excluded: chain g residue 231 ASN Chi-restraints excluded: chain g residue 297 GLN Chi-restraints excluded: chain g residue 383 GLU Chi-restraints excluded: chain g residue 433 VAL Chi-restraints excluded: chain g residue 435 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 461 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 272 optimal weight: 0.7980 chunk 349 optimal weight: 3.9990 chunk 270 optimal weight: 0.9990 chunk 403 optimal weight: 0.0020 chunk 267 optimal weight: 5.9990 chunk 477 optimal weight: 2.9990 chunk 298 optimal weight: 0.6980 chunk 290 optimal weight: 0.0040 chunk 220 optimal weight: 4.9990 overall best weight: 0.5002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 GLN B 246 GLN B 297 GLN F 246 GLN F 269 GLN G 269 GLN H 231 ASN H 246 GLN H 297 GLN M 246 GLN M 297 GLN N 231 ASN N 269 GLN N 297 GLN O 246 GLN S 246 GLN S 297 GLN V 246 GLN V 269 GLN W 297 GLN X 246 GLN c 246 GLN c 297 GLN e 231 ASN e 269 GLN f 246 GLN f 297 GLN g 231 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 39765 Z= 0.121 Angle : 0.409 5.501 53592 Z= 0.220 Chirality : 0.038 0.125 6138 Planarity : 0.002 0.029 7194 Dihedral : 4.136 16.190 5379 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % Rotamer: Outliers : 1.72 % Allowed : 17.59 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.13), residues: 4785 helix: 3.38 (0.15), residues: 1320 sheet: 1.01 (0.11), residues: 2442 loop : -0.40 (0.19), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 281 PHE 0.009 0.001 PHE R 422 TYR 0.005 0.001 TYR O 393 ARG 0.008 0.000 ARG L 356 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9570 Ramachandran restraints generated. 4785 Oldfield, 0 Emsley, 4785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9570 Ramachandran restraints generated. 4785 Oldfield, 0 Emsley, 4785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1296 residues out of total 4422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 1220 time to evaluate : 4.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 GLN cc_start: 0.8481 (tt0) cc_final: 0.8121 (tt0) REVERT: A 376 LYS cc_start: 0.7892 (tttt) cc_final: 0.7563 (mttp) REVERT: A 409 MET cc_start: 0.8101 (mmm) cc_final: 0.7869 (mmm) REVERT: B 297 GLN cc_start: 0.7446 (OUTLIER) cc_final: 0.6997 (tt0) REVERT: B 376 LYS cc_start: 0.7781 (tttt) cc_final: 0.7401 (mttp) REVERT: B 409 MET cc_start: 0.8318 (mmm) cc_final: 0.7883 (mmm) REVERT: C 269 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7509 (mp10) REVERT: C 376 LYS cc_start: 0.7851 (tttt) cc_final: 0.7612 (mttp) REVERT: D 246 GLN cc_start: 0.8486 (tt0) cc_final: 0.8219 (tt0) REVERT: D 376 LYS cc_start: 0.7786 (tttt) cc_final: 0.7453 (mttp) REVERT: E 376 LYS cc_start: 0.7913 (tttt) cc_final: 0.7540 (mttp) REVERT: F 246 GLN cc_start: 0.8473 (tt0) cc_final: 0.7980 (tt0) REVERT: F 376 LYS cc_start: 0.7928 (tttt) cc_final: 0.7555 (mttp) REVERT: F 435 SER cc_start: 0.8400 (OUTLIER) cc_final: 0.7983 (t) REVERT: G 235 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8701 (mp) REVERT: G 376 LYS cc_start: 0.7839 (tttt) cc_final: 0.7415 (mttp) REVERT: G 409 MET cc_start: 0.8178 (mmm) cc_final: 0.7915 (mmm) REVERT: H 376 LYS cc_start: 0.7923 (tttt) cc_final: 0.7485 (mttp) REVERT: I 376 LYS cc_start: 0.7975 (tttt) cc_final: 0.7624 (mttp) REVERT: J 246 GLN cc_start: 0.8495 (tt0) cc_final: 0.8029 (tt0) REVERT: J 269 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.7544 (mp10) REVERT: J 376 LYS cc_start: 0.7792 (tttt) cc_final: 0.7395 (mttp) REVERT: K 235 LEU cc_start: 0.8965 (mt) cc_final: 0.8509 (mp) REVERT: K 246 GLN cc_start: 0.8360 (tt0) cc_final: 0.8075 (tt0) REVERT: K 269 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7548 (mp10) REVERT: K 296 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.6655 (ttp-170) REVERT: K 376 LYS cc_start: 0.7934 (tttt) cc_final: 0.7619 (mttp) REVERT: L 246 GLN cc_start: 0.8525 (tt0) cc_final: 0.8283 (tt0) REVERT: L 297 GLN cc_start: 0.7606 (tt0) cc_final: 0.7405 (tp-100) REVERT: L 376 LYS cc_start: 0.7812 (tttt) cc_final: 0.7444 (mttp) REVERT: M 376 LYS cc_start: 0.7813 (tttt) cc_final: 0.7418 (mttp) REVERT: N 246 GLN cc_start: 0.8423 (tt0) cc_final: 0.8057 (tt0) REVERT: N 303 GLN cc_start: 0.7212 (OUTLIER) cc_final: 0.6562 (mt0) REVERT: N 376 LYS cc_start: 0.7820 (tttt) cc_final: 0.7469 (mttp) REVERT: O 246 GLN cc_start: 0.8403 (tt0) cc_final: 0.8138 (tt0) REVERT: O 376 LYS cc_start: 0.7956 (tttt) cc_final: 0.7607 (mttp) REVERT: P 376 LYS cc_start: 0.7998 (tttt) cc_final: 0.7605 (mttp) REVERT: P 435 SER cc_start: 0.8307 (t) cc_final: 0.8074 (t) REVERT: Q 235 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8476 (mp) REVERT: Q 297 GLN cc_start: 0.7567 (tt0) cc_final: 0.7359 (tp40) REVERT: Q 376 LYS cc_start: 0.7851 (tttt) cc_final: 0.7403 (mttp) REVERT: Q 420 MET cc_start: 0.8590 (ptm) cc_final: 0.8376 (ptm) REVERT: R 246 GLN cc_start: 0.8475 (tt0) cc_final: 0.8115 (tt0) REVERT: R 376 LYS cc_start: 0.7862 (tttt) cc_final: 0.7501 (mttp) REVERT: S 276 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6916 (tp30) REVERT: S 376 LYS cc_start: 0.7845 (tttt) cc_final: 0.7466 (mttp) REVERT: S 377 MET cc_start: 0.7797 (mpt) cc_final: 0.7387 (mpt) REVERT: T 246 GLN cc_start: 0.8452 (tt0) cc_final: 0.8150 (tt0) REVERT: T 297 GLN cc_start: 0.7578 (tt0) cc_final: 0.7360 (tp-100) REVERT: T 376 LYS cc_start: 0.7769 (tttt) cc_final: 0.7381 (mttp) REVERT: U 279 GLU cc_start: 0.7202 (mt-10) cc_final: 0.6996 (mp0) REVERT: U 376 LYS cc_start: 0.7807 (tttt) cc_final: 0.7435 (mttp) REVERT: V 246 GLN cc_start: 0.8469 (tt0) cc_final: 0.8055 (tt0) REVERT: V 297 GLN