Starting phenix.real_space_refine (version: dev) on Wed Apr 6 22:37:10 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w5f_8767/04_2022/5w5f_8767.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w5f_8767/04_2022/5w5f_8767.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w5f_8767/04_2022/5w5f_8767.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w5f_8767/04_2022/5w5f_8767.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w5f_8767/04_2022/5w5f_8767.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w5f_8767/04_2022/5w5f_8767.pdb" } resolution = 3.4 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= 0.002 sd= 0.007 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 8": "NH1" <-> "NH2" Residue "A ARG 17": "NH1" <-> "NH2" Residue "A ARG 82": "NH1" <-> "NH2" Residue "A TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 118": "NH1" <-> "NH2" Residue "R ARG 8": "NH1" <-> "NH2" Residue "R ARG 17": "NH1" <-> "NH2" Residue "R ARG 82": "NH1" <-> "NH2" Residue "R TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 118": "NH1" <-> "NH2" Residue "C ARG 8": "NH1" <-> "NH2" Residue "C ARG 17": "NH1" <-> "NH2" Residue "C ARG 82": "NH1" <-> "NH2" Residue "C TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 118": "NH1" <-> "NH2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 17": "NH1" <-> "NH2" Residue "B ARG 82": "NH1" <-> "NH2" Residue "B TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 118": "NH1" <-> "NH2" Residue "D ARG 8": "NH1" <-> "NH2" Residue "D ARG 17": "NH1" <-> "NH2" Residue "D ARG 82": "NH1" <-> "NH2" Residue "D TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 118": "NH1" <-> "NH2" Residue "E ARG 8": "NH1" <-> "NH2" Residue "E ARG 17": "NH1" <-> "NH2" Residue "E ARG 82": "NH1" <-> "NH2" Residue "E TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 118": "NH1" <-> "NH2" Residue "F ARG 8": "NH1" <-> "NH2" Residue "F ARG 17": "NH1" <-> "NH2" Residue "F ARG 82": "NH1" <-> "NH2" Residue "F TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 118": "NH1" <-> "NH2" Residue "G ARG 8": "NH1" <-> "NH2" Residue "G ARG 17": "NH1" <-> "NH2" Residue "G ARG 82": "NH1" <-> "NH2" Residue "G TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 118": "NH1" <-> "NH2" Residue "H ARG 8": "NH1" <-> "NH2" Residue "H ARG 17": "NH1" <-> "NH2" Residue "H ARG 82": "NH1" <-> "NH2" Residue "H TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 118": "NH1" <-> "NH2" Residue "I ARG 8": "NH1" <-> "NH2" Residue "I ARG 17": "NH1" <-> "NH2" Residue "I ARG 82": "NH1" <-> "NH2" Residue "I TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 118": "NH1" <-> "NH2" Residue "J ARG 8": "NH1" <-> "NH2" Residue "J ARG 17": "NH1" <-> "NH2" Residue "J ARG 82": "NH1" <-> "NH2" Residue "J TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 118": "NH1" <-> "NH2" Residue "K ARG 8": "NH1" <-> "NH2" Residue "K ARG 17": "NH1" <-> "NH2" Residue "K ARG 82": "NH1" <-> "NH2" Residue "K TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 118": "NH1" <-> "NH2" Residue "L ARG 8": "NH1" <-> "NH2" Residue "L ARG 17": "NH1" <-> "NH2" Residue "L ARG 82": "NH1" <-> "NH2" Residue "L TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 118": "NH1" <-> "NH2" Residue "M ARG 8": "NH1" <-> "NH2" Residue "M ARG 17": "NH1" <-> "NH2" Residue "M ARG 82": "NH1" <-> "NH2" Residue "M TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 118": "NH1" <-> "NH2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ARG 17": "NH1" <-> "NH2" Residue "N ARG 82": "NH1" <-> "NH2" Residue "N TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "O ARG 8": "NH1" <-> "NH2" Residue "O ARG 17": "NH1" <-> "NH2" Residue "O ARG 82": "NH1" <-> "NH2" Residue "O TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 118": "NH1" <-> "NH2" Residue "P ARG 8": "NH1" <-> "NH2" Residue "P ARG 17": "NH1" <-> "NH2" Residue "P ARG 82": "NH1" <-> "NH2" Residue "P TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 118": "NH1" <-> "NH2" Residue "Q ARG 8": "NH1" <-> "NH2" Residue "Q ARG 17": "NH1" <-> "NH2" Residue "Q ARG 82": "NH1" <-> "NH2" Residue "Q TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 118": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 23472 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1304 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 157} Chain: "R" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1304 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 157} Chain: "C" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1304 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 157} Chain: "B" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1304 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 157} Chain: "D" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1304 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 157} Chain: "E" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1304 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 157} Chain: "F" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1304 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 157} Chain: "G" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1304 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 157} Chain: "H" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1304 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 157} Chain: "I" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1304 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 157} Chain: "J" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1304 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 157} Chain: "K" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1304 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 157} Chain: "L" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1304 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 157} Chain: "M" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1304 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 157} Chain: "N" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1304 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 157} Chain: "O" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1304 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 157} Chain: "P" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1304 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 157} Chain: "Q" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1304 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 157} Time building chain proxies: 12.73, per 1000 atoms: 0.54 Number of scatterers: 23472 At special positions: 0 Unit cell: (102.96, 101.64, 146.52, 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 72 16.00 O 4554 8.00 N 3942 7.00 C 14904 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: 8.52 Conformation dependent library (CDL) restraints added in 3.5 seconds 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5472 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 36 sheets defined 22.1% alpha, 49.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'A' and resid 4 through 10 removed outlier: 3.642A pdb=" N ARG A 8 " --> pdb=" O ASP A 4 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE A 10 " --> pdb=" O VAL A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 14 removed outlier: 3.725A pdb=" N ASP A 14 " --> pdb=" O GLU A 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 11 through 14' Processing helix chain 'A' and resid 31 through 34 removed outlier: 3.543A pdb=" N PHE A 34 " --> pdb=" O ASN A 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 31 through 34' Processing helix chain 'A' and resid 79 through 93 removed outlier: 4.242A pdb=" N PHE A 85 " --> pdb=" O ALA A 81 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TRP A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA A 92 " --> pdb=" O TRP A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.512A pdb=" N TYR A 107 " --> pdb=" O LYS A 103 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS A 108 " --> pdb=" O PRO A 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 108' Processing helix chain 'R' and resid 4 through 10 removed outlier: 3.642A pdb=" N ARG R 8 " --> pdb=" O ASP R 4 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE R 10 " --> pdb=" O VAL R 6 " (cutoff:3.500A) Processing helix chain 'R' and resid 11 through 14 removed outlier: 3.725A pdb=" N ASP R 14 " --> pdb=" O GLU R 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 11 through 14' Processing helix chain 'R' and resid 31 through 34 removed outlier: 3.543A pdb=" N PHE R 34 " --> pdb=" O ASN R 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 31 through 34' Processing helix chain 'R' and resid 79 through 93 removed outlier: 4.242A pdb=" N PHE R 85 " --> pdb=" O ALA R 81 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP R 88 " --> pdb=" O LYS R 84 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA R 92 " --> pdb=" O TRP R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 108 removed outlier: 3.512A pdb=" N TYR R 107 " --> pdb=" O LYS R 103 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS R 108 " --> pdb=" O PRO R 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 103 through 108' Processing helix chain 'C' and resid 4 through 10 removed outlier: 3.642A pdb=" N ARG C 8 " --> pdb=" O ASP C 4 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE C 10 " --> pdb=" O VAL C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 14 removed outlier: 3.726A pdb=" N ASP C 14 " --> pdb=" O GLU C 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 11 through 14' Processing helix chain 'C' and resid 31 through 34 removed outlier: 3.543A pdb=" N PHE C 34 " --> pdb=" O ASN C 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 31 through 34' Processing helix chain 'C' and resid 79 through 93 removed outlier: 4.243A pdb=" N PHE C 85 " --> pdb=" O ALA C 81 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TRP C 88 " --> pdb=" O LYS C 84 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA C 92 " --> pdb=" O TRP C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.512A pdb=" N TYR C 107 " --> pdb=" O LYS C 103 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS C 108 " --> pdb=" O PRO C 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 103 through 108' Processing helix chain 'B' and resid 4 through 10 removed outlier: 3.642A pdb=" N ARG B 8 " --> pdb=" O ASP B 4 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE B 10 " --> pdb=" O VAL B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 14 removed outlier: 3.725A pdb=" N ASP B 14 " --> pdb=" O GLU B 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 11 through 14' Processing helix chain 'B' and resid 31 through 34 removed outlier: 3.543A pdb=" N PHE B 34 " --> pdb=" O ASN B 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 31 through 34' Processing helix chain 'B' and resid 79 through 93 removed outlier: 4.242A pdb=" N PHE B 85 " --> pdb=" O ALA B 81 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TRP B 88 " --> pdb=" O LYS B 84 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA B 92 " --> pdb=" O TRP B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.512A pdb=" N TYR B 107 " --> pdb=" O LYS B 103 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS B 108 " --> pdb=" O PRO B 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 108' Processing helix chain 'D' and resid 4 through 10 removed outlier: 3.642A pdb=" N ARG D 8 " --> pdb=" O ASP D 4 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE D 10 " --> pdb=" O VAL D 6 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 14 removed outlier: 3.724A pdb=" N ASP D 14 " --> pdb=" O GLU D 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 11 through 14' Processing helix chain 'D' and resid 31 through 34 removed outlier: 3.543A pdb=" N PHE D 34 " --> pdb=" O ASN D 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 31 through 34' Processing helix chain 'D' and resid 79 through 93 removed outlier: 4.242A pdb=" N PHE D 85 " --> pdb=" O ALA D 81 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP D 88 " --> pdb=" O LYS D 84 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA D 92 " --> pdb=" O TRP D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.512A pdb=" N TYR D 107 " --> pdb=" O LYS D 103 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS D 108 " --> pdb=" O PRO D 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 108' Processing helix chain 'E' and resid 4 through 10 removed outlier: 3.642A pdb=" N ARG E 8 " --> pdb=" O ASP