Starting phenix.real_space_refine (version: dev) on Thu Feb 23 18:23:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l7c_0842/02_2023/6l7c_0842.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l7c_0842/02_2023/6l7c_0842.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l7c_0842/02_2023/6l7c_0842.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l7c_0842/02_2023/6l7c_0842.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l7c_0842/02_2023/6l7c_0842.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l7c_0842/02_2023/6l7c_0842.pdb" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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 Process input model Symmetric amino acids flipped Residue "A ASP 74": "OD1" <-> "OD2" Residue "A GLU 82": "OE1" <-> "OE2" Residue "A GLU 101": "OE1" <-> "OE2" Residue "A ASP 149": "OD1" <-> "OD2" Residue "A TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 192": "NH1" <-> "NH2" Residue "A ASP 195": "OD1" <-> "OD2" Residue "A GLU 203": "OE1" <-> "OE2" Residue "A ASP 238": "OD1" <-> "OD2" Residue "A GLU 261": "OE1" <-> "OE2" Residue "B ASP 74": "OD1" <-> "OD2" Residue "B GLU 82": "OE1" <-> "OE2" Residue "B GLU 101": "OE1" <-> "OE2" Residue "B ASP 149": "OD1" <-> "OD2" Residue "B TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 192": "NH1" <-> "NH2" Residue "B ASP 195": "OD1" <-> "OD2" Residue "B GLU 203": "OE1" <-> "OE2" Residue "B ASP 238": "OD1" <-> "OD2" Residue "B GLU 261": "OE1" <-> "OE2" Residue "C ASP 74": "OD1" <-> "OD2" Residue "C GLU 82": "OE1" <-> "OE2" Residue "C GLU 101": "OE1" <-> "OE2" Residue "C ASP 149": "OD1" <-> "OD2" Residue "C TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 192": "NH1" <-> "NH2" Residue "C ASP 195": "OD1" <-> "OD2" Residue "C GLU 203": "OE1" <-> "OE2" Residue "C ASP 238": "OD1" <-> "OD2" Residue "C GLU 261": "OE1" <-> "OE2" Residue "D ASP 74": "OD1" <-> "OD2" Residue "D GLU 82": "OE1" <-> "OE2" Residue "D GLU 101": "OE1" <-> "OE2" Residue "D ASP 149": "OD1" <-> "OD2" Residue "D TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 192": "NH1" <-> "NH2" Residue "D ASP 195": "OD1" <-> "OD2" Residue "D GLU 203": "OE1" <-> "OE2" Residue "D ASP 238": "OD1" <-> "OD2" Residue "D GLU 261": "OE1" <-> "OE2" Residue "E ASP 74": "OD1" <-> "OD2" Residue "E GLU 82": "OE1" <-> "OE2" Residue "E GLU 101": "OE1" <-> "OE2" Residue "E ASP 149": "OD1" <-> "OD2" Residue "E TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 192": "NH1" <-> "NH2" Residue "E ASP 195": "OD1" <-> "OD2" Residue "E GLU 203": "OE1" <-> "OE2" Residue "E ASP 238": "OD1" <-> "OD2" Residue "E GLU 261": "OE1" <-> "OE2" Residue "F ASP 74": "OD1" <-> "OD2" Residue "F GLU 82": "OE1" <-> "OE2" Residue "F GLU 101": "OE1" <-> "OE2" Residue "F ASP 149": "OD1" <-> "OD2" Residue "F TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 192": "NH1" <-> "NH2" Residue "F ASP 195": "OD1" <-> "OD2" Residue "F GLU 203": "OE1" <-> "OE2" Residue "F ASP 238": "OD1" <-> "OD2" Residue "F GLU 261": "OE1" <-> "OE2" Residue "G ASP 74": "OD1" <-> "OD2" Residue "G GLU 82": "OE1" <-> "OE2" Residue "G GLU 101": "OE1" <-> "OE2" Residue "G ASP 149": "OD1" <-> "OD2" Residue "G TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 192": "NH1" <-> "NH2" Residue "G ASP 195": "OD1" <-> "OD2" Residue "G GLU 203": "OE1" <-> "OE2" Residue "G ASP 238": "OD1" <-> "OD2" Residue "G GLU 261": "OE1" <-> "OE2" Residue "H ASP 74": "OD1" <-> "OD2" Residue "H GLU 82": "OE1" <-> "OE2" Residue "H GLU 101": "OE1" <-> "OE2" Residue "H ASP 149": "OD1" <-> "OD2" Residue "H TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 192": "NH1" <-> "NH2" Residue "H ASP 195": "OD1" <-> "OD2" Residue "H GLU 203": "OE1" <-> "OE2" Residue "H ASP 238": "OD1" <-> "OD2" Residue "H GLU 261": "OE1" <-> "OE2" Residue "I ASP 74": "OD1" <-> "OD2" Residue "I GLU 82": "OE1" <-> "OE2" Residue "I GLU 101": "OE1" <-> "OE2" Residue "I ASP 149": "OD1" <-> "OD2" Residue "I TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 192": "NH1" <-> "NH2" Residue "I ASP 195": "OD1" <-> "OD2" Residue "I GLU 203": "OE1" <-> "OE2" Residue "I ASP 238": "OD1" <-> "OD2" Residue "I GLU 261": "OE1" <-> "OE2" Residue "J ARG 8": "NH1" <-> "NH2" Residue "J ASP 34": "OD1" <-> "OD2" Residue "K ARG 8": "NH1" <-> "NH2" Residue "K ASP 34": "OD1" <-> "OD2" Residue "L ARG 8": "NH1" <-> "NH2" Residue "L ASP 34": "OD1" <-> "OD2" Residue "M ARG 8": "NH1" <-> "NH2" Residue "M ASP 34": "OD1" <-> "OD2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ASP 34": "OD1" <-> "OD2" Residue "O ARG 8": "NH1" <-> "NH2" Residue "O ASP 34": "OD1" <-> "OD2" Residue "P ARG 8": "NH1" <-> "NH2" Residue "P ASP 34": "OD1" <-> "OD2" Residue "Q ARG 8": "NH1" <-> "NH2" Residue "Q ASP 34": "OD1" <-> "OD2" Residue "R ARG 8": "NH1" <-> "NH2" Residue "R ASP 34": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 20601 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 1968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1968 Classifications: {'peptide': 253} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 240} Chain: "B" Number of atoms: 1968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1968 Classifications: {'peptide': 253} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 240} Chain: "C" Number of atoms: 1968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1968 Classifications: {'peptide': 253} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 240} Chain: "D" Number of atoms: 1968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1968 Classifications: {'peptide': 253} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 240} Chain: "E" Number of atoms: 1968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1968 Classifications: {'peptide': 253} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 240} Chain: "F" Number of atoms: 1968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1968 Classifications: {'peptide': 253} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 240} Chain: "G" Number of atoms: 1968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1968 Classifications: {'peptide': 253} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 240} Chain: "H" Number of atoms: 1968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1968 Classifications: {'peptide': 253} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 240} Chain: "I" Number of atoms: 1968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1968 Classifications: {'peptide': 253} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 240} Chain: "J" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 275 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "K" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 275 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "L" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 275 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "M" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 275 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "N" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 275 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "O" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 275 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "P" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 275 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "Q" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 275 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "R" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 275 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "S" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 46 Classifications: {'peptide': 6} Link IDs: {'PTRANS': 1, 'TRANS': 4} Chain: "T" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 46 Classifications: {'peptide': 6} Link IDs: {'PTRANS': 1, 'TRANS': 4} Chain: "U" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 46 Classifications: {'peptide': 6} Link IDs: {'PTRANS': 1, 'TRANS': 4} Chain: "V" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 46 Classifications: {'peptide': 6} Link IDs: {'PTRANS': 1, 'TRANS': 4} Chain: "W" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 46 Classifications: {'peptide': 6} Link IDs: {'PTRANS': 1, 'TRANS': 4} Chain: "X" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 46 Classifications: {'peptide': 6} Link IDs: {'PTRANS': 1, 'TRANS': 4} Chain: "Y" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 46 Classifications: {'peptide': 6} Link IDs: {'PTRANS': 1, 'TRANS': 4} Chain: "Z" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 46 Classifications: {'peptide': 6} Link IDs: {'PTRANS': 1, 'TRANS': 4} Chain: "a" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 46 Classifications: {'peptide': 6} Link IDs: {'PTRANS': 1, 'TRANS': 4} Time building chain proxies: 11.59, per 1000 atoms: 0.56 Number of scatterers: 20601 At special positions: 0 Unit cell: (133.32, 134.64, 121.44, 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 3942 8.00 N 3582 7.00 C 13005 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: 7.79 Conformation dependent library (CDL) restraints added in 2.9 seconds 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4896 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 27 sheets defined 31.2% alpha, 134.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.05 Creating SS restraints... Processing helix chain 'A' and resid 18 through 26 removed outlier: 3.935A pdb=" N LYS A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N HIS A 26 " --> pdb=" O LYS A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 75 removed outlier: 3.667A pdb=" N THR A 70 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 102 removed outlier: 3.552A pdb=" N ASN A 91 " --> pdb=" O GLN A 87 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 99 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU A 101 " --> pdb=" O ARG A 97 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASN A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 234 removed outlier: 3.530A pdb=" N MET A 217 " --> pdb=" O MET A 213 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE A 225 " --> pdb=" O GLU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 247 removed outlier: 3.824A pdb=" N GLN A 246 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN A 247 " --> pdb=" O GLU A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 255 Processing helix chain 'B' and resid 18 through 26 removed outlier: 3.935A pdb=" N LYS B 22 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N HIS B 26 " --> pdb=" O LYS B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 75 removed outlier: 3.668A pdb=" N THR B 70 " --> pdb=" O ALA B 66 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER B 75 " --> pdb=" O ALA B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 102 removed outlier: 3.552A pdb=" N ASN B 91 " --> pdb=" O GLN B 87 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA B 99 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU B 101 " --> pdb=" O ARG B 97 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASN B 102 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 234 removed outlier: 3.531A pdb=" N MET B 217 " --> pdb=" O MET B 213 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE B 225 " --> pdb=" O GLU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 247 removed outlier: 3.825A pdb=" N GLN B 246 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN B 247 " --> pdb=" O GLU B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 255 Processing helix chain 'C' and resid 18 through 26 removed outlier: 3.935A pdb=" N LYS C 22 " --> pdb=" O ALA C 18 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N HIS C 26 " --> pdb=" O LYS C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 75 removed outlier: 3.667A pdb=" N THR C 70 " --> pdb=" O ALA C 66 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER C 75 " --> pdb=" O ALA C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 102 removed outlier: 3.551A pdb=" N ASN C 91 " --> pdb=" O GLN C 87 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA C 99 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU C 101 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASN C 102 " --> pdb=" O ALA C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 234 removed outlier: 3.530A pdb=" N MET C 217 " --> pdb=" O MET C 213 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE C 225 " --> pdb=" O GLU C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 247 removed outlier: 3.824A pdb=" N GLN C 246 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN C 247 " --> pdb=" O GLU C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 255 Processing helix chain 'D' and resid 18 through 26 removed outlier: 3.935A pdb=" N LYS D 22 " --> pdb=" O ALA D 18 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N HIS D 26 " --> pdb=" O LYS D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 