Starting phenix.real_space_refine on Sun Feb 18 03:53:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l7c_0842/02_2024/6l7c_0842.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l7c_0842/02_2024/6l7c_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_2024/6l7c_0842.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l7c_0842/02_2024/6l7c_0842.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l7c_0842/02_2024/6l7c_0842.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l7c_0842/02_2024/6l7c_0842.pdb" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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 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. 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 10.81, per 1000 atoms: 0.52 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: 7.54 Conformation dependent library (CDL) restraints added in 3.8 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: 3.55 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: 9.30 Time building geometry restraints manager: 8.14 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 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: 0.020 Extract box with map and model: 4.660 Check model and map are aligned: 0.350 Set scattering table: 0.200 Process input model: 57.850 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 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 % Allowed : 5.20 % Favored : 93.60 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP D 237 HIS 0.002 0.001 HIS E 26 PHE 0.019 0.002 PHE F 144 TYR 0.013 0.002 TYR I 196 ARG 0.006 0.001 ARG B 93 *********************** 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 : 2.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 LYS cc_start: 0.8614 (ttmt) cc_final: 0.8107 (tptm) REVERT: A 42 GLN cc_start: 0.8659 (mp10) cc_final: 0.8381 (mp10) REVERT: A 56 PHE cc_start: 0.9072 (m-10) cc_final: 0.8839 (m-10) REVERT: A 82 GLU cc_start: 0.7657 (tp30) cc_final: 0.7437 (tp30) REVERT: A 124 GLU cc_start: 0.8419 (pt0) cc_final: 0.8121 (pt0) REVERT: A 203 GLU cc_start: 0.7830 (tt0) cc_final: 0.7448 (tt0) REVERT: A 230 ASP cc_start: 0.8509 (t70) cc_final: 0.8092 (t70) REVERT: A 261 GLU cc_start: 0.3168 (OUTLIER) cc_final: 0.2524 (tp30) REVERT: B 22 LYS cc_start: 0.8487 (ttmt) cc_final: 0.8086 (tptm) REVERT: B 44 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7979 (mt-10) REVERT: B 131 GLU cc_start: 0.7676 (tp30) cc_final: 0.7418 (tp30) REVERT: B 135 LYS cc_start: 0.8759 (mttt) cc_final: 0.8494 (mttp) REVERT: B 155 ASP cc_start: 0.8609 (m-30) cc_final: 0.8390 (m-30) REVERT: B 194 ILE cc_start: 0.8563 (OUTLIER) cc_final: 0.8239 (pt) REVERT: B 230 ASP cc_start: 0.8584 (t70) cc_final: 0.8339 (t70) REVERT: B 261 GLU cc_start: 0.3124 (OUTLIER) cc_final: 0.1902 (tp30) REVERT: C 22 LYS cc_start: 0.8507 (ttmt) cc_final: 0.8101 (tptp) REVERT: C 51 TYR cc_start: 0.8600 (t80) cc_final: 0.8313 (t80) REVERT: C 194 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.7898 (pt) REVERT: C 221 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8507 (mt-10) REVERT: C 230 ASP cc_start: 0.8530 (t70) cc_final: 0.8175 (t0) REVERT: C 261 GLU cc_start: 0.3427 (OUTLIER) cc_final: 0.2837 (tp30) REVERT: D 22 LYS cc_start: 0.8419 (ttmt) cc_final: 0.8066 (tptp) REVERT: D 44 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7751 (mt-10) REVERT: D 192 ARG cc_start: 0.7892 (ttt180) cc_final: 0.7555 (ttp80) REVERT: D 194 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.8137 (pt) REVERT: D 230 ASP cc_start: 0.8392 (t70) cc_final: 0.7961 (t0) REVERT: D 261 GLU cc_start: 0.3159 (OUTLIER) cc_final: 0.1527 (tp30) REVERT: E 22 LYS cc_start: 0.8589 (ttmt) cc_final: 0.8139 (tptm) REVERT: E 42 GLN cc_start: 0.8515 (mp10) cc_final: 0.8001 (mp10) REVERT: E 44 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7890 (mt-10) REVERT: E 51 TYR cc_start: 0.8518 (t80) cc_final: 0.8238 (t80) REVERT: E 135 LYS cc_start: 0.8751 (mttt) cc_final: 0.8467 (mttm) REVERT: E 194 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.7916 (pt) REVERT: E 203 GLU cc_start: 0.7621 (tt0) cc_final: 0.7375 (tt0) REVERT: E 221 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8117 (mt-10) REVERT: E 261 GLU cc_start: 0.3054 (OUTLIER) cc_final: 0.1188 (tp30) REVERT: F 22 LYS cc_start: 0.8412 (ttmt) cc_final: 0.8094 (tptm) REVERT: F 44 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7736 (mt-10) REVERT: F 51 TYR cc_start: 0.8549 (t80) cc_final: 0.8267 (t80) REVERT: F 82 GLU cc_start: 0.7671 (tp30) cc_final: 0.7313 (tp30) REVERT: F 194 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.8163 (pt) REVERT: F 230 ASP cc_start: 0.8419 (t70) cc_final: 0.7977 (t0) REVERT: F 261 GLU cc_start: 0.3660 (OUTLIER) cc_final: 0.1349 (tp30) REVERT: G 22 LYS cc_start: 0.8534 (ttmt) cc_final: 0.8110 (tptm) REVERT: G 56 PHE cc_start: 0.9063 (m-10) cc_final: 0.8811 (m-10) REVERT: G 105 VAL cc_start: 0.7367 (t) cc_final: 0.7106 (t) REVERT: G 155 ASP cc_start: 0.8583 (m-30) cc_final: 0.8316 (m-30) REVERT: G 192 ARG cc_start: 0.7793 (ttt180) cc_final: 0.7567 (ttp80) REVERT: G 194 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.8100 (pt) REVERT: G 221 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8162 (mt-10) REVERT: G 261 GLU cc_start: 0.3244 (OUTLIER) cc_final: 0.1569 (tp30) REVERT: H 22 LYS cc_start: 0.8809 (ttmt) cc_final: 0.8272 (tptm) REVERT: H 131 GLU cc_start: 0.7763 (tp30) cc_final: 0.7455 (tp30) REVERT: H 194 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8298 (pt) REVERT: H 261 GLU cc_start: 0.2946 (OUTLIER) cc_final: 0.2522 (tp30) REVERT: I 22 LYS cc_start: 0.8719 (ttmt) cc_final: 0.8225 (tptm) REVERT: I 44 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7840 (mt-10) REVERT: I 230 ASP cc_start: 0.8515 (t70) cc_final: 0.8008 (t0) REVERT: I 261 GLU cc_start: 0.3287 (OUTLIER) cc_final: 0.1712 (tp30) REVERT: J 4 THR cc_start: 0.8825 (OUTLIER) cc_final: 0.8566 (p) REVERT: K 6 GLN cc_start: 0.8100 (mt0) cc_final: 0.7852 (mm-40) REVERT: M 17 ASN cc_start: 0.9079 (m110) cc_final: 0.8858 (m-40) outliers start: 27 outliers final: 5 residues processed: 519 average time/residue: 0.3731 time to fit residues: 281.1892 Evaluate side-chains 374 residues out of total 2250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 352 time to evaluate : 2.