E 4 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE E 10 " --> pdb=" O VAL E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 14 removed outlier: 3.724A pdb=" N ASP E 14 " --> pdb=" O GLU E 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 11 through 14' Processing helix chain 'E' and resid 31 through 34 removed outlier: 3.543A pdb=" N PHE E 34 " --> pdb=" O ASN E 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 31 through 34' Processing helix chain 'E' and resid 79 through 93 removed outlier: 4.242A pdb=" N PHE E 85 " --> pdb=" O ALA E 81 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP E 88 " --> pdb=" O LYS E 84 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA E 92 " --> pdb=" O TRP E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 108 removed outlier: 3.512A pdb=" N TYR E 107 " --> pdb=" O LYS E 103 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS E 108 " --> pdb=" O PRO E 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 103 through 108' Processing helix chain 'F' and resid 4 through 10 removed outlier: 3.642A pdb=" N ARG F 8 " --> pdb=" O ASP F 4 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE F 10 " --> pdb=" O VAL F 6 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 14 removed outlier: 3.725A pdb=" N ASP F 14 " --> pdb=" O GLU F 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 11 through 14' Processing helix chain 'F' and resid 31 through 34 removed outlier: 3.543A pdb=" N PHE F 34 " --> pdb=" O ASN F 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 31 through 34' Processing helix chain 'F' and resid 79 through 93 removed outlier: 4.242A pdb=" N PHE F 85 " --> pdb=" O ALA F 81 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP F 88 " --> pdb=" O LYS F 84 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA F 92 " --> pdb=" O TRP F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 108 removed outlier: 3.511A pdb=" N TYR F 107 " --> pdb=" O LYS F 103 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS F 108 " --> pdb=" O PRO F 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 103 through 108' Processing helix chain 'G' and resid 4 through 10 removed outlier: 3.642A pdb=" N ARG G 8 " --> pdb=" O ASP G 4 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE G 10 " --> pdb=" O VAL G 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 14 removed outlier: 3.725A pdb=" N ASP G 14 " --> pdb=" O GLU G 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 11 through 14' Processing helix chain 'G' and resid 31 through 34 removed outlier: 3.543A pdb=" N PHE G 34 " --> pdb=" O ASN G 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 31 through 34' Processing helix chain 'G' and resid 79 through 93 removed outlier: 4.242A pdb=" N PHE G 85 " --> pdb=" O ALA G 81 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP G 88 " --> pdb=" O LYS G 84 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA G 92 " --> pdb=" O TRP G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 108 removed outlier: 3.512A pdb=" N TYR G 107 " --> pdb=" O LYS G 103 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS G 108 " --> pdb=" O PRO G 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 103 through 108' Processing helix chain 'H' and resid 4 through 10 removed outlier: 3.642A pdb=" N ARG H 8 " --> pdb=" O ASP H 4 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE H 10 " --> pdb=" O VAL H 6 " (cutoff:3.500A) Processing helix chain 'H' and resid 11 through 14 removed outlier: 3.725A pdb=" N ASP H 14 " --> pdb=" O GLU H 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 11 through 14' Processing helix chain 'H' and resid 31 through 34 removed outlier: 3.544A pdb=" N PHE H 34 " --> pdb=" O ASN H 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 31 through 34' Processing helix chain 'H' and resid 79 through 93 removed outlier: 4.242A pdb=" N PHE H 85 " --> pdb=" O ALA H 81 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP H 88 " --> pdb=" O LYS H 84 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA H 92 " --> pdb=" O TRP H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 108 removed outlier: 3.512A pdb=" N TYR H 107 " --> pdb=" O LYS H 103 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS H 108 " --> pdb=" O PRO H 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 103 through 108' Processing helix chain 'I' and resid 4 through 10 removed outlier: 3.642A pdb=" N ARG I 8 " --> pdb=" O ASP I 4 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE I 10 " --> pdb=" O VAL I 6 " (cutoff:3.500A) Processing helix chain 'I' and resid 11 through 14 removed outlier: 3.725A pdb=" N ASP I 14 " --> pdb=" O GLU I 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 11 through 14' Processing helix chain 'I' and resid 31 through 34 removed outlier: 3.543A pdb=" N PHE I 34 " --> pdb=" O ASN I 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 31 through 34' Processing helix chain 'I' and resid 79 through 93 removed outlier: 4.242A pdb=" N PHE I 85 " --> pdb=" O ALA I 81 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP I 88 " --> pdb=" O LYS I 84 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA I 92 " --> pdb=" O TRP I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 103 through 108 removed outlier: 3.512A pdb=" N TYR I 107 " --> pdb=" O LYS I 103 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS I 108 " --> pdb=" O PRO I 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 103 through 108' Processing helix chain 'J' and resid 4 through 10 removed outlier: 3.642A pdb=" N ARG J 8 " --> pdb=" O ASP J 4 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE J 10 " --> pdb=" O VAL J 6 " (cutoff:3.500A) Processing helix chain 'J' and resid 11 through 14 removed outlier: 3.724A pdb=" N ASP J 14 " --> pdb=" O GLU J 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 11 through 14' Processing helix chain 'J' and resid 31 through 34 removed outlier: 3.543A pdb=" N PHE J 34 " --> pdb=" O ASN J 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 31 through 34' Processing helix chain 'J' and resid 79 through 93 removed outlier: 4.242A pdb=" N PHE J 85 " --> pdb=" O ALA J 81 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP J 88 " --> pdb=" O LYS J 84 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA J 92 " --> pdb=" O TRP J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 108 removed outlier: 3.511A pdb=" N TYR J 107 " --> pdb=" O LYS J 103 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS J 108 " --> pdb=" O PRO J 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 103 through 108' Processing helix chain 'K' and resid 4 through 10 removed outlier: 3.642A pdb=" N ARG K 8 " --> pdb=" O ASP K 4 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE K 10 " --> pdb=" O VAL K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 11 through 14 removed outlier: 3.724A pdb=" N ASP K 14 " --> pdb=" O GLU K 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 11 through 14' Processing helix chain 'K' and resid 31 through 34 removed outlier: 3.542A pdb=" N PHE K 34 " --> pdb=" O ASN K 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 31 through 34' Processing helix chain 'K' and resid 79 through 93 removed outlier: 4.242A pdb=" N PHE K 85 " --> pdb=" O ALA K 81 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP K 88 " --> pdb=" O LYS K 84 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA K 92 " --> pdb=" O TRP K 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 103 through 108 removed outlier: 3.512A pdb=" N TYR K 107 " --> pdb=" O LYS K 103 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS K 108 " --> pdb=" O PRO K 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 103 through 108' Processing helix chain 'L' and resid 4 through 10 removed outlier: 3.642A pdb=" N ARG L 8 " --> pdb=" O ASP L 4 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE L 10 " --> pdb=" O VAL L 6 " (cutoff:3.500A) Processing helix chain 'L' and resid 11 through 14 removed outlier: 3.724A pdb=" N ASP L 14 " --> pdb=" O GLU L 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 11 through 14' Processing helix chain 'L' and resid 31 through 34 removed outlier: 3.543A pdb=" N PHE L 34 " --> pdb=" O ASN L 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 31 through 34' Processing helix chain 'L' and resid 79 through 93 removed outlier: 4.241A pdb=" N PHE L 85 " --> pdb=" O ALA L 81 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TRP L 88 " --> pdb=" O LYS L 84 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA L 92 " --> pdb=" O TRP L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 103 through 108 removed outlier: 3.512A pdb=" N TYR L 107 " --> pdb=" O LYS L 103 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS L 108 " --> pdb=" O PRO L 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 103 through 108' Processing helix chain 'M' and resid 4 through 10 removed outlier: 3.643A pdb=" N ARG M 8 " --> pdb=" O ASP M 4 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE M 10 " --> pdb=" O VAL M 6 " (cutoff:3.500A) Processing helix chain 'M' and resid 11 through 14 removed outlier: 3.725A pdb=" N ASP M 14 " --> pdb=" O GLU M 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 11 through 14' Processing helix chain 'M' and resid 31 through 34 removed outlier: 3.542A pdb=" N PHE M 34 " --> pdb=" O ASN M 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 31 through 34' Processing helix chain 'M' and resid 79 through 93 removed outlier: 4.242A pdb=" N PHE M 85 " --> pdb=" O ALA M 81 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP M 88 " --> pdb=" O LYS M 84 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA M 92 " --> pdb=" O TRP M 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 103 through 108 removed outlier: 3.512A pdb=" N TYR M 107 " --> pdb=" O LYS M 103 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS M 108 " --> pdb=" O PRO M 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 103 through 108' Processing helix chain 'N' and resid 4 through 10 removed outlier: 3.642A pdb=" N ARG N 8 " --> pdb=" O ASP N 4 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE N 10 " --> pdb=" O VAL N 6 " (cutoff:3.500A) Processing helix chain 'N' and resid 11 through 14 removed outlier: 3.725A pdb=" N ASP N 14 " --> pdb=" O GLU N 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 11 through 14' Processing helix chain 'N' and resid 31 through 34 removed outlier: 3.543A pdb=" N PHE N 34 " --> pdb=" O ASN N 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 31 through 34' Processing helix chain 'N' and resid 79 through 93 removed outlier: 4.242A pdb=" N PHE N 85 " --> pdb=" O ALA N 81 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP N 88 " --> pdb=" O LYS N 84 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA N 92 " --> pdb=" O TRP N 88 " (cutoff:3.500A) Processing helix chain 'N' and resid 103 through 108 removed outlier: 3.512A pdb=" N TYR N 107 " --> pdb=" O LYS N 103 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS N 108 " --> pdb=" O PRO N 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 103 through 108' Processing helix chain 'O' and resid 4 through 10 removed outlier: 3.642A pdb=" N ARG O 8 " --> pdb=" O ASP O 4 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE O 10 " --> pdb=" O VAL O 6 " (cutoff:3.500A) Processing helix chain 'O' and resid 11 through 14 removed outlier: 3.725A pdb=" N ASP O 14 " --> pdb=" O GLU O 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 11 through 14' Processing helix chain 'O' and resid 31 through 34 removed outlier: 3.543A pdb=" N PHE O 34 " --> pdb=" O ASN O 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 31 through 34' Processing helix chain 'O' and resid 79 through 93 removed outlier: 4.243A pdb=" N PHE O 85 " --> pdb=" O ALA O 81 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TRP O 88 " --> pdb=" O LYS O 84 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA O 92 " --> pdb=" O TRP O 88 " (cutoff:3.500A) Processing helix chain 'O' and resid 103 through 108 removed outlier: 3.512A pdb=" N TYR O 107 " --> pdb=" O LYS O 103 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS O 108 " --> pdb=" O PRO O 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 103 through 108' Processing helix chain 'P' and resid 4 through 10 removed outlier: 3.642A pdb=" N ARG P 8 " --> pdb=" O ASP P 4 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE P 10 " --> pdb=" O VAL P 6 " (cutoff:3.500A) Processing helix chain 