75 removed outlier: 3.667A pdb=" N THR D 70 " --> pdb=" O ALA D 66 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER D 75 " --> pdb=" O ALA D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 102 removed outlier: 3.552A pdb=" N ASN D 91 " --> pdb=" O GLN D 87 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA D 99 " --> pdb=" O ILE D 95 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU D 101 " --> pdb=" O ARG D 97 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASN D 102 " --> pdb=" O ALA D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 234 removed outlier: 3.530A pdb=" N MET D 217 " --> pdb=" O MET D 213 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE D 225 " --> pdb=" O GLU D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 247 removed outlier: 3.824A pdb=" N GLN D 246 " --> pdb=" O ALA D 243 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN D 247 " --> pdb=" O GLU D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 255 Processing helix chain 'E' and resid 18 through 26 removed outlier: 3.936A pdb=" N LYS E 22 " --> pdb=" O ALA E 18 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N HIS E 26 " --> pdb=" O LYS E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 75 removed outlier: 3.667A pdb=" N THR E 70 " --> pdb=" O ALA E 66 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER E 75 " --> pdb=" O ALA E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 102 removed outlier: 3.551A pdb=" N ASN E 91 " --> pdb=" O GLN E 87 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA E 99 " --> pdb=" O ILE E 95 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU E 101 " --> pdb=" O ARG E 97 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASN E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 234 removed outlier: 3.530A pdb=" N MET E 217 " --> pdb=" O MET E 213 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE E 225 " --> pdb=" O GLU E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 247 removed outlier: 3.824A pdb=" N GLN E 246 " --> pdb=" O ALA E 243 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN E 247 " --> pdb=" O GLU E 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 255 Processing helix chain 'F' and resid 18 through 26 removed outlier: 3.935A pdb=" N LYS F 22 " --> pdb=" O ALA F 18 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N HIS F 26 " --> pdb=" O LYS F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 75 removed outlier: 3.667A pdb=" N THR F 70 " --> pdb=" O ALA F 66 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER F 75 " --> pdb=" O ALA F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 102 removed outlier: 3.552A pdb=" N ASN F 91 " --> pdb=" O GLN F 87 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA F 99 " --> pdb=" O ILE F 95 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU F 101 " --> pdb=" O ARG F 97 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASN F 102 " --> pdb=" O ALA F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 234 removed outlier: 3.531A pdb=" N MET F 217 " --> pdb=" O MET F 213 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE F 225 " --> pdb=" O GLU F 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 247 removed outlier: 3.825A pdb=" N GLN F 246 " --> pdb=" O ALA F 243 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN F 247 " --> pdb=" O GLU F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 255 Processing helix chain 'G' and resid 18 through 26 removed outlier: 3.936A pdb=" N LYS G 22 " --> pdb=" O ALA G 18 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N HIS G 26 " --> pdb=" O LYS G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 75 removed outlier: 3.667A pdb=" N THR G 70 " --> pdb=" O ALA G 66 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER G 75 " --> pdb=" O ALA G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 102 removed outlier: 3.552A pdb=" N ASN G 91 " --> pdb=" O GLN G 87 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA G 99 " --> pdb=" O ILE G 95 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU G 101 " --> pdb=" O ARG G 97 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASN G 102 " --> pdb=" O ALA G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 234 removed outlier: 3.531A pdb=" N MET G 217 " --> pdb=" O MET G 213 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE G 225 " --> pdb=" O GLU G 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 241 through 247 removed outlier: 3.824A pdb=" N GLN G 246 " --> pdb=" O ALA G 243 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN G 247 " --> pdb=" O GLU G 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 249 through 255 Processing helix chain 'H' and resid 18 through 26 removed outlier: 3.936A pdb=" N LYS H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N HIS H 26 " --> pdb=" O LYS H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 75 removed outlier: 3.668A pdb=" N THR H 70 " --> pdb=" O ALA H 66 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER H 75 " --> pdb=" O ALA H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 102 removed outlier: 3.552A pdb=" N ASN H 91 " --> pdb=" O GLN H 87 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA H 99 " --> pdb=" O ILE H 95 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU H 101 " --> pdb=" O ARG H 97 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASN H 102 " --> pdb=" O ALA H 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 234 removed outlier: 3.531A pdb=" N MET H 217 " --> pdb=" O MET H 213 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE H 225 " --> pdb=" O GLU H 221 " (cutoff:3.500A) Processing helix chain 'H' and resid 241 through 247 removed outlier: 3.825A pdb=" N GLN H 246 " --> pdb=" O ALA H 243 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN H 247 " --> pdb=" O GLU H 244 " (cutoff:3.500A) Processing helix chain 'H' and resid 249 through 255 Processing helix chain 'I' and resid 18 through 26 removed outlier: 3.936A pdb=" N LYS I 22 " --> pdb=" O ALA I 18 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N HIS I 26 " --> pdb=" O LYS I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 75 removed outlier: 3.667A pdb=" N THR I 70 " --> pdb=" O ALA I 66 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER I 75 " --> pdb=" O ALA I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 102 removed outlier: 3.552A pdb=" N ASN I 91 " --> pdb=" O GLN I 87 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA I 99 " --> pdb=" O ILE I 95 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU I 101 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASN I 102 " --> pdb=" O ALA I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 211 through 234 removed outlier: 3.531A pdb=" N MET I 217 " --> pdb=" O MET I 213 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE I 225 " --> pdb=" O GLU I 221 " (cutoff:3.500A) Processing helix chain 'I' and resid 241 through 247 removed outlier: 3.825A pdb=" N GLN I 246 " --> pdb=" O ALA I 243 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN I 247 " --> pdb=" O GLU I 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 249 through 255 Processing helix chain 'J' and resid 15 through 17 No H-bonds generated for 'chain 'J' and resid 15 through 17' Processing helix chain 'J' and resid 18 through 28 Processing helix chain 'K' and resid 15 through 17 No H-bonds generated for 'chain 'K' and resid 15 through 17' Processing helix chain 'K' and resid 18 through 28 Processing helix chain 'L' and resid 15 through 17 No H-bonds generated for 'chain 'L' and resid 15 through 17' Processing helix chain 'L' and resid 18 through 28 Processing helix chain 'M' and resid 15 through 17 No H-bonds generated for 'chain 'M' and resid 15 through 17' Processing helix chain 'M' and resid 18 through 28 Processing helix chain 'N' and resid 15 through 17 No H-bonds generated for 'chain 'N' and resid 15 through 17' Processing helix chain 'N' and resid 18 through 28 Processing helix chain 'O' and resid 15 through 17 No H-bonds generated for 'chain 'O' and resid 15 through 17' Processing helix chain 'O' and resid 18 through 28 Processing helix chain 'P' and resid 15 through 17 No H-bonds generated for 'chain 'P' and resid 15 through 17' Processing helix chain 'P' and resid 18 through 28 Processing helix chain 'Q' and resid 15 through 17 No H-bonds generated for 'chain 'Q' and resid 15 through 17' Processing helix chain 'Q' and resid 18 through 28 Processing helix chain 'R' and resid 15 through 17 No H-bonds generated for 'chain 'R' and resid 15 through 17' Processing helix chain 'R' and resid 18 through 28 Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 14 removed outlier: 6.239A pdb=" N ILE B 171 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN B 165 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER B 173 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE B 146 " --> pdb=" O GLY B 140 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY B 140 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 11.532A pdb=" N ALA B 148 " --> pdb=" O GLY B 138 " (cutoff:3.500A) removed outlier: 10.482A pdb=" N GLY B 138 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N THR B 150 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N SER B 136 " --> pdb=" O THR B 150 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N TYR B 152 " --> pdb=" O VAL B 134 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL B 134 " --> pdb=" O TYR B 152 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LEU B 154 " --> pdb=" O SER B 132 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER B 132 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN B 156 " --> pdb=" O TYR B 130 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR B 130 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA B 158 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN B 42 " --> pdb=" O GLY B 125 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 41 through 42 removed outlier: 3.906A pdb=" N GLN B 42 " --> pdb=" O GLY B 125 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N VAL B 134 " --> pdb=" O ASN A 209 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 42 removed outlier: 3.907A pdb=" N GLN A 42 " --> pdb=" O GLY A 125 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA A 158 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TYR A 130 " --> pdb=" O GLN A 156 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN A 156 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER A 132 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU A 154 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL A 134 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 11.332A pdb=" N TYR A 152 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N SER A 136 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N THR A 150 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 10.481A pdb=" N GLY A 138 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ALA A 148 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY A 140 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE A 146 " --> pdb=" O GLY A 140 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER A 173 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN A 165 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE A 171 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N VAL B 134 " --> pdb=" O ASN A 209 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN B 42 " --> pdb=" O GLY B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 13 through 14 removed outlier: 3.520A pdb=" N SER A 136 " --> pdb=" O THR I 207 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VAL A 134 " --> pdb=" O ASN I 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA A 158 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TYR A 130 " --> pdb=" O GLN A 156 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN A 156 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER A 132 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU A 154 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL A 134 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 11.332A pdb=" N TYR A 152 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N SER A 136 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N THR A 150 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 10.481A pdb=" N GLY A 138 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ALA A 148 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY A 140 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE A 146 " --> pdb=" O GLY A 140 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER A 173 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN A 165 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE A 171 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N VAL