cc_start: 0.7675 (tt0) cc_final: 0.7465 (tp40) REVERT: V 376 LYS cc_start: 0.7904 (tttt) cc_final: 0.7526 (mttp) REVERT: W 231 ASN cc_start: 0.4643 (OUTLIER) cc_final: 0.4354 (p0) REVERT: W 269 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7809 (mp10) REVERT: W 376 LYS cc_start: 0.7966 (tttt) cc_final: 0.7489 (mttp) REVERT: X 269 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7721 (mp10) REVERT: X 279 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.7031 (mp0) REVERT: X 376 LYS cc_start: 0.7950 (tttt) cc_final: 0.7498 (mttp) REVERT: Y 246 GLN cc_start: 0.8449 (tt0) cc_final: 0.8069 (tt0) REVERT: Y 297 GLN cc_start: 0.7535 (tt0) cc_final: 0.7329 (tp-100) REVERT: Y 376 LYS cc_start: 0.7930 (tttt) cc_final: 0.7587 (mttp) REVERT: Y 420 MET cc_start: 0.8366 (ptm) cc_final: 0.8000 (ptm) REVERT: Z 246 GLN cc_start: 0.8542 (tt0) cc_final: 0.8149 (tt0) REVERT: Z 296 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.6716 (ttp-170) REVERT: Z 376 LYS cc_start: 0.7877 (tttt) cc_final: 0.7589 (mttp) REVERT: a 235 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8646 (mp) REVERT: a 246 GLN cc_start: 0.8463 (tt0) cc_final: 0.8010 (tt0) REVERT: a 376 LYS cc_start: 0.7751 (tttt) cc_final: 0.7381 (mttp) REVERT: b 246 GLN cc_start: 0.8493 (tt0) cc_final: 0.8052 (tt0) REVERT: b 297 GLN cc_start: 0.7538 (tt0) cc_final: 0.7260 (tp40) REVERT: b 376 LYS cc_start: 0.7671 (tttt) cc_final: 0.7334 (mttp) REVERT: c 279 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6930 (mp0) REVERT: c 376 LYS cc_start: 0.7831 (tttt) cc_final: 0.7523 (mttp) REVERT: d 279 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6966 (mp0) REVERT: d 376 LYS cc_start: 0.7742 (tttt) cc_final: 0.7432 (mttp) REVERT: e 297 GLN cc_start: 0.7558 (tt0) cc_final: 0.7347 (tp-100) REVERT: e 376 LYS cc_start: 0.7827 (tttt) cc_final: 0.7523 (mttp) REVERT: f 296 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7265 (tpp-160) REVERT: f 376 LYS cc_start: 0.7903 (tttt) cc_final: 0.7588 (mttp) REVERT: f 409 MET cc_start: 0.8264 (mmm) cc_final: 0.7994 (mmm) REVERT: g 246 GLN cc_start: 0.8453 (tt0) cc_final: 0.8036 (tt0) REVERT: g 376 LYS cc_start: 0.7964 (tttt) cc_final: 0.7557 (mttp) REVERT: g 383 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7555 (mt-10) outliers start: 76 outliers final: 25 residues processed: 1242 average time/residue: 1.7110 time to fit residues: 2503.7583 Evaluate side-chains 1252 residues out of total 4422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 1208 time to evaluate : 4.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 297 GLN Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 435 SER Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain J residue 269 GLN Chi-restraints excluded: chain J residue 435 SER Chi-restraints excluded: chain K residue 269 GLN Chi-restraints excluded: chain K residue 296 ARG Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain N residue 303 GLN Chi-restraints excluded: chain N residue 363 THR Chi-restraints excluded: chain P residue 363 THR Chi-restraints excluded: chain Q residue 235 LEU Chi-restraints excluded: chain Q residue 363 THR Chi-restraints excluded: chain Q residue 433 VAL Chi-restraints excluded: chain S residue 276 GLU Chi-restraints excluded: chain U residue 363 THR Chi-restraints excluded: chain U residue 429 THR Chi-restraints excluded: chain V residue 435 SER Chi-restraints excluded: chain W residue 231 ASN Chi-restraints excluded: chain W residue 269 GLN Chi-restraints excluded: chain W residue 435 SER Chi-restraints excluded: chain X residue 269 GLN Chi-restraints excluded: chain X residue 276 GLU Chi-restraints excluded: chain X residue 279 GLU Chi-restraints excluded: chain Z residue 296 ARG Chi-restraints excluded: chain Z residue 363 THR Chi-restraints excluded: chain a residue 235 LEU Chi-restraints excluded: chain b residue 363 THR Chi-restraints excluded: chain c residue 235 LEU Chi-restraints excluded: chain c residue 405 THR Chi-restraints excluded: chain d residue 279 GLU Chi-restraints excluded: chain d residue 363 THR Chi-restraints excluded: chain d residue 402 LEU Chi-restraints excluded: chain d residue 435 SER Chi-restraints excluded: chain e residue 363 THR Chi-restraints excluded: chain e residue 433 VAL Chi-restraints excluded: chain f residue 276 GLU Chi-restraints excluded: chain f residue 296 ARG Chi-restraints excluded: chain f residue 435 SER Chi-restraints excluded: chain g residue 383 GLU Chi-restraints excluded: chain g residue 435 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 295 optimal weight: 5.9990 chunk 190 optimal weight: 5.9990 chunk 284 optimal weight: 0.8980 chunk 143 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 303 optimal weight: 10.0000 chunk 325 optimal weight: 8.9990 chunk 235 optimal weight: 0.7980 chunk 44 optimal weight: 10.0000 chunk 375 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 246 GLN C 246 GLN C 297 GLN E 246 GLN F 269 GLN G 246 GLN G 269 GLN H 231 ASN H 246 GLN ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 411 GLN I 246 GLN M 246 GLN M 297 GLN N 231 ASN N 269 GLN N 297 GLN O 297 GLN O 299 ASN Q 246 GLN S 246 GLN T 269 GLN U 246 GLN V 269 GLN W 297 GLN X 246 GLN Z 261 ASN c 246 GLN c 297 GLN d 246 GLN d 374 HIS e 231 ASN e 269 GLN f 246 GLN f 297 GLN g 231 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 39765 Z= 0.310 Angle : 0.490 4.964 53592 Z= 0.262 Chirality : 0.039 0.130 6138 Planarity : 0.003 0.032 7194 Dihedral : 4.629 17.083 5379 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 2.01 % Allowed : 17.59 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.13), residues: 4785 helix: 3.07 (0.14), residues: 1320 sheet: 1.02 (0.11), residues: 2442 loop : -0.55 (0.18), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS W 281 PHE 0.011 0.001 PHE P 422 TYR 0.011 0.001 TYR a 393 ARG 0.006 0.001 ARG L 356 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9570 Ramachandran restraints generated. 