Starting phenix.real_space_refine (version: 1.21rc1) on Tue Jul 18 06:18:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sd1_10145/07_2023/6sd1_10145.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sd1_10145/07_2023/6sd1_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_10145/07_2023/6sd1_10145.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sd1_10145/07_2023/6sd1_10145.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sd1_10145/07_2023/6sd1_10145.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sd1_10145/07_2023/6sd1_10145.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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: 17.68, per 1000 atoms: 0.45 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: 13.45 Conformation dependent library (CDL) restraints added in 5.8 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: 1.60 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: 12.95 Time building geometry restraints manager: 14.55 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: 3.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 19.680 Check model and map are aligned: 0.570 Set scattering table: 0.310 Process input model: 88.100 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:11.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 127.120 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 4.969 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 outliers start: 0 outliers final: 0 residues processed: 1388 average time/residue: 1.9529 time to fit residues: 3155.0516 Evaluate side-chains 1230 residues out of total 4422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1230 time to evaluate : 4.865 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.6262 ------------------------------------------------------------------------------- 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: 0.7980 chunk 375 optimal weight: 0.5980 chunk 208 optimal weight: 5.9990 chunk 128 optimal weight: 0.9990 chunk 253 optimal weight: 5.9990 chunk 200 optimal weight: 2.9990 chunk 387 optimal weight: 0.8980 chunk 150 optimal weight: 0.9980 chunk 235 optimal weight: 5.9990 chunk 288 optimal weight: 9.9990 chunk 449 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN 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 246 GLN D 261 ASN 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 269 GLN ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 297 GLN ** 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 246 GLN J 261 ASN J 263 HIS J 434 ASN K 246 GLN K 263 HIS ** K 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 246 GLN 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 269 GLN ** N 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 297 GLN ** N 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 246 GLN O 261 ASN O 263 HIS ** 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 297 GLN Q 299 ASN Q 365 ASN ** Q 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 246 GLN 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 246 GLN T 261 ASN T 263 HIS ** T 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 246 GLN U 261 ASN U 263 HIS U 434 ASN V 246 GLN V 261 ASN V 263 HIS V 297 GLN 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 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 246 GLN Y 261 ASN Y 263 HIS ** Y 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 246 GLN Z 263 HIS Z 365 ASN Z 431 ASN Z 434 ASN a 246 GLN a 261 ASN a 263 HIS ** a 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 246 GLN b 261 ASN b 263 HIS b 365 ASN b 434 ASN c 246 GLN c 261 ASN c 297 GLN c 365 ASN ** c 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 246 GLN d 261 ASN d 263 HIS d 269 GLN ** 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 246 GLN 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: 145 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 39765 Z= 0.179 Angle : 0.466 4.946 53592 Z= 0.251 Chirality : 0.038 0.124 6138 Planarity : 0.003 0.034 7194 Dihedral : 4.588 17.335 5379 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.13), residues: 4785 helix: 0.35 (0.13), residues: 1320 sheet: -0.08 (0.11), residues: 2475 loop : -0.83 (0.20), residues: 990 *********************** 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 1264 residues out of total 4422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 1221 time to evaluate : 4.446 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 outliers start: 43 outliers final: 8 residues processed: 1231 average time/residue: 1.7924 time to fit residues: 2599.1504 Evaluate side-chains 1190 residues