B 134 " --> pdb=" O ASN A 209 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN B 42 " --> pdb=" O GLY B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 41 through 42 removed outlier: 3.907A pdb=" N GLN I 42 " --> pdb=" O GLY I 125 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA I 158 " --> pdb=" O ILE I 128 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR I 130 " --> pdb=" O GLN I 156 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN I 156 " --> pdb=" O TYR I 130 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N SER I 132 " --> pdb=" O LEU I 154 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU I 154 " --> pdb=" O SER I 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL I 134 " --> pdb=" O TYR I 152 " (cutoff:3.500A) removed outlier: 11.332A pdb=" N TYR I 152 " --> pdb=" O VAL I 134 " (cutoff:3.500A) removed outlier: 10.636A pdb=" N SER I 136 " --> pdb=" O THR I 150 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N THR I 150 " --> pdb=" O SER I 136 " (cutoff:3.500A) removed outlier: 10.482A pdb=" N GLY I 138 " --> pdb=" O ALA I 148 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ALA I 148 " --> pdb=" O GLY I 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY I 140 " --> pdb=" O ILE I 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE I 146 " --> pdb=" O GLY I 140 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER I 173 " --> pdb=" O VAL I 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN I 165 " --> pdb=" O ILE I 171 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE I 171 " --> pdb=" O ASN I 165 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 136 " --> pdb=" O THR I 207 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VAL A 134 " --> pdb=" O ASN I 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA A 158 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TYR A 130 " --> pdb=" O GLN A 156 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN A 156 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER A 132 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU A 154 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL A 134 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 11.332A pdb=" N TYR A 152 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N SER A 136 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N THR A 150 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 10.481A pdb=" N GLY A 138 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ALA A 148 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY A 140 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE A 146 " --> pdb=" O GLY A 140 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER A 173 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN A 165 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE A 171 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N VAL B 134 " --> pdb=" O ASN A 209 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN B 42 " --> pdb=" O GLY B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 13 through 14 removed outlier: 3.520A pdb=" N SER I 136 " --> pdb=" O THR H 207 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N VAL I 134 " --> pdb=" O ASN H 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA I 158 " --> pdb=" O ILE I 128 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR I 130 " --> pdb=" O GLN I 156 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN I 156 " --> pdb=" O TYR I 130 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N SER I 132 " --> pdb=" O LEU I 154 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU I 154 " --> pdb=" O SER I 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL I 134 " --> pdb=" O TYR I 152 " (cutoff:3.500A) removed outlier: 11.332A pdb=" N TYR I 152 " --> pdb=" O VAL I 134 " (cutoff:3.500A) removed outlier: 10.636A pdb=" N SER I 136 " --> pdb=" O THR I 150 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N THR I 150 " --> pdb=" O SER I 136 " (cutoff:3.500A) removed outlier: 10.482A pdb=" N GLY I 138 " --> pdb=" O ALA I 148 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ALA I 148 " --> pdb=" O GLY I 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY I 140 " --> pdb=" O ILE I 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE I 146 " --> pdb=" O GLY I 140 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER I 173 " --> pdb=" O VAL I 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN I 165 " --> pdb=" O ILE I 171 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE I 171 " --> pdb=" O ASN I 165 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 136 " --> pdb=" O THR I 207 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VAL A 134 " --> pdb=" O ASN I 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA A 158 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TYR A 130 " --> pdb=" O GLN A 156 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN A 156 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER A 132 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU A 154 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL A 134 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 11.332A pdb=" N TYR A 152 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N SER A 136 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N THR A 150 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 10.481A pdb=" N GLY A 138 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ALA A 148 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY A 140 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE A 146 " --> pdb=" O GLY A 140 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER A 173 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN A 165 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE A 171 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N VAL B 134 " --> pdb=" O ASN A 209 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN B 42 " --> pdb=" O GLY B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 41 through 42 removed outlier: 3.907A pdb=" N GLN H 42 " --> pdb=" O GLY H 125 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ALA H 158 " --> pdb=" O ILE H 128 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TYR H 130 " --> pdb=" O GLN H 156 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN H 156 " --> pdb=" O TYR H 130 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N SER H 132 " --> pdb=" O LEU H 154 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU H 154 " --> pdb=" O SER H 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL H 134 " --> pdb=" O TYR H 152 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N TYR H 152 " --> pdb=" O VAL H 134 " (cutoff:3.500A) removed outlier: 10.636A pdb=" N SER H 136 " --> pdb=" O THR H 150 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N THR H 150 " --> pdb=" O SER H 136 " (cutoff:3.500A) removed outlier: 10.482A pdb=" N GLY H 138 " --> pdb=" O ALA H 148 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ALA H 148 " --> pdb=" O GLY H 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY H 140 " --> pdb=" O ILE H 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE H 146 " --> pdb=" O GLY H 140 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER H 173 " --> pdb=" O VAL H 163 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN H 165 " --> pdb=" O ILE H 171 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE H 171 " --> pdb=" O ASN H 165 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER I 136 " --> pdb=" O THR H 207 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N VAL I 134 " --> pdb=" O ASN H 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA I 158 " --> pdb=" O ILE I 128 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR I 130 " --> pdb=" O GLN I 156 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN I 156 " --> pdb=" O TYR I 130 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N SER I 132 " --> pdb=" O LEU I 154 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU I 154 " --> pdb=" O SER I 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL I 134 " --> pdb=" O TYR I 152 " (cutoff:3.500A) removed outlier: 11.332A pdb=" N TYR I 152 " --> pdb=" O VAL I 134 " (cutoff:3.500A) removed outlier: 10.636A pdb=" N SER I 136 " --> pdb=" O THR I 150 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N THR I 150 " --> pdb=" O SER I 136 " (cutoff:3.500A) removed outlier: 10.482A pdb=" N GLY I 138 " --> pdb=" O ALA I 148 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ALA I 148 " --> pdb=" O GLY I 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY I 140 " --> pdb=" O ILE I 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE I 146 " --> pdb=" O GLY I 140 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER I 173 " --> pdb=" O VAL I 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN I 165 " --> pdb=" O ILE I 171 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE I 171 " --> pdb=" O ASN I 165 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 136 " --> pdb=" O THR I 207 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VAL A 134 " --> pdb=" O ASN I 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA A 158 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TYR A 130 " --> pdb=" O GLN A 156 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN A 156 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER A 132 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU A 154 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL A 134 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 11.332A pdb=" N TYR A 152 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N SER A 136 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N THR A 150 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 10.481A pdb=" N GLY A 138 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ALA A 148 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY A 140 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE A 146 " --> pdb=" O GLY A 140 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER A 173 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN A 165 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE A 171 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N VAL B 134 " --> pdb=" O ASN A 209 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN B 42 " --> pdb=" O GLY B 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 13 through 14 removed outlier: 3.527A pdb=" N SER H 136 " --> pdb=" O THR G 207 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N VAL H 134 " --> pdb=" O ASN G 209 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ALA H 158 " --> pdb=" O ILE H 128 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TYR H 130 " --> pdb=" O GLN H 156 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN H 156 " --> pdb=" O TYR H 130 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N SER H 132 " --> pdb=" O LEU H 154 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU H 154 " --> pdb=" O SER H 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL H 134 " --> pdb=" O TYR H 152 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N TYR H 152 " --> pdb=" O VAL H 134 " (cutoff:3.500A) removed outlier: 10.636A pdb=" N SER H 136 " --> pdb=" O THR H 150 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N THR H 150 " --> pdb=" O SER H 136 " (cutoff:3.500A) removed outlier: 10.482A pdb=" N GLY H 138 " --> pdb=" O ALA H 148 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ALA H 148 " --> pdb=" O GLY H 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY H 140 " --> pdb=" O ILE H 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE H 146 " --> pdb=" O GLY H 140 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER H 173 " --> pdb=" O VAL H 163 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN H 165 " --> pdb=" O ILE H 171 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE H 171 " --> pdb=" O ASN H 165 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER I 136 " --> pdb=" O THR H 207 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N VAL I 134 " --> pdb=" O ASN H 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA I 158 " --> pdb=" O ILE I 128 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR I 130 " --> pdb=" O GLN I 156 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN I 156 " --> pdb=" O TYR I 130 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N SER I 132 " --> pdb=" O LEU I 154 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU I 154 " --> pdb=" O SER I 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL I 134 " --> pdb=" O TYR I 152 " (cutoff:3.500A) removed outlier: 11.332A pdb=" N TYR I 152 " --> pdb=" O VAL I 134 " (cutoff:3.500A) removed outlier: 10.636A pdb=" N SER I 136 " --> pdb=" O THR I 150 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N