Starting phenix.real_space_refine on Fri Apr 12 15:30:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nht_9373/04_2024/6nht_9373.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nht_9373/04_2024/6nht_9373.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nht_9373/04_2024/6nht_9373.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nht_9373/04_2024/6nht_9373.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nht_9373/04_2024/6nht_9373.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nht_9373/04_2024/6nht_9373.pdb" } resolution = 2.9 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= 0.014 sd= 0.205 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 108 5.16 5 C 16476 2.51 5 N 4524 2.21 5 O 5028 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 49": "OD1" <-> "OD2" Residue "A GLU 50": "OE1" <-> "OE2" Residue "A GLU 51": "OE1" <-> "OE2" Residue "A GLU 135": "OE1" <-> "OE2" Residue "A GLU 141": "OE1" <-> "OE2" Residue "A GLU 163": "OE1" <-> "OE2" Residue "A ASP 178": "OD1" <-> "OD2" Residue "B ASP 49": "OD1" <-> "OD2" Residue "B GLU 50": "OE1" <-> "OE2" Residue "B GLU 51": "OE1" <-> "OE2" Residue "B GLU 135": "OE1" <-> "OE2" Residue "B GLU 141": "OE1" <-> "OE2" Residue "B GLU 163": "OE1" <-> "OE2" Residue "B ASP 178": "OD1" <-> "OD2" Residue "C ASP 49": "OD1" <-> "OD2" Residue "C GLU 50": "OE1" <-> "OE2" Residue "C GLU 51": "OE1" <-> "OE2" Residue "C GLU 135": "OE1" <-> "OE2" Residue "C GLU 141": "OE1" <-> "OE2" Residue "C GLU 163": "OE1" <-> "OE2" Residue "C ASP 178": "OD1" <-> "OD2" Residue "D ASP 49": "OD1" <-> "OD2" Residue "D GLU 50": "OE1" <-> "OE2" Residue "D GLU 51": "OE1" <-> "OE2" Residue "D GLU 135": "OE1" <-> "OE2" Residue "D GLU 141": "OE1" <-> "OE2" Residue "D GLU 163": "OE1" <-> "OE2" Residue "D ASP 178": "OD1" <-> "OD2" Residue "E GLU 7": "OE1" <-> "OE2" Residue "E GLU 23": "OE1" <-> "OE2" Residue "E TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 73": "OD1" <-> "OD2" Residue "E GLU 90": "OE1" <-> "OE2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "E GLU 98": "OE1" <-> "OE2" Residue "F GLU 7": "OE1" <-> "OE2" Residue "F GLU 23": "OE1" <-> "OE2" Residue "F TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 73": "OD1" <-> "OD2" Residue "F GLU 90": "OE1" <-> "OE2" Residue "F GLU 97": "OE1" <-> "OE2" Residue "F GLU 98": "OE1" <-> "OE2" Residue "G GLU 7": "OE1" <-> "OE2" Residue "G GLU 23": "OE1" <-> "OE2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 73": "OD1" <-> "OD2" Residue "G GLU 90": "OE1" <-> "OE2" Residue "G GLU 97": "OE1" <-> "OE2" Residue "G GLU 98": "OE1" <-> "OE2" Residue "H GLU 7": "OE1" <-> "OE2" Residue "H GLU 23": "OE1" <-> "OE2" Residue "H TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 73": "OD1" <-> "OD2" Residue "H GLU 90": "OE1" <-> "OE2" Residue "H GLU 97": "OE1" <-> "OE2" Residue "H GLU 98": "OE1" <-> "OE2" Residue "I ASP 49": "OD1" <-> "OD2" Residue "I GLU 50": "OE1" <-> "OE2" Residue "I GLU 51": "OE1" <-> "OE2" Residue "I GLU 135": "OE1" <-> "OE2" Residue "I GLU 141": "OE1" <-> "OE2" Residue "I GLU 163": "OE1" <-> "OE2" Residue "I ASP 178": "OD1" <-> "OD2" Residue "J ASP 49": "OD1" <-> "OD2" Residue "J GLU 50": "OE1" <-> "OE2" Residue "J GLU 51": "OE1" <-> "OE2" Residue "J GLU 135": "OE1" <-> "OE2" Residue "J GLU 141": "OE1" <-> "OE2" Residue "J GLU 163": "OE1" <-> "OE2" Residue "J ASP 178": "OD1" <-> "OD2" Residue "K ASP 49": "OD1" <-> "OD2" Residue "K GLU 50": "OE1" <-> "OE2" Residue "K GLU 51": "OE1" <-> "OE2" Residue "K GLU 135": "OE1" <-> "OE2" Residue "K GLU 141": "OE1" <-> "OE2" Residue "K GLU 163": "OE1" <-> "OE2" Residue "K ASP 178": "OD1" <-> "OD2" Residue "L ASP 49": "OD1" <-> "OD2" Residue "L GLU 50": "OE1" <-> "OE2" Residue "L GLU 51": "OE1" <-> "OE2" Residue "L GLU 135": "OE1" <-> "OE2" Residue "L GLU 141": "OE1" <-> "OE2" Residue "L GLU 163": "OE1" <-> "OE2" Residue "L ASP 178": "OD1" <-> "OD2" Residue "M GLU 7": "OE1" <-> "OE2" Residue "M GLU 23": "OE1" <-> "OE2" Residue "M TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 73": "OD1" <-> "OD2" Residue "M GLU 90": "OE1" <-> "OE2" Residue "M GLU 97": "OE1" <-> "OE2" Residue "M GLU 98": "OE1" <-> "OE2" Residue "N GLU 7": "OE1" <-> "OE2" Residue "N GLU 23": "OE1" <-> "OE2" Residue "N TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 73": "OD1" <-> "OD2" Residue "N GLU 90": "OE1" <-> "OE2" Residue "N GLU 97": "OE1" <-> "OE2" Residue "N GLU 98": "OE1" <-> "OE2" Residue "O GLU 7": "OE1" <-> "OE2" Residue "O GLU 23": "OE1" <-> "OE2" Residue "O TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 73": "OD1" <-> "OD2" Residue "O GLU 90": "OE1" <-> "OE2" Residue "O GLU 97": "OE1" <-> "OE2" Residue "O GLU 98": "OE1" <-> "OE2" Residue "P GLU 7": "OE1" <-> "OE2" Residue "P GLU 23": "OE1" <-> "OE2" Residue "P TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 73": "OD1" <-> "OD2" Residue "P GLU 90": "OE1" <-> "OE2" Residue "P GLU 97": "OE1" <-> "OE2" Residue "P GLU 98": "OE1" <-> "OE2" Residue "Q ASP 49": "OD1" <-> "OD2" Residue "Q GLU 50": "OE1" <-> "OE2" Residue "Q GLU 51": "OE1" <-> "OE2" Residue "Q GLU 135": "OE1" <-> "OE2" Residue "Q GLU 141": "OE1" <-> "OE2" Residue "Q GLU 163": "OE1" <-> "OE2" Residue "Q ASP 178": "OD1" <-> "OD2" Residue "R ASP 49": "OD1" <-> "OD2" Residue "R GLU 50": "OE1" <-> "OE2" Residue "R GLU 51": "OE1" <-> "OE2" Residue "R GLU 135": "OE1" <-> "OE2" Residue "R GLU 141": "OE1" <-> "OE2" Residue "R GLU 163": "OE1" <-> "OE2" Residue "R ASP 178": "OD1" <-> "OD2" Residue "S ASP 49": "OD1" <-> "OD2" Residue "S GLU 50": "OE1" <-> "OE2" Residue "S GLU 51": "OE1" <-> "OE2" Residue "S GLU 135": "OE1" <-> "OE2" Residue "S GLU 141": "OE1" <-> "OE2" Residue "S GLU 163": "OE1" <-> "OE2" Residue "S ASP 178": "OD1" <-> "OD2" Residue "T ASP 49": "OD1" <-> "OD2" Residue "T GLU 50": "OE1" <-> "OE2" Residue "T GLU 51": "OE1" <-> "OE2" Residue "T GLU 135": "OE1" <-> "OE2" Residue "T GLU 141": "OE1" <-> "OE2" Residue "T GLU 163": "OE1" <-> "OE2" Residue "T ASP 178": "OD1" <-> "OD2" Residue "U GLU 7": "OE1" <-> "OE2" Residue "U GLU 23": "OE1" <-> "OE2" Residue "U TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 73": "OD1" <-> "OD2" Residue "U GLU 90": "OE1" <-> "OE2" Residue "U GLU 97": "OE1" <-> "OE2" Residue "U GLU 98": "OE1" <-> "OE2" Residue "V GLU 7": "OE1" <-> "OE2" Residue "V GLU 23": "OE1" <-> "OE2" Residue "V TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 73": "OD1" <-> "OD2" Residue "V GLU 90": "OE1" <-> "OE2" Residue "V GLU 97": "OE1" <-> "OE2" Residue "V GLU 98": "OE1" <-> "OE2" Residue "W GLU 7": "OE1" <-> "OE2" Residue "W GLU 23": "OE1" <-> "OE2" Residue "W TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 73": "OD1" <-> "OD2" Residue "W GLU 90": "OE1" <-> "OE2" Residue "W GLU 97": "OE1" <-> "OE2" Residue "W GLU 98": "OE1" <-> "OE2" Residue "X GLU 7": "OE1" <-> "OE2" Residue "X GLU 23": "OE1" <-> "OE2" Residue "X TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 73": "OD1" <-> "OD2" Residue "X GLU 90": "OE1" <-> "OE2" Residue "X GLU 97": "OE1" <-> "OE2" Residue "X GLU 98": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 26136 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1293 Classifications: {'peptide': 168} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 165} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1293 Classifications: {'peptide': 168} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 165} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1293 Classifications: {'peptide': 168} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 165} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1293 Classifications: {'peptide': 168} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 165} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "F" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "G" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "H" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "I" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1293 Classifications: {'peptide': 168} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 165} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1293 Classifications: {'peptide': 168} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 165} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "K" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1293 Classifications: {'peptide': 168} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 165} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "L" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1293 Classifications: {'peptide': 168} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 165} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "M" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "N" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "O" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "P" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "Q" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1293 Classifications: {'peptide': 168} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 165} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "R" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1293 Classifications: {'peptide': 168} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 165} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "S" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1293 Classifications: {'peptide': 168} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 165} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "T" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1293 Classifications: {'peptide': 168} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 165} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "U" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "V" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "W" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "X" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Time building chain proxies: 12.80, per 1000 atoms: 0.49 Number of scatterers: 26136 At special positions: 0 Unit cell: (153.7, 152.64, 147.34, 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 108 16.00 O 5028 8.00 N 4524 7.00 C 16476 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: 10.94 Conformation dependent library (CDL) restraints added in 4.9 seconds 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6288 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 24 sheets defined 58.4% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.54 Creating SS restraints... Processing helix chain 'A' and resid 24 through 45 removed outlier: 3.540A pdb=" N GLU A 29 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER A 39 " --> pdb=" O ASP A 35 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY A 42 " --> pdb=" O THR A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 72 removed outlier: 3.759A pdb=" N GLY A 54 " --> pdb=" O GLU A 50 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 55 " --> pdb=" O GLU A 51 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU A 58 " --> pdb=" O