out of total 4422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1182 time to evaluate : 4.724 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 2 residues processed: 6 average time/residue: 0.6260 time to fit residues: 12.1671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 374 optimal weight: 10.0000 chunk 306 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 450 optimal weight: 0.8980 chunk 486 optimal weight: 1.9990 chunk 401 optimal weight: 8.9990 chunk 446 optimal weight: 1.9990 chunk 153 optimal weight: 6.9990 chunk 361 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN A 365 ASN B 246 GLN B 434 ASN C 246 GLN C 365 ASN C 434 ASN D 246 GLN D 434 ASN E 246 GLN E 365 ASN E 434 ASN F 246 GLN F 269 GLN F 365 ASN F 434 ASN G 246 GLN G 269 GLN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 434 ASN H 231 ASN H 246 GLN H 263 HIS H 434 ASN I 246 GLN J 246 GLN K 365 ASN K 434 ASN L 246 GLN M 246 GLN M 297 GLN M 434 ASN N 246 GLN ** N 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 297 GLN N 365 ASN N 434 ASN O 246 GLN O 365 ASN O 434 ASN P 246 GLN P 269 GLN P 434 ASN Q 246 GLN Q 299 ASN Q 434 ASN S 246 GLN S 434 ASN T 269 GLN T 434 ASN V 246 GLN V 269 GLN V 297 GLN V 434 ASN W 297 GLN W 365 ASN W 434 ASN X 239 ASN X 246 GLN X 269 GLN X 434 ASN Y 246 GLN Y 434 ASN Z 246 GLN a 246 GLN a 365 ASN a 434 ASN b 246 GLN c 246 GLN c 263 HIS c 297 GLN c 434 ASN d 246 GLN d 434 ASN e 231 ASN e 246 GLN e 269 GLN f 246 GLN f 434 ASN g 231 ASN g 246 GLN ** g 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 79 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 39765 Z= 0.287 Angle : 0.493 4.908 53592 Z= 0.264 Chirality : 0.039 0.128 6138 Planarity : 0.003 0.028 7194 Dihedral : 4.758 17.176 5379 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer Outliers : 1.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.13), residues: 4785 helix: 1.71 (0.14), residues: 1320 sheet: 0.22 (0.11), residues: 2442 loop : -0.78 (0.18), residues: 1023 *********************** 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 1266 residues out of total 4422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 1198 time to evaluate : 4.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 24 residues processed: 1219 average time/residue: 1.8711 time to fit residues: 2674.5615 Evaluate side-chains 1196 residues out of total 4422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1172 time to evaluate : 4.598 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 10 residues processed: 16 average time/residue: 0.7448 time to fit residues: 23.2484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 444 optimal weight: 5.9990 chunk 338 optimal weight: 2.9990 chunk 233 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 214 optimal weight: 1.9990 chunk 302 optimal weight: 10.0000 chunk 451 optimal weight: 0.9990 chunk 478 optimal weight: 5.9990 chunk 236 optimal weight: 9.9990 chunk 428 optimal weight: 1.9990 chunk 128 optimal weight: 0.0060 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN B 246 GLN B 297 GLN C 246 GLN D 246 GLN E 246 GLN F 269 GLN G 246 GLN G 269 GLN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 297 GLN H 231 ASN H 246 GLN H 297 GLN I 246 GLN J 246 GLN J 411 GLN N 246 GLN N 269 GLN ** N 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 297 GLN O 246 GLN P 269 GLN Q 246 GLN S 246 GLN V 246 GLN V 269 GLN V 297 GLN X 246 GLN Y 246 GLN Y 297 GLN Z 246 GLN a 246 GLN b 246 GLN c 246 GLN d 246 GLN e 231 ASN e 269 GLN f 246 GLN g 231 ASN g 246 GLN ** g 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 39765 Z= 0.238 Angle : 0.464 5.081 53592 Z= 0.249 Chirality : 0.038 0.126 6138 Planarity : 0.002 0.020 7194 Dihedral : 4.630 17.038 5379 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Rotamer Outliers : 1.88 % 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: 1.09 (0.13), residues: 4785 helix: 2.42 (0.15), residues: 1320 sheet: 0.45 (0.12), residues: 2442 loop : -0.69 (0.18), residues: 1023 *********************** 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 1268 residues out of total 4422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 1185 time to evaluate : 4.