'P' and resid 11 through 14 removed outlier: 3.726A pdb=" N ASP P 14 " --> pdb=" O GLU P 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 11 through 14' Processing helix chain 'P' and resid 31 through 34 removed outlier: 3.543A pdb=" N PHE P 34 " --> pdb=" O ASN P 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 31 through 34' Processing helix chain 'P' and resid 79 through 93 removed outlier: 4.242A pdb=" N PHE P 85 " --> pdb=" O ALA P 81 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP P 88 " --> pdb=" O LYS P 84 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA P 92 " --> pdb=" O TRP P 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 103 through 108 removed outlier: 3.512A pdb=" N TYR P 107 " --> pdb=" O LYS P 103 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS P 108 " --> pdb=" O PRO P 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 103 through 108' Processing helix chain 'Q' and resid 4 through 10 removed outlier: 3.641A pdb=" N ARG Q 8 " --> pdb=" O ASP Q 4 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE Q 10 " --> pdb=" O VAL Q 6 " (cutoff:3.500A) Processing helix chain 'Q' and resid 11 through 14 removed outlier: 3.725A pdb=" N ASP Q 14 " --> pdb=" O GLU Q 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 11 through 14' Processing helix chain 'Q' and resid 31 through 34 removed outlier: 3.543A pdb=" N PHE Q 34 " --> pdb=" O ASN Q 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 31 through 34' Processing helix chain 'Q' and resid 79 through 93 removed outlier: 4.242A pdb=" N PHE Q 85 " --> pdb=" O ALA Q 81 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP Q 88 " --> pdb=" O LYS Q 84 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ALA Q 92 " --> pdb=" O TRP Q 88 " (cutoff:3.500A) Processing helix chain 'Q' and resid 103 through 108 removed outlier: 3.512A pdb=" N TYR Q 107 " --> pdb=" O LYS Q 103 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS Q 108 " --> pdb=" O PRO Q 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 103 through 108' Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 24 removed outlier: 6.744A pdb=" N ALA A 111 " --> pdb=" O LYS A 130 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N LYS A 130 " --> pdb=" O ALA A 111 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL A 113 " --> pdb=" O GLU A 128 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N GLU A 128 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLN A 115 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLU A 126 " --> pdb=" O GLN A 115 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR A 156 " --> pdb=" O THR A 135 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N VAL A 137 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N GLU A 154 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N THR A 70 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N MET A 74 " --> pdb=" O CYS A 36 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N CYS A 36 " --> pdb=" O MET A 74 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU D 142 " --> pdb=" O THR A 39 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU D 140 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 161 through 163 removed outlier: 3.711A pdb=" N TYR A 161 " --> pdb=" O LYS A 130 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU A 128 " --> pdb=" O GLU A 163 " (cutoff:3.500A) removed outlier: 22.513A pdb=" N ILE A 129 " --> pdb=" O GLY P 52 " (cutoff:3.500A) removed outlier: 20.122A pdb=" N GLY P 52 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 16.307A pdb=" N GLY A 131 " --> pdb=" O PRO P 50 " (cutoff:3.500A) removed outlier: 12.473A pdb=" N TRP A 133 " --> pdb=" O LYS P 48 " (cutoff:3.500A) removed outlier: 9.012A pdb=" N LYS P 48 " --> pdb=" O TRP A 133 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N THR A 135 " --> pdb=" O VAL P 46 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE P 45 " --> pdb=" O THR P 65 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP P 63 " --> pdb=" O GLU P 47 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ILE P 49 " --> pdb=" O ALA P 61 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ALA P 61 " --> pdb=" O ILE P 49 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL P 51 " --> pdb=" O ASN P 59 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ASN P 59 " --> pdb=" O VAL P 51 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N PHE P 53 " --> pdb=" O LYS P 57 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N LYS P 57 " --> pdb=" O PHE P 53 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 56 through 66 removed outlier: 5.104A pdb=" N LYS A 57 " --> pdb=" O PHE A 53 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N PHE A 53 " --> pdb=" O LYS A 57 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ASN A 59 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL A 51 " --> pdb=" O ASN A 59 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ALA A 61 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ILE A 49 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP A 63 " --> pdb=" O GLU A 47 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE A 45 " --> pdb=" O THR A 65 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N THR D 135 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 8.999A pdb=" N LYS A 48 " --> pdb=" O TRP D 133 " (cutoff:3.500A) removed outlier: 12.454A pdb=" N TRP D 133 " --> pdb=" O LYS A 48 " (cutoff:3.500A) removed outlier: 16.301A pdb=" N GLY D 131 " --> pdb=" O PRO A 50 " (cutoff:3.500A) removed outlier: 20.125A pdb=" N GLY A 52 " --> pdb=" O ILE D 129 " (cutoff:3.500A) removed outlier: 22.526A pdb=" N ILE D 129 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU D 128 " --> pdb=" O GLU D 163 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR D 161 " --> pdb=" O LYS D 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 21 through 24 removed outlier: 6.745A pdb=" N ALA D 111 " --> pdb=" O LYS D 130 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS D 130 " --> pdb=" O ALA D 111 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL D 113 " --> pdb=" O GLU D 128 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N GLU D 128 " --> pdb=" O VAL D 113 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLN D 115 " --> pdb=" O GLU D 126 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLU D 126 " --> pdb=" O GLN D 115 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR D 156 " --> pdb=" O THR D 135 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N VAL D 137 " --> pdb=" O GLU D 154 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N GLU D 154 " --> pdb=" O VAL D 137 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N THR D 70 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N MET D 74 " --> pdb=" O CYS D 36 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N CYS D 36 " --> pdb=" O MET D 74 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU G 142 " --> pdb=" O THR D 39 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU G 140 " --> pdb=" O LEU D 41 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 140 through 143 removed outlier: 3.723A pdb=" N LEU A 140 " --> pdb=" O LEU P 41 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU A 142 " --> pdb=" O THR P 39 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N CYS P 36 " --> pdb=" O MET P 74 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N MET P 74 " --> pdb=" O CYS P 36 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N THR P 70 " --> pdb=" O ALA P 40 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N GLU P 154 " --> pdb=" O VAL P 137 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N VAL P 137 " --> pdb=" O GLU P 154 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR P 156 " --> pdb=" O THR P 135 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLU P 126 " --> pdb=" O GLN P 115 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLN P 115 " --> pdb=" O GLU P 126 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N GLU P 128 " --> pdb=" O VAL P 113 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL P 113 " --> pdb=" O GLU P 128 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS P 130 " --> pdb=" O ALA P 111 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ALA P 111 " --> pdb=" O LYS P 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 56 through 66 removed outlier: 5.103A pdb=" N LYS M 57 " --> pdb=" O PHE M 53 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N PHE M 53 " --> pdb=" O LYS M 57 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ASN M 59 " --> pdb=" O VAL M 51 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL M 51 " --> pdb=" O ASN M 59 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ALA M 61 " --> pdb=" O ILE M 49 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ILE M 49 " --> pdb=" O ALA M 61 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP M 63 " --> pdb=" O GLU M 47 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE M 45 " --> pdb=" O THR M 65 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N THR P 135 " --> pdb=" O VAL M 46 " (cutoff:3.500A) removed outlier: 9.045A pdb=" N LYS M 48 " --> pdb=" O TRP P 133 " (cutoff:3.500A) removed outlier: 12.516A pdb=" N TRP P 133 " --> pdb=" O LYS M 48 " (cutoff:3.500A) removed outlier: 16.370A pdb=" N GLY P 131 " --> pdb=" O PRO M 50 " (cutoff:3.500A) removed outlier: 20.190A pdb=" N GLY M 52 " --> pdb=" O ILE P 129 " (cutoff:3.500A) removed outlier: 22.579A pdb=" N ILE P 129 " --> pdb=" O GLY M 52 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU P 128 " --> pdb=" O GLU P 163 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR P 161 " --> pdb=" O LYS P 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'R' and resid 21 through 24 removed outlier: 6.744A pdb=" N ALA R 111 " --> pdb=" O LYS R 130 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N LYS R 130 " --> pdb=" O ALA R 111 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL R 113 " --> pdb=" O GLU R 128 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N GLU R 128 " --> pdb=" O VAL R 113 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLN R 115 " --> pdb=" O GLU R 126 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N GLU R 126 " --> pdb=" O GLN R 115 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR R 156 " --> pdb=" O THR R 135 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N VAL R 137 " --> pdb=" O GLU R 154 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N GLU R 154 " --> pdb=" O VAL R 137 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N THR R 70 " --> pdb=" O ALA R 40 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N MET R 74 " --> pdb=" O CYS R 36 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N CYS R 36 " --> pdb=" O MET R 74 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU B 142 " --> pdb=" O THR R 39 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU B 140 " --> pdb=" O LEU R 41 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 161 through 163 removed outlier: 3.711A pdb=" N TYR R 161 " --> pdb=" O LYS R 130 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU R 128 " --> pdb=" O GLU R 163 " (cutoff:3.500A) removed outlier: 22.580A pdb=" N ILE R 129 " --> pdb=" O GLY O 52 " (cutoff:3.500A) removed outlier: 20.181A pdb=" N GLY O 52 " --> pdb=" O ILE R 129 " (cutoff:3.500A) removed outlier: 16.352A pdb=" N GLY R 131 " --> pdb=" O PRO O 50 " (cutoff:3.500A) removed outlier: 12.494A pdb=" N TRP R 133 " --> pdb=" O LYS O 48 " (cutoff:3.500A) removed outlier: 9.027A pdb=" N LYS O 48 " --> pdb=" O TRP R 133 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N THR R 135 " --> pdb=" O VAL O 46 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE O 45 " --> pdb=" O THR O 65 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP O 63 " --> pdb=" O GLU O 47 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ILE O 49 " --> pdb=" O ALA O 61 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ALA O 61 " --> pdb=" O ILE O 49 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N VAL O 51 " --> pdb=" O ASN O 59 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ASN O 59 " --> pdb=" O VAL O 51 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N PHE O 53 " --> pdb=" O LYS O 57 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N LYS O 57 " --> pdb=" O PHE O 53 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 56 through 66 removed outlier: 5.104A pdb=" N LYS R 57 " --> pdb=" O PHE R 53 