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 261 GLU Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 261 GLU Chi-restraints excluded: chain F residue 194 ILE Chi-restraints excluded: chain F residue 261 GLU Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 261 GLU Chi-restraints excluded: chain H residue 194 ILE Chi-restraints excluded: chain H residue 261 GLU Chi-restraints excluded: chain I residue 261 GLU Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain M residue 4 THR Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain O residue 4 THR Chi-restraints excluded: chain P residue 4 THR Chi-restraints excluded: chain Q residue 4 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 1.9990 chunk 191 optimal weight: 0.4980 chunk 105 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 197 optimal weight: 0.6980 chunk 76 optimal weight: 0.0870 chunk 120 optimal weight: 0.8980 chunk 147 optimal weight: 0.9980 chunk 228 optimal weight: 0.7980 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 M 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: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20988 Z= 0.183 Angle : 0.587 7.557 28485 Z= 0.314 Chirality : 0.044 0.167 3204 Planarity : 0.004 0.034 3762 Dihedral : 5.478 35.796 2918 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.47 % Allowed : 10.76 % Favored : 87.78 % 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: -1.50 (0.16), residues: 2601 helix: -1.50 (0.15), residues: 765 sheet: 0.18 (0.19), residues: 756 loop : -1.35 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 237 HIS 0.001 0.001 HIS G 255 PHE 0.024 0.001 PHE E 144 TYR 0.011 0.001 TYR A 184 ARG 0.007 0.000 ARG G 245 *********************** 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 408 residues out of total 2250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 375 time to evaluate : 2.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 LYS cc_start: 0.8603 (ttmt) cc_final: 0.8123 (tptm) REVERT: A 230 ASP cc_start: 0.8628 (t70) cc_final: 0.8296 (t70) REVERT: B 22 LYS cc_start: 0.8510 (ttmt) cc_final: 0.8128 (tptm) REVERT: B 44 GLU cc_start: 0.8322 (mt-10) cc_final: 0.8063 (mt-10) REVERT: B 131 GLU cc_start: 0.7621 (tp30) cc_final: 0.7419 (mm-30) REVERT: B 238 ASP cc_start: 0.8166 (m-30) cc_final: 0.7850 (t0) REVERT: C 22 LYS cc_start: 0.8315 (ttmt) cc_final: 0.8001 (tptp) REVERT: D 22 LYS cc_start: 0.8443 (ttmt) cc_final: 0.8105 (tptm) REVERT: E 22 LYS cc_start: 0.8589 (ttmt) cc_final: 0.8178 (tptm) REVERT: E 44 GLU cc_start: 0.8321 (mt-10) cc_final: 0.8049 (mt-10) REVERT: E 51 TYR cc_start: 0.8575 (t80) cc_final: 0.8169 (t80) REVERT: E 67 MET cc_start: 0.9171 (mtt) cc_final: 0.8924 (mtt) REVERT: E 135 LYS cc_start: 0.8396 (mttt) cc_final: 0.8060 (mttm) REVERT: E 201 GLU cc_start: 0.6628 (tm-30) cc_final: 0.5904 (tm-30) REVERT: F 22 LYS cc_start: 0.8386 (ttmt) cc_final: 0.8110 (tptm) REVERT: F 230 ASP cc_start: 0.8490 (t70) cc_final: 0.7740 (t70) REVERT: G 22 LYS cc_start: 0.8531 (ttmt) cc_final: 0.8117 (tptm) REVERT: G 122 MET cc_start: 0.7973 (ptp) cc_final: 0.7764 (ptm) REVERT: G 230 ASP cc_start: 0.8516 (t70) cc_final: 0.8265 (t70) REVERT: H 22 LYS cc_start: 0.8709 (ttmt) cc_final: 0.8194 (tptm) REVERT: H 217 MET cc_start: 0.8221 (tpp) cc_final: 0.7735 (tpp) REVERT: H 238 ASP cc_start: 0.7538 (t0) cc_final: 0.7222 (t0) REVERT: I 22 LYS cc_start: 0.8711 (ttmt) cc_final: 0.8258 (tptm) REVERT: I 43 ASP cc_start: 0.8081 (t70) cc_final: 0.7774 (t70) REVERT: I 44 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7904 (mt-10) REVERT: J 4 THR cc_start: 0.8716 (OUTLIER) cc_final: 0.8497 (p) REVERT: K 27 GLN cc_start: 0.8823 (mt0) cc_final: 0.8487 (mm110) REVERT: O 4 THR cc_start: 0.8783 (OUTLIER) cc_final: 0.8581 (p) REVERT: V 5 GLN cc_start: 0.7024 (mt0) cc_final: 0.6786 (mt0) outliers start: 33 outliers final: 15 residues processed: 397 average time/residue: 0.3370 time to fit residues: 201.8835 Evaluate side-chains 345 residues out of total 2250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 328 time to evaluate : 2.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 TYR Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 144 PHE Chi-restraints excluded: chain C residue 144 PHE Chi-restraints excluded: chain D residue 144 PHE Chi-restraints excluded: chain E residue 155 ASP Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain F residue 144 PHE Chi-restraints excluded: chain F residue 155 ASP Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain G residue 144 PHE Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain J residue 4 THR Chi-restraints excluded: chain O residue 4 THR Chi-restraints excluded: chain P residue 4 THR Chi-restraints excluded: chain Q residue 4 THR 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: 2.9990 chunk 190 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 229 optimal weight: 0.8980 chunk 247 optimal weight: 0.6980 chunk 204 optimal weight: 1.9990 chunk 227 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 183 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 29 GLN K 29 GLN L 29 GLN N 29 GLN O 29 GLN P 29 GLN R 29 GLN ** T 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 5 GLN W 5 GLN X 5 GLN Z 5 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20988 Z= 0.202 Angle : 0.566 7.434 28485 Z= 0.302 Chirality : 0.044 0.163 3204 Planarity : 0.004 0.032 3762 Dihedral : 4.600 27.448 2875 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.33 % Allowed : 15.42 % Favored : 83.24 % 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: -0.32 (0.16), residues: 2601 helix: 0.47 (0.18), residues: 765 sheet: 0.41 (0.19), residues: 756 loop : -1.12 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 237 HIS 0.001 0.001 HIS E 26 PHE 0.026 0.002 PHE C 144 TYR 0.019 0.001 TYR B 184 ARG 0.004 0.000 ARG P 8 *********************** 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 397 residues out of total 2250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 367 time to evaluate : 2.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 LYS cc_start: 0.8541 (ttmt) cc_final: 0.8033 (tptm) REVERT: A 230 ASP cc_start: 0.8681 (t70) cc_final: 0.8271 (t70) REVERT: B 22 LYS cc_start: 0.8434 (ttmt) cc_final: 0.8048 (tptm) REVERT: B 44 GLU cc_start: 0.8256 (mt-10) cc_final: 0.8004 (mt-10) REVERT: B 82 GLU cc_start: 0.7738 (tp30) cc_final: 0.7438 (tp30) REVERT: B 122 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.8061 (ptm) REVERT: B 238 ASP cc_start: 0.8242 (m-30) cc_final: 0.7899 (t0) REVERT: C 22 LYS cc_start: 0.8335 (ttmt) cc_final: 0.7986 (tptp) REVERT: C 37 SER cc_start: 0.9026 (m) cc_final: 0.8716 (p) REVERT: C 55 ASN cc_start: 0.8612 (m110) cc_final: 0.8246 (m-40) REVERT: D 22 LYS cc_start: 0.8372 (ttmt) cc_final: 0.8064 (tptm) REVERT: D 213 MET cc_start: 0.8127 (OUTLIER) cc_final: 0.7724 (ptt) REVERT: E 22 LYS cc_start: 0.8534 (ttmt) cc_final: 0.8182 (tptm) REVERT: E 37 SER cc_start: 0.9041 (m) cc_final: 0.8776 (p) REVERT: E 44 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8285 (mt-10) REVERT: E 51 TYR cc_start: 0.8496 (t80) cc_final: 0.8064 (t80) REVERT: E 135 LYS cc_start: 0.8436 (mttt) cc_final: 0.8232 (mttm) REVERT: E 193 PHE cc_start: 0.9215 (OUTLIER) cc_final: 0.7681 (t80) REVERT: E 201 GLU cc_start: 0.6722 (tm-30) cc_final: 0.5997 (tm-30) REVERT: F 22 LYS cc_start: 0.8409 (ttmt) cc_final: 0.8071 (tptm) REVERT: F 230 ASP cc_start: 0.8464 (t70) cc_final: 0.8059 (t70) REVERT: F 238 ASP cc_start: 0.8130 (m-30) cc_final: 0.7756 (t0) REVERT: G 22 LYS cc_start: 0.8498 (ttmt) cc_final: 0.8268 (tmtt) REVERT: G 122 MET cc_start: 0.8110 (ptp) cc_final: 0.7909 (ptm) REVERT: G 