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 83 outliers final: 32 residues processed: 1214 average time/residue: 1.8193 time to fit residues: 2591.0647 Evaluate side-chains 1203 residues out of total 4422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 1171 time to evaluate : 4.594 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 17 residues processed: 16 average time/residue: 0.5244 time to fit residues: 19.3281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 398 optimal weight: 2.9990 chunk 271 optimal weight: 0.7980 chunk 6 optimal weight: 0.0970 chunk 356 optimal weight: 10.0000 chunk 197 optimal weight: 5.9990 chunk 408 optimal weight: 9.9990 chunk 330 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 244 optimal weight: 0.8980 chunk 429 optimal weight: 0.4980 chunk 120 optimal weight: 0.2980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN B 246 GLN C 246 GLN C 297 GLN D 246 GLN E 246 GLN F 269 GLN G 246 GLN G 269 GLN G 277 GLN G 297 GLN H 231 ASN H 246 GLN H 297 GLN I 246 GLN J 246 GLN N 246 GLN N 269 GLN ** N 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 297 GLN O 246 GLN O 297 GLN P 269 GLN Q 246 GLN S 246 GLN V 269 GLN V 297 GLN X 246 GLN Y 246 GLN Y 297 GLN Y 299 ASN Z 246 GLN Z 261 ASN a 246 GLN b 246 GLN c 246 GLN c 297 GLN d 246 GLN e 231 ASN e 269 GLN f 246 GLN g 231 ASN g 246 GLN ** 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: 0.8003 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.019 39765 Z= 0.118 Angle : 0.409 5.005 53592 Z= 0.220 Chirality : 0.037 0.121 6138 Planarity : 0.002 0.020 7194 Dihedral : 4.188 16.422 5379 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 1.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.13), residues: 4785 helix: 3.02 (0.15), residues: 1320 sheet: 0.68 (0.11), residues: 2442 loop : -0.50 (0.18), residues: 1023 *********************** 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 1315 residues out of total 4422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 1238 time to evaluate : 4.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 27 residues processed: 1269 average time/residue: 1.7789 time to fit residues: 2663.3375 Evaluate side-chains 1234 residues out of total 4422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 1207 time to evaluate : 4.739 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 15 residues processed: 13 average time/residue: 0.8804 time to fit residues: 22.2869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 160 optimal weight: 2.9990 chunk 430 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 280 optimal weight: 9.9990 chunk 118 optimal weight: 3.9990 chunk 478 optimal weight: 6.9990 chunk 397 optimal weight: 5.9990 chunk 221 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 158 optimal weight: 4.9990 chunk 251 optimal weight: 10.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN A 261 ASN A 269 GLN A 411 GLN B 246 GLN B 297 GLN C 246 GLN D 246 GLN ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN F 269 GLN G 246 GLN G 269 GLN G 297 GLN H 231 ASN H 246 GLN ** H 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 297 GLN H 365 ASN I 246 GLN ** I 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 365 ASN J 246 GLN K 246 GLN M 297 GLN N 231 ASN N 246 GLN N 269 GLN ** N 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 297 GLN O 246 GLN P 246 GLN P 269 GLN Q 246 GLN Q 261 ASN R 277 GLN S 246 GLN ** T 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 365 ASN U 239 ASN U 365 ASN V 269 GLN V 297 GLN X 246 GLN Y 246 GLN ** Y 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 299 ASN Y 365 ASN Z 246 GLN Z 261 ASN Z 411 GLN a 246 GLN b 246 GLN c 246 GLN ** c 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 297 GLN d 246 GLN ** d 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 231 ASN ** e 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 269 GLN f 246 GLN g 231 ASN g 246 GLN ** g 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 434 ASN Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.049 39765 Z= 0.455 Angle : 0.559 5.239 53592 Z= 0.298 Chirality : 0.041 0.130 6138 Planarity : 0.003 0.034 7194 Dihedral : 4.980 17.845 5379 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer Outliers : 2.49 % 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: 1.23 (0.13), residues: 4785 helix: 2.40 (0.15), residues: 1320 sheet: 0.62 (0.11), residues: 2442 loop : -0.71 (0.17), residues: 1023 *********************** 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 1323 residues out of total 4422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 1213 time to evaluate : 4.846 Fit side-chains revert: symmetry clash outliers start: 110 outliers final: 48 residues processed: 1260 average time/residue: 1.8094 time to fit residues: 2680.7278 Evaluate side-chains 1225 residues out of total 4422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 1177 time to evaluate : 4.660 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 26 residues processed: 22 average time/residue: 