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N PHE R 53 " --> pdb=" O LYS R 57 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ASN R 59 " --> pdb=" O VAL R 51 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL R 51 " --> pdb=" O ASN R 59 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ALA R 61 " --> pdb=" O ILE R 49 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ILE R 49 " --> pdb=" O ALA R 61 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP R 63 " --> pdb=" O GLU R 47 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE R 45 " --> pdb=" O THR R 65 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N THR B 135 " --> pdb=" O VAL R 46 " (cutoff:3.500A) removed outlier: 9.011A pdb=" N LYS R 48 " --> pdb=" O TRP B 133 " (cutoff:3.500A) removed outlier: 12.475A pdb=" N TRP B 133 " --> pdb=" O LYS R 48 " (cutoff:3.500A) removed outlier: 16.326A pdb=" N GLY B 131 " --> pdb=" O PRO R 50 " (cutoff:3.500A) removed outlier: 20.156A pdb=" N GLY R 52 " --> pdb=" O ILE B 129 " (cutoff:3.500A) removed outlier: 22.554A pdb=" N ILE B 129 " --> pdb=" O GLY R 52 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU B 128 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR B 161 " --> pdb=" O LYS B 130 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 21 through 24 removed outlier: 6.744A pdb=" N ALA B 111 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS B 130 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL B 113 " --> pdb=" O GLU B 128 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N GLU B 128 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N GLN B 115 " --> pdb=" O GLU B 126 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLU B 126 " --> pdb=" O GLN B 115 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR B 156 " --> pdb=" O THR B 135 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N VAL B 137 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N GLU B 154 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N THR B 70 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N MET B 74 " --> pdb=" O CYS B 36 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N CYS B 36 " --> pdb=" O MET B 74 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU F 142 " --> pdb=" O THR B 39 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU F 140 " --> pdb=" O LEU B 41 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 140 through 143 removed outlier: 3.685A pdb=" N LEU R 140 " --> pdb=" O LEU O 41 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU R 142 " --> pdb=" O THR O 39 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N CYS O 36 " --> pdb=" O MET O 74 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N MET O 74 " --> pdb=" O CYS O 36 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N THR O 70 " --> pdb=" O ALA O 40 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N GLU O 154 " --> pdb=" O VAL O 137 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N VAL O 137 " --> pdb=" O GLU O 154 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR O 156 " --> pdb=" O THR O 135 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLU O 126 " --> pdb=" O GLN O 115 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLN O 115 " --> pdb=" O GLU O 126 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N GLU O 128 " --> pdb=" O VAL O 113 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL O 113 " --> pdb=" O GLU O 128 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS O 130 " --> pdb=" O ALA O 111 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ALA O 111 " --> pdb=" O LYS O 130 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 56 through 66 removed outlier: 5.104A pdb=" N LYS L 57 " --> pdb=" O PHE L 53 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N PHE L 53 " --> pdb=" O LYS L 57 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ASN L 59 " --> pdb=" O VAL L 51 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL L 51 " --> pdb=" O ASN L 59 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ALA L 61 " --> pdb=" O ILE L 49 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ILE L 49 " --> pdb=" O ALA L 61 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP L 63 " --> pdb=" O GLU L 47 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE L 45 " --> pdb=" O THR L 65 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N THR O 135 " --> pdb=" O VAL L 46 " (cutoff:3.500A) removed outlier: 9.018A pdb=" N LYS L 48 " --> pdb=" O TRP O 133 " (cutoff:3.500A) removed outlier: 12.482A pdb=" N TRP O 133 " --> pdb=" O LYS L 48 " (cutoff:3.500A) removed outlier: 16.340A pdb=" N GLY O 131 " --> pdb=" O PRO L 50 " (cutoff:3.500A) removed outlier: 20.170A pdb=" N GLY L 52 " --> pdb=" O ILE O 129 " (cutoff:3.500A) removed outlier: 22.568A pdb=" N ILE O 129 " --> pdb=" O GLY L 52 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU O 128 " --> pdb=" O GLU O 163 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR O 161 " --> pdb=" O LYS O 130 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 21 through 24 removed outlier: 6.744A pdb=" N ALA C 111 " --> pdb=" O LYS C 130 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS C 130 " --> pdb=" O ALA C 111 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL C 113 " --> pdb=" O GLU C 128 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N GLU C 128 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N GLN C 115 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N GLU C 126 " --> pdb=" O GLN C 115 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR C 156 " --> pdb=" O THR C 135 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N VAL C 137 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N GLU C 154 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N THR C 70 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N MET C 74 " --> pdb=" O CYS C 36 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N CYS C 36 " --> pdb=" O MET C 74 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU E 142 " --> pdb=" O THR C 39 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU E 140 " --> pdb=" O LEU C 41 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 161 through 163 removed outlier: 3.710A pdb=" N TYR C 161 " --> pdb=" O LYS C 130 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU C 128 " --> pdb=" O GLU C 163 " (cutoff:3.500A) removed outlier: 22.505A pdb=" N ILE C 129 " --> pdb=" O GLY Q 52 " (cutoff:3.500A) removed outlier: 20.109A pdb=" N GLY Q 52 " --> pdb=" O ILE C 129 " (cutoff:3.500A) removed outlier: 16.293A pdb=" N GLY C 131 " --> pdb=" O PRO Q 50 " (cutoff:3.500A) removed outlier: 12.446A pdb=" N TRP C 133 " --> pdb=" O LYS Q 48 " (cutoff:3.500A) removed outlier: 8.983A pdb=" N LYS Q 48 " --> pdb=" O TRP C 133 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N THR C 135 " --> pdb=" O VAL Q 46 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE Q 45 " --> pdb=" O THR Q 65 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP Q 63 " --> pdb=" O GLU Q 47 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ILE Q 49 " --> pdb=" O ALA Q 61 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ALA Q 61 " --> pdb=" O ILE Q 49 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL Q 51 " --> pdb=" O ASN Q 59 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ASN Q 59 " --> pdb=" O VAL Q 51 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N PHE Q 53 " --> pdb=" O LYS Q 57 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N LYS Q 57 " --> pdb=" O PHE Q 53 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 56 through 66 removed outlier: 5.104A pdb=" N LYS C 57 " --> pdb=" O PHE C 53 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N PHE C 53 " --> pdb=" O LYS C 57 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ASN C 59 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N VAL C 51 " --> pdb=" O ASN C 59 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ALA C 61 " --> pdb=" O ILE C 49 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ILE C 49 " --> pdb=" O ALA C 61 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP C 63 " --> pdb=" O GLU C 47 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE C 45 " --> pdb=" O THR C 65 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N THR E 135 " --> pdb=" O VAL C 46 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N LYS C 48 " --> pdb=" O TRP E 133 " (cutoff:3.500A) removed outlier: 12.446A pdb=" N TRP E 133 " --> pdb=" O LYS C 48 " (cutoff:3.500A) removed outlier: 16.295A pdb=" N GLY E 131 " --> pdb=" O PRO C 50 " (cutoff:3.500A) removed outlier: 20.112A pdb=" N GLY C 52 " --> pdb=" O ILE E 129 " (cutoff:3.500A) removed outlier: 22.508A pdb=" N ILE E 129 " --> pdb=" O GLY C 52 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU E 128 " --> pdb=" O GLU E 163 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR E 161 " --> pdb=" O LYS E 130 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 21 through 24 removed outlier: 6.744A pdb=" N ALA E 111 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS E 130 " --> pdb=" O ALA E 111 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL E 113 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N GLU E 128 " --> pdb=" O VAL E 113 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLN E 115 " --> pdb=" O GLU E 126 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLU E 126 " --> pdb=" O GLN E 115 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR E 156 " --> pdb=" O THR E 135 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N VAL E 137 " --> pdb=" O GLU E 154 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N GLU E 154 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N THR E 70 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N MET E 74 " --> pdb=" O CYS E 36 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N CYS E 36 " --> pdb=" O MET E 74 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU H 142 " --> pdb=" O THR E 39 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU H 140 " --> pdb=" O LEU E 41 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 140 through 143 removed outlier: 3.679A pdb=" N LEU C 140 " --> pdb=" O LEU Q 41 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU C 142 " --> pdb=" O THR Q 39 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N CYS Q 36 " --> pdb=" O MET Q 74 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N MET Q 74 " --> pdb=" O CYS Q 36 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N THR Q 70 " --> pdb=" O ALA Q 40 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N GLU Q 154 " --> pdb=" O VAL Q 137 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N VAL Q 137 " --> pdb=" O GLU Q 154 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR Q 156 " --> pdb=" O THR Q 135 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLU Q 126 " --> pdb=" O GLN Q 115 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLN Q 115 " --> pdb=" O GLU Q 126 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N GLU Q 128 " --> pdb=" O VAL Q 113 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL Q 113 " --> pdb=" O GLU Q 128 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS Q 130 " --> pdb=" O ALA Q 111 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ALA Q 111 " --> pdb=" O LYS Q 130 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 56 through 66 removed outlier: 5.104A pdb=" N LYS N 57 " --> pdb=" O PHE N 53 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N PHE N 53 " --> pdb=" O LYS N 57 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ASN N 59 " --> pdb=" O VAL N 51 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL N 51 " --> pdb=" O ASN N 59 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ALA N 61 " --> pdb=" O ILE N 49 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ILE N 49 " --> pdb=" O ALA N 61 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP N 63 " --> pdb=" O GLU N 47 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE N 45 " --> pdb=" O THR N 65 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N THR Q 135 " --> pdb=" O VAL N 46 " (cutoff:3.500A) removed outlier: 8.996A pdb=" N LYS N 48 " --> pdb=" O TRP Q 133 " (cutoff:3.500A) removed outlier: 12.459A pdb=" N TRP Q 133 " --> pdb=" O LYS N 48 " (cutoff:3.500A) removed outlier: 16.307A pdb=" N GLY Q 131 " --> pdb=" O PRO N 50 " (cutoff:3.500A) removed outlier: 20.122A pdb=" N GLY N 52 " --> pdb=" O ILE Q 129 " (cutoff:3.500A) removed outlier: 22.514A pdb=" N