230 ASP cc_start: 0.8550 (t70) cc_final: 0.8302 (t70) REVERT: H 22 LYS cc_start: 0.8693 (ttmt) cc_final: 0.8251 (tptm) REVERT: H 217 MET cc_start: 0.8154 (tpp) cc_final: 0.7626 (tpp) REVERT: H 238 ASP cc_start: 0.7463 (t0) cc_final: 0.7234 (t0) REVERT: I 22 LYS cc_start: 0.8532 (ttmt) cc_final: 0.8147 (tptm) REVERT: I 42 GLN cc_start: 0.8038 (mp10) cc_final: 0.7782 (mt0) REVERT: I 43 ASP cc_start: 0.7951 (t70) cc_final: 0.7661 (t70) REVERT: I 44 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7623 (mt-10) REVERT: I 82 GLU cc_start: 0.7764 (tp30) cc_final: 0.7438 (tp30) REVERT: I 203 GLU cc_start: 0.7818 (tt0) cc_final: 0.7393 (tt0) REVERT: I 238 ASP cc_start: 0.7405 (t0) cc_final: 0.7194 (t0) REVERT: J 11 ASN cc_start: 0.8889 (m-40) cc_final: 0.8643 (m-40) REVERT: K 6 GLN cc_start: 0.8088 (mt0) cc_final: 0.7786 (mm-40) REVERT: K 27 GLN cc_start: 0.8837 (mt0) cc_final: 0.8551 (mm110) REVERT: P 4 THR cc_start: 0.8882 (m) cc_final: 0.8668 (p) REVERT: Q 27 GLN cc_start: 0.8921 (mt0) cc_final: 0.8681 (mm-40) REVERT: R 27 GLN cc_start: 0.8580 (mt0) cc_final: 0.8238 (mm110) REVERT: X 5 GLN cc_start: 0.7170 (OUTLIER) cc_final: 0.6861 (mp10) outliers start: 30 outliers final: 13 residues processed: 383 average time/residue: 0.3342 time to fit residues: 194.5997 Evaluate side-chains 347 residues out of total 2250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 330 time to evaluate : 2.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain D residue 213 MET Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 155 ASP Chi-restraints excluded: chain E residue 193 PHE Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain F residue 155 ASP Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain X residue 5 GLN Chi-restraints excluded: chain a residue 5 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 109 optimal weight: 0.4980 chunk 153 optimal weight: 0.0670 chunk 230 optimal weight: 3.9990 chunk 243 optimal weight: 4.9990 chunk 120 optimal weight: 0.9980 chunk 218 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 overall best weight: 1.3122 ------------------------------------------------------------------------------- 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 29 GLN M 29 GLN Q 29 GLN R 11 ASN U 5 GLN V 5 GLN W 5 GLN X 5 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20988 Z= 0.279 Angle : 0.604 7.916 28485 Z= 0.318 Chirality : 0.045 0.169 3204 Planarity : 0.004 0.047 3762 Dihedral : 4.660 23.610 2871 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.36 % Allowed : 17.16 % Favored : 80.49 % 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: 0.19 (0.17), residues: 2601 helix: 1.20 (0.19), residues: 765 sheet: 0.54 (0.19), residues: 756 loop : -0.93 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 237 HIS 0.002 0.001 HIS F 26 PHE 0.024 0.002 PHE D 144 TYR 0.021 0.001 TYR X 6 ARG 0.007 0.000 ARG P 8 *********************** 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 386 residues out of total 2250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 333 time to evaluate : 2.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 LYS cc_start: 0.8490 (ttmt) cc_final: 0.7956 (tptm) REVERT: A 49 LYS cc_start: 0.8687 (mttt) cc_final: 0.8317 (mtpp) REVERT: A 230 ASP cc_start: 0.8744 (t70) cc_final: 0.8354 (t70) REVERT: B 22 LYS cc_start: 0.8419 (ttmt) cc_final: 0.7999 (tptm) REVERT: B 113 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8791 (pp) REVERT: B 135 LYS cc_start: 0.8639 (mttt) cc_final: 0.8340 (mttp) REVERT: C 22 LYS cc_start: 0.8340 (ttmt) cc_final: 0.7987 (tptp) REVERT: C 37 SER cc_start: 0.9011 (m) cc_final: 0.8673 (p) REVERT: C 109 ASN cc_start: 0.8425 (m-40) cc_final: 0.8016 (m110) REVERT: D 22 LYS cc_start: 0.8362 (ttmt) cc_final: 0.8102 (tptp) REVERT: D 113 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8220 (pp) REVERT: D 213 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7749 (ptm) REVERT: D 256 MET cc_start: 0.7889 (ttm) cc_final: 0.7406 (mtt) REVERT: E 22 LYS cc_start: 0.8511 (ttmt) cc_final: 0.8134 (tptm) REVERT: E 37 SER cc_start: 0.9045 (m) cc_final: 0.8778 (p) REVERT: E 44 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8075 (mt-10) REVERT: E 51 TYR cc_start: 0.8483 (t80) cc_final: 0.8076 (t80) REVERT: E 67 MET cc_start: 0.9258 (mtt) cc_final: 0.9002 (mtt) REVERT: E 196 TYR cc_start: 0.8330 (t80) cc_final: 0.8034 (t80) REVERT: E 201 GLU cc_start: 0.6813 (tm-30) cc_final: 0.6113 (tm-30) REVERT: E 238 ASP cc_start: 0.8128 (m-30) cc_final: 0.7917 (m-30) REVERT: E 256 MET cc_start: 0.7977 (ttm) cc_final: 0.7776 (ttm) REVERT: F 22 LYS cc_start: 0.8368 (ttmt) cc_final: 0.8041 (tptm) REVERT: F 230 ASP cc_start: 0.8504 (t70) cc_final: 0.8159 (t70) REVERT: G 22 LYS cc_start: 0.8412 (ttmt) cc_final: 0.8137 (tmtt) REVERT: G 113 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8592 (pp) REVERT: G 122 MET cc_start: 0.8228 (ptp) cc_final: 0.7976 (ptm) REVERT: G 166 VAL cc_start: 0.9182 (OUTLIER) cc_final: 0.8929 (p) REVERT: G 230 ASP cc_start: 0.8590 (t70) cc_final: 0.8362 (t70) REVERT: G 245 ARG cc_start: 0.8406 (ttm-80) cc_final: 0.8119 (ttm-80) REVERT: H 22 LYS cc_start: 0.8691 (ttmt) cc_final: 0.8168 (tptm) REVERT: H 113 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8606 (pp) REVERT: H 238 ASP cc_start: 0.7618 (t0) cc_final: 0.7335 (t0) REVERT: I 22 LYS cc_start: 0.8389 (ttmt) cc_final: 0.8046 (tptm) REVERT: I 42 GLN cc_start: 0.8132 (mp10) cc_final: 0.7847 (mt0) REVERT: I 43 ASP cc_start: 0.7994 (t70) cc_final: 0.7703 (t70) REVERT: I 44 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7598 (mt-10) REVERT: I 113 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8788 (pp) REVERT: I 203 GLU cc_start: 0.7811 (tt0) cc_final: 0.7353 (tt0) REVERT: I 238 ASP cc_start: 0.7435 (t0) cc_final: 0.7228 (t0) REVERT: J 11 ASN cc_start: 0.8967 (m-40) cc_final: 0.8702 (m-40) REVERT: K 6 GLN cc_start: 0.7865 (mt0) cc_final: 0.7625 (mm-40) REVERT: K 27 GLN cc_start: 0.8881 (mt0) cc_final: 0.8560 (mm110) REVERT: Q 27 GLN cc_start: 0.8948 (mt0) cc_final: 0.8714 (mm-40) REVERT: R 27 GLN cc_start: 0.8620 (mt0) cc_final: 0.8303 (mm-40) REVERT: V 5 GLN cc_start: 0.7186 (mt0) cc_final: 0.6736 (mt0) REVERT: W 5 GLN cc_start: 0.7340 (OUTLIER) cc_final: 0.7119 (mt0) outliers start: 53 outliers final: 31 residues processed: 359 average time/residue: 0.3256 time to fit residues: 178.6105 Evaluate side-chains 354 residues out of total 2250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 315 time to evaluate : 2.