0.7902 time to fit residues: 30.6375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 461 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 272 optimal weight: 0.9990 chunk 349 optimal weight: 0.9990 chunk 270 optimal weight: 2.9990 chunk 403 optimal weight: 0.0170 chunk 267 optimal weight: 0.9990 chunk 477 optimal weight: 5.9990 chunk 298 optimal weight: 0.9980 chunk 290 optimal weight: 1.9990 chunk 220 optimal weight: 0.9990 overall best weight: 0.8024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN A 261 ASN B 246 GLN F 269 GLN G 231 ASN G 269 GLN H 231 ASN H 246 GLN H 277 GLN I 246 GLN J 246 GLN J 411 GLN K 246 GLN N 269 GLN ** N 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 297 GLN O 246 GLN P 269 GLN Q 261 ASN Q 297 GLN T 277 GLN V 269 GLN V 297 GLN W 246 GLN Y 246 GLN Z 246 GLN Z 261 ASN a 246 GLN b 246 GLN c 246 GLN e 231 ASN f 246 GLN g 231 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 39765 Z= 0.161 Angle : 0.435 4.877 53592 Z= 0.234 Chirality : 0.038 0.125 6138 Planarity : 0.002 0.022 7194 Dihedral : 4.385 16.729 5379 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 1.88 % 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: 3.00 (0.15), residues: 1320 sheet: 0.83 (0.12), residues: 2442 loop : -0.52 (0.18), residues: 1023 *********************** 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 1291 residues out of total 4422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 1208 time to evaluate : 4.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 83 outliers final: 38 residues processed: 1248 average time/residue: 1.7745 time to fit residues: 2617.3682 Evaluate side-chains 1238 residues out of total 4422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 1200 time to evaluate : 4.378 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 28 residues processed: 11 average time/residue: 0.9638 time to fit residues: 20.4122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 295 optimal weight: 2.9990 chunk 190 optimal weight: 6.9990 chunk 284 optimal weight: 10.0000 chunk 143 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 303 optimal weight: 10.0000 chunk 325 optimal weight: 8.9990 chunk 235 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 375 optimal weight: 0.0970 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN B 246 GLN B 297 GLN C 246 GLN D 246 GLN E 246 GLN F 269 GLN G 269 GLN H 231 ASN H 246 GLN I 246 GLN J 246 GLN J 411 GLN L 231 ASN M 297 GLN N 231 ASN N 246 GLN N 269 GLN ** N 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 246 GLN P 269 GLN Q 246 GLN S 246 GLN T 269 GLN U 239 ASN V 269 GLN V 297 GLN X 246 GLN Y 246 GLN Z 246 GLN Z 261 ASN Z 411 GLN a 246 GLN b 246 GLN c 246 GLN d 246 GLN e 231 ASN f 246 GLN g 231 ASN g 246 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 39765 Z= 0.292 Angle : 0.488 5.149 53592 Z= 0.261 Chirality : 0.039 0.129 6138 Planarity : 0.003 0.048 7194 Dihedral : 4.655 17.171 5379 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.13), residues: 4785 helix: 2.83 (0.15), residues: 1320 sheet: 0.87 (0.11), residues: 2442 loop : -0.56 (0.18), residues: 1023 *********************** 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 1288 residues out of total 4422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 1209 time to evaluate : 4.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 79 outliers final: 46 residues processed: 1255 average time/residue: 1.7837 time to fit residues: 2641.7596 Evaluate side-chains 1247 residues out of total 4422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 1201 time to evaluate : 4.449 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 35 residues processed: 12 average time/residue: 0.8627 time to fit residues: 20.3083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 434 optimal weight: 4.9990 chunk 457 optimal weight: 0.8980 chunk 417 optimal weight: 0.4980 chunk 444 optimal weight: 2.9990 chunk 456 optimal weight: 0.5980 chunk 267 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 349 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 chunk 401 optimal weight: 6.9990 chunk 420 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN A 269 GLN B 246 GLN D 246 GLN F 269 GLN G 269 GLN H 231 ASN H 246 GLN I 246 GLN J 246 GLN J 411 GLN N 246 GLN N 269 GLN ** N 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 246 GLN Q 246 GLN S 246 GLN U 239 ASN V 269 GLN V 297 GLN X 246 GLN Y 246 GLN Z 246 GLN Z 261 ASN Z 411 GLN a 246 GLN b 246 GLN c 246 GLN e 231 ASN f 246 GLN g 231 ASN g 246 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 39765 Z= 0.153 Angle : 0.431 5.023 53592 Z= 0.231 Chirality : 0.038 0.124 6138 Planarity : 0.002 0.021 7194 Dihedral : 4.302 16.710 5379 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 1.42 % 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: 2.00 (0.13), residues: 4785 helix: 3.21 (0.15), residues: 1320 sheet: 1.02 (0.11), residues: 2442 loop : -0.45 (0.18), residues: 1023 *********************** 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 1279 residues out of total 4422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 1216 time to evaluate : 4.