ILE Q 129 " --> pdb=" O GLY N 52 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU Q 128 " --> pdb=" O GLU Q 163 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR Q 161 " --> pdb=" O LYS Q 130 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 56 through 66 removed outlier: 5.104A pdb=" N LYS B 57 " --> pdb=" O PHE B 53 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N PHE B 53 " --> pdb=" O LYS B 57 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ASN B 59 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL B 51 " --> pdb=" O ASN B 59 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ALA B 61 " --> pdb=" O ILE B 49 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ILE B 49 " --> pdb=" O ALA B 61 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP B 63 " --> pdb=" O GLU B 47 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE B 45 " --> pdb=" O THR B 65 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N THR F 135 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 9.021A pdb=" N LYS B 48 " --> pdb=" O TRP F 133 " (cutoff:3.500A) removed outlier: 12.484A pdb=" N TRP F 133 " --> pdb=" O LYS B 48 " (cutoff:3.500A) removed outlier: 16.340A pdb=" N GLY F 131 " --> pdb=" O PRO B 50 " (cutoff:3.500A) removed outlier: 20.170A pdb=" N GLY B 52 " --> pdb=" O ILE F 129 " (cutoff:3.500A) removed outlier: 22.569A pdb=" N ILE F 129 " --> pdb=" O GLY B 52 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU F 128 " --> pdb=" O GLU F 163 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR F 161 " --> pdb=" O LYS F 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 21 through 24 removed outlier: 6.744A pdb=" N ALA F 111 " --> pdb=" O LYS F 130 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS F 130 " --> pdb=" O ALA F 111 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL F 113 " --> pdb=" O GLU F 128 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N GLU F 128 " --> pdb=" O VAL F 113 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N GLN F 115 " --> pdb=" O GLU F 126 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLU F 126 " --> pdb=" O GLN F 115 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR F 156 " --> pdb=" O THR F 135 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N VAL F 137 " --> pdb=" O GLU F 154 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N GLU F 154 " --> pdb=" O VAL F 137 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N THR F 70 " --> pdb=" O ALA F 40 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N MET F 74 " --> pdb=" O CYS F 36 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N CYS F 36 " --> pdb=" O MET F 74 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU I 142 " --> pdb=" O THR F 39 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU I 140 " --> pdb=" O LEU F 41 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 56 through 66 removed outlier: 5.103A pdb=" N LYS D 57 " --> pdb=" O PHE D 53 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N PHE D 53 " --> pdb=" O LYS D 57 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ASN D 59 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N VAL D 51 " --> pdb=" O ASN D 59 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ALA D 61 " --> pdb=" O ILE D 49 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ILE D 49 " --> pdb=" O ALA D 61 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP D 63 " --> pdb=" O GLU D 47 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE D 45 " --> pdb=" O THR D 65 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N THR G 135 " --> pdb=" O VAL D 46 " (cutoff:3.500A) removed outlier: 9.010A pdb=" N LYS D 48 " --> pdb=" O TRP G 133 " (cutoff:3.500A) removed outlier: 12.472A pdb=" N TRP G 133 " --> pdb=" O LYS D 48 " (cutoff:3.500A) removed outlier: 16.316A pdb=" N GLY G 131 " --> pdb=" O PRO D 50 " (cutoff:3.500A) removed outlier: 20.142A pdb=" N GLY D 52 " --> pdb=" O ILE G 129 " (cutoff:3.500A) removed outlier: 22.536A pdb=" N ILE G 129 " --> pdb=" O GLY D 52 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU G 128 " --> pdb=" O GLU G 163 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR G 161 " --> pdb=" O LYS G 130 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 21 through 24 removed outlier: 6.744A pdb=" N ALA G 111 " --> pdb=" O LYS G 130 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS G 130 " --> pdb=" O ALA G 111 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL G 113 " --> pdb=" O GLU G 128 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N GLU G 128 " --> pdb=" O VAL G 113 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLN G 115 " --> pdb=" O GLU G 126 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N GLU G 126 " --> pdb=" O GLN G 115 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR G 156 " --> pdb=" O THR G 135 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N VAL G 137 " --> pdb=" O GLU G 154 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N GLU G 154 " --> pdb=" O VAL G 137 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N THR G 70 " --> pdb=" O ALA G 40 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N MET G 74 " --> pdb=" O CYS G 36 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N CYS G 36 " --> pdb=" O MET G 74 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU J 142 " --> pdb=" O THR G 39 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU J 140 " --> pdb=" O LEU G 41 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 56 through 66 removed outlier: 5.104A pdb=" N LYS E 57 " --> pdb=" O PHE E 53 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N PHE E 53 " --> pdb=" O LYS E 57 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ASN E 59 " --> pdb=" O VAL E 51 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL E 51 " --> pdb=" O ASN E 59 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ALA E 61 " --> pdb=" O ILE E 49 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ILE E 49 " --> pdb=" O ALA E 61 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP E 63 " --> pdb=" O GLU E 47 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE E 45 " --> pdb=" O THR E 65 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N THR H 135 " --> pdb=" O VAL E 46 " (cutoff:3.500A) removed outlier: 8.990A pdb=" N LYS E 48 " --> pdb=" O TRP H 133 " (cutoff:3.500A) removed outlier: 12.451A pdb=" N TRP H 133 " --> pdb=" O LYS E 48 " (cutoff:3.500A) removed outlier: 16.299A pdb=" N GLY H 131 " --> pdb=" O PRO E 50 " (cutoff:3.500A) removed outlier: 20.117A pdb=" N GLY E 52 " --> pdb=" O ILE H 129 " (cutoff:3.500A) removed outlier: 22.513A pdb=" N ILE H 129 " --> pdb=" O GLY E 52 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU H 128 " --> pdb=" O GLU H 163 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR H 161 " --> pdb=" O LYS H 130 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 21 through 24 removed outlier: 6.744A pdb=" N ALA H 111 " --> pdb=" O LYS H 130 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS H 130 " --> pdb=" O ALA H 111 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL H 113 " --> pdb=" O GLU H 128 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N GLU H 128 " --> pdb=" O VAL H 113 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLN H 115 " --> pdb=" O GLU H 126 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N GLU H 126 " --> pdb=" O GLN H 115 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR H 156 " --> pdb=" O THR H 135 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N VAL H 137 " --> pdb=" O GLU H 154 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N GLU H 154 " --> pdb=" O VAL H 137 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N THR H 70 " --> pdb=" O ALA H 40 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N MET H 74 " --> pdb=" O CYS H 36 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N CYS H 36 " --> pdb=" O MET H 74 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU K 142 " --> pdb=" O THR H 39 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU K 140 " --> pdb=" O LEU H 41 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 56 through 66 removed outlier: 5.103A pdb=" N LYS F 57 " --> pdb=" O PHE F 53 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N PHE F 53 " --> pdb=" O LYS F 57 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ASN F 59 " --> pdb=" O VAL F 51 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL F 51 " --> pdb=" O ASN F 59 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ALA F 61 " --> pdb=" O ILE F 49 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ILE F 49 " --> pdb=" O ALA F 61 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP F 63 " --> pdb=" O GLU F 47 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE F 45 " --> pdb=" O THR F 65 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N THR I 135 " --> pdb=" O VAL F 46 " (cutoff:3.500A) removed outlier: 9.029A pdb=" N LYS F 48 " --> pdb=" O TRP I 133 " (cutoff:3.500A) removed outlier: 12.494A pdb=" N TRP I 133 " --> pdb=" O LYS F 48 " (cutoff:3.500A) removed outlier: 16.347A pdb=" N GLY I 131 " --> pdb=" O PRO F 50 " (cutoff:3.500A) removed outlier: 20.174A pdb=" N GLY F 52 " --> pdb=" O ILE I 129 " (cutoff:3.500A) removed outlier: 22.572A pdb=" N ILE I 129 " --> pdb=" O GLY F 52 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU I 128 " --> pdb=" O GLU I 163 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR I 161 " --> pdb=" O LYS I 130 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 21 through 24 removed outlier: 6.743A pdb=" N ALA I 111 " --> pdb=" O LYS I 130 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS I 130 " --> pdb=" O ALA I 111 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL I 113 " --> pdb=" O GLU I 128 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N GLU I 128 " --> pdb=" O VAL I 113 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLN I 115 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLU I 126 " --> pdb=" O GLN I 115 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR I 156 " --> pdb=" O THR I 135 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N VAL I 137 " --> pdb=" O GLU I 154 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N GLU I 154 " --> pdb=" O VAL I 137 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N THR I 70 " --> pdb=" O ALA I 40 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N MET I 74 " --> pdb=" O CYS I 36 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N CYS I 36 " --> pdb=" O MET I 74 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU L 142 " --> pdb=" O THR I 39 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU L 140 " --> pdb=" O LEU I 41 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 56 through 66 removed outlier: 5.103A pdb=" N LYS G 57 " --> pdb=" O PHE G 53 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N PHE G 53 " --> pdb=" O LYS G 57 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ASN G 59 " --> pdb=" O VAL G 51 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL G 51 " --> pdb=" O ASN G 59 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ALA G 61 " --> pdb=" O ILE G 49 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ILE G 49 " --> pdb=" O ALA G 61 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP G 63 " --> pdb=" O GLU G 47 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE G 45 " --> pdb=" O THR G 65 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N THR J 135 " --> pdb=" O VAL G 46 " (cutoff:3.500A) removed outlier: 9.005A pdb=" N LYS G 48 " --> pdb=" O TRP J 133 " (cutoff:3.500A) removed outlier: 12.465A pdb=" N TRP J 133 " --> pdb=" O LYS G 48 " (cutoff:3.500A) removed outlier: 16.308A pdb=" N GLY J 131 " --> pdb=" O PRO G 50 " (cutoff:3.500A) removed outlier: 20.128A pdb=" N GLY G 52 " --> pdb=" O ILE J 129 " (cutoff:3.500A) removed outlier: 22.524A pdb=" N ILE J 129 " --> pdb=" O GLY G 52 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU J 128 " --> pdb=" O GLU J 163 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR J 161 " --> pdb=" O LYS J 130 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 21 through 24 removed outlier: 6.744A pdb=" N ALA J 111 " --> pdb=" O LYS J 130 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N LYS J 130 " --> pdb=" O ALA J 111 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL J 113 " --> pdb=" O GLU J 128 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N GLU J 128 " --> pdb=" O VAL J 113 