THR I 150 " --> pdb=" O SER I 136 " (cutoff:3.500A) removed outlier: 10.482A pdb=" N GLY I 138 " --> pdb=" O ALA I 148 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ALA I 148 " --> pdb=" O GLY I 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY I 140 " --> pdb=" O ILE I 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE I 146 " --> pdb=" O GLY I 140 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER I 173 " --> pdb=" O VAL I 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN I 165 " --> pdb=" O ILE I 171 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE I 171 " --> pdb=" O ASN I 165 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 136 " --> pdb=" O THR I 207 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VAL A 134 " --> pdb=" O ASN I 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA A 158 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TYR A 130 " --> pdb=" O GLN A 156 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN A 156 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER A 132 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU A 154 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL A 134 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 11.332A pdb=" N TYR A 152 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N SER A 136 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N THR A 150 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 10.481A pdb=" N GLY A 138 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ALA A 148 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY A 140 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE A 146 " --> pdb=" O GLY A 140 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER A 173 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN A 165 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE A 171 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N VAL B 134 " --> pdb=" O ASN A 209 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN B 42 " --> pdb=" O GLY B 125 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 41 through 42 removed outlier: 3.907A pdb=" N GLN G 42 " --> pdb=" O GLY G 125 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA G 158 " --> pdb=" O ILE G 128 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR G 130 " --> pdb=" O GLN G 156 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN G 156 " --> pdb=" O TYR G 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER G 132 " --> pdb=" O LEU G 154 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU G 154 " --> pdb=" O SER G 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL G 134 " --> pdb=" O TYR G 152 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N TYR G 152 " --> pdb=" O VAL G 134 " (cutoff:3.500A) removed outlier: 10.634A pdb=" N SER G 136 " --> pdb=" O THR G 150 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N THR G 150 " --> pdb=" O SER G 136 " (cutoff:3.500A) removed outlier: 10.482A pdb=" N GLY G 138 " --> pdb=" O ALA G 148 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ALA G 148 " --> pdb=" O GLY G 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY G 140 " --> pdb=" O ILE G 146 " (cutoff:3.500A) removed outlier: 11.785A pdb=" N ILE G 146 " --> pdb=" O GLY G 140 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER G 173 " --> pdb=" O VAL G 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN G 165 " --> pdb=" O ILE G 171 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE G 171 " --> pdb=" O ASN G 165 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER H 136 " --> pdb=" O THR G 207 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N VAL H 134 " --> pdb=" O ASN G 209 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ALA H 158 " --> pdb=" O ILE H 128 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TYR H 130 " --> pdb=" O GLN H 156 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN H 156 " --> pdb=" O TYR H 130 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N SER H 132 " --> pdb=" O LEU H 154 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU H 154 " --> pdb=" O SER H 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL H 134 " --> pdb=" O TYR H 152 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N TYR H 152 " --> pdb=" O VAL H 134 " (cutoff:3.500A) removed outlier: 10.636A pdb=" N SER H 136 " --> pdb=" O THR H 150 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N THR H 150 " --> pdb=" O SER H 136 " (cutoff:3.500A) removed outlier: 10.482A pdb=" N GLY H 138 " --> pdb=" O ALA H 148 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ALA H 148 " --> pdb=" O GLY H 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY H 140 " --> pdb=" O ILE H 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE H 146 " --> pdb=" O GLY H 140 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER H 173 " --> pdb=" O VAL H 163 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN H 165 " --> pdb=" O ILE H 171 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE H 171 " --> pdb=" O ASN H 165 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER I 136 " --> pdb=" O THR H 207 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N VAL I 134 " --> pdb=" O ASN H 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA I 158 " --> pdb=" O ILE I 128 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR I 130 " --> pdb=" O GLN I 156 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN I 156 " --> pdb=" O TYR I 130 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N SER I 132 " --> pdb=" O LEU I 154 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU I 154 " --> pdb=" O SER I 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL I 134 " --> pdb=" O TYR I 152 " (cutoff:3.500A) removed outlier: 11.332A pdb=" N TYR I 152 " --> pdb=" O VAL I 134 " (cutoff:3.500A) removed outlier: 10.636A pdb=" N SER I 136 " --> pdb=" O THR I 150 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N THR I 150 " --> pdb=" O SER I 136 " (cutoff:3.500A) removed outlier: 10.482A pdb=" N GLY I 138 " --> pdb=" O ALA I 148 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ALA I 148 " --> pdb=" O GLY I 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY I 140 " --> pdb=" O ILE I 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE I 146 " --> pdb=" O GLY I 140 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER I 173 " --> pdb=" O VAL I 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN I 165 " --> pdb=" O ILE I 171 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE I 171 " --> pdb=" O ASN I 165 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 136 " --> pdb=" O THR I 207 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VAL A 134 " --> pdb=" O ASN I 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA A 158 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TYR A 130 " --> pdb=" O GLN A 156 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN A 156 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER A 132 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU A 154 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL A 134 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 11.332A pdb=" N TYR A 152 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N SER A 136 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N THR A 150 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 10.481A pdb=" N GLY A 138 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ALA A 148 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY A 140 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE A 146 " --> pdb=" O GLY A 140 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER A 173 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN A 165 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE A 171 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N VAL B 134 " --> pdb=" O ASN A 209 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN B 42 " --> pdb=" O GLY B 125 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 13 through 14 removed outlier: 5.089A pdb=" N VAL C 134 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN C 42 " --> pdb=" O GLY C 125 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 13 through 14 removed outlier: 5.089A pdb=" N VAL C 134 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA C 158 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR C 130 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN C 156 " --> pdb=" O TYR C 130 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N SER C 132 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU C 154 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL C 134 " --> pdb=" O TYR C 152 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N TYR C 152 " --> pdb=" O VAL C 134 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N SER C 136 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 11.726A pdb=" N THR C 150 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 10.483A pdb=" N GLY C 138 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 11.532A pdb=" N ALA C 148 " --> pdb=" O GLY C 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY C 140 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE C 146 " --> pdb=" O GLY C 140 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER C 173 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN C 165 " --> pdb=" O ILE C 171 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE C 171 " --> pdb=" O ASN C 165 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 13 through 14 removed outlier: 5.089A pdb=" N VAL C 134 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA C 158 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR C 130 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN C 156 " --> pdb=" O TYR C 130 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N SER C 132 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU C 154 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL C 134 " --> pdb=" O TYR C 152 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N TYR C 152 " --> pdb=" O VAL C 134 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N SER C 136 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 11.726A pdb=" N THR C 150 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 10.483A pdb=" N GLY C 138 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 11.532A pdb=" N ALA C 148 " --> pdb=" O GLY C 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY C 140 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE C 146 " --> pdb=" O GLY C 140 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER C 173 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN C 165 " --> pdb=" O ILE C 171 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE C 171 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N VAL D 134 " --> pdb=" O ASN C 209 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN D 42 " --> pdb=" O GLY D 125 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 13 through 14 removed outlier: 5.089A pdb=" N VAL C 134 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA C 158 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR C 130 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN C 156 " --> pdb=" O TYR C 130 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N SER C 132 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU C 154 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL C 134 " --> pdb=" O TYR C 152 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N TYR C 152 " --> pdb=" O VAL C 134 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N SER C 136 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 11.726A pdb=" N THR C 150 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 10.483A pdb=" N GLY C 138 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 11.532A pdb=" N ALA C 148 " --> pdb=" O GLY C 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY C 140 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE C 146 " --> pdb=" O GLY C 140 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER C 173 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN C 165 " --> pdb=" O ILE C 171 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE C 171 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N VAL D 134 " --> pdb=" O ASN C 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA D 158 " --> pdb=" O ILE D 128 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TYR D 130 " --> pdb=" O GLN D 156 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN D 156 " --> pdb=" O TYR D 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER D 132 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU D 154 " --> pdb=" O SER D 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL D 134 " --> pdb=" O TYR D 152 " (cutoff:3.500A) removed outlier: 11.332A pdb=" N TYR