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 38 residues processed: 1258 average time/residue: 1.7332 time to fit residues: 2586.6793 Evaluate side-chains 1243 residues out of total 4422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 1205 time to evaluate : 4.552 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 33 residues processed: 6 average time/residue: 0.8845 time to fit residues: 13.5666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 443 optimal weight: 2.9990 chunk 291 optimal weight: 2.9990 chunk 470 optimal weight: 0.4980 chunk 286 optimal weight: 0.9980 chunk 223 optimal weight: 7.9990 chunk 326 optimal weight: 8.9990 chunk 493 optimal weight: 2.9990 chunk 453 optimal weight: 6.9990 chunk 392 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 303 optimal weight: 6.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN A 269 GLN B 246 GLN B 297 GLN C 246 GLN D 246 GLN E 246 GLN F 269 GLN G 231 ASN G 269 GLN H 231 ASN H 246 GLN ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 411 GLN I 246 GLN J 246 GLN J 411 GLN L 246 GLN M 239 ASN M 297 GLN N 246 GLN N 269 GLN ** N 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 246 GLN Q 246 GLN S 246 GLN T 269 GLN V 269 GLN V 297 GLN X 246 GLN Y 246 GLN Z 246 GLN Z 261 ASN Z 411 GLN a 246 GLN b 246 GLN c 246 GLN d 246 GLN e 231 ASN f 246 GLN g 231 ASN g 246 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 39765 Z= 0.331 Angle : 0.505 5.650 53592 Z= 0.270 Chirality : 0.040 0.129 6138 Planarity : 0.003 0.062 7194 Dihedral : 4.677 17.204 5379 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer Outliers : 1.42 % 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: 1.81 (0.13), residues: 4785 helix: 2.90 (0.14), residues: 1320 sheet: 1.00 (0.11), residues: 2442 loop : -0.57 (0.18), residues: 1023 ********************** 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 1275 residues out of total 4422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 1212 time to evaluate : 5.151 Fit side-chains revert: symmetry clash outliers start: 63 outliers final: 39 residues processed: 1259 average time/residue: 1.7749 time to fit residues: 2638.8708 Evaluate side-chains 1239 residues out of total 4422 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 1200 time to evaluate : 4.955 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 36 residues processed: 4 average time/residue: 0.3930 time to fit residues: 10.0156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 240 optimal weight: 1.9990 chunk 311 optimal weight: 8.9990 chunk 418 optimal weight: 1.9990 chunk 120 optimal weight: 0.0270 chunk 362 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 393 optimal weight: 5.9990 chunk 164 optimal weight: 10.0000 chunk 403 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN A 269 GLN B 246 GLN F 269 GLN G 231 ASN G 269 GLN H 231 ASN H 246 GLN H 277 GLN I 246 GLN J 246 GLN J 411 GLN L 246 GLN M 239 ASN N 246 GLN N 269 GLN ** N 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 246 GLN Q 246 GLN T 269 GLN U 239 ASN V 269 GLN V 297 GLN W 281 HIS X 246 GLN X 269 GLN Z 246 GLN Z 261 ASN Z 411 GLN a 246 GLN b 231 ASN b 246 GLN c 246 GLN d 246 GLN e 231 ASN f 246 GLN g 231 ASN g 246 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.145690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.120674 restraints weight = 46322.103| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.67 r_work: 0.3349 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 39765 Z= 0.207 Angle : 0.458 5.392 53592 Z= 0.246 Chirality : 0.038 0.128 6138 Planarity : 0.002 0.020 7194 Dihedral : 4.464 21.693 5379 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 1.42 % 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: 2.00 (0.13), residues: 4785 helix: 3.11 (0.14), residues: 1320 sheet: 1.10 (0.11), residues: 2442 loop : -0.52 (0.18), residues: 1023 =============================================================================== Job complete usr+sys time: 31220.79 seconds wall clock time: 546 minutes 26.06 seconds (32786.06 seconds total)