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain D residue 213 MET Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 155 ASP Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 155 ASP Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 122 MET Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 155 ASP Chi-restraints excluded: chain I residue 230 ASP Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain L residue 11 ASN Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain O residue 6 GLN Chi-restraints excluded: chain R residue 4 THR Chi-restraints excluded: chain R residue 11 ASN Chi-restraints excluded: chain W residue 5 GLN Chi-restraints excluded: chain a residue 5 GLN 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: 0.8980 chunk 181 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 207 optimal weight: 0.7980 chunk 168 optimal weight: 0.0670 chunk 0 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 218 optimal weight: 0.0270 chunk 61 optimal weight: 3.9990 overall best weight: 0.5376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 11 ASN M 29 GLN R 11 ASN W 5 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2946 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= 0.161 Angle : 0.535 6.905 28485 Z= 0.283 Chirality : 0.044 0.155 3204 Planarity : 0.003 0.029 3762 Dihedral : 4.435 26.254 2871 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.09 % Allowed : 18.04 % Favored : 79.87 % 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: 0.60 (0.17), residues: 2601 helix: 1.67 (0.20), residues: 765 sheet: 0.65 (0.19), residues: 765 loop : -0.69 (0.19), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 77 HIS 0.001 0.000 HIS H 255 PHE 0.019 0.001 PHE D 144 TYR 0.019 0.001 TYR H 184 ARG 0.008 0.000 ARG P 8 *********************** 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 381 residues out of total 2250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 334 time to evaluate : 2.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 LYS cc_start: 0.8456 (ttmt) cc_final: 0.7947 (tptm) REVERT: A 230 ASP cc_start: 0.8704 (t70) cc_final: 0.8308 (t70) REVERT: A 241 ASN cc_start: 0.8235 (OUTLIER) cc_final: 0.7887 (m-40) REVERT: B 22 LYS cc_start: 0.8392 (ttmt) cc_final: 0.7990 (tptm) REVERT: B 82 GLU cc_start: 0.7857 (tp30) cc_final: 0.7458 (tp30) REVERT: B 122 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7990 (ptm) REVERT: C 22 LYS cc_start: 0.8360 (ttmt) cc_final: 0.8023 (tptp) REVERT: C 37 SER cc_start: 0.9028 (m) cc_final: 0.8505 (p) REVERT: C 109 ASN cc_start: 0.8370 (m-40) cc_final: 0.7971 (m110) REVERT: D 22 LYS cc_start: 0.8386 (ttmt) cc_final: 0.8053 (tptm) REVERT: D 213 MET cc_start: 0.8093 (ptp) cc_final: 0.7707 (ptt) REVERT: D 256 MET cc_start: 0.7870 (ttm) cc_final: 0.7432 (mtp) REVERT: E 22 LYS cc_start: 0.8509 (ttmt) cc_final: 0.8106 (tptm) REVERT: E 37 SER cc_start: 0.9019 (m) cc_final: 0.8775 (p) REVERT: E 44 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8166 (mt-10) REVERT: E 51 TYR cc_start: 0.8456 (t80) cc_final: 0.8055 (t80) REVERT: E 192 ARG cc_start: 0.7891 (ttp80) cc_final: 0.7512 (ttt180) REVERT: E 201 GLU cc_start: 0.6640 (tm-30) cc_final: 0.5836 (tm-30) REVERT: E 238 ASP cc_start: 0.8108 (m-30) cc_final: 0.7896 (m-30) REVERT: F 22 LYS cc_start: 0.8337 (ttmt) cc_final: 0.8015 (tptm) REVERT: F 230 ASP cc_start: 0.8504 (t70) cc_final: 0.8137 (t70) REVERT: G 22 LYS cc_start: 0.8354 (ttmt) cc_final: 0.8142 (tmtt) REVERT: G 113 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8623 (pp) REVERT: G 122 MET cc_start: 0.8188 (ptp) cc_final: 0.7918 (ptm) REVERT: G 166 VAL cc_start: 0.9130 (OUTLIER) cc_final: 0.8907 (p) REVERT: G 230 ASP cc_start: 0.8552 (t70) cc_final: 0.8319 (t70) REVERT: G 245 ARG cc_start: 0.8212 (ttm-80) cc_final: 0.7729 (ttm-80) REVERT: H 22 LYS cc_start: 0.8665 (ttmt) cc_final: 0.8152 (tptm) REVERT: H 44 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7401 (mt-10) REVERT: H 113 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8588 (pp) REVERT: H 238 ASP cc_start: 0.7589 (t0) cc_final: 0.7312 (t0) REVERT: I 22 LYS cc_start: 0.8342 (ttmt) cc_final: 0.8003 (tptm) REVERT: I 43 ASP cc_start: 0.8008 (t70) cc_final: 0.7763 (t70) REVERT: I 44 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7759 (mt-10) REVERT: I 113 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8728 (pp) REVERT: I 166 VAL cc_start: 0.9034 (OUTLIER) cc_final: 0.8769 (p) REVERT: I 203 GLU cc_start: 0.7804 (tt0) cc_final: 0.7259 (tt0) REVERT: J 11 ASN cc_start: 0.8850 (m-40) cc_final: 0.8625 (m-40) REVERT: K 27 GLN cc_start: 0.8843 (mt0) cc_final: 0.8577 (mm110) REVERT: Q 11 ASN cc_start: 0.8904 (m-40) cc_final: 0.8693 (m-40) REVERT: Q 27 GLN cc_start: 0.8908 (mt0) cc_final: 0.8696 (mm-40) REVERT: R 27 GLN cc_start: 0.8647 (mt0) cc_final: 0.8333 (mm-40) REVERT: V 5 GLN cc_start: 0.7154 (mt0) cc_final: 0.6723 (mt0) outliers start: 47 outliers final: 31 residues processed: 359 average time/residue: 0.3261 time to fit residues: 179.6428 Evaluate side-chains 352 residues out of total 2250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 314 time to evaluate : 2.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 155 ASP Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 155 ASP Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 122 MET Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 155 ASP Chi-restraints excluded: chain I residue 166 VAL Chi-restraints excluded: chain I residue 201 GLU Chi-restraints excluded: chain I residue 258 VAL Chi-restraints excluded: chain L residue 11 ASN Chi-restraints excluded: chain M residue 29 GLN Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain O residue 2 THR Chi-restraints excluded: chain R residue 4 THR Chi-restraints excluded: chain R residue 11 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 0.6980 chunk 219 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 243 optimal weight: 2.9990 chunk 202 optimal weight: 1.9990 chunk 112 optimal weight: 0.0010 chunk 20 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 128 optimal weight: 0.8980 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 27 GLN L 11 ASN M 29 GLN Y 5 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20988 Z= 0.178 Angle : 0.547 11.867 28485 Z= 0.286 Chirality : 0.044 0.155 3204 Planarity : 0.003 0.027 3762 Dihedral : 4.350 24.992 2871 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.89 % Allowed : 17.38 % Favored : 79.73 % 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: 0.88 (0.17), residues: 2601 helix: 1.93 (0.20), residues: 765 sheet: 0.84 (0.19), residues: 756 loop : -0.57 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 77 HIS 0.001 0.000 HIS E 26 PHE 0.020 0.001 PHE D 144 TYR 0.016 0.001 TYR H 184 ARG 0.005 0.000 ARG P 8 *********************** 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 397 residues out of total 2250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 332 time to evaluate : 2.