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLN J 115 " --> pdb=" O GLU J 126 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLU J 126 " --> pdb=" O GLN J 115 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR J 156 " --> pdb=" O THR J 135 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N VAL J 137 " --> pdb=" O GLU J 154 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N GLU J 154 " --> pdb=" O VAL J 137 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N THR J 70 " --> pdb=" O ALA J 40 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N MET J 74 " --> pdb=" O CYS J 36 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N CYS J 36 " --> pdb=" O MET J 74 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU M 142 " --> pdb=" O THR J 39 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU M 140 " --> pdb=" O LEU J 41 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 56 through 66 removed outlier: 5.103A pdb=" N LYS H 57 " --> pdb=" O PHE H 53 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N PHE H 53 " --> pdb=" O LYS H 57 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ASN H 59 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL H 51 " --> pdb=" O ASN H 59 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ALA H 61 " --> pdb=" O ILE H 49 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ILE H 49 " --> pdb=" O ALA H 61 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP H 63 " --> pdb=" O GLU H 47 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE H 45 " --> pdb=" O THR H 65 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N THR K 135 " --> pdb=" O VAL H 46 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N LYS H 48 " --> pdb=" O TRP K 133 " (cutoff:3.500A) removed outlier: 12.448A pdb=" N TRP K 133 " --> pdb=" O LYS H 48 " (cutoff:3.500A) removed outlier: 16.291A pdb=" N GLY K 131 " --> pdb=" O PRO H 50 " (cutoff:3.500A) removed outlier: 20.110A pdb=" N GLY H 52 " --> pdb=" O ILE K 129 " (cutoff:3.500A) removed outlier: 22.506A pdb=" N ILE K 129 " --> pdb=" O GLY H 52 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU K 128 " --> pdb=" O GLU K 163 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR K 161 " --> pdb=" O LYS K 130 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 21 through 24 removed outlier: 6.743A pdb=" N ALA K 111 " --> pdb=" O LYS K 130 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS K 130 " --> pdb=" O ALA K 111 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL K 113 " --> pdb=" O GLU K 128 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N GLU K 128 " --> pdb=" O VAL K 113 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLN K 115 " --> pdb=" O GLU K 126 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N GLU K 126 " --> pdb=" O GLN K 115 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR K 156 " --> pdb=" O THR K 135 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N VAL K 137 " --> pdb=" O GLU K 154 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N GLU K 154 " --> pdb=" O VAL K 137 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N THR K 70 " --> pdb=" O ALA K 40 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N MET K 74 " --> pdb=" O CYS K 36 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N CYS K 36 " --> pdb=" O MET K 74 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU N 142 " --> pdb=" O THR K 39 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU N 140 " --> pdb=" O LEU K 41 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 56 through 66 removed outlier: 5.104A pdb=" N LYS I 57 " --> pdb=" O PHE I 53 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N PHE I 53 " --> pdb=" O LYS I 57 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ASN I 59 " --> pdb=" O VAL I 51 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL I 51 " --> pdb=" O ASN I 59 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ALA I 61 " --> pdb=" O ILE I 49 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ILE I 49 " --> pdb=" O ALA I 61 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP I 63 " --> pdb=" O GLU I 47 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE I 45 " --> pdb=" O THR I 65 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N THR L 135 " --> pdb=" O VAL I 46 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N LYS I 48 " --> pdb=" O TRP L 133 " (cutoff:3.500A) removed outlier: 12.479A pdb=" N TRP L 133 " --> pdb=" O LYS I 48 " (cutoff:3.500A) removed outlier: 16.326A pdb=" N GLY L 131 " --> pdb=" O PRO I 50 " (cutoff:3.500A) removed outlier: 20.150A pdb=" N GLY I 52 " --> pdb=" O ILE L 129 " (cutoff:3.500A) removed outlier: 22.544A pdb=" N ILE L 129 " --> pdb=" O GLY I 52 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU L 128 " --> pdb=" O GLU L 163 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR L 161 " --> pdb=" O LYS L 130 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 21 through 24 removed outlier: 6.744A pdb=" N ALA L 111 " --> pdb=" O LYS L 130 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS L 130 " --> pdb=" O ALA L 111 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL L 113 " --> pdb=" O GLU L 128 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N GLU L 128 " --> pdb=" O VAL L 113 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N GLN L 115 " --> pdb=" O GLU L 126 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLU L 126 " --> pdb=" O GLN L 115 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR L 156 " --> pdb=" O THR L 135 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N VAL L 137 " --> pdb=" O GLU L 154 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N GLU L 154 " --> pdb=" O VAL L 137 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N THR L 70 " --> pdb=" O ALA L 40 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N MET L 74 " --> pdb=" O CYS L 36 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N CYS L 36 " --> pdb=" O MET L 74 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU O 142 " --> pdb=" O THR L 39 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU O 140 " --> pdb=" O LEU L 41 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 56 through 66 removed outlier: 5.104A pdb=" N LYS J 57 " --> pdb=" O PHE J 53 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N PHE J 53 " --> pdb=" O LYS J 57 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ASN J 59 " --> pdb=" O VAL J 51 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N VAL J 51 " --> pdb=" O ASN J 59 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ALA J 61 " --> pdb=" O ILE J 49 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ILE J 49 " --> pdb=" O ALA J 61 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP J 63 " --> pdb=" O GLU J 47 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE J 45 " --> pdb=" O THR J 65 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N THR M 135 " --> pdb=" O VAL J 46 " (cutoff:3.500A) removed outlier: 8.940A pdb=" N LYS J 48 " --> pdb=" O TRP M 133 " (cutoff:3.500A) removed outlier: 12.403A pdb=" N TRP M 133 " --> pdb=" O LYS J 48 " (cutoff:3.500A) removed outlier: 16.242A pdb=" N GLY M 131 " --> pdb=" O PRO J 50 " (cutoff:3.500A) removed outlier: 20.086A pdb=" N GLY J 52 " --> pdb=" O ILE M 129 " (cutoff:3.500A) removed outlier: 22.485A pdb=" N ILE M 129 " --> pdb=" O GLY J 52 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU M 128 " --> pdb=" O GLU M 163 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TYR M 161 " --> pdb=" O LYS M 130 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 21 through 24 removed outlier: 6.744A pdb=" N ALA M 111 " --> pdb=" O LYS M 130 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N LYS M 130 " --> pdb=" O ALA M 111 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL M 113 " --> pdb=" O GLU M 128 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N GLU M 128 " --> pdb=" O VAL M 113 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLN M 115 " --> pdb=" O GLU M 126 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N GLU M 126 " --> pdb=" O GLN M 115 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR M 156 " --> pdb=" O THR M 135 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N VAL M 137 " --> pdb=" O GLU M 154 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N GLU M 154 " --> pdb=" O VAL M 137 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N THR M 70 " --> pdb=" O ALA M 40 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N MET M 74 " --> pdb=" O CYS M 36 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N CYS M 36 " --> pdb=" O MET M 74 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU P 142 " --> pdb=" O THR M 39 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU P 140 " --> pdb=" O LEU M 41 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 56 through 66 removed outlier: 5.104A pdb=" N LYS K 57 " --> pdb=" O PHE K 53 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N PHE K 53 " --> pdb=" O LYS K 57 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ASN K 59 " --> pdb=" O VAL K 51 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL K 51 " --> pdb=" O ASN K 59 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ALA K 61 " --> pdb=" O ILE K 49 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ILE K 49 " --> pdb=" O ALA K 61 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP K 63 " --> pdb=" O GLU K 47 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE K 45 " --> pdb=" O THR K 65 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N THR N 135 " --> pdb=" O VAL K 46 " (cutoff:3.500A) removed outlier: 8.999A pdb=" N LYS K 48 " --> pdb=" O TRP N 133 " (cutoff:3.500A) removed outlier: 12.458A pdb=" N TRP N 133 " --> pdb=" O LYS K 48 " (cutoff:3.500A) removed outlier: 16.302A pdb=" N GLY N 131 " --> pdb=" O PRO K 50 " (cutoff:3.500A) removed outlier: 20.120A pdb=" N GLY K 52 " --> pdb=" O ILE N 129 " (cutoff:3.500A) removed outlier: 22.517A pdb=" N ILE N 129 " --> pdb=" O GLY K 52 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU N 128 " --> pdb=" O GLU N 163 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR N 161 " --> pdb=" O LYS N 130 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 21 through 24 removed outlier: 6.743A pdb=" N ALA N 111 " --> pdb=" O LYS N 130 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS N 130 " --> pdb=" O ALA N 111 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL N 113 " --> pdb=" O GLU N 128 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N GLU N 128 " --> pdb=" O VAL N 113 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N GLN N 115 " --> pdb=" O GLU N 126 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLU N 126 " --> pdb=" O GLN N 115 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR N 156 " --> pdb=" O THR N 135 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N VAL N 137 " --> pdb=" O GLU N 154 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N GLU N 154 " --> pdb=" O VAL N 137 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N THR N 70 " --> pdb=" O ALA N 40 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N MET N 74 " --> pdb=" O CYS N 36 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N CYS N 36 " --> pdb=" O MET N 74 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU Q 142 " --> pdb=" O THR N 39 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU Q 140 " --> pdb=" O LEU N 41 " (cutoff:3.500A) 648 hydrogen bonds defined for protein. 1782 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: 8.33 Time building geometry restraints manager: 9.