4785 Oldfield, 0 Emsley, 4785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9570 Ramachandran restraints generated. 4785 Oldfield, 0 Emsley, 4785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1307 residues out of total 4422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 1218 time to evaluate : 4.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 GLN cc_start: 0.8587 (tt0) cc_final: 0.8282 (tt0) REVERT: A 376 LYS cc_start: 0.7931 (tttt) cc_final: 0.7583 (mttp) REVERT: B 297 GLN cc_start: 0.7562 (OUTLIER) cc_final: 0.6856 (tp40) REVERT: B 376 LYS cc_start: 0.7882 (tttt) cc_final: 0.7412 (mttp) REVERT: B 409 MET cc_start: 0.8294 (mmm) cc_final: 0.7802 (mmm) REVERT: C 269 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7651 (mp10) REVERT: C 297 GLN cc_start: 0.7410 (OUTLIER) cc_final: 0.6972 (tt0) REVERT: C 376 LYS cc_start: 0.7987 (tttt) cc_final: 0.7709 (mttp) REVERT: C 383 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7554 (mt-10) REVERT: D 376 LYS cc_start: 0.7857 (tttt) cc_final: 0.7499 (mttp) REVERT: E 376 LYS cc_start: 0.7976 (tttt) cc_final: 0.7584 (mttp) REVERT: F 376 LYS cc_start: 0.7991 (tttt) cc_final: 0.7563 (mttp) REVERT: G 235 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8854 (mp) REVERT: G 376 LYS cc_start: 0.7894 (tttt) cc_final: 0.7457 (mttp) REVERT: G 409 MET cc_start: 0.8194 (mmm) cc_final: 0.7871 (mmm) REVERT: H 376 LYS cc_start: 0.8010 (tttt) cc_final: 0.7562 (mttp) REVERT: I 246 GLN cc_start: 0.8526 (tt0) cc_final: 0.8214 (tt0) REVERT: I 376 LYS cc_start: 0.8021 (tttt) cc_final: 0.7629 (mttp) REVERT: J 246 GLN cc_start: 0.8601 (tt0) cc_final: 0.8201 (tt0) REVERT: J 269 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7591 (mp10) REVERT: J 376 LYS cc_start: 0.7916 (tttt) cc_final: 0.7453 (mttp) REVERT: K 235 LEU cc_start: 0.9036 (mt) cc_final: 0.8551 (mp) REVERT: K 246 GLN cc_start: 0.8481 (tt0) cc_final: 0.8157 (tt0) REVERT: K 269 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7561 (mp10) REVERT: K 296 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.6721 (ttp-170) REVERT: K 376 LYS cc_start: 0.7998 (tttt) cc_final: 0.7665 (mttp) REVERT: L 246 GLN cc_start: 0.8599 (tt0) cc_final: 0.8364 (tt0) REVERT: L 297 GLN cc_start: 0.7629 (tt0) cc_final: 0.7404 (tp-100) REVERT: L 376 LYS cc_start: 0.7896 (tttt) cc_final: 0.7479 (mttp) REVERT: M 297 GLN cc_start: 0.7629 (OUTLIER) cc_final: 0.7182 (tt0) REVERT: M 376 LYS cc_start: 0.7890 (tttt) cc_final: 0.7474 (mttp) REVERT: N 246 GLN cc_start: 0.8516 (tt0) cc_final: 0.8225 (tt0) REVERT: N 297 GLN cc_start: 0.7624 (OUTLIER) cc_final: 0.7023 (tt0) REVERT: N 376 LYS cc_start: 0.7942 (tttt) cc_final: 0.7528 (mttp) REVERT: O 275 LYS cc_start: 0.8234 (ttmt) cc_final: 0.8028 (tttt) REVERT: O 297 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.6913 (tp-100) REVERT: O 376 LYS cc_start: 0.8014 (tttt) cc_final: 0.7640 (mttp) REVERT: P 376 LYS cc_start: 0.8049 (tttt) cc_final: 0.7657 (mttp) REVERT: P 435 SER cc_start: 0.8363 (t) cc_final: 0.8157 (t) REVERT: Q 235 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8593 (mp) REVERT: Q 297 GLN cc_start: 0.7569 (tt0) cc_final: 0.7332 (tp40) REVERT: Q 376 LYS cc_start: 0.7920 (tttt) cc_final: 0.7399 (mttp) REVERT: R 246 GLN cc_start: 0.8562 (tt0) cc_final: 0.8178 (tt0) REVERT: R 376 LYS cc_start: 0.7926 (tttt) cc_final: 0.7552 (mttp) REVERT: S 376 LYS cc_start: 0.7933 (tttt) cc_final: 0.7590 (mttp) REVERT: T 246 GLN cc_start: 0.8604 (tt0) cc_final: 0.8335 (tt0) REVERT: T 297 GLN cc_start: 0.7599 (tt0) cc_final: 0.7392 (tp-100) REVERT: T 376 LYS cc_start: 0.7862 (tttt) cc_final: 0.7516 (mttp) REVERT: U 246 GLN cc_start: 0.8509 (tt0) cc_final: 0.8027 (tt0) REVERT: U 279 GLU cc_start: 0.7433 (mt-10) cc_final: 0.7209 (mp0) REVERT: U 376 LYS cc_start: 0.7926 (tttt) cc_final: 0.7538 (mttp) REVERT: V 235 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8735 (mp) REVERT: V 297 GLN cc_start: 0.7704 (tt0) cc_final: 0.7483 (tp40) REVERT: V 376 LYS cc_start: 0.7981 (tttt) cc_final: 0.7564 (mttp) REVERT: W 231 ASN cc_start: 0.4847 (OUTLIER) cc_final: 0.4600 (p0) REVERT: W 269 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7879 (mp10) REVERT: W 376 LYS cc_start: 0.8018 (tttt) cc_final: 0.7563 (mttp) REVERT: X 269 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7728 (mp10) REVERT: X 279 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.7124 (mp0) REVERT: X 376 LYS cc_start: 0.8036 (tttt) cc_final: 0.7567 (mttp) REVERT: Y 246 GLN cc_start: 0.8523 (tt0) cc_final: 0.8130 (tt0) REVERT: Y 297 GLN cc_start: 0.7577 (tt0) cc_final: 0.7348 (tp40) REVERT: Y 376 LYS cc_start: 0.7973 (tttt) cc_final: 0.7644 (mttp) REVERT: Y 420 MET cc_start: 0.8592 (ptm) cc_final: 0.8194 (ptm) REVERT: Z 246 GLN cc_start: 0.8550 (tt0) cc_final: 0.8228 (tt0) REVERT: Z 296 ARG cc_start: 0.7710 (OUTLIER) cc_final: 0.6874 (ttp-170) REVERT: Z 376 LYS cc_start: 0.7921 (tttt) cc_final: 0.7629 (mttp) REVERT: a 246 GLN cc_start: 0.8500 (tt0) cc_final: 0.8224 (tt0) REVERT: a 376 LYS cc_start: 0.7823 (tttt) cc_final: 0.7433 (mttp) REVERT: b 246 GLN cc_start: 0.8571 (tt0) cc_final: 0.8152 (tt0) REVERT: b 376 LYS cc_start: 0.7799 (tttt) cc_final: 0.7439 (mttp) REVERT: c 279 