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 LYS cc_start: 0.8473 (ttmt) cc_final: 0.7997 (tptm) REVERT: A 203 GLU cc_start: 0.7769 (tt0) cc_final: 0.7407 (tt0) REVERT: A 230 ASP cc_start: 0.8717 (t70) cc_final: 0.8321 (t70) REVERT: A 241 ASN cc_start: 0.8232 (OUTLIER) cc_final: 0.7886 (m-40) REVERT: B 22 LYS cc_start: 0.8392 (ttmt) cc_final: 0.7970 (tptm) REVERT: B 82 GLU cc_start: 0.7872 (tp30) cc_final: 0.7506 (tp30) REVERT: B 113 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8749 (pp) REVERT: B 122 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.8030 (ptm) REVERT: B 213 MET cc_start: 0.8499 (ptp) cc_final: 0.8102 (ptp) REVERT: C 22 LYS cc_start: 0.8341 (ttmt) cc_final: 0.8012 (tptp) REVERT: C 37 SER cc_start: 0.8985 (m) cc_final: 0.8685 (p) REVERT: C 39 TYR cc_start: 0.8940 (m-80) cc_final: 0.8658 (m-80) REVERT: C 109 ASN cc_start: 0.8325 (m-40) cc_final: 0.7938 (m110) REVERT: D 22 LYS cc_start: 0.8371 (ttmt) cc_final: 0.8046 (tptm) REVERT: D 113 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8238 (pp) REVERT: D 213 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7701 (ptt) REVERT: D 245 ARG cc_start: 0.8041 (ttm110) cc_final: 0.7779 (mtt-85) REVERT: D 256 MET cc_start: 0.7797 (ttm) cc_final: 0.7355 (mtp) REVERT: E 22 LYS cc_start: 0.8493 (ttmt) cc_final: 0.8093 (tptm) REVERT: E 37 SER cc_start: 0.9017 (m) cc_final: 0.8776 (p) REVERT: E 51 TYR cc_start: 0.8459 (t80) cc_final: 0.8059 (t80) REVERT: E 192 ARG cc_start: 0.7877 (ttp80) cc_final: 0.7519 (ttt180) REVERT: E 201 GLU cc_start: 0.6641 (tm-30) cc_final: 0.5814 (tm-30) REVERT: E 238 ASP cc_start: 0.8102 (m-30) cc_final: 0.7532 (t0) REVERT: F 22 LYS cc_start: 0.8258 (ttmt) cc_final: 0.7908 (tptm) REVERT: F 166 VAL cc_start: 0.9058 (OUTLIER) cc_final: 0.8815 (p) REVERT: F 230 ASP cc_start: 0.8438 (t70) cc_final: 0.8090 (t70) REVERT: G 22 LYS cc_start: 0.8312 (ttmt) cc_final: 0.8110 (tmtt) REVERT: G 113 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8608 (pp) REVERT: G 122 MET cc_start: 0.8245 (ptp) cc_final: 0.7972 (ptm) REVERT: G 166 VAL cc_start: 0.9129 (OUTLIER) cc_final: 0.8904 (p) REVERT: G 230 ASP cc_start: 0.8561 (t70) cc_final: 0.8323 (t70) REVERT: G 238 ASP cc_start: 0.6883 (t0) cc_final: 0.6607 (t0) REVERT: G 245 ARG cc_start: 0.8193 (ttm-80) cc_final: 0.7680 (ttm-80) REVERT: H 22 LYS cc_start: 0.8660 (ttmt) cc_final: 0.8145 (tptm) REVERT: H 44 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7405 (mt-10) REVERT: H 113 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8629 (pp) REVERT: H 238 ASP cc_start: 0.7634 (t0) cc_final: 0.7241 (t0) REVERT: I 22 LYS cc_start: 0.8330 (ttmt) cc_final: 0.7992 (tptm) REVERT: I 42 GLN cc_start: 0.7993 (mp10) cc_final: 0.7746 (mt0) REVERT: I 43 ASP cc_start: 0.8004 (t70) cc_final: 0.7760 (t70) REVERT: I 44 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7606 (mt-10) REVERT: I 113 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8736 (pp) REVERT: I 166 VAL cc_start: 0.9050 (OUTLIER) cc_final: 0.8798 (p) REVERT: I 203 GLU cc_start: 0.7722 (tt0) cc_final: 0.7175 (tt0) REVERT: J 11 ASN cc_start: 0.8881 (m-40) cc_final: 0.8661 (m-40) REVERT: K 6 GLN cc_start: 0.7813 (mt0) cc_final: 0.7569 (mm-40) REVERT: K 27 GLN cc_start: 0.8838 (mt0) cc_final: 0.8625 (mm-40) REVERT: K 32 TYR cc_start: 0.8423 (m-80) cc_final: 0.8043 (m-80) REVERT: Q 11 ASN cc_start: 0.8919 (m-40) cc_final: 0.8700 (m-40) REVERT: Q 27 GLN cc_start: 0.8909 (mt0) cc_final: 0.8706 (mm-40) REVERT: R 27 GLN cc_start: 0.8656 (mt0) cc_final: 0.8351 (mm-40) REVERT: V 5 GLN cc_start: 0.7269 (mt0) cc_final: 0.6889 (mt0) outliers start: 65 outliers final: 41 residues processed: 373 average time/residue: 0.3212 time to fit residues: 184.4634 Evaluate side-chains 372 residues out of total 2250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 320 time to evaluate : 2.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 213 MET Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 155 ASP Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 155 ASP Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 155 ASP Chi-restraints excluded: chain I residue 166 VAL Chi-restraints excluded: chain I residue 201 GLU Chi-restraints excluded: chain I residue 258 VAL Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain L residue 11 ASN Chi-restraints excluded: chain M residue 29 GLN Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain O residue 2 THR Chi-restraints excluded: chain Q residue 31 SER Chi-restraints excluded: chain R residue 4 THR Chi-restraints excluded: chain a residue 5 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 178 optimal weight: 0.4980 chunk 137 optimal weight: 3.9990 chunk 205 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 242 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 29 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 20988 Z= 0.295 Angle : 0.613 12.184 28485 Z= 0.320 Chirality : 0.045 0.170 3204 Planarity : 0.004 0.031 3762 Dihedral : 4.596 24.293 2871 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.89 % Allowed : 17.69 % Favored : 79.42 % 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: 0.89 (0.17), residues: 2601 helix: 1.95 (0.20), residues: 765 sheet: 0.78 (0.19), residues: 756 loop : -0.52 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 77 HIS 0.002 0.001 HIS F 26 PHE 0.022 0.002 PHE E 144 TYR 0.016 0.001 TYR H 184 ARG 0.005 0.000 ARG P 8 *********************** 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 394 residues out of total 2250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 329 time to evaluate : 2.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 LYS cc_start: 0.8494 (ttmt) cc_final: 0.7894 (tptm) REVERT: A 230 ASP cc_start: 0.8767 (t70) cc_final: 0.8375 (t70) REVERT: B 22 LYS cc_start: 0.8394 (ttmt) cc_final: 0.7958 (tptm) REVERT: B 82 GLU cc_start: 0.7932 (tp30) cc_final: 0.7495 (tp30) REVERT: B 113 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8780 (pp) REVERT: B 135 LYS cc_start: 0.8656 (mttt) cc_final: 0.8351 (mttp) REVERT: B 213 MET cc_start: 0.8454 (ptp) cc_final: 0.8096 (ptp) REVERT: C 22 LYS cc_start: 0.8343 (ttmt) cc_final: 0.8014 (tptp) REVERT: C 37 SER cc_start: 0.9016 (m) cc_final: 0.8737 (p) REVERT: C 109 ASN cc_start: 0.8319 (m-40) cc_final: 0.7910 (m110) REVERT: C 256 MET cc_start: 0.7776 (ttm) cc_final: 0.7399 (ttt) REVERT: D 22 LYS cc_start: 0.8381 (ttmt) cc_final: 0.8094 (tptp) REVERT: D 51 TYR cc_start: 0.8677 (t80) cc_final: 0.8281 (t80) REVERT: D 113 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8323 (pp) REVERT: D 213 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7790 (ptt) REVERT: D 256 MET cc_start: 0.7837 (ttm) cc_final: 0.7374 (mtp) REVERT: E 22 LYS cc_start: 0.8493 (ttmt) cc_final: 0.8084 (tptm) REVERT: E 44 GLU cc_start: 0.8361 (mt-10) cc_final: 0.8013 (mt-10) REVERT: E 51 TYR cc_start: 0.8497 (t80) cc_final: 0.8128 (t80) REVERT: E 201 GLU cc_start: 0.6871 (tm-30) cc_final: 0.6043 (tm-30) REVERT: E 238 ASP cc_start: 0.8227 (m-30) cc_final: 0.7587 (t0) REVERT: F 22 LYS cc_start: 0.8270 (ttmt) cc_final: 0.7926 (tptm) REVERT: F 230 ASP cc_start: 0.8564 (t70) cc_final: 0.8236 (t70) REVERT: G 22 LYS cc_start: 0.8333 (ttmt) cc_final: 0.8125 (tmtt) REVERT: G 113 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8625 (pp) REVERT: G 122 MET cc_start: 0.8273 (ptp) cc_final: 0.8006 (ptm) REVERT: G 166 VAL cc_start: 0.9191 (OUTLIER) cc_final: 0.8946 (p) REVERT: G 230 ASP cc_start: 