D 152 " --> pdb=" O VAL D 134 " (cutoff:3.500A) removed outlier: 10.636A pdb=" N SER D 136 " --> pdb=" O THR D 150 " (cutoff:3.500A) removed outlier: 11.724A pdb=" N THR D 150 " --> pdb=" O SER D 136 " (cutoff:3.500A) removed outlier: 10.483A pdb=" N GLY D 138 " --> pdb=" O ALA D 148 " (cutoff:3.500A) removed outlier: 11.532A pdb=" N ALA D 148 " --> pdb=" O GLY D 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY D 140 " --> pdb=" O ILE D 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE D 146 " --> pdb=" O GLY D 140 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER D 173 " --> pdb=" O VAL D 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN D 165 " --> pdb=" O ILE D 171 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE D 171 " --> pdb=" O ASN D 165 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 13 through 14 removed outlier: 5.089A pdb=" N VAL C 134 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA C 158 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR C 130 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN C 156 " --> pdb=" O TYR C 130 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N SER C 132 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU C 154 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL C 134 " --> pdb=" O TYR C 152 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N TYR C 152 " --> pdb=" O VAL C 134 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N SER C 136 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 11.726A pdb=" N THR C 150 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 10.483A pdb=" N GLY C 138 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 11.532A pdb=" N ALA C 148 " --> pdb=" O GLY C 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY C 140 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE C 146 " --> pdb=" O GLY C 140 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER C 173 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN C 165 " --> pdb=" O ILE C 171 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE C 171 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N VAL D 134 " --> pdb=" O ASN C 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA D 158 " --> pdb=" O ILE D 128 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TYR D 130 " --> pdb=" O GLN D 156 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN D 156 " --> pdb=" O TYR D 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER D 132 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU D 154 " --> pdb=" O SER D 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL D 134 " --> pdb=" O TYR D 152 " (cutoff:3.500A) removed outlier: 11.332A pdb=" N TYR D 152 " --> pdb=" O VAL D 134 " (cutoff:3.500A) removed outlier: 10.636A pdb=" N SER D 136 " --> pdb=" O THR D 150 " (cutoff:3.500A) removed outlier: 11.724A pdb=" N THR D 150 " --> pdb=" O SER D 136 " (cutoff:3.500A) removed outlier: 10.483A pdb=" N GLY D 138 " --> pdb=" O ALA D 148 " (cutoff:3.500A) removed outlier: 11.532A pdb=" N ALA D 148 " --> pdb=" O GLY D 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY D 140 " --> pdb=" O ILE D 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE D 146 " --> pdb=" O GLY D 140 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER D 173 " --> pdb=" O VAL D 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN D 165 " --> pdb=" O ILE D 171 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE D 171 " --> pdb=" O ASN D 165 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N VAL E 134 " --> pdb=" O ASN D 209 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN E 42 " --> pdb=" O GLY E 125 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 13 through 14 removed outlier: 5.089A pdb=" N VAL C 134 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA C 158 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR C 130 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN C 156 " --> pdb=" O TYR C 130 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N SER C 132 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU C 154 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL C 134 " --> pdb=" O TYR C 152 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N TYR C 152 " --> pdb=" O VAL C 134 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N SER C 136 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 11.726A pdb=" N THR C 150 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 10.483A pdb=" N GLY C 138 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 11.532A pdb=" N ALA C 148 " --> pdb=" O GLY C 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY C 140 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE C 146 " --> pdb=" O GLY C 140 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER C 173 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN C 165 " --> pdb=" O ILE C 171 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE C 171 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N VAL D 134 " --> pdb=" O ASN C 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA D 158 " --> pdb=" O ILE D 128 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TYR D 130 " --> pdb=" O GLN D 156 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN D 156 " --> pdb=" O TYR D 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER D 132 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU D 154 " --> pdb=" O SER D 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL D 134 " --> pdb=" O TYR D 152 " (cutoff:3.500A) removed outlier: 11.332A pdb=" N TYR D 152 " --> pdb=" O VAL D 134 " (cutoff:3.500A) removed outlier: 10.636A pdb=" N SER D 136 " --> pdb=" O THR D 150 " (cutoff:3.500A) removed outlier: 11.724A pdb=" N THR D 150 " --> pdb=" O SER D 136 " (cutoff:3.500A) removed outlier: 10.483A pdb=" N GLY D 138 " --> pdb=" O ALA D 148 " (cutoff:3.500A) removed outlier: 11.532A pdb=" N ALA D 148 " --> pdb=" O GLY D 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY D 140 " --> pdb=" O ILE D 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE D 146 " --> pdb=" O GLY D 140 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER D 173 " --> pdb=" O VAL D 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN D 165 " --> pdb=" O ILE D 171 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE D 171 " --> pdb=" O ASN D 165 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N VAL E 134 " --> pdb=" O ASN D 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA E 158 " --> pdb=" O ILE E 128 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR E 130 " --> pdb=" O GLN E 156 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN E 156 " --> pdb=" O TYR E 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER E 132 " --> pdb=" O LEU E 154 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU E 154 " --> pdb=" O SER E 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL E 134 " --> pdb=" O TYR E 152 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N TYR E 152 " --> pdb=" O VAL E 134 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N SER E 136 " --> pdb=" O THR E 150 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N THR E 150 " --> pdb=" O SER E 136 " (cutoff:3.500A) removed outlier: 10.482A pdb=" N GLY E 138 " --> pdb=" O ALA E 148 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ALA E 148 " --> pdb=" O GLY E 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY E 140 " --> pdb=" O ILE E 146 " (cutoff:3.500A) removed outlier: 11.785A pdb=" N ILE E 146 " --> pdb=" O GLY E 140 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER E 173 " --> pdb=" O VAL E 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN E 165 " --> pdb=" O ILE E 171 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE E 171 " --> pdb=" O ASN E 165 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 13 through 14 removed outlier: 5.089A pdb=" N VAL C 134 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA C 158 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR C 130 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN C 156 " --> pdb=" O TYR C 130 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N SER C 132 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU C 154 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL C 134 " --> pdb=" O TYR C 152 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N TYR C 152 " --> pdb=" O VAL C 134 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N SER C 136 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 11.726A pdb=" N THR C 150 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 10.483A pdb=" N GLY C 138 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 11.532A pdb=" N ALA C 148 " --> pdb=" O GLY C 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY C 140 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE C 146 " --> pdb=" O GLY C 140 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER C 173 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN C 165 " --> pdb=" O ILE C 171 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE C 171 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N VAL D 134 " --> pdb=" O ASN C 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA D 158 " --> pdb=" O ILE D 128 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TYR D 130 " --> pdb=" O GLN D 156 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN D 156 " --> pdb=" O TYR D 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER D 132 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU D 154 " --> pdb=" O SER D 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL D 134 " --> pdb=" O TYR D 152 " (cutoff:3.500A) removed outlier: 11.332A pdb=" N TYR D 152 " --> pdb=" O VAL D 134 " (cutoff:3.500A) removed outlier: 10.636A pdb=" N SER D 136 " --> pdb=" O THR D 150 " (cutoff:3.500A) removed outlier: 11.724A pdb=" N THR D 150 " --> pdb=" O SER D 136 " (cutoff:3.500A) removed outlier: 10.483A pdb=" N GLY D 138 " --> pdb=" O ALA D 148 " (cutoff:3.500A) removed outlier: 11.532A pdb=" N ALA D 148 " --> pdb=" O GLY D 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY D 140 " --> pdb=" O ILE D 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE D 146 " --> pdb=" O GLY D 140 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER D 173 " --> pdb=" O VAL D 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN D 165 " --> pdb=" O ILE D 171 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE D 171 " --> pdb=" O ASN D 165 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N VAL E 134 " --> pdb=" O ASN D 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA E 158 " --> pdb=" O ILE E 128 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR E 130 " --> pdb=" O GLN E 156 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN E 156 " --> pdb=" O TYR E 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER E 132 " --> pdb=" O LEU E 154 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU E 154 " --> pdb=" O SER E 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL E 134 " --> pdb=" O TYR E 152 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N TYR E 152 " --> pdb=" O VAL E 134 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N SER E 136 " --> pdb=" O THR E 150 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N THR E 150 " --> pdb=" O SER E 136 " (cutoff:3.500A) removed outlier: 10.482A pdb=" N GLY E 138 " --> pdb=" O ALA E 148 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ALA E 148 " --> pdb=" O GLY E 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY E 140 " --> pdb=" O ILE E 146 " (cutoff:3.500A) removed outlier: 11.785A pdb=" N ILE E 146 " --> pdb=" O GLY E 140 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER E 173 " --> pdb=" O VAL E 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN E 165 " --> pdb=" O ILE E 171 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE E 171 " --> pdb=" O ASN E 165 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER F 136 " --> pdb=" O THR E 207 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N VAL F 134 " --> pdb=" O ASN E 209 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN F 42 " --> pdb=" O GLY F 125 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 13 through 14 removed outlier: 5.089A pdb=" N VAL C 134 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA C 158 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR C 130 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN C 156 " --> pdb=" O TYR C 130 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N SER C 132 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU C 154 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL C 134 " --> pdb=" O TYR C 152 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N TYR C 152 " --> pdb=" O VAL C 134 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N SER C 136 