GLY A 54 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER A 72 " --> pdb=" O GLY A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 98 removed outlier: 4.077A pdb=" N ILE A 84 " --> pdb=" O SER A 80 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG A 93 " --> pdb=" O LYS A 89 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLU A 96 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N MET A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 137 removed outlier: 3.510A pdb=" N LYS A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP A 116 " --> pdb=" O SER A 112 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL A 117 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS A 118 " --> pdb=" O LYS A 114 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR A 120 " --> pdb=" O ASP A 116 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR A 131 " --> pdb=" O ARG A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 150 removed outlier: 3.513A pdb=" N ALA A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 174 removed outlier: 3.562A pdb=" N LEU A 155 " --> pdb=" O ASP A 151 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE A 162 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 168 " --> pdb=" O GLN A 164 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 169 " --> pdb=" O GLY A 165 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU A 170 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A 171 " --> pdb=" O LYS A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'B' and resid 24 through 45 removed outlier: 3.541A pdb=" N GLU B 29 " --> pdb=" O SER B 25 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER B 39 " --> pdb=" O ASP B 35 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY B 42 " --> pdb=" O THR B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 72 removed outlier: 3.759A pdb=" N GLY B 54 " --> pdb=" O GLU B 50 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B 55 " --> pdb=" O GLU B 51 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU B 58 " --> pdb=" O GLY B 54 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER B 72 " --> pdb=" O GLY B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 98 removed outlier: 4.078A pdb=" N ILE B 84 " --> pdb=" O SER B 80 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS B 89 " --> pdb=" O ALA B 85 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG B 93 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLU B 96 " --> pdb=" O LEU B 92 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N MET B 97 " --> pdb=" O ARG B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 137 removed outlier: 3.510A pdb=" N LYS B 114 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP B 116 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL B 117 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N CYS B 118 " --> pdb=" O LYS B 114 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR B 120 " --> pdb=" O ASP B 116 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR B 131 " --> pdb=" O ARG B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 150 removed outlier: 3.513A pdb=" N ALA B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 174 removed outlier: 3.563A pdb=" N LEU B 155 " --> pdb=" O ASP B 151 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE B 160 " --> pdb=" O LEU B 156 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU B 161 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE B 162 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU B 168 " --> pdb=" O GLN B 164 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU B 169 " --> pdb=" O GLY B 165 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU B 170 " --> pdb=" O LYS B 166 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA B 171 " --> pdb=" O LYS B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 Processing helix chain 'C' and resid 24 through 45 removed outlier: 3.540A pdb=" N GLU C 29 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER C 39 " --> pdb=" O ASP C 35 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY C 42 " --> pdb=" O THR C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 72 removed outlier: 3.760A pdb=" N GLY C 54 " --> pdb=" O GLU C 50 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE C 55 " --> pdb=" O GLU C 51 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU C 58 " --> pdb=" O GLY C 54 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER C 72 " --> pdb=" O GLY C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 98 removed outlier: 4.077A pdb=" N ILE C 84 " --> pdb=" O SER C 80 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS C 89 " --> pdb=" O ALA C 85 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG C 93 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLU C 96 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N MET C 97 " --> pdb=" O ARG C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 137 removed outlier: 3.511A pdb=" N LYS C 114 " --> pdb=" O LEU C 110 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU C 115 " --> pdb=" O GLU C 111 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP C 116 " --> pdb=" O SER C 112 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL C 117 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS C 118 " --> pdb=" O LYS C 114 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR C 120 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR C 131 " --> pdb=" O ARG C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 