0.8609 (t70) cc_final: 0.8383 (t70) REVERT: G 238 ASP cc_start: 0.7150 (t0) cc_final: 0.6808 (t0) REVERT: G 245 ARG cc_start: 0.8324 (ttm-80) cc_final: 0.7805 (ttm-80) REVERT: H 22 LYS cc_start: 0.8667 (ttmt) cc_final: 0.8143 (tptm) REVERT: H 44 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7535 (mt-10) REVERT: H 238 ASP cc_start: 0.7417 (t0) cc_final: 0.7094 (t0) REVERT: I 22 LYS cc_start: 0.8302 (ttmt) cc_final: 0.7980 (tptm) REVERT: I 42 GLN cc_start: 0.8092 (mp10) cc_final: 0.7800 (mt0) REVERT: I 43 ASP cc_start: 0.8019 (t70) cc_final: 0.7726 (t70) REVERT: I 44 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7642 (mt-10) REVERT: I 113 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8788 (pp) REVERT: I 166 VAL cc_start: 0.9120 (OUTLIER) cc_final: 0.8829 (p) REVERT: I 203 GLU cc_start: 0.7791 (tt0) cc_final: 0.7349 (tt0) REVERT: J 11 ASN cc_start: 0.8972 (m-40) cc_final: 0.8706 (m-40) REVERT: K 6 GLN cc_start: 0.7827 (mt0) cc_final: 0.7594 (mm-40) REVERT: K 27 GLN cc_start: 0.8912 (mt0) cc_final: 0.8671 (mm-40) REVERT: Q 27 GLN cc_start: 0.8973 (mt0) cc_final: 0.8757 (mm-40) REVERT: R 27 GLN cc_start: 0.8627 (mt0) cc_final: 0.8348 (mm-40) outliers start: 65 outliers final: 49 residues processed: 370 average time/residue: 0.3251 time to fit residues: 184.2410 Evaluate side-chains 379 residues out of total 2250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 323 time to evaluate : 2.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 213 MET Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 155 ASP Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 155 ASP Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 155 ASP Chi-restraints excluded: chain I residue 166 VAL Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 201 GLU Chi-restraints excluded: chain I residue 230 ASP Chi-restraints excluded: chain I residue 258 VAL Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain L residue 11 ASN Chi-restraints excluded: chain M residue 29 GLN Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain O residue 2 THR Chi-restraints excluded: chain O residue 6 GLN Chi-restraints excluded: chain P residue 4 THR Chi-restraints excluded: chain Q residue 31 SER Chi-restraints excluded: chain R residue 4 THR Chi-restraints excluded: chain a residue 5 GLN 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: 2.9990 chunk 145 optimal weight: 2.9990 chunk 73 optimal weight: 0.0770 chunk 47 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 190 optimal weight: 1.9990 chunk 220 optimal weight: 0.9980 overall best weight: 0.9740 ------------------------------------------------------------------------------- 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 L 11 ASN M 29 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20988 Z= 0.225 Angle : 0.580 11.357 28485 Z= 0.304 Chirality : 0.044 0.161 3204 Planarity : 0.003 0.029 3762 Dihedral : 4.524 25.523 2871 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.76 % Allowed : 18.18 % Favored : 79.07 % 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: 1.00 (0.17), residues: 2601 helix: 2.07 (0.20), residues: 765 sheet: 0.83 (0.19), residues: 756 loop : -0.46 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 77 HIS 0.001 0.001 HIS F 26 PHE 0.022 0.001 PHE R 5 TYR 0.017 0.001 TYR E 184 ARG 0.007 0.000 ARG I 245 *********************** 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 387 residues out of total 2250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 325 time to evaluate : 2.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 LYS cc_start: 0.8467 (ttmt) cc_final: 0.7945 (tptm) REVERT: A 143 TYR cc_start: 0.8424 (t80) cc_final: 0.8099 (t80) REVERT: A 230 ASP cc_start: 0.8747 (t70) cc_final: 0.8352 (t70) REVERT: B 22 LYS cc_start: 0.8384 (ttmt) cc_final: 0.7953 (tptm) REVERT: B 82 GLU cc_start: 0.7925 (tp30) cc_final: 0.7495 (tp30) REVERT: B 113 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8782 (pp) REVERT: B 135 LYS cc_start: 0.8712 (mttt) cc_final: 0.8409 (mttp) REVERT: B 213 MET cc_start: 0.8432 (ptp) cc_final: 0.8089 (ptp) REVERT: B 245 ARG cc_start: 0.7531 (ttm-80) cc_final: 0.7284 (ttm-80) REVERT: C 22 LYS cc_start: 0.8334 (ttmt) cc_final: 0.8006 (tptp) REVERT: C 37 SER cc_start: 0.9050 (m) cc_final: 0.8773 (p) REVERT: C 109 ASN cc_start: 0.8241 (m-40) cc_final: 0.7884 (m110) REVERT: C 256 MET cc_start: 0.7782 (ttm) cc_final: 0.7401 (ttt) REVERT: D 22 LYS cc_start: 0.8379 (ttmt) cc_final: 0.8023 (tptm) REVERT: D 51 TYR cc_start: 0.8650 (t80) cc_final: 0.8252 (t80) REVERT: D 113 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8350 (pp) REVERT: D 213 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.7679 (ptt) REVERT: D 256 MET cc_start: 0.7824 (ttm) cc_final: 0.7358 (mtp) REVERT: E 22 LYS cc_start: 0.8485 (ttmt) cc_final: 0.8085 (tptm) REVERT: E 51 TYR cc_start: 0.8496 (t80) cc_final: 0.8170 (t80) REVERT: E 192 ARG cc_start: 0.7954 (ttp80) cc_final: 0.7560 (ttt180) REVERT: E 193 PHE cc_start: 0.9200 (OUTLIER) cc_final: 0.7555 (t80) REVERT: E 201 GLU cc_start: 0.6843 (tm-30) cc_final: 0.5986 (tm-30) REVERT: E 238 ASP cc_start: 0.8228 (m-30) cc_final: 0.7605 (t0) REVERT: F 22 LYS cc_start: 0.8290 (ttmt) cc_final: 0.7954 (tptm) REVERT: F 230 ASP cc_start: 0.8549 (t70) cc_final: 0.8218 (t70) REVERT: G 22 LYS cc_start: 0.8336 (ttmt) cc_final: 0.8104 (tmtt) REVERT: G 113 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8621 (pp) REVERT: G 122 MET cc_start: 0.8302 (ptp) cc_final: 0.8039 (ptm) REVERT: G 166 VAL cc_start: 0.9153 (OUTLIER) cc_final: 0.8876 (p) REVERT: G 230 ASP cc_start: 0.8593 (t70) cc_final: 0.8369 (t70) REVERT: G 238 ASP cc_start: 0.7205 (t0) cc_final: 0.6853 (t0) REVERT: G 245 ARG cc_start: 0.8286 (ttm-80) cc_final: 0.7750 (ttm-80) REVERT: H 22 LYS cc_start: 0.8659 (ttmt) cc_final: 0.8138 (tptm) REVERT: H 44 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7502 (mt-10) REVERT: H 238 ASP cc_start: 0.7408 (t0) cc_final: 0.7080 (t0) REVERT: I 22 LYS cc_start: 0.8307 (ttmt) cc_final: 0.7998 (tptm) REVERT: I 42 GLN cc_start: 0.8066 (mp10) cc_final: 0.7772 (mt0) REVERT: I 43 ASP cc_start: 0.8081 (t70) cc_final: 0.7826 (t70) REVERT: I 44 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7608 (mt-10) REVERT: I 113 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8730 (pp) REVERT: I 166 VAL cc_start: 0.9114 (OUTLIER) cc_final: 0.8833 (p) REVERT: I 203 GLU cc_start: 0.7768 (tt0) cc_final: 0.7387 (tt0) REVERT: J 11 ASN cc_start: 0.8918 (m-40) cc_final: 0.8697 (m-40) REVERT: K 6 GLN cc_start: 0.7821 (mt0) cc_final: 0.7578 (mm-40) REVERT: K 27 GLN cc_start: 0.8896 (mt0) cc_final: 0.8659 (mm-40) REVERT: K 32 TYR cc_start: 0.8457 (m-80) cc_final: 0.8070 (m-80) REVERT: Q 27 GLN cc_start: 0.8959 (mt0) cc_final: 0.8751 (mm-40) REVERT: R 27 GLN cc_start: 0.8600 (mt0) cc_final: 0.8336 (mm-40) outliers start: 62 outliers final: 50 residues processed: 362 average time/residue: 0.3279 time to fit residues: 181.5721 Evaluate side-chains 373 residues out of total 2250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 315 time to evaluate : 2.