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 11.726A pdb=" N THR C 150 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 10.483A pdb=" N GLY C 138 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 11.532A pdb=" N ALA C 148 " --> pdb=" O GLY C 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY C 140 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE C 146 " --> pdb=" O GLY C 140 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER C 173 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN C 165 " --> pdb=" O ILE C 171 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE C 171 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N VAL D 134 " --> pdb=" O ASN C 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA D 158 " --> pdb=" O ILE D 128 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TYR D 130 " --> pdb=" O GLN D 156 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN D 156 " --> pdb=" O TYR D 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER D 132 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU D 154 " --> pdb=" O SER D 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL D 134 " --> pdb=" O TYR D 152 " (cutoff:3.500A) removed outlier: 11.332A pdb=" N TYR D 152 " --> pdb=" O VAL D 134 " (cutoff:3.500A) removed outlier: 10.636A pdb=" N SER D 136 " --> pdb=" O THR D 150 " (cutoff:3.500A) removed outlier: 11.724A pdb=" N THR D 150 " --> pdb=" O SER D 136 " (cutoff:3.500A) removed outlier: 10.483A pdb=" N GLY D 138 " --> pdb=" O ALA D 148 " (cutoff:3.500A) removed outlier: 11.532A pdb=" N ALA D 148 " --> pdb=" O GLY D 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY D 140 " --> pdb=" O ILE D 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE D 146 " --> pdb=" O GLY D 140 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER D 173 " --> pdb=" O VAL D 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN D 165 " --> pdb=" O ILE D 171 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE D 171 " --> pdb=" O ASN D 165 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N VAL E 134 " --> pdb=" O ASN D 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA E 158 " --> pdb=" O ILE E 128 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR E 130 " --> pdb=" O GLN E 156 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN E 156 " --> pdb=" O TYR E 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER E 132 " --> pdb=" O LEU E 154 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU E 154 " --> pdb=" O SER E 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL E 134 " --> pdb=" O TYR E 152 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N TYR E 152 " --> pdb=" O VAL E 134 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N SER E 136 " --> pdb=" O THR E 150 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N THR E 150 " --> pdb=" O SER E 136 " (cutoff:3.500A) removed outlier: 10.482A pdb=" N GLY E 138 " --> pdb=" O ALA E 148 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ALA E 148 " --> pdb=" O GLY E 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY E 140 " --> pdb=" O ILE E 146 " (cutoff:3.500A) removed outlier: 11.785A pdb=" N ILE E 146 " --> pdb=" O GLY E 140 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER E 173 " --> pdb=" O VAL E 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN E 165 " --> pdb=" O ILE E 171 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE E 171 " --> pdb=" O ASN E 165 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER F 136 " --> pdb=" O THR E 207 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N VAL F 134 " --> pdb=" O ASN E 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA F 158 " --> pdb=" O ILE F 128 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR F 130 " --> pdb=" O GLN F 156 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN F 156 " --> pdb=" O TYR F 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER F 132 " --> pdb=" O LEU F 154 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU F 154 " --> pdb=" O SER F 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL F 134 " --> pdb=" O TYR F 152 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N TYR F 152 " --> pdb=" O VAL F 134 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N SER F 136 " --> pdb=" O THR F 150 " (cutoff:3.500A) removed outlier: 11.726A pdb=" N THR F 150 " --> pdb=" O SER F 136 " (cutoff:3.500A) removed outlier: 10.483A pdb=" N GLY F 138 " --> pdb=" O ALA F 148 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ALA F 148 " --> pdb=" O GLY F 138 " (cutoff:3.500A) removed outlier: 10.987A pdb=" N GLY F 140 " --> pdb=" O ILE F 146 " (cutoff:3.500A) removed outlier: 11.785A pdb=" N ILE F 146 " --> pdb=" O GLY F 140 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER F 173 " --> pdb=" O VAL F 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN F 165 " --> pdb=" O ILE F 171 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE F 171 " --> pdb=" O ASN F 165 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 13 through 14 removed outlier: 5.089A pdb=" N VAL C 134 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA C 158 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR C 130 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN C 156 " --> pdb=" O TYR C 130 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N SER C 132 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU C 154 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL C 134 " --> pdb=" O TYR C 152 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N TYR C 152 " --> pdb=" O VAL C 134 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N SER C 136 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 11.726A pdb=" N THR C 150 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 10.483A pdb=" N GLY C 138 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 11.532A pdb=" N ALA C 148 " --> pdb=" O GLY C 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY C 140 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE C 146 " --> pdb=" O GLY C 140 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER C 173 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN C 165 " --> pdb=" O ILE C 171 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE C 171 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N VAL D 134 " --> pdb=" O ASN C 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA D 158 " --> pdb=" O ILE D 128 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TYR D 130 " --> pdb=" O GLN D 156 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN D 156 " --> pdb=" O TYR D 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER D 132 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU D 154 " --> pdb=" O SER D 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL D 134 " --> pdb=" O TYR D 152 " (cutoff:3.500A) removed outlier: 11.332A pdb=" N TYR D 152 " --> pdb=" O VAL D 134 " (cutoff:3.500A) removed outlier: 10.636A pdb=" N SER D 136 " --> pdb=" O THR D 150 " (cutoff:3.500A) removed outlier: 11.724A pdb=" N THR D 150 " --> pdb=" O SER D 136 " (cutoff:3.500A) removed outlier: 10.483A pdb=" N GLY D 138 " --> pdb=" O ALA D 148 " (cutoff:3.500A) removed outlier: 11.532A pdb=" N ALA D 148 " --> pdb=" O GLY D 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY D 140 " --> pdb=" O ILE D 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE D 146 " --> pdb=" O GLY D 140 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER D 173 " --> pdb=" O VAL D 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN D 165 " --> pdb=" O ILE D 171 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE D 171 " --> pdb=" O ASN D 165 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N VAL E 134 " --> pdb=" O ASN D 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA E 158 " --> pdb=" O ILE E 128 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR E 130 " --> pdb=" O GLN E 156 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN E 156 " --> pdb=" O TYR E 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER E 132 " --> pdb=" O LEU E 154 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU E 154 " --> pdb=" O SER E 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL E 134 " --> pdb=" O TYR E 152 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N TYR E 152 " --> pdb=" O VAL E 134 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N SER E 136 " --> pdb=" O THR E 150 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N THR E 150 " --> pdb=" O SER E 136 " (cutoff:3.500A) removed outlier: 10.482A pdb=" N GLY E 138 " --> pdb=" O ALA E 148 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ALA E 148 " --> pdb=" O GLY E 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY E 140 " --> pdb=" O ILE E 146 " (cutoff:3.500A) removed outlier: 11.785A pdb=" N ILE E 146 " --> pdb=" O GLY E 140 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER E 173 " --> pdb=" O VAL E 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN E 165 " --> pdb=" O ILE E 171 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE E 171 " --> pdb=" O ASN E 165 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER F 136 " --> pdb=" O THR E 207 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N VAL F 134 " --> pdb=" O ASN E 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA F 158 " --> pdb=" O ILE F 128 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR F 130 " --> pdb=" O GLN F 156 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN F 156 " --> pdb=" O TYR F 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER F 132 " --> pdb=" O LEU F 154 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU F 154 " --> pdb=" O SER F 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL F 134 " --> pdb=" O TYR F 152 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N TYR F 152 " --> pdb=" O VAL F 134 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N SER F 136 " --> pdb=" O THR F 150 " (cutoff:3.500A) removed outlier: 11.726A pdb=" N THR F 150 " --> pdb=" O SER F 136 " (cutoff:3.500A) removed outlier: 10.483A pdb=" N GLY F 138 " --> pdb=" O ALA F 148 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ALA F 148 " --> pdb=" O GLY F 138 " (cutoff:3.500A) removed outlier: 10.987A pdb=" N GLY F 140 " --> pdb=" O ILE F 146 " (cutoff:3.500A) removed outlier: 11.785A pdb=" N ILE F 146 " --> pdb=" O GLY F 140 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER F 173 " --> pdb=" O VAL F 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN F 165 " --> pdb=" O ILE F 171 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE F 171 " --> pdb=" O ASN F 165 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER G 136 " --> pdb=" O THR F 207 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VAL G 134 " --> pdb=" O ASN F 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA G 158 " --> pdb=" O ILE G 128 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR G 130 " --> pdb=" O GLN G 156 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN G 156 " --> pdb=" O TYR G 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER G 132 " --> pdb=" O LEU G 154 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU G 154 " --> pdb=" O SER G 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL G 134 " --> pdb=" O TYR G 152 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N TYR G 152 " --> pdb=" O VAL G 134 " (cutoff:3.500A) removed outlier: 10.634A pdb=" N SER G 136 " --> pdb=" O THR G 150 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N THR G 150 " --> pdb=" O SER G 136 " (cutoff:3.500A) removed outlier: 10.482A pdb=" N GLY G 138 " --> pdb=" O ALA G 148 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ALA G 148 " --> pdb=" O GLY G 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY G 140 " --> pdb=" O ILE G 146 " (cutoff:3.500A) removed outlier: 11.785A pdb=" N ILE G 146 " --> pdb=" O GLY G 140 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER G 173 " --> pdb=" O VAL G 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN G 165 " --> pdb=" O ILE G 171 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE G 171 " --> pdb=" O ASN G 165 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER H 136 " --> pdb=" O THR G 207 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N VAL H 134 " --> pdb=" O ASN G 209 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ALA H 158 " --> pdb=" O ILE H 128 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TYR H 130 " --> pdb=" O GLN H 156 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN H 156 " --> pdb=" O TYR H 130 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N SER H 132 " --> pdb=" O LEU H 154 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU H 154 " --> pdb=" O SER H 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL H 134 " --> pdb=" O TYR H 152 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N