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.7081 (mp0) REVERT: c 297 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.6950 (tt0) REVERT: c 376 LYS cc_start: 0.7914 (tttt) cc_final: 0.7484 (mttp) REVERT: d 279 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7162 (mp0) REVERT: d 356 ARG cc_start: 0.6195 (mpp-170) cc_final: 0.5779 (mpp-170) REVERT: d 376 LYS cc_start: 0.7897 (tttt) cc_final: 0.7557 (mttp) REVERT: e 297 GLN cc_start: 0.7601 (tt0) cc_final: 0.7379 (tp-100) REVERT: e 376 LYS cc_start: 0.7872 (tttt) cc_final: 0.7576 (mttp) REVERT: f 296 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7212 (tpp-160) REVERT: f 297 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.7129 (tt0) REVERT: f 376 LYS cc_start: 0.7939 (tttt) cc_final: 0.7599 (mttp) REVERT: f 409 MET cc_start: 0.8224 (mmm) cc_final: 0.7884 (mmm) REVERT: g 246 GLN cc_start: 0.8563 (tt0) cc_final: 0.8180 (tt0) REVERT: g 297 GLN cc_start: 0.7527 (OUTLIER) cc_final: 0.6765 (tp-100) REVERT: g 376 LYS cc_start: 0.8026 (tttt) cc_final: 0.7643 (mttp) REVERT: g 383 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7536 (mt-10) outliers start: 89 outliers final: 41 residues processed: 1247 average time/residue: 1.7595 time to fit residues: 2586.9474 Evaluate side-chains 1265 residues out of total 4422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 1200 time to evaluate : 4.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 297 GLN Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain C residue 297 GLN Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 435 SER Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain H residue 297 GLN Chi-restraints excluded: chain I residue 276 GLU Chi-restraints excluded: chain I residue 405 THR Chi-restraints excluded: chain J residue 269 GLN Chi-restraints excluded: chain J residue 435 SER Chi-restraints excluded: chain K residue 269 GLN Chi-restraints excluded: chain K residue 296 ARG Chi-restraints excluded: chain K residue 429 THR Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain M residue 297 GLN Chi-restraints excluded: chain N residue 297 GLN Chi-restraints excluded: chain N residue 363 THR Chi-restraints excluded: chain O residue 235 LEU Chi-restraints excluded: chain O residue 297 GLN Chi-restraints excluded: chain O residue 429 THR Chi-restraints excluded: chain P residue 363 THR Chi-restraints excluded: chain Q residue 235 LEU Chi-restraints excluded: chain Q residue 363 THR Chi-restraints excluded: chain Q residue 433 VAL Chi-restraints excluded: chain S residue 276 GLU Chi-restraints excluded: chain S residue 429 THR Chi-restraints excluded: chain U residue 429 THR Chi-restraints excluded: chain V residue 235 LEU Chi-restraints excluded: chain V residue 429 THR Chi-restraints excluded: chain V residue 435 SER Chi-restraints excluded: chain W residue 231 ASN Chi-restraints excluded: chain W residue 269 GLN Chi-restraints excluded: chain W residue 429 THR Chi-restraints excluded: chain W residue 435 SER Chi-restraints excluded: chain X residue 269 GLN Chi-restraints excluded: chain X residue 276 GLU Chi-restraints excluded: chain X residue 279 GLU Chi-restraints excluded: chain X residue 429 THR Chi-restraints excluded: chain Z residue 235 LEU Chi-restraints excluded: chain Z residue 296 ARG Chi-restraints excluded: chain Z residue 363 THR Chi-restraints excluded: chain Z residue 433 VAL Chi-restraints excluded: chain c residue 235 LEU Chi-restraints excluded: chain c residue 279 GLU Chi-restraints excluded: chain c residue 297 GLN Chi-restraints excluded: chain c residue 405 THR Chi-restraints excluded: chain d residue 279 GLU Chi-restraints excluded: chain d residue 363 THR Chi-restraints excluded: chain d residue 402 LEU Chi-restraints excluded: chain d residue 435 SER Chi-restraints excluded: chain e residue 405 THR Chi-restraints excluded: chain e residue 412 ILE Chi-restraints excluded: chain e residue 429 THR Chi-restraints excluded: chain e residue 433 VAL Chi-restraints excluded: chain f residue 296 ARG Chi-restraints excluded: chain f residue 297 GLN Chi-restraints excluded: chain f residue 435 SER Chi-restraints excluded: chain g residue 231 ASN Chi-restraints excluded: chain g residue 297 GLN Chi-restraints excluded: chain g residue 383 GLU Chi-restraints excluded: chain g residue 433 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 434 optimal weight: 1.9990 chunk 457 optimal weight: 5.9990 chunk 417 optimal weight: 6.9990 chunk 444 optimal weight: 2.9990 chunk 456 optimal weight: 0.9990 chunk 267 optimal weight: 4.9990 chunk 193 optimal weight: 0.7980 chunk 349 optimal weight: 3.9990 chunk 136 optimal weight: 0.6980 chunk 401 optimal weight: 7.9990 chunk 420 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 GLN B 246 GLN B 297 GLN C 246 GLN C 297 GLN D 246 GLN F 269 GLN G 231 ASN G 269 GLN H 231 ASN H 246 GLN H 277 GLN J 411 GLN M 246 GLN M 297 GLN N 231 ASN N 269 GLN N 297 GLN O 246 GLN O 297 GLN O 299 ASN Q 246 GLN S 246 GLN V 246 GLN X 246 GLN Z 261 ASN c 246 GLN c 297 GLN d 246 GLN e 231 ASN f 246 GLN f 297 GLN g 231 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 39765 Z= 0.195 Angle : 0.442 5.016 53592 Z= 0.237 Chirality : 0.038 0.127 6138 Planarity : 0.002 0.028 7194 Dihedral : 4.388 17.029 5379 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.88 % Allowed : 18.14 % Favored : 79.99 % 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: 2.10 (0.13), residues: 4785 helix: 3.30 (0.14), residues: 1320 sheet: 1.11 (0.11), residues: 2442 loop : -0.50 (0.18), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.000 HIS W 281 PHE 0.009 0.001 PHE P 422 TYR 0.007 0.001 TYR B 393 ARG 0.007 0.000 ARG L 356 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9570 Ramachandran restraints generated. 