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 213 MET Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 155 ASP Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 193 PHE Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 155 ASP Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 155 ASP Chi-restraints excluded: chain I residue 166 VAL Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 201 GLU Chi-restraints excluded: chain I residue 258 VAL Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain L residue 11 ASN Chi-restraints excluded: chain M residue 29 GLN Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain O residue 2 THR Chi-restraints excluded: chain O residue 6 GLN Chi-restraints excluded: chain P residue 4 THR Chi-restraints excluded: chain Q residue 31 SER Chi-restraints excluded: chain a residue 5 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 0.0970 chunk 212 optimal weight: 4.9990 chunk 226 optimal weight: 0.1980 chunk 136 optimal weight: 4.9990 chunk 98 optimal weight: 0.3980 chunk 177 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 204 optimal weight: 5.9990 chunk 214 optimal weight: 1.9990 chunk 225 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 L 11 ASN ** Q 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3167 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= 0.218 Angle : 0.573 11.167 28485 Z= 0.301 Chirality : 0.044 0.161 3204 Planarity : 0.003 0.030 3762 Dihedral : 4.493 24.809 2871 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.71 % Allowed : 18.44 % Favored : 78.84 % 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: 1.06 (0.17), residues: 2601 helix: 2.16 (0.20), residues: 765 sheet: 0.85 (0.20), residues: 756 loop : -0.45 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 77 HIS 0.001 0.001 HIS F 26 PHE 0.022 0.001 PHE R 5 TYR 0.017 0.001 TYR E 184 ARG 0.006 0.000 ARG P 8 *********************** 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 378 residues out of total 2250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 317 time to evaluate : 2.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 LYS cc_start: 0.8462 (ttmt) cc_final: 0.7944 (tptm) REVERT: A 143 TYR cc_start: 0.8412 (t80) cc_final: 0.8096 (t80) REVERT: A 230 ASP cc_start: 0.8745 (t70) cc_final: 0.8353 (t70) REVERT: B 22 LYS cc_start: 0.8344 (ttmt) cc_final: 0.7901 (tptm) REVERT: B 82 GLU cc_start: 0.7929 (tp30) cc_final: 0.7502 (tp30) REVERT: B 113 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8774 (pp) REVERT: B 213 MET cc_start: 0.8431 (ptp) cc_final: 0.8095 (ptp) REVERT: B 245 ARG cc_start: 0.7494 (ttm-80) cc_final: 0.7286 (ttm-80) REVERT: C 22 LYS cc_start: 0.8321 (ttmt) cc_final: 0.7997 (tptp) REVERT: C 37 SER cc_start: 0.9050 (m) cc_final: 0.8783 (p) REVERT: C 109 ASN cc_start: 0.8292 (m-40) cc_final: 0.7920 (m110) REVERT: C 256 MET cc_start: 0.7694 (ttm) cc_final: 0.7315 (ttt) REVERT: D 22 LYS cc_start: 0.8375 (ttmt) cc_final: 0.8089 (tptp) REVERT: D 51 TYR cc_start: 0.8673 (t80) cc_final: 0.8292 (t80) REVERT: D 113 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8350 (pp) REVERT: D 213 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7655 (ptt) REVERT: D 256 MET cc_start: 0.7816 (ttm) cc_final: 0.7343 (mtp) REVERT: E 22 LYS cc_start: 0.8484 (ttmt) cc_final: 0.8094 (tptm) REVERT: E 44 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7984 (mt-10) REVERT: E 51 TYR cc_start: 0.8495 (t80) cc_final: 0.8178 (t80) REVERT: E 192 ARG cc_start: 0.7945 (ttp80) cc_final: 0.7550 (ttt180) REVERT: E 193 PHE cc_start: 0.9230 (OUTLIER) cc_final: 0.7633 (t80) REVERT: E 201 GLU cc_start: 0.6720 (tm-30) cc_final: 0.5871 (tm-30) REVERT: F 22 LYS cc_start: 0.8286 (ttmt) cc_final: 0.7952 (tptm) REVERT: F 230 ASP cc_start: 0.8548 (t70) cc_final: 0.8218 (t70) REVERT: G 22 LYS cc_start: 0.8323 (ttmt) cc_final: 0.8099 (tmtt) REVERT: G 113 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8615 (pp) REVERT: G 122 MET cc_start: 0.8304 (ptp) cc_final: 0.8045 (ptm) REVERT: G 166 VAL cc_start: 0.9159 (OUTLIER) cc_final: 0.8884 (p) REVERT: G 230 ASP cc_start: 0.8592 (t70) cc_final: 0.8364 (t70) REVERT: G 238 ASP cc_start: 0.7283 (t0) cc_final: 0.6961 (t0) REVERT: G 245 ARG cc_start: 0.8270 (ttm-80) cc_final: 0.7773 (ttm-80) REVERT: H 22 LYS cc_start: 0.8656 (ttmt) cc_final: 0.8136 (tptm) REVERT: H 44 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7506 (mt-10) REVERT: H 238 ASP cc_start: 0.7500 (t0) cc_final: 0.7182 (t0) REVERT: I 22 LYS cc_start: 0.8324 (ttmt) cc_final: 0.8028 (tptm) REVERT: I 42 GLN cc_start: 0.8066 (mp10) cc_final: 0.7769 (mt0) REVERT: I 43 ASP cc_start: 0.8074 (t70) cc_final: 0.7798 (t70) REVERT: I 44 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7603 (mt-10) REVERT: I 113 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8734 (pp) REVERT: I 166 VAL cc_start: 0.9111 (OUTLIER) cc_final: 0.8830 (p) REVERT: I 203 GLU cc_start: 0.7769 (tt0) cc_final: 0.7403 (tt0) REVERT: J 11 ASN cc_start: 0.8909 (m-40) cc_final: 0.8692 (m-40) REVERT: K 6 GLN cc_start: 0.7824 (mt0) cc_final: 0.7586 (mm-40) REVERT: K 27 GLN cc_start: 0.8898 (mt0) cc_final: 0.8666 (mm-40) REVERT: K 32 TYR cc_start: 0.8477 (m-80) cc_final: 0.8134 (m-80) REVERT: L 25 SER cc_start: 0.9052 (p) cc_final: 0.8824 (p) REVERT: Q 27 GLN cc_start: 0.8959 (mt0) cc_final: 0.8755 (mm-40) REVERT: R 27 GLN cc_start: 0.8599 (mt0) cc_final: 0.8334 (mm-40) outliers start: 61 outliers final: 50 residues processed: 352 average time/residue: 0.3186 time to fit residues: 172.3804 Evaluate side-chains 377 residues out of total 2250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 319 time to evaluate : 2.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 213 MET Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 155 ASP Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 193 PHE Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 155 ASP Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 213 MET Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 155 ASP Chi-restraints excluded: chain I residue 166 VAL Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 201 GLU Chi-restraints excluded: chain I residue 258 VAL Chi-restraints excluded: chain J residue 2 THR Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain L residue 11 ASN Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain O residue 2 THR Chi-restraints excluded: chain O residue 6 GLN Chi-restraints excluded: chain P residue 4 THR Chi-restraints excluded: chain Q residue 31 SER Chi-restraints excluded: chain a residue 5 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 chunk 251 optimal weight: 0.8980 chunk 231 optimal weight: 3.9990 chunk 199 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 154 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 109 ASN F 100 GLN L 11 ASN L 27 GLN M 29 GLN ** Q 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 20988 Z= 0.310 Angle : 0.625 11.825 28485 Z= 0.327 Chirality : 0.046 0.170 3204 Planarity : 0.004 0.033 3762 Dihedral : 4.685 25.520 2871 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.80 % Allowed : 18.53 % Favored : 78.67 % 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: 0.81 (0.17), residues: 2601 helix: 1.89 (0.20), residues: 783 sheet: 0.77 (0.20), residues: 756 loop : -0.65 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 237 HIS 0.002 0.001 HIS F 26 PHE 0.023 0.002 PHE R 5 TYR 0.018 0.001 TYR E 184 ARG 0.006 0.000 ARG D 142 ********************** 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 379 residues out of total 2250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 316 time to evaluate : 2.