TYR H 152 " --> pdb=" O VAL H 134 " (cutoff:3.500A) removed outlier: 10.636A pdb=" N SER H 136 " --> pdb=" O THR H 150 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N THR H 150 " --> pdb=" O SER H 136 " (cutoff:3.500A) removed outlier: 10.482A pdb=" N GLY H 138 " --> pdb=" O ALA H 148 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ALA H 148 " --> pdb=" O GLY H 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY H 140 " --> pdb=" O ILE H 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE H 146 " --> pdb=" O GLY H 140 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER H 173 " --> pdb=" O VAL H 163 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASN H 165 " --> pdb=" O ILE H 171 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE H 171 " --> pdb=" O ASN H 165 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER I 136 " --> pdb=" O THR H 207 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N VAL I 134 " --> pdb=" O ASN H 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA I 158 " --> pdb=" O ILE I 128 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR I 130 " --> pdb=" O GLN I 156 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN I 156 " --> pdb=" O TYR I 130 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N SER I 132 " --> pdb=" O LEU I 154 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU I 154 " --> pdb=" O SER I 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL I 134 " --> pdb=" O TYR I 152 " (cutoff:3.500A) removed outlier: 11.332A pdb=" N TYR I 152 " --> pdb=" O VAL I 134 " (cutoff:3.500A) removed outlier: 10.636A pdb=" N SER I 136 " --> pdb=" O THR I 150 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N THR I 150 " --> pdb=" O SER I 136 " (cutoff:3.500A) removed outlier: 10.482A pdb=" N GLY I 138 " --> pdb=" O ALA I 148 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ALA I 148 " --> pdb=" O GLY I 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY I 140 " --> pdb=" O ILE I 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE I 146 " --> pdb=" O GLY I 140 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER I 173 " --> pdb=" O VAL I 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN I 165 " --> pdb=" O ILE I 171 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE I 171 " --> pdb=" O ASN I 165 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 136 " --> pdb=" O THR I 207 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VAL A 134 " --> pdb=" O ASN I 209 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ALA A 158 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TYR A 130 " --> pdb=" O GLN A 156 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLN A 156 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N SER A 132 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU A 154 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL A 134 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 11.332A pdb=" N TYR A 152 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 10.635A pdb=" N SER A 136 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 11.725A pdb=" N THR A 150 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 10.481A pdb=" N GLY A 138 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 11.533A pdb=" N ALA A 148 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 10.988A pdb=" N GLY A 140 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 11.784A pdb=" N ILE A 146 " --> pdb=" O GLY A 140 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER A 173 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN A 165 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE A 171 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N VAL B 134 " --> pdb=" O ASN A 209 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN B 42 " --> pdb=" O GLY B 125 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 34 through 37 removed outlier: 6.359A pdb=" N ILE A 34 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N LEU A 81 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL A 36 " --> pdb=" O LEU A 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 34 through 37 removed outlier: 6.359A pdb=" N ILE B 34 " --> pdb=" O ILE B 79 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N LEU B 81 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL B 36 " --> pdb=" O LEU B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 34 through 37 removed outlier: 6.359A pdb=" N ILE C 34 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N LEU C 81 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL C 36 " --> pdb=" O LEU C 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'D' and resid 34 through 37 removed outlier: 6.358A pdb=" N ILE D 34 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N LEU D 81 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL D 36 " --> pdb=" O LEU D 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'E' and resid 34 through 37 removed outlier: 6.359A pdb=" N ILE E 34 " --> pdb=" O ILE E 79 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LEU E 81 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL E 36 " --> pdb=" O LEU E 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'F' and resid 34 through 37 removed outlier: 6.359A pdb=" N ILE F 34 " --> pdb=" O ILE F 79 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N LEU F 81 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL F 36 " --> pdb=" O LEU F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'G' and resid 34 through 37 removed outlier: 6.359A pdb=" N ILE G 34 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N LEU G 81 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL G 36 " --> pdb=" O LEU G 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'H' and resid 34 through 37 removed outlier: 6.359A pdb=" N ILE H 34 " --> pdb=" O ILE H 79 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LEU H 81 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL H 36 " --> pdb=" O LEU H 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'I' and resid 34 through 37 removed outlier: 6.360A pdb=" N ILE I 34 " --> pdb=" O ILE I 79 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N LEU I 81 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL I 36 " --> pdb=" O LEU I 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 2400 hydrogen bonds defined for protein. 6945 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: 8.66 Time building geometry restraints manager: 8.42 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: 6889 1.34 - 1.45: 2714 1.45 - 1.57: 11250 1.57 - 1.68: 0 1.68 - 1.80: 135 Bond restraints: 20988 Sorted by residual: bond pdb=" N ASP D 195 " pdb=" CA ASP D 195 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.32e-02 5.74e+03 8.75e+00 bond pdb=" N ASP E 195 " pdb=" CA ASP E 195 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.32e-02 5.74e+03 8.72e+00 bond pdb=" N ASP A 195 " pdb=" CA ASP A 195 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.32e-02 5.74e+03 8.43e+00 bond pdb=" N ASP F 195 " pdb=" CA ASP F 195 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.32e-02 5.74e+03 8.38e+00 bond pdb=" N ASP I 195 " pdb=" CA ASP I 195 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.32e-02 5.74e+03 8.35e+00 ... (remaining 20983 not shown) Histogram of bond angle deviations from ideal: 99.69 - 106.55: 648 106.55 - 113.41: 11322 113.41 - 120.26: 7486 120.26 - 127.12: 8809 127.12 - 133.98: 220 Bond angle restraints: 28485 Sorted by residual: angle pdb=" C ILE C 194 " pdb=" N ASP C 195 " pdb=" CA ASP C 195 " ideal model delta sigma weight residual 121.31 132.20 -10.89 1.49e+00 4.50e-01 5.35e+01 angle pdb=" C ILE I 194 " pdb=" N ASP I 195 " pdb=" CA ASP I 195 " ideal model delta sigma weight residual 121.31 132.18 -10.87 1.49e+00 4.50e-01 5.32e+01 angle pdb=" C ILE G 194 " pdb=" N ASP G 195 " pdb=" CA ASP G 195 " ideal model delta sigma weight residual 121.31 132.17 -10.86 1.49e+00 4.50e-01 5.31e+01 angle pdb=" C ILE A 194 " pdb=" N ASP A 195 " pdb=" CA ASP A 195 " ideal model delta sigma weight residual 121.31 132.16 -10.85 1.49e+00 4.50e-01 5.30e+01 angle pdb=" C ILE E 194 " pdb=" N ASP E 195 " pdb=" CA ASP E 195 " ideal model delta sigma weight residual 121.31 132.16 -10.85 1.49e+00 4.50e-01 5.30e+01 ... (remaining 28480 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.33: 10890 15.33 - 30.67: 1332 30.67 - 46.00: 345 46.00 - 61.33: 60 61.33 - 76.67: 36 Dihedral angle restraints: 12663 sinusoidal: 5031 harmonic: 7632 Sorted by residual: dihedral pdb=" CA ASP F 195 " pdb=" C ASP F 195 " pdb=" N TYR F 196 " pdb=" CA TYR F 196 " ideal model delta harmonic sigma weight residual -180.00 -149.64 -30.36 0 5.00e+00 4.00e-02 3.69e+01 dihedral pdb=" CA ASP A 195 " pdb=" C ASP A 195 " pdb=" N TYR A 196 " pdb=" CA TYR A 196 " ideal model delta harmonic sigma weight residual -180.00 -149.69 -30.31 0 5.00e+00 4.00e-02 3.68e+01 dihedral pdb=" CA ASP E 195 " pdb=" C ASP E 195 " pdb=" N TYR E 196 " pdb=" CA TYR E 196 " ideal model delta harmonic sigma weight residual -180.00 -149.71 -30.29 0 5.00e+00 4.00e-02 3.67e+01 ... (remaining 12660 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2058 0.038 - 0.076: 761 0.076 - 0.114: 240 0.114 - 0.152: 126 0.152 - 0.190: 19 Chirality restraints: 3204 Sorted by residual: chirality pdb=" CA ILE F 194 " pdb=" N ILE F 194 " pdb=" C ILE F 194 " pdb=" CB ILE F 194 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.03e-01 chirality pdb=" CA ILE I 194 " pdb=" N ILE I 194 " pdb=" C ILE I 194 " pdb=" CB ILE I 194 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.03e-01 chirality pdb=" CA ILE D 194 " pdb=" N ILE D 194 " pdb=" C ILE D 194 " pdb=" CB ILE D 194 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.00e-01 ... (remaining 3201 not shown) Planarity restraints: 3762 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 195 " 0.011 2.00e-02 2.50e+03 2.16e-02 4.65e+00 pdb=" C ASP C 195 " -0.037 2.00e-02 2.50e+03 pdb=" O ASP C 195 " 0.014 2.00e-02 2.50e+03 pdb=" N TYR C 196 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP H 195 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.65e+00 pdb=" C ASP H 195 " 0.037 2.00e-02 2.50e+03 pdb=" O ASP H 195 " -0.014 2.00e-02 2.50e+03 pdb=" N TYR H 196 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP E 195 " -0.010 2.00e-02 2.50e+03 2.14e-02 4.59e+00 pdb=" C ASP E 195 " 0.037 2.00e-02 2.50e+03 pdb=" O ASP E 195 " -0.014 2.00e-02 2.50e+03 pdb=" N TYR E 196 " -0.013 2.00e-02 2.50e+03 ... (remaining 3759 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 7157 2.86 - 3.37: 17935 3.37 - 3.88: 33553 3.88 - 4.39: 38638 4.39 - 4.90: 68404 Nonbonded interactions: 165687 Sorted by model distance: nonbonded pdb=" O THR E 104 " pdb=" OG SER F 115 " model vdw 2.347 2.440 nonbonded pdb=" O LEU E 72 " pdb=" OG SER E 75 " model vdw 2.366 2.440 nonbonded pdb=" O LEU F 72 " pdb=" OG SER F 75 " model vdw 2.366 2.440 nonbonded pdb=" O LEU A 72 " pdb=" OG SER A 75 " model vdw 2.366 2.440 nonbonded pdb=" O LEU I 72 " pdb=" OG SER I 75 " model vdw 2.366 2.440 ... (remaining 165682 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' } ncs_group { reference = 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' } ncs_group { reference = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' } 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 13005 2.51 5 N 3582 2.21 5 O 3942 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: 0.900 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: 0.010 Extract box with map and model: 5.910 Check model and map are aligned: 0.230 Process input model: 54.220 Find NCS groups from input model: 1.320 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Set scattering table: 0.190 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 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 : 0.006 0.039 20988 Z= 0.364 Angle : 0.855 11.086 28485 Z= 0.498 Chirality : 0.051 0.190 3204 Planarity : 0.006 0.045 3762 Dihedral : 14.849 76.668 7767 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer Outliers : 1.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: -3.41 (0.15), residues: 2601 helix: -4.22 (0.07), residues: 738 sheet: -0.53 (0.19), residues: 765 loop : -1.94 (0.18), residues: 1098 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 507 time to evaluate : 2.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 5 residues processed: 519 average time/residue: 0.3750 time to fit residues: 282.6141 Evaluate side-chains 346 residues out of total 2250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 341 time to evaluate : 2.431 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1856 time to fit residues: 5.0200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 2.9990 chunk 191 optimal weight: 0.4980 chunk 105 optimal weight: 0.0570 chunk 65 optimal weight: 2.9990 chunk 128 optimal weight: 0.3980 chunk 102 optimal weight: 1.9990 chunk 197 optimal weight: 0.9980 chunk 76 optimal weight: 0.0470 chunk 120 optimal weight: 0.9980 chunk 147 optimal weight: 0.9990 chunk 228 optimal weight: 3.