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7628 1.34 - 1.45: 3591 1.45 - 1.57: 12649 1.57 - 1.68: 0 1.68 - 1.80: 126 Bond restraints: 23994 Sorted by residual: bond pdb=" CA ASN G 55 " pdb=" CB ASN G 55 " ideal model delta sigma weight residual 1.535 1.553 -0.018 1.37e-02 5.33e+03 1.77e+00 bond pdb=" CA ASN Q 55 " pdb=" CB ASN Q 55 " ideal model delta sigma weight residual 1.535 1.553 -0.018 1.37e-02 5.33e+03 1.76e+00 bond pdb=" CA ASN P 55 " pdb=" CB ASN P 55 " ideal model delta sigma weight residual 1.535 1.553 -0.018 1.37e-02 5.33e+03 1.73e+00 bond pdb=" CA ASN B 55 " pdb=" CB ASN B 55 " ideal model delta sigma weight residual 1.535 1.553 -0.018 1.37e-02 5.33e+03 1.70e+00 bond pdb=" CA ASN K 55 " pdb=" CB ASN K 55 " ideal model delta sigma weight residual 1.535 1.553 -0.018 1.37e-02 5.33e+03 1.69e+00 ... (remaining 23989 not shown) Histogram of bond angle deviations from ideal: 98.62 - 105.70: 354 105.70 - 112.79: 12486 112.79 - 119.87: 7805 119.87 - 126.96: 11576 126.96 - 134.04: 341 Bond angle restraints: 32562 Sorted by residual: angle pdb=" CA ASN H 55 " pdb=" CB ASN H 55 " pdb=" CG ASN H 55 " ideal model delta sigma weight residual 112.60 115.58 -2.98 1.00e+00 1.00e+00 8.88e+00 angle pdb=" CA ASN I 55 " pdb=" CB ASN I 55 " pdb=" CG ASN I 55 " ideal model delta sigma weight residual 112.60 115.57 -2.97 1.00e+00 1.00e+00 8.79e+00 angle pdb=" CA ASN F 55 " pdb=" CB ASN F 55 " pdb=" CG ASN F 55 " ideal model delta sigma weight residual 112.60 115.56 -2.96 1.00e+00 1.00e+00 8.75e+00 angle pdb=" CA ASN R 55 " pdb=" CB ASN R 55 " pdb=" CG ASN R 55 " ideal model delta sigma weight residual 112.60 115.56 -2.96 1.00e+00 1.00e+00 8.74e+00 angle pdb=" CA ASN J 55 " pdb=" CB ASN J 55 " pdb=" CG ASN J 55 " ideal model delta sigma weight residual 112.60 115.54 -2.94 1.00e+00 1.00e+00 8.66e+00 ... (remaining 32557 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.76: 13110 14.76 - 29.52: 678 29.52 - 44.28: 216 44.28 - 59.04: 36 59.04 - 73.80: 72 Dihedral angle restraints: 14112 sinusoidal: 5652 harmonic: 8460 Sorted by residual: dihedral pdb=" CA ARG G 118 " pdb=" C ARG G 118 " pdb=" N ASP G 119 " pdb=" CA ASP G 119 " ideal model delta harmonic sigma weight residual 180.00 158.06 21.94 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA ARG M 118 " pdb=" C ARG M 118 " pdb=" N ASP M 119 " pdb=" CA ASP M 119 " ideal model delta harmonic sigma weight residual 180.00 158.06 21.94 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA ARG H 118 " pdb=" C ARG H 118 " pdb=" N ASP H 119 " pdb=" CA ASP H 119 " ideal model delta harmonic sigma weight residual 180.00 158.07 21.93 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 14109 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2244 0.041 - 0.082: 691 0.082 - 0.123: 431 0.123 - 0.164: 108 0.164 - 0.205: 36 Chirality restraints: 3510 Sorted by residual: chirality pdb=" CB ILE E 99 " pdb=" CA ILE E 99 " pdb=" CG1 ILE E 99 " pdb=" CG2 ILE E 99 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB ILE O 99 " pdb=" CA ILE O 99 " pdb=" CG1 ILE O 99 " pdb=" CG2 ILE O 99 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CB ILE R 99 " pdb=" CA ILE R 99 " pdb=" CG1 ILE R 99 " pdb=" CG2 ILE R 99 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 3507 not shown) Planarity restraints: 4284 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET J 54 " 0.015 2.00e-02 2.50e+03 3.08e-02 9.50e+00 pdb=" C MET J 54 " -0.053 2.00e-02 2.50e+03 pdb=" O MET J 54 " 0.020 2.00e-02 2.50e+03 pdb=" N ASN J 55 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET I 54 " 0.015 2.00e-02 2.50e+03 3.08e-02 9.49e+00 pdb=" C MET I 54 " -0.053 2.00e-02 2.50e+03 pdb=" O MET I 54 " 0.020 2.00e-02 2.50e+03 pdb=" N ASN I 55 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 54 " -0.015 2.00e-02 2.50e+03 3.08e-02 9.46e+00 pdb=" C MET B 54 " 0.053 2.00e-02 2.50e+03 pdb=" O MET B 54 " -0.020 2.00e-02 2.50e+03 pdb=" N ASN B 55 " -0.018 2.00e-02 2.50e+03 ... (remaining 4281 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1702 2.72 - 3.26: 21811 3.26 - 3.81: 38063 3.81 - 4.35: 46128 4.35 - 4.90: 80194 Nonbonded interactions: 187898 Sorted by model distance: nonbonded pdb=" OE1 GLN J 115 " pdb=" NE2 HIS M 79 " model vdw 2.171 2.520 nonbonded pdb=" NE2 HIS R 79 " pdb=" OE1 GLN O 115 " model vdw 2.271 2.520 nonbonded pdb=" OE1 GLN A 115 " pdb=" NE2 HIS D 79 " model vdw 2.278 2.520 nonbonded pdb=" OE1 GLN R 115 " pdb=" NE2 HIS B 79 " model vdw 2.282 2.520 nonbonded pdb=" OE1 GLN I 115 " pdb=" NE2 HIS L 79 " model vdw 2.283 2.520 ... (remaining 187893 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 14904 2.51 5 N 3942 2.21 5 O 4554 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 2.840 Check model and map are aligned: 0.360 Convert atoms to be neutral: 0.210 Process input model: 57.840 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.040 23994 Z= 0.453 Angle : 0.913 9.378 32562 Z= 0.524 Chirality : 0.057 0.205 3510 Planarity : 0.006 0.041 4284 Dihedral : 12.301 73.804 8640 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % 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: -2.49 (0.13), residues: 2898 helix: -4.29 (0.12), residues: 288 sheet: 0.13 (0.22), residues: 666 loop : -2.01 (0.11), residues: 1944 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1309 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1309 time to evaluate : 2.850 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 outliers start: 0 outliers final: 0 residues processed: 1309 average time/residue: 0.3527 time to fit residues: 698.7956 Evaluate side-chains 872 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 872 time to evaluate : 2.781 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.7833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 6.9990 chunk 218 optimal weight: 9.9990 chunk 121 optimal weight: 8.9990 chunk 74 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 116 optimal weight: 8.9990 chunk 225 optimal weight: 8.9990 chunk 87 optimal weight: 20.0000 chunk 137 optimal weight: 8.9990 chunk 168 optimal weight: 5.9990 chunk 261 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 ASN ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 89 GLN ** R 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 ASN B 30 GLN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 ASN ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 ASN H 35 GLN ** H 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN M 75 ASN M 83 GLN M 89 GLN N 35 GLN ** N 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 89 GLN ** N 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 55 ASN O 147 ASN ** P 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 89 GLN Q 75 ASN Q 89 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.7275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.079 23994 Z= 0.328 Angle : 0.722 10.583 32562 Z= 0.385 Chirality : 0.052 0.187 3510 Planarity : 0.006 0.109 4284 Dihedral : 7.261 76.138 3132 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer Outliers : 7.54 % 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: -2.18 (0.14), residues: 2898 helix: -3.52 (0.18), residues: 306 sheet: -0.24 (0.19), residues: 756 loop : -1.66 (0.12), residues: 1836 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1368 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 1182 time to evaluate : 2.687 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 outliers start: 186 outliers final: 112 residues processed: 1296 average time/residue: 0.3490 time to fit residues: 691.8859 Evaluate side-chains 1056 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 944 time to evaluate : 2.816 Switching outliers to nearest non-outliers outliers start: 112 outliers final: 0 residues processed: 112 average time/residue: 0.2021 time to fit residues: 47.1217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 145 optimal weight: 7.9990 chunk 81 optimal weight: 20.0000 chunk 217 optimal weight: 20.0000 chunk 178 optimal weight: 10.0000 chunk 72 optimal weight: 8.9990 chunk 262 optimal weight: 20.0000 chunk 283 optimal weight: 8.9990 chunk 233 optimal weight: 30.0000 chunk 259 optimal weight: 6.9990 chunk 89 optimal weight: 40.0000 chunk 210 optimal weight: 7.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 ASN ** A 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN C 148 ASN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 ASN ** D 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 ASN F 95 GLN ** G 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 95 GLN ** G 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 22 GLN H 55 ASN ** H 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 89 GLN ** I 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 75 ASN I 89 GLN ** I 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 ASN ** J 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 83 GLN O 35 GLN ** O 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 148 ASN Q 115 GLN Q 148 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.9611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.041 23994 Z= 0.359 Angle : 0.699 10.282 32562 Z= 0.374 Chirality : 0.050 0.195 3510 Planarity : 0.005 0.068 4284 Dihedral : 7.522 83.535 3132 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer Outliers : 5.64 % 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: -2.14 (0.14), residues: 2898 helix: -3.13 (0.18), residues: 360 sheet: -0.12 (0.20), residues: 756 loop : -1.70 (0.13), residues: 1782 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1186 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 1047 time to evaluate : 2.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 139 outliers final: 84 residues processed: 1141 average time/residue: 0.3511 time to fit residues: 613.5486 Evaluate side-chains 953 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 869 time to evaluate : 2.836 Switching outliers to nearest non-outliers outliers start: 84 outliers final: 0 residues processed: 84 average time/residue: 0.2056 time to fit residues: 36.2078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 258 optimal weight: 5.9990 chunk 196 optimal weight: 10.0000 chunk 135 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 125 optimal weight: 10.0000 chunk 175 optimal weight: 10.0000 chunk 262 optimal weight: 6.9990 chunk 278 optimal weight: 20.0000 chunk 137 optimal weight: 30.0000 chunk 249 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 55 ASN ** R 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 97 ASN C 148 ASN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 GLN B 147 ASN D 22 GLN ** D 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 136 ASN ** G 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN ** H 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 GLN I 136 ASN ** J 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 147 ASN K 22 GLN ** K 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 147 ASN ** L 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 GLN ** N 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 83 GLN ** N 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 22 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 1.0221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.066 23994 Z= 0.290 Angle : 0.635 9.316 32562 Z= 0.335 Chirality : 0.048 0.221 3510 Planarity : 0.004 0.055 4284 Dihedral : 7.334 83.542 3132 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer Outliers : 4.95 % 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 (0.14), residues: 2898 helix: -2.17 (0.24), residues: 306 sheet: -0.04 (0.19), residues: 756 loop : -1.44 (0.13), residues: 1836 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1099 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 977 time to evaluate : 3.001 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 outliers start: 122 outliers final: 78 residues processed: 1041 average time/residue: 0.3677 time to fit residues: 584.6693 Evaluate side-chains 946 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 868 time to evaluate : 2.838 Switching outliers to nearest non-outliers outliers start: 78 outliers final: 0 residues processed: 78 average time/residue: 0.2159 time to fit residues: 35.5256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 231 optimal weight: 9.9990 chunk 158 optimal weight: 5.9990 chunk 4 optimal weight: 20.0000 chunk 207 optimal weight: 10.0000 chunk 114 optimal weight: 7.9990 chunk 237 optimal weight: 7.9990 chunk 192 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 142 optimal weight: 9.9990 chunk 249 optimal weight: 10.0000 chunk 70 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN ** R 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 97 ASN C 148 ASN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 GLN B 147 ASN ** D 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 ASN F 55 ASN ** F 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN ** H 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 75 ASN K 22 GLN K 75 ASN K 79 HIS ** L 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 83 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 1.0683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 23994 Z= 0.316 Angle : 0.644 9.044 32562 Z= 0.341 Chirality : 0.049 0.204 3510 Planarity : 0.004 0.048 4284 Dihedral : 7.376 86.510 3132 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer Outliers : 4.30 % 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: -1.77 (0.14), residues: 2898 helix: -1.93 (0.24), residues: 360 sheet: -0.05 (0.19), residues: 756 loop : -1.57 (0.13), residues: 1782 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1052 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 946 time to evaluate : 2.