150 removed outlier: 3.513A pdb=" N ALA C 148 " --> pdb=" O ALA C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 174 removed outlier: 3.563A pdb=" N LEU C 155 " --> pdb=" O ASP C 151 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE C 160 " --> pdb=" O LEU C 156 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU C 161 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE C 162 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU C 168 " --> pdb=" O GLN C 164 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU C 169 " --> pdb=" O GLY C 165 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU C 170 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA C 171 " --> pdb=" O LYS C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 185 Processing helix chain 'D' and resid 24 through 45 removed outlier: 3.541A pdb=" N GLU D 29 " --> pdb=" O SER D 25 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER D 39 " --> pdb=" O ASP D 35 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY D 42 " --> pdb=" O THR D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 72 removed outlier: 3.759A pdb=" N GLY D 54 " --> pdb=" O GLU D 50 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE D 55 " --> pdb=" O GLU D 51 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU D 58 " --> pdb=" O GLY D 54 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER D 72 " --> pdb=" O GLY D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 98 removed outlier: 4.078A pdb=" N ILE D 84 " --> pdb=" O SER D 80 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS D 89 " --> pdb=" O ALA D 85 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG D 93 " --> pdb=" O LYS D 89 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLU D 96 " --> pdb=" O LEU D 92 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N MET D 97 " --> pdb=" O ARG D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 137 removed outlier: 3.509A pdb=" N LYS D 114 " --> pdb=" O LEU D 110 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS D 118 " --> pdb=" O LYS D 114 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR D 120 " --> pdb=" O ASP D 116 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR D 131 " --> pdb=" O ARG D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 150 removed outlier: 3.513A pdb=" N ALA D 148 " --> pdb=" O ALA D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 174 removed outlier: 3.562A pdb=" N LEU D 155 " --> pdb=" O ASP D 151 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE D 160 " --> pdb=" O LEU D 156 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU D 161 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE D 162 " --> pdb=" O ARG D 158 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU D 168 " --> pdb=" O GLN D 164 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU D 169 " --> pdb=" O GLY D 165 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU D 170 " --> pdb=" O LYS D 166 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA D 171 " --> pdb=" O LYS D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 185 Processing helix chain 'E' and resid 17 through 31 removed outlier: 3.860A pdb=" N LEU E 22 " --> pdb=" O PRO E 18 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN E 24 " --> pdb=" O GLU E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 89 removed outlier: 3.730A pdb=" N ALA E 86 " --> pdb=" O ALA E 82 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL E 87 " --> pdb=" O SER E 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 31 removed outlier: 3.860A pdb=" N LEU F 22 " --> pdb=" O PRO F 18 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN F 24 " --> pdb=" O GLU F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 89 removed outlier: 3.729A pdb=" N ALA F 86 " --> pdb=" O ALA F 82 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL F 87 " --> pdb=" O SER F 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 31 removed outlier: 3.860A pdb=" N LEU G 22 " --> pdb=" O PRO G 18 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN G 24 " --> pdb=" O GLU G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 89 removed outlier: 3.730A pdb=" N ALA G 86 " --> pdb=" O ALA G 82 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL G 87 " --> pdb=" O SER G 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 17 through 31 removed outlier: 3.860A pdb=" N LEU H 22 " --> pdb=" O PRO H 18 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN H 24 " --> pdb=" O GLU H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 89 removed outlier: 3.730A pdb=" N ALA H 86 " --> pdb=" O ALA H 82 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL H 87 " --> pdb=" O SER H 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 45 removed outlier: 3.541A pdb=" N GLU I 29 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER I 39 " --> pdb=" O ASP I 35 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY I 42 " --> pdb=" O THR I 38 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 72 removed outlier: 3.760A pdb=" N GLY I 54 " --> pdb=" O GLU I 50 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE I 55 " --> pdb=" O GLU I 51 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU I 58 " --> pdb=" O GLY I 54 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN I 61 " --> pdb=" O GLU I 57 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER I 72 " --> pdb=" O GLY I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 80 through 