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN B 100 GLN C 100 GLN D 100 GLN E 100 GLN F 100 GLN G 100 GLN H 100 GLN I 100 GLN K 17 ASN O 17 ASN Q 17 ASN R 17 ASN ** Y 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 5 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 20988 Z= 0.165 Angle : 0.574 7.580 28485 Z= 0.308 Chirality : 0.044 0.164 3204 Planarity : 0.004 0.035 3762 Dihedral : 4.782 23.448 2871 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer Outliers : 1.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -1.42 (0.16), residues: 2601 helix: -1.47 (0.15), residues: 765 sheet: 0.27 (0.20), residues: 756 loop : -1.33 (0.19), residues: 1080 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 383 time to evaluate : 2.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 9 residues processed: 403 average time/residue: 0.3395 time to fit residues: 211.9470 Evaluate side-chains 336 residues out of total 2250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 327 time to evaluate : 2.411 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2196 time to fit residues: 6.8583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 190 optimal weight: 0.9980 chunk 155 optimal weight: 0.2980 chunk 63 optimal weight: 1.9990 chunk 229 optimal weight: 0.5980 chunk 247 optimal weight: 3.9990 chunk 204 optimal weight: 0.0980 chunk 227 optimal weight: 2.9990 chunk 78 optimal weight: 0.4980 chunk 183 optimal weight: 0.7980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 29 GLN K 27 GLN R 29 GLN ** T 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 5 GLN V 5 GLN W 5 GLN X 5 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 20988 Z= 0.152 Angle : 0.538 7.688 28485 Z= 0.288 Chirality : 0.043 0.164 3204 Planarity : 0.004 0.042 3762 Dihedral : 4.478 27.630 2871 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer Outliers : 0.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.16), residues: 2601 helix: 0.42 (0.18), residues: 765 sheet: 0.59 (0.19), residues: 747 loop : -1.09 (0.19), residues: 1089 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 384 time to evaluate : 2.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 11 residues processed: 395 average time/residue: 0.3138 time to fit residues: 194.4044 Evaluate side-chains 330 residues out of total 2250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 319 time to evaluate : 2.386 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1956 time to fit residues: 7.2177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 0.6980 chunk 172 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 153 optimal weight: 0.8980 chunk 230 optimal weight: 2.9990 chunk 243 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 218 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 100 GLN J 27 GLN K 27 GLN K 29 GLN ** L 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 29 GLN M 27 GLN M 29 GLN N 29 GLN O 29 GLN ** P 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 27 GLN U 5 GLN ** V 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 5 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.066 20988 Z= 0.479 Angle : 0.703 9.387 28485 Z= 0.369 Chirality : 0.048 0.158 3204 Planarity : 0.004 0.035 3762 Dihedral : 5.010 23.420 2871 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer Outliers : 2.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.17), residues: 2601 helix: 1.06 (0.19), residues: 765 sheet: 0.43 (0.19), residues: 756 loop : -1.06 (0.18), residues: 1080 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 330 time to evaluate : 2.525 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 30 residues processed: 361 average time/residue: 0.3404 time to fit residues: 191.6073 Evaluate side-chains 331 residues out of total 2250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 301 time to evaluate : 2.623 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.2048 time to fit residues: 14.6079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 181 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 207 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 218 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 11 ASN ** M 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 27 GLN P 29 GLN Q 29 GLN R 27 GLN V 5 GLN ** W 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 5 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 20988 Z= 0.238 Angle : 0.587 7.577 28485 Z= 0.309 Chirality : 0.044 0.153 3204 Planarity : 0.003 0.045 3762 Dihedral : 4.729 25.128 2871 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.17), residues: 2601 helix: 1.57 (0.20), residues: 765 sheet: 0.52 (0.19), residues: 765 loop : -0.89 (0.18), residues: 1071 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 312 time to evaluate : 2.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 17 residues processed: 337 average time/residue: 0.3438 time to fit residues: 180.9773 Evaluate side-chains 317 residues out of total 2250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 300 time to evaluate : 2.413 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1874 time to fit residues: 9.4990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 2.9990 chunk 219 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 143 optimal weight: 0.8980 chunk 60 optimal weight: 0.0970 chunk 243 optimal weight: 3.9990 chunk 202 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 128 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 100 GLN K 29 GLN R 11 ASN Y 5 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 20988 Z= 0.214 Angle : 0.565 7.422 28485 Z= 0.298 Chirality : 0.044 0.149 3204 Planarity : 0.003 0.035 3762 Dihedral : 4.604 25.447 2871 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer Outliers : 1.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.17), residues: 2601 helix: 1.88 (0.20), residues: 765 sheet: 0.60 (0.19), residues: 765 loop : -0.70 (0.19), residues: 1071 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 316 time to evaluate : 2.361 Fit side-chains revert: symmetry clash outliers start: 42 outliers final: 23 residues processed: 340 average time/residue: 0.3273 time to fit residues: 174.0290 Evaluate side-chains 319 residues out of total 2250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 296 time to evaluate : 2.443 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.2057 time to fit residues: 12.0994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 0.0870 chunk 27 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 205 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 242 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 100 GLN L 11 ASN L 27 GLN ** M 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 27 GLN R 27 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 20988 Z= 0.295 Angle : 0.613 8.078 28485 Z= 0.323 Chirality : 0.045 0.157 3204 Planarity : 0.004 0.033 3762 Dihedral : 4.741 23.947 2871 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.17), residues: 2601 helix: 1.88 (0.20), residues: 765 sheet: 0.64 (0.19), residues: 756 loop : -0.64 (0.19), residues: 1080 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 304 time to evaluate : 2.867 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 10 residues processed: 314 average time/residue: 0.3252 time to fit residues: 157.8901 Evaluate side-chains 305 residues out of total 2250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 295 time to evaluate : 2.466 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1883 time to fit residues: 6.8836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 4.9990 chunk 96 optimal weight: 0.6980 chunk 145 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 154 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 190 optimal weight: 2.9990 chunk 220 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 100 GLN K 11 ASN L 11 ASN ** P 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 11 ASN a 5 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 20988 Z= 0.197 Angle : 0.568 7.285 28485 Z= 0.301 Chirality : 0.043 0.149 3204 Planarity : 0.003 0.030 3762 Dihedral : 4.569 25.322 2871 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.17), residues: 2601 helix: 2.12 (0.20), residues: 765 sheet: 0.67 (0.19), residues: 765 loop : -0.56 (0.19), residues: 1071 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 310 time to evaluate : 2.643 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 10 residues processed: 318 average time/residue: 0.3237 time to fit residues: 159.4998 Evaluate side-chains 310 residues out of total 2250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 300 time to evaluate : 2.433 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1915 time to fit residues: 6.8116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 3.9990 chunk 212 optimal weight: 5.9990 chunk 226 optimal weight: 0.6980 chunk 136 optimal weight: 4.9990 chunk 98 optimal weight: 0.4980 chunk 177 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 204 optimal weight: 0.2980 chunk 214 optimal weight: 0.8980 chunk 225 optimal weight: 3.9990 chunk 148 optimal weight: 0.0870 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 100 GLN L 11 ASN ** P 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 20988 Z= 0.159 Angle : 0.548 11.776 28485 Z= 0.290 Chirality : 0.043 0.145 3204 Planarity : 0.003 0.031 3762 Dihedral : 4.379 25.712 2871 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.17), residues: 2601 helix: 2.19 (0.20), residues: 783 sheet: 0.81 (0.20), residues: 756 loop : -0.69 (0.18), residues: 1062 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 329 time to evaluate : 2.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 331 average time/residue: 0.3244 time to fit residues: 165.9479 Evaluate side-chains 311 residues out of total 2250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 307 time to evaluate : 2.165 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1956 time to fit residues: 4.5258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 5.9990 chunk 146 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 251 optimal weight: 5.9990 chunk 231 optimal weight: 0.9990 chunk 199 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 154 optimal weight: 0.3980 chunk 122 optimal weight: 0.9990 chunk 158 optimal weight: 2.9990 overall best weight: 0.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 100 GLN K 11 ASN L 11 ASN L 27 GLN ** P 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 27 GLN a 5 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 20988 Z= 0.214 Angle : 0.591 12.363 28485 Z= 0.311 Chirality : 0.044 0.149 3204 Planarity : 0.004 0.031 3762 Dihedral : 4.459 25.526 2871 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer Outliers : 0.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.17), residues: 2601 helix: 2.17 (0.20), residues: 783 sheet: 0.75 (0.19), residues: 765 loop : -0.63 (0.19), residues: 1053 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5202 Ramachandran restraints generated. 2601 Oldfield, 0 Emsley, 2601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 310 time to evaluate : 2.256 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 313 average time/residue: 0.3291 time to fit residues: 158.8341 Evaluate side-chains 307 residues out of total 2250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 301 time to evaluate : 2.516 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2015 time to fit residues: 5.6359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 184 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 55 optimal weight: 0.0980 chunk 200 optimal weight: 0.0670 chunk 83 optimal weight: 0.9980 chunk 205 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 175 optimal weight: 5.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 100 GLN H 109 ASN ** P 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.115619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.100993 restraints weight = 32093.559| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.23 r_work: 0.3002 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 20988 Z= 0.168 Angle : 0.565 11.744 28485 Z= 0.299 Chirality : 0.043 0.155 3204 Planarity : 0.004 0.032 3762 Dihedral : 4.383 26.593 2871 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1.03 (0.17), residues: 2601 helix: 2.22 (0.20), residues: 783 sheet: 0.83 (0.20), residues: 756 loop : -0.59 (0.19), residues: 1062 =============================================================================== Job complete usr+sys time: 4205.59 seconds wall clock time: 77 minutes 7.22 seconds (4627.22 seconds total)