4785 Oldfield, 0 Emsley, 4785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9570 Ramachandran restraints generated. 4785 Oldfield, 0 Emsley, 4785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1284 residues out of total 4422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 1201 time to evaluate : 4.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 GLN cc_start: 0.8527 (tt0) cc_final: 0.8210 (tt0) REVERT: A 376 LYS cc_start: 0.7891 (tttt) cc_final: 0.7606 (mttp) REVERT: B 297 GLN cc_start: 0.7496 (OUTLIER) cc_final: 0.7032 (tt0) REVERT: B 376 LYS cc_start: 0.7855 (tttt) cc_final: 0.7471 (mttp) REVERT: B 409 MET cc_start: 0.8328 (mmm) cc_final: 0.7798 (mmm) REVERT: C 269 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7528 (mp10) REVERT: C 297 GLN cc_start: 0.7411 (OUTLIER) cc_final: 0.6918 (tt0) REVERT: C 376 LYS cc_start: 0.7891 (tttt) cc_final: 0.7623 (mttp) REVERT: D 376 LYS cc_start: 0.7830 (tttt) cc_final: 0.7499 (mttp) REVERT: E 376 LYS cc_start: 0.7930 (tttt) cc_final: 0.7553 (mttp) REVERT: F 296 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.7259 (ttp-170) REVERT: F 376 LYS cc_start: 0.7961 (tttt) cc_final: 0.7563 (mttp) REVERT: G 235 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8814 (mp) REVERT: G 376 LYS cc_start: 0.7902 (tttt) cc_final: 0.7468 (mttp) REVERT: G 409 MET cc_start: 0.8177 (mmm) cc_final: 0.7867 (mmm) REVERT: H 296 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.7124 (ttp-170) REVERT: H 376 LYS cc_start: 0.7954 (tttt) cc_final: 0.7503 (mttp) REVERT: I 246 GLN cc_start: 0.8442 (tt0) cc_final: 0.8178 (tt0) REVERT: I 376 LYS cc_start: 0.7993 (tttt) cc_final: 0.7656 (mttp) REVERT: J 246 GLN cc_start: 0.8564 (tt0) cc_final: 0.8156 (tt0) REVERT: J 269 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7646 (mp10) REVERT: J 376 LYS cc_start: 0.7869 (tttt) cc_final: 0.7419 (mttp) REVERT: K 235 LEU cc_start: 0.8996 (mt) cc_final: 0.8510 (mp) REVERT: K 246 GLN cc_start: 0.8401 (tt0) cc_final: 0.8040 (tt0) REVERT: K 269 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7537 (mp10) REVERT: K 296 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.6694 (ttp-170) REVERT: K 376 LYS cc_start: 0.7977 (tttt) cc_final: 0.7633 (mttp) REVERT: L 246 GLN cc_start: 0.8570 (tt0) cc_final: 0.8321 (tt0) REVERT: L 297 GLN cc_start: 0.7601 (tt0) cc_final: 0.7390 (tp-100) REVERT: L 376 LYS cc_start: 0.7877 (tttt) cc_final: 0.7464 (mttp) REVERT: M 297 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.7127 (tt0) REVERT: M 376 LYS cc_start: 0.7891 (tttt) cc_final: 0.7490 (mttp) REVERT: N 246 GLN cc_start: 0.8465 (tt0) cc_final: 0.8138 (tt0) REVERT: N 376 LYS cc_start: 0.7849 (tttt) cc_final: 0.7500 (mttp) REVERT: O 275 LYS cc_start: 0.8222 (ttmt) cc_final: 0.8009 (tttt) REVERT: O 297 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.6905 (tp-100) REVERT: O 376 LYS cc_start: 0.7978 (tttt) cc_final: 0.7636 (mttp) REVERT: P 376 LYS cc_start: 0.8021 (tttt) cc_final: 0.7622 (mttp) REVERT: P 435 SER cc_start: 0.8343 (t) cc_final: 0.8135 (t) REVERT: Q 235 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8527 (mp) REVERT: Q 297 GLN cc_start: 0.7566 (tt0) cc_final: 0.7346 (tp40) REVERT: Q 376 LYS cc_start: 0.7890 (tttt) cc_final: 0.7432 (mttp) REVERT: R 246 GLN cc_start: 0.8560 (tt0) cc_final: 0.8169 (tt0) REVERT: R 376 LYS cc_start: 0.7917 (tttt) cc_final: 0.7543 (mttp) REVERT: S 376 LYS cc_start: 0.7889 (tttt) cc_final: 0.7561 (mttp) REVERT: S 377 MET cc_start: 0.7774 (mpt) cc_final: 0.7483 (mpt) REVERT: T 246 GLN cc_start: 0.8568 (tt0) cc_final: 0.8264 (tt0) REVERT: T 297 GLN cc_start: 0.7592 (tt0) cc_final: 0.7374 (tp-100) REVERT: T 376 LYS cc_start: 0.7752 (tttt) cc_final: 0.7381 (mttp) REVERT: U 279 GLU cc_start: 0.7347 (mt-10) cc_final: 0.7125 (mp0) REVERT: U 376 LYS cc_start: 0.7870 (tttt) cc_final: 0.7499 (mttp) REVERT: V 235 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8630 (mp) REVERT: V 246 GLN cc_start: 0.8452 (tt0) cc_final: 0.8068 (tt0) REVERT: V 297 GLN cc_start: 0.7694 (tt0) cc_final: 0.7477 (tp40) REVERT: V 376 LYS cc_start: 0.7953 (tttt) cc_final: 0.7552 (mttp) REVERT: W 231 ASN cc_start: 0.4749 (OUTLIER) cc_final: 0.4516 (p0) REVERT: W 269 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7869 (mp10) REVERT: W 376 LYS cc_start: 0.8010 (tttt) cc_final: 0.7552 (mttp) REVERT: X 269 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7703 (mp10) REVERT: X 279 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.7025 (mp0) REVERT: X 376 LYS cc_start: 0.7994 (tttt) cc_final: 0.7553 (mttp) REVERT: Y 246 GLN cc_start: 0.8483 (tt0) cc_final: 0.8064 (tt0) REVERT: Y 287 ASP cc_start: 0.7513 (t0) cc_final: 0.7289 (t70) REVERT: Y 297 GLN cc_start: 0.7564 (tt0) cc_final: 0.7346 (tp40) REVERT: Y 376 LYS cc_start: 0.7959 (tttt) cc_final: 0.7635 (mttp) REVERT: Y 420 MET cc_start: 0.8494 (ptm) cc_final: 0.8031 (ptm) REVERT: Z 246 GLN cc_start: 0.8525 (tt0) cc_final: 0.8168 (tt0) REVERT: Z 296 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.6820 (ttp-170) REVERT: Z 376 LYS cc_start: 0.7899 (tttt) cc_final: 0.7640 (mttp) REVERT: a 246 GLN cc_start: 0.8450 (tt0) cc_final: 0.8156 (tt0) REVERT: a 376 LYS cc_start: 0.7773 (tttt) cc_final: 0.7434 (mttp) REVERT: b 246 GLN cc_start: 0.8517 (tt0) cc_final: 0.8063 (tt0) REVERT: b 376 LYS cc_start: 0.7771 (tttt) cc_final: 0.7414 (mttp) REVERT: c 279 GLU cc_start: 0.7315 (mt-10) cc_final: 0.6997 (mp0) REVERT: c 297 GLN cc_start: 0.7557 (OUTLIER) cc_final: 0.6888 (tt0) REVERT: c 376 LYS cc_start: 0.7869 (tttt) cc_final: 0.7495 (mttp) REVERT: c 425 LYS cc_start: 0.8874 (mtmt) cc_final: 0.8615 (mtmm) REVERT: d 279 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7089 (mp0) REVERT: d 376 LYS cc_start: 0.7869 (tttt) cc_final: 0.7550 (mttp) REVERT: e 297 GLN cc_start: 0.7574 (tt0) cc_final: 0.7361 (tp-100) REVERT: e 376 LYS cc_start: 0.7870 (tttt) cc_final: 0.7572 (mttp) REVERT: f 296 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.7190 (tpp-160) REVERT: f 297 GLN cc_start: 0.7539 (OUTLIER) cc_final: 0.7076 (tt0) REVERT: f 376 LYS cc_start: 0.7899 (tttt) cc_final: 0.7554 (mttp) REVERT: f 409 MET cc_start: 0.8213 (mmm) cc_final: 0.7896 (mmm) REVERT: g 246 GLN cc_start: 0.8514 (tt0) cc_final: 0.8107 (tt0) REVERT: g 376 LYS cc_start: 0.7991 (tttt) cc_final: 0.7608 (mttp) REVERT: g 383 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7488 (mt-10) outliers start: 83 outliers final: 44 residues processed: 1229 average time/residue: 1.6944 time to fit residues: 2452.2821 Evaluate side-chains 1264 residues out of total 4422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 1197 time to evaluate : 4.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 297 GLN Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 297 GLN Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain F residue 296 ARG Chi-restraints excluded: chain F residue 412 ILE Chi-restraints excluded: chain F residue 435 SER Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain H residue 296 ARG Chi-restraints excluded: chain H residue 297 GLN Chi-restraints excluded: chain J residue 269 GLN Chi-restraints excluded: chain J residue 435 SER Chi-restraints excluded: chain K residue 269 GLN Chi-restraints excluded: chain K residue 296 ARG Chi-restraints excluded: chain K residue 429 THR Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain M residue 297 GLN Chi-restraints excluded: chain N residue 363 THR Chi-restraints excluded: chain O residue 235 LEU Chi-restraints excluded: chain O residue 297 GLN Chi-restraints excluded: chain O residue 429 THR Chi-restraints excluded: chain P residue 363 THR Chi-restraints excluded: chain Q residue 235 LEU Chi-restraints excluded: chain Q residue 363 THR Chi-restraints excluded: chain Q residue 433 VAL Chi-restraints excluded: chain S residue 276 GLU Chi-restraints excluded: chain S residue 405 THR Chi-restraints excluded: chain S residue 429 THR Chi-restraints excluded: chain U residue 363 THR Chi-restraints excluded: chain U residue 429 THR Chi-restraints excluded: chain V residue 235 LEU Chi-restraints excluded: chain V residue 429 THR Chi-restraints excluded: chain V residue 435 SER Chi-restraints excluded: chain W residue 231 ASN Chi-restraints excluded: chain W residue 269 GLN Chi-restraints excluded: chain W residue 429 THR Chi-restraints excluded: chain W residue 435 SER Chi-restraints excluded: chain X residue 269 GLN Chi-restraints excluded: chain X residue 276 GLU Chi-restraints excluded: chain X residue 279 GLU Chi-restraints excluded: chain Z residue 235 LEU Chi-restraints excluded: chain Z residue 296 ARG Chi-restraints excluded: chain Z residue 363 THR Chi-restraints excluded: chain Z residue 405 THR Chi-restraints excluded: chain Z residue 429 THR Chi-restraints excluded: chain Z residue 433 VAL Chi-restraints excluded: chain c residue 235 LEU Chi-restraints excluded: chain c residue 297 GLN Chi-restraints excluded: chain c residue 405 THR Chi-restraints excluded: chain d residue 279 GLU Chi-restraints excluded: chain d residue 363 THR Chi-restraints excluded: chain d residue 402 LEU Chi-restraints excluded: chain d residue 435 SER Chi-restraints excluded: chain e residue 412 ILE Chi-restraints excluded: chain e residue 433 VAL Chi-restraints excluded: chain f residue 296 ARG Chi-restraints excluded: chain f residue 297 GLN Chi-restraints excluded: chain f residue 405 THR Chi-restraints excluded: chain f residue 429 THR Chi-restraints excluded: chain f residue 435 SER Chi-restraints excluded: chain g residue 235 LEU Chi-restraints excluded: chain g residue 383 GLU Chi-restraints excluded: chain g residue 433 VAL Chi-restraints excluded: chain g residue 435 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 443 optimal weight: 0.9990 chunk 291 optimal weight: 0.9990 chunk 470 optimal weight: 0.6980 chunk 286 optimal weight: 0.9990 chunk 223 optimal weight: 7.9990 chunk 326 optimal weight: 4.9990 chunk 493 optimal weight: 6.9990 chunk 453 optimal weight: 0.0010 chunk 392 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 303 optimal weight: 7.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 GLN B 246 GLN B 297 GLN C 246 GLN C 297 GLN D 246 GLN E 246 GLN F 269 GLN G 269 GLN H 231 ASN H 246 GLN J 411 GLN M 246 GLN M 297 GLN N 231 ASN N 269 GLN N 297 GLN O 246 GLN O 297 GLN Q 246 GLN S 246 GLN U 246 GLN X 239 ASN X 246 GLN c 246 GLN c 297 GLN c 299 ASN e 231 ASN f 246 GLN f 297 GLN g 231 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 39765 Z= 0.151 Angle : 0.427 5.100 53592 Z= 0.229 Chirality : 0.038 0.127 6138 Planarity : 0.002 0.028 7194 Dihedral : 4.256 17.380 5379 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.81 % Allowed : 18.43 % Favored : 79.76 % 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: 2.28 (0.13), residues: 4785 helix: 3.49 (0.14), residues: 1320 sheet: 1.20 (0.11), residues: 2442 loop : -0.44 (0.18), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS W 281 PHE 0.009 0.001 PHE R 422 TYR 0.006 0.001 TYR H 393 ARG 0.006 0.000 ARG L 356 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9570 Ramachandran restraints generated. 