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 LYS cc_start: 0.8468 (ttmt) cc_final: 0.7905 (tptm) REVERT: A 143 TYR cc_start: 0.8450 (t80) cc_final: 0.8141 (t80) REVERT: A 230 ASP cc_start: 0.8784 (t70) cc_final: 0.8398 (t70) REVERT: B 22 LYS cc_start: 0.8348 (ttmt) cc_final: 0.7899 (tptm) REVERT: B 82 GLU cc_start: 0.7928 (tp30) cc_final: 0.7457 (tp30) REVERT: B 113 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8749 (pp) REVERT: B 135 LYS cc_start: 0.8692 (mttt) cc_final: 0.8371 (mttp) REVERT: B 213 MET cc_start: 0.8490 (ptp) cc_final: 0.8139 (ptp) REVERT: B 245 ARG cc_start: 0.7557 (ttm-80) cc_final: 0.7353 (ttm-80) REVERT: B 256 MET cc_start: 0.7657 (ttm) cc_final: 0.7367 (ttt) REVERT: C 22 LYS cc_start: 0.8258 (ttmt) cc_final: 0.7914 (tptp) REVERT: C 109 ASN cc_start: 0.8258 (m-40) cc_final: 0.7917 (m110) REVERT: C 214 LEU cc_start: 0.8256 (tp) cc_final: 0.7760 (mt) REVERT: C 256 MET cc_start: 0.7828 (ttm) cc_final: 0.7446 (ttt) REVERT: D 22 LYS cc_start: 0.8378 (ttmt) cc_final: 0.8086 (tptp) REVERT: D 51 TYR cc_start: 0.8678 (t80) cc_final: 0.8287 (t80) REVERT: D 213 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7718 (ptt) REVERT: D 256 MET cc_start: 0.7831 (ttm) cc_final: 0.7351 (mtp) REVERT: E 22 LYS cc_start: 0.8493 (ttmt) cc_final: 0.8083 (tptm) REVERT: E 44 GLU cc_start: 0.8260 (mt-10) cc_final: 0.8015 (mt-10) REVERT: E 51 TYR cc_start: 0.8482 (t80) cc_final: 0.8148 (t80) REVERT: E 193 PHE cc_start: 0.9235 (OUTLIER) cc_final: 0.7545 (t80) REVERT: E 201 GLU cc_start: 0.6887 (tm-30) cc_final: 0.6087 (tm-30) REVERT: F 22 LYS cc_start: 0.8297 (ttmt) cc_final: 0.8029 (tptm) REVERT: F 230 ASP cc_start: 0.8579 (t70) cc_final: 0.8251 (t70) REVERT: G 22 LYS cc_start: 0.8319 (ttmt) cc_final: 0.8118 (tmtt) REVERT: G 113 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8627 (pp) REVERT: G 122 MET cc_start: 0.8298 (ptp) cc_final: 0.8021 (ptm) REVERT: G 166 VAL cc_start: 0.9214 (OUTLIER) cc_final: 0.8922 (p) REVERT: G 230 ASP cc_start: 0.8614 (t70) cc_final: 0.8404 (t70) REVERT: G 238 ASP cc_start: 0.7354 (t0) cc_final: 0.7092 (t0) REVERT: G 245 ARG cc_start: 0.8426 (ttm-80) cc_final: 0.7913 (ttm-80) REVERT: H 22 LYS cc_start: 0.8626 (ttmt) cc_final: 0.8095 (tptm) REVERT: H 43 ASP cc_start: 0.8240 (t70) cc_final: 0.7995 (t70) REVERT: H 44 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7482 (mt-10) REVERT: H 238 ASP cc_start: 0.7457 (t0) cc_final: 0.7098 (t0) REVERT: H 245 ARG cc_start: 0.8066 (ttm170) cc_final: 0.7726 (ttm110) REVERT: I 22 LYS cc_start: 0.8371 (ttmt) cc_final: 0.8054 (tptm) REVERT: I 43 ASP cc_start: 0.8053 (t70) cc_final: 0.7756 (t70) REVERT: I 44 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7793 (mt-10) REVERT: I 82 GLU cc_start: 0.7965 (tp30) cc_final: 0.7543 (tp30) REVERT: I 113 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8715 (pp) REVERT: I 166 VAL cc_start: 0.9147 (OUTLIER) cc_final: 0.8847 (p) REVERT: I 203 GLU cc_start: 0.7785 (tt0) cc_final: 0.7411 (tt0) REVERT: J 11 ASN cc_start: 0.8963 (m-40) cc_final: 0.8708 (m-40) REVERT: K 6 GLN cc_start: 0.7943 (mt0) cc_final: 0.7698 (mm-40) REVERT: K 27 GLN cc_start: 0.8914 (mt0) cc_final: 0.8496 (mm110) REVERT: Q 27 GLN cc_start: 0.8979 (mt0) cc_final: 0.8675 (mm-40) REVERT: R 27 GLN cc_start: 0.8633 (mt0) cc_final: 0.8139 (mm110) outliers start: 63 outliers final: 52 residues processed: 352 average time/residue: 0.3256 time to fit residues: 175.1661 Evaluate side-chains 373 residues out of total 2250 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 314 time to evaluate : 2.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 213 MET Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 155 ASP Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 193 PHE Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 155 ASP Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 201 GLU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 178 SER Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 213 MET Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 155 ASP Chi-restraints excluded: chain I residue 166 VAL Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain I residue 201 GLU Chi-restraints excluded: chain I residue 258 VAL Chi-restraints excluded: chain J residue 2 THR Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain L residue 11 ASN Chi-restraints excluded: chain M residue 29 GLN Chi-restraints excluded: chain N residue 4 THR Chi-restraints excluded: chain O residue 2 THR Chi-restraints excluded: chain O residue 6 GLN Chi-restraints excluded: chain P residue 4 THR Chi-restraints excluded: chain Q residue 31 SER Chi-restraints excluded: chain a residue 5 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 0.0040 chunk 61 optimal weight: 1.9990 chunk 184 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 55 optimal weight: 0.4980 chunk 200 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 205 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 175 optimal weight: 4.9990 overall best weight: 1.0796 ------------------------------------------------------------------------------- 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 ** Q 11 ASN ** 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 = 0.3267 r_free = 0.3267 target = 0.110827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.096303 restraints weight = 32500.811| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.22 r_work: 0.2932 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 20988 Z= 0.275 Angle : 0.768 59.199 28485 Z= 0.424 Chirality : 0.045 0.341 3204 Planarity : 0.004 0.090 3762 Dihedral : 4.687 25.353 2871 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.67 % Allowed : 18.76 % Favored : 78.58 % Cbeta Deviations : 0.04 % 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: 0.81 (0.17), residues: 2601 helix: 1.89 (0.20), residues: 783 sheet: 0.76 (0.20), residues: 756 loop : -0.64 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 237 HIS 0.002 0.001 HIS F 26 PHE 0.021 0.002 PHE C 144 TYR 0.016 0.001 TYR E 184 ARG 0.035 0.000 ARG I 245 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4674.53 seconds wall clock time: 85 minutes 36.45 seconds (5136.45 seconds total)