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 106 outliers final: 71 residues processed: 997 average time/residue: 0.3575 time to fit residues: 542.8909 Evaluate side-chains 944 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 873 time to evaluate : 2.982 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 0 residues processed: 71 average time/residue: 0.2082 time to fit residues: 31.4881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 93 optimal weight: 20.0000 chunk 250 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 163 optimal weight: 0.9980 chunk 68 optimal weight: 20.0000 chunk 278 optimal weight: 10.0000 chunk 231 optimal weight: 7.9990 chunk 129 optimal weight: 20.0000 chunk 23 optimal weight: 9.9990 chunk 92 optimal weight: 8.9990 chunk 146 optimal weight: 6.9990 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN A 148 ASN ** R 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 ASN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 GLN B 147 ASN B 148 ASN ** D 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 ASN ** F 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 148 ASN ** G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN ** H 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 19 ASN ** J 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 83 GLN J 147 ASN K 22 GLN K 79 HIS ** L 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 30 GLN ** N 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 83 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 1.0922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 23994 Z= 0.283 Angle : 0.639 9.046 32562 Z= 0.337 Chirality : 0.048 0.233 3510 Planarity : 0.004 0.046 4284 Dihedral : 7.179 80.407 3132 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer Outliers : 3.49 % 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: -1.73 (0.14), residues: 2898 helix: -1.70 (0.25), residues: 360 sheet: -0.07 (0.20), residues: 756 loop : -1.57 (0.13), residues: 1782 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1054 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 968 time to evaluate : 2.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 86 outliers final: 55 residues processed: 1010 average time/residue: 0.3609 time to fit residues: 556.8832 Evaluate side-chains 931 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 876 time to evaluate : 2.884 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 0 residues processed: 55 average time/residue: 0.2052 time to fit residues: 25.1127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 268 optimal weight: 40.0000 chunk 31 optimal weight: 9.9990 chunk 158 optimal weight: 0.7980 chunk 203 optimal weight: 20.0000 chunk 157 optimal weight: 6.9990 chunk 234 optimal weight: 0.4980 chunk 155 optimal weight: 10.0000 chunk 277 optimal weight: 10.0000 chunk 173 optimal weight: 5.9990 chunk 169 optimal weight: 20.0000 chunk 128 optimal weight: 30.0000 overall best weight: 4.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 ASN R 31 ASN ** R 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 ASN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 ASN ** D 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN ** G 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 147 ASN N 55 ASN ** N 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 83 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 1.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 23994 Z= 0.245 Angle : 0.635 10.651 32562 Z= 0.332 Chirality : 0.048 0.208 3510 Planarity : 0.004 0.045 4284 Dihedral : 6.949 77.421 3132 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer Outliers : 3.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.14), residues: 2898 helix: -1.58 (0.25), residues: 360 sheet: -0.25 (0.18), residues: 864 loop : -1.53 (0.13), residues: 1674 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1007 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 931 time to evaluate : 2.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 76 outliers final: 51 residues processed: 971 average time/residue: 0.3813 time to fit residues: 565.7513 Evaluate side-chains 932 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 881 time to evaluate : 2.770 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 0 residues processed: 51 average time/residue: 0.2172 time to fit residues: 24.5063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 171 optimal weight: 6.9990 chunk 110 optimal weight: 6.9990 chunk 165 optimal weight: 0.0370 chunk 83 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 176 optimal weight: 30.0000 chunk 189 optimal weight: 3.9990 chunk 137 optimal weight: 40.0000 chunk 25 optimal weight: 5.9990 chunk 218 optimal weight: 1.9990 overall best weight: 2.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 GLN A 148 ASN R 31 ASN ** R 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 136 ASN R 148 ASN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 ASN B 147 ASN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 83 GLN ** N 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 1.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 23994 Z= 0.188 Angle : 0.634 9.636 32562 Z= 0.328 Chirality : 0.048 0.208 3510 Planarity : 0.004 0.043 4284 Dihedral : 6.451 72.376 3132 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer Outliers : 2.03 % 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: -1.56 (0.14), residues: 2898 helix: -1.41 (0.25), residues: 360 sheet: -0.16 (0.18), residues: 864 loop : -1.45 (0.13), residues: 1674 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1027 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 977 time to evaluate : 2.813 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 27 residues processed: 1000 average time/residue: 0.3673 time to fit residues: 555.0503 Evaluate side-chains 928 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 901 time to evaluate : 2.950 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.2129 time to fit residues: 14.6009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 10.0000 chunk 265 optimal weight: 20.0000 chunk 242 optimal weight: 20.0000 chunk 258 optimal weight: 20.0000 chunk 155 optimal weight: 9.9990 chunk 112 optimal weight: 30.0000 chunk 203 optimal weight: 9.9990 chunk 79 optimal weight: 9.9990 chunk 233 optimal weight: 9.9990 chunk 244 optimal weight: 10.0000 chunk 257 optimal weight: 10.0000 overall best weight: 9.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN ** R 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 30 GLN ** G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 147 ASN I 97 ASN I 147 ASN J 19 ASN ** J 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 55 ASN K 22 GLN ** K 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 147 ASN ** N 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 83 GLN O 22 GLN O 55 ASN ** O 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 89 GLN ** Q 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 1.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.050 23994 Z= 0.418 Angle : 0.730 9.672 32562 Z= 0.384 Chirality : 0.051 0.230 3510 Planarity : 0.005 0.050 4284 Dihedral : 7.368 84.965 3132 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 19.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer Outliers : 2.51 % 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 (0.14), residues: 2898 helix: -1.28 (0.25), residues: 360 sheet: -0.17 (0.20), residues: 756 loop : -1.60 (0.13), residues: 1782 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 948 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 886 time to evaluate : 2.889 Fit side-chains revert: symmetry clash outliers start: 62 outliers final: 43 residues processed: 922 average time/residue: 0.3695 time to fit residues: 512.9451 Evaluate side-chains 861 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 818 time to evaluate : 2.741 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.2139 time to fit residues: 20.5828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 169 optimal weight: 9.9990 chunk 273 optimal weight: 4.9990 chunk 166 optimal weight: 20.0000 chunk 129 optimal weight: 9.9990 chunk 190 optimal weight: 7.9990 chunk 286 optimal weight: 0.6980 chunk 264 optimal weight: 2.9990 chunk 228 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 176 optimal weight: 30.0000 chunk 140 optimal weight: 20.0000 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN ** R 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 ASN ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 ASN ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 GLN ** G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 147 ASN ** J 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 79 HIS ** L 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 147 ASN ** N 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 83 GLN N 115 GLN ** O 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 1.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 23994 Z= 0.235 Angle : 0.701 10.475 32562 Z= 0.364 Chirality : 0.049 0.242 3510 Planarity : 0.004 0.050 4284 Dihedral : 6.886 79.235 3132 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer Outliers : 0.85 % 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: -1.63 (0.14), residues: 2898 helix: -1.16 (0.25), residues: 360 sheet: -0.37 (0.18), residues: 864 loop : -1.47 (0.13), residues: 1674 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 924 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 903 time to evaluate : 2.989 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 16 residues processed: 914 average time/residue: 0.3790 time to fit residues: 522.5646 Evaluate side-chains 893 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 877 time to evaluate : 2.801 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2249 time to fit residues: 10.4599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 181 optimal weight: 7.9990 chunk 243 optimal weight: 8.9990 chunk 69 optimal weight: 5.9990 chunk 210 optimal weight: 5.9990 chunk 33 optimal weight: 20.0000 chunk 63 optimal weight: 20.0000 chunk 228 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 234 optimal weight: 0.9990 chunk 28 optimal weight: 20.0000 chunk 42 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 97 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 ASN ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 147 ASN J 35 GLN ** J 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 22 GLN ** O 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.098406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.087936 restraints weight = 49836.240| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 3.13 r_work: 0.3193 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work: 0.3171 rms_B_bonded: 2.85 restraints_weight: 0.1250 r_work: 0.3159 rms_B_bonded: 2.91 restraints_weight: 0.0625 r_work: 0.3147 rms_B_bonded: 3.01 restraints_weight: 0.0312 r_work: 0.3134 rms_B_bonded: 3.14 restraints_weight: 0.0156 r_work: 0.3120 rms_B_bonded: 3.29 restraints_weight: 0.0078 r_work: 0.3106 rms_B_bonded: 3.47 restraints_weight: 0.0039 r_work: 0.3092 rms_B_bonded: 3.68 restraints_weight: 0.0020 r_work: 0.3076 rms_B_bonded: 3.91 restraints_weight: 0.0010 r_work: 0.3060 rms_B_bonded: 4.17 restraints_weight: 0.0005 r_work: 0.3043 rms_B_bonded: 4.46 restraints_weight: 0.0002 r_work: 0.3025 rms_B_bonded: 4.78 restraints_weight: 0.0001 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 1.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 23994 Z= 0.267 Angle : 0.708 10.814 32562 Z= 0.367 Chirality : 0.049 0.265 3510 Planarity : 0.004 0.051 4284 Dihedral : 6.914 79.262 3132 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer Outliers : 1.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.14), residues: 2898 helix: -1.58 (0.21), residues: 468 sheet: -0.37 (0.18), residues: 864 loop : -1.73 (0.13), residues: 1566 =============================================================================== Job complete usr+sys time: 7975.96 seconds wall clock time: 143 minutes 1.71 seconds (8581.71 seconds total)