4785 Oldfield, 0 Emsley, 4785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9570 Ramachandran restraints generated. 4785 Oldfield, 0 Emsley, 4785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1297 residues out of total 4422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 1217 time to evaluate : 4.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 GLN cc_start: 0.8499 (tt0) cc_final: 0.8197 (tt0) REVERT: A 376 LYS cc_start: 0.7882 (tttt) cc_final: 0.7565 (mttp) REVERT: B 376 LYS cc_start: 0.7834 (tttt) cc_final: 0.7450 (mttp) REVERT: B 409 MET cc_start: 0.8280 (mmm) cc_final: 0.7787 (mmm) REVERT: C 269 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7524 (mp10) REVERT: C 376 LYS cc_start: 0.7850 (tttt) cc_final: 0.7616 (mttp) REVERT: D 376 LYS cc_start: 0.7811 (tttt) cc_final: 0.7500 (mttp) REVERT: E 376 LYS cc_start: 0.7925 (tttt) cc_final: 0.7547 (mttp) REVERT: F 296 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.7230 (ttp-170) REVERT: F 376 LYS cc_start: 0.7951 (tttt) cc_final: 0.7567 (mttp) REVERT: G 235 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8779 (mp) REVERT: G 376 LYS cc_start: 0.7878 (tttt) cc_final: 0.7438 (mttp) REVERT: G 409 MET cc_start: 0.8177 (mmm) cc_final: 0.7888 (mmm) REVERT: H 296 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.7104 (ttp-170) REVERT: H 376 LYS cc_start: 0.7961 (tttt) cc_final: 0.7498 (mttp) REVERT: I 376 LYS cc_start: 0.7966 (tttt) cc_final: 0.7639 (mttp) REVERT: J 246 GLN cc_start: 0.8540 (tt0) cc_final: 0.8126 (tt0) REVERT: J 269 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7650 (mp10) REVERT: J 376 LYS cc_start: 0.7837 (tttt) cc_final: 0.7428 (mttp) REVERT: K 235 LEU cc_start: 0.8986 (mt) cc_final: 0.8522 (mp) REVERT: K 246 GLN cc_start: 0.8379 (tt0) cc_final: 0.8042 (tt0) REVERT: K 269 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7580 (mp10) REVERT: K 296 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.6673 (ttp-170) REVERT: K 376 LYS cc_start: 0.7956 (tttt) cc_final: 0.7616 (mttp) REVERT: L 246 GLN cc_start: 0.8545 (tt0) cc_final: 0.8300 (tt0) REVERT: L 297 GLN cc_start: 0.7587 (tt0) cc_final: 0.7384 (tp-100) REVERT: L 376 LYS cc_start: 0.7841 (tttt) cc_final: 0.7456 (mttp) REVERT: M 297 GLN cc_start: 0.7555 (OUTLIER) cc_final: 0.7159 (tt0) REVERT: M 376 LYS cc_start: 0.7848 (tttt) cc_final: 0.7459 (mttp) REVERT: N 246 GLN cc_start: 0.8482 (tt0) cc_final: 0.8129 (tt0) REVERT: N 297 GLN cc_start: 0.7578 (OUTLIER) cc_final: 0.6982 (tt0) REVERT: N 376 LYS cc_start: 0.7805 (tttt) cc_final: 0.7468 (mttp) REVERT: O 275 LYS cc_start: 0.8211 (ttmt) cc_final: 0.8006 (tttt) REVERT: O 297 GLN cc_start: 0.7607 (OUTLIER) cc_final: 0.6970 (tp-100) REVERT: O 376 LYS cc_start: 0.7970 (tttt) cc_final: 0.7625 (mttp) REVERT: P 376 LYS cc_start: 0.8008 (tttt) cc_final: 0.7629 (mttp) REVERT: P 435 SER cc_start: 0.8321 (t) cc_final: 0.8099 (t) REVERT: Q 235 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8503 (mp) REVERT: Q 297 GLN cc_start: 0.7562 (tt0) cc_final: 0.7340 (tp40) REVERT: Q 376 LYS cc_start: 0.7860 (tttt) cc_final: 0.7409 (mttp) REVERT: R 246 GLN cc_start: 0.8501 (tt0) cc_final: 0.8106 (tt0) REVERT: R 376 LYS cc_start: 0.7875 (tttt) cc_final: 0.7522 (mttp) REVERT: S 376 LYS cc_start: 0.7890 (tttt) cc_final: 0.7555 (mttp) REVERT: S 377 MET cc_start: 0.7771 (mpt) cc_final: 0.7478 (mpt) REVERT: T 246 GLN cc_start: 0.8520 (tt0) cc_final: 0.8191 (tt0) REVERT: T 297 GLN cc_start: 0.7583 (tt0) cc_final: 0.7369 (tp-100) REVERT: T 376 LYS cc_start: 0.7770 (tttt) cc_final: 0.7401 (mttp) REVERT: U 246 GLN cc_start: 0.8431 (tt0) cc_final: 0.7991 (tt0) REVERT: U 279 GLU cc_start: 0.7265 (mt-10) cc_final: 0.7033 (mp0) REVERT: U 376 LYS cc_start: 0.7852 (tttt) cc_final: 0.7471 (mttp) REVERT: V 235 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8621 (mp) REVERT: V 297 GLN cc_start: 0.7687 (tt0) cc_final: 0.7475 (tp40) REVERT: V 376 LYS cc_start: 0.7931 (tttt) cc_final: 0.7534 (mttp) REVERT: W 231 ASN cc_start: 0.4661 (OUTLIER) cc_final: 0.4443 (p0) REVERT: W 269 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7816 (mp10) REVERT: W 376 LYS cc_start: 0.7982 (tttt) cc_final: 0.7512 (mttp) REVERT: X 269 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7699 (mp10) REVERT: X 279 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.7025 (mp0) REVERT: X 376 LYS cc_start: 0.7968 (tttt) cc_final: 0.7523 (mttp) REVERT: Y 246 GLN cc_start: 0.8469 (tt0) cc_final: 0.8090 (tt0) REVERT: Y 297 GLN cc_start: 0.7550 (tt0) cc_final: 0.7342 (tp40) REVERT: Y 376 LYS cc_start: 0.7940 (tttt) cc_final: 0.7602 (mttp) REVERT: Y 420 MET cc_start: 0.8492 (ptm) cc_final: 0.8005 (ptm) REVERT: Z 246 GLN cc_start: 0.8576 (tt0) cc_final: 0.8202 (tt0) REVERT: Z 296 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.6801 (ttp-170) REVERT: Z 376 LYS cc_start: 0.7875 (tttt) cc_final: 0.7624 (mttp) REVERT: a 235 LEU cc_start: 0.8972 (mp) cc_final: 0.8700 (mp) REVERT: a 246 GLN cc_start: 0.8428 (tt0) cc_final: 0.8043 (tt0) REVERT: a 376 LYS cc_start: 0.7763 (tttt) cc_final: 0.7407 (mttp) REVERT: b 246 GLN cc_start: 0.8485 (tt0) cc_final: 0.8020 (tt0) REVERT: b 376 LYS cc_start: 0.7749 (tttt) cc_final: 0.7401 (mttp) REVERT: c 279 GLU cc_start: 0.7224 (mt-10) cc_final: 0.6916 (mp0) REVERT: c 376 LYS cc_start: 0.7850 (tttt) cc_final: 0.7516 (mttp) REVERT: c 425 LYS cc_start: 0.8882 (mtmt) cc_final: 0.8617 (mtmm) REVERT: d 279 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6995 (mp0) REVERT: d 376 LYS cc_start: 0.7850 (tttt) cc_final: 0.7543 (mttp) REVERT: e 297 GLN cc_start: 0.7578 (tt0) cc_final: 0.7359 (tp-100) REVERT: e 376 LYS cc_start: 0.7852 (tttt) cc_final: 0.7548 (mttp) REVERT: f 297 GLN cc_start: 0.7539 (OUTLIER) cc_final: 0.7191 (tt0) REVERT: f 376 LYS cc_start: 0.7889 (tttt) cc_final: 0.7542 (mttp) REVERT: f 409 MET cc_start: 0.8213 (mmm) cc_final: 0.7915 (mmm) REVERT: g 246 GLN cc_start: 0.8473 (tt0) cc_final: 0.8055 (tt0) REVERT: g 376 LYS cc_start: 0.7939 (tttt) cc_final: 0.7566 (mttp) REVERT: g 383 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7540 (mt-10) outliers start: 80 outliers final: 44 residues processed: 1246 average time/residue: 1.7129 time to fit residues: 2514.5327 Evaluate side-chains 1272 residues out of total 4422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 1208 time to evaluate : 4.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain C residue 269 GLN Chi-restraints excluded: chain D residue 433 VAL Chi-restraints excluded: chain F residue 296 ARG Chi-restraints excluded: chain F residue 435 SER Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain H residue 296 ARG Chi-restraints excluded: chain H residue 297 GLN Chi-restraints excluded: chain I residue 276 GLU Chi-restraints excluded: chain J residue 269 GLN Chi-restraints excluded: chain J residue 435 SER Chi-restraints excluded: chain K residue 269 GLN Chi-restraints excluded: chain K residue 296 ARG Chi-restraints excluded: chain K residue 429 THR Chi-restraints excluded: chain L residue 363 THR Chi-restraints excluded: chain M residue 297 GLN Chi-restraints excluded: chain N residue 297 GLN Chi-restraints excluded: chain N residue 363 THR Chi-restraints excluded: chain O residue 235 LEU Chi-restraints excluded: chain O residue 297 GLN Chi-restraints excluded: chain O residue 429 THR Chi-restraints excluded: chain P residue 363 THR Chi-restraints excluded: chain Q residue 235 LEU Chi-restraints excluded: chain Q residue 363 THR Chi-restraints excluded: chain Q residue 433 VAL Chi-restraints excluded: chain S residue 276 GLU Chi-restraints excluded: chain S residue 405 THR Chi-restraints excluded: chain S residue 429 THR Chi-restraints excluded: chain U residue 405 THR Chi-restraints excluded: chain U residue 429 THR Chi-restraints excluded: chain V residue 235 LEU Chi-restraints excluded: chain V residue 429 THR Chi-restraints excluded: chain V residue 435 SER Chi-restraints excluded: chain W residue 231 ASN Chi-restraints excluded: chain W residue 269 GLN Chi-restraints excluded: chain W residue 429 THR Chi-restraints excluded: chain W residue 435 SER Chi-restraints excluded: chain X residue 269 GLN Chi-restraints excluded: chain X residue 276 GLU Chi-restraints excluded: chain X residue 279 GLU Chi-restraints excluded: chain Z residue 235 LEU Chi-restraints excluded: chain Z residue 296 ARG Chi-restraints excluded: chain Z residue 363 THR Chi-restraints excluded: chain Z residue 429 THR Chi-restraints excluded: chain Z residue 433 VAL Chi-restraints excluded: chain b residue 231 ASN Chi-restraints excluded: chain c residue 235 LEU Chi-restraints excluded: chain c residue 405 THR Chi-restraints excluded: chain d residue 279 GLU Chi-restraints excluded: chain d residue 363 THR Chi-restraints excluded: chain d residue 402 LEU Chi-restraints excluded: chain d residue 435 SER Chi-restraints excluded: chain e residue 405 THR Chi-restraints excluded: chain e residue 433 VAL Chi-restraints excluded: chain f residue 276 GLU Chi-restraints excluded: chain f residue 297 GLN Chi-restraints excluded: chain f residue 405 THR Chi-restraints excluded: chain f residue 429 THR Chi-restraints excluded: chain f residue 435 SER Chi-restraints excluded: chain g residue 235 LEU Chi-restraints excluded: chain g residue 383 GLU Chi-restraints excluded: chain g residue 433 VAL Chi-restraints excluded: chain g residue 435 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 240 optimal weight: 4.9990 chunk 311 optimal weight: 4.9990 chunk 418 optimal weight: 3.9990 chunk 120 optimal weight: 0.0070 chunk 362 optimal weight: 8.9990 chunk 57 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 393 optimal weight: 0.0370 chunk 164 optimal weight: 3.9990 chunk 403 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.0082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 GLN B 246 GLN C 246 GLN C 297 GLN D 246 GLN E 246 GLN F 269 GLN G 231 ASN G 246 GLN G 269 GLN H 231 ASN H 246 GLN H 277 GLN I 246 GLN J 411 GLN M 246 GLN M 297 GLN N 231 ASN N 269 GLN N 297 GLN O 246 GLN O 297 GLN Q 246 GLN S 246 GLN V 246 GLN X 246 GLN c 246 GLN c 297 GLN c 299 ASN e 231 ASN f 246 GLN f 297 GLN g 231 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.146054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.121217 restraints weight = 46234.817| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.61 r_work: 0.3364 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 39765 Z= 0.185 Angle : 0.436 5.114 53592 Z= 0.233 Chirality : 0.038 0.127 6138 Planarity : 0.002 0.027 7194 Dihedral : 4.286 17.323 5379 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.81 % Allowed : 18.66 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.13), residues: 4785 helix: 3.46 (0.14), residues: 1320 sheet: 1.26 (0.11), residues: 2442 loop : -0.44 (0.18), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS W 281 PHE 0.009 0.001 PHE P 422 TYR 0.007 0.001 TYR d 393 ARG 0.006 0.000 ARG L 356 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 30626.77 seconds wall clock time: 537 minutes 22.41 seconds (32242.41 seconds total)