98 removed outlier: 4.078A pdb=" N ILE I 84 " --> pdb=" O SER I 80 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS I 89 " --> pdb=" O ALA I 85 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG I 93 " --> pdb=" O LYS I 89 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLU I 96 " --> pdb=" O LEU I 92 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N MET I 97 " --> pdb=" O ARG I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 110 through 137 removed outlier: 3.510A pdb=" N LYS I 114 " --> pdb=" O LEU I 110 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU I 115 " --> pdb=" O GLU I 111 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP I 116 " --> pdb=" O SER I 112 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL I 117 " --> pdb=" O ALA I 113 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N CYS I 118 " --> pdb=" O LYS I 114 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR I 120 " --> pdb=" O ASP I 116 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR I 131 " --> pdb=" O ARG I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 139 through 150 removed outlier: 3.512A pdb=" N ALA I 148 " --> pdb=" O ALA I 144 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 174 removed outlier: 3.563A pdb=" N LEU I 155 " --> pdb=" O ASP I 151 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE I 160 " --> pdb=" O LEU I 156 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU I 161 " --> pdb=" O ALA I 157 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE I 162 " --> pdb=" O ARG I 158 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU I 168 " --> pdb=" O GLN I 164 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU I 169 " --> pdb=" O GLY I 165 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU I 170 " --> pdb=" O LYS I 166 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA I 171 " --> pdb=" O LYS I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 180 through 185 Processing helix chain 'J' and resid 24 through 45 removed outlier: 3.541A pdb=" N GLU J 29 " --> pdb=" O SER J 25 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER J 39 " --> pdb=" O ASP J 35 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY J 42 " --> pdb=" O THR J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 72 removed outlier: 3.761A pdb=" N GLY J 54 " --> pdb=" O GLU J 50 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE J 55 " --> pdb=" O GLU J 51 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU J 58 " --> pdb=" O GLY J 54 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN J 61 " --> pdb=" O GLU J 57 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER J 72 " --> pdb=" O GLY J 68 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 98 removed outlier: 4.078A pdb=" N ILE J 84 " --> pdb=" O SER J 80 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS J 89 " --> pdb=" O ALA J 85 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG J 93 " --> pdb=" O LYS J 89 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLU J 96 " --> pdb=" O LEU J 92 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N MET J 97 " --> pdb=" O ARG J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 110 through 137 removed outlier: 3.511A pdb=" N LYS J 114 " --> pdb=" O LEU J 110 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU J 115 " --> pdb=" O GLU J 111 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP J 116 " --> pdb=" O SER J 112 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL J 117 " --> pdb=" O ALA J 113 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N CYS J 118 " --> pdb=" O LYS J 114 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR J 120 " --> pdb=" O ASP J 116 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR J 131 " --> pdb=" O ARG J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 139 through 150 removed outlier: 3.513A pdb=" N ALA J 148 " --> pdb=" O ALA J 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 174 removed outlier: 3.562A pdb=" N LEU J 155 " --> pdb=" O ASP J 151 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE J 160 " --> pdb=" O LEU J 156 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU J 161 " --> pdb=" O ALA J 157 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE J 162 " --> pdb=" O ARG J 158 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU J 168 " --> pdb=" O GLN J 164 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU J 169 " --> pdb=" O GLY J 165 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU J 170 " --> pdb=" O LYS J 166 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA J 171 " --> pdb=" O LYS J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 180 through 185 Processing helix chain 'K' and resid 24 through 45 removed outlier: 3.541A pdb=" N GLU K 29 " --> pdb=" O SER K 25 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER K 39 " --> pdb=" O ASP K 35 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY K 42 " --> pdb=" O THR K 38 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 72 removed outlier: 3.760A pdb=" N GLY K 54 " --> pdb=" O GLU K 50 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE K 55 " --> pdb=" O GLU K 51 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU K 58 " --> pdb=" O GLY K 54 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN K 61 " --> pdb=" O GLU K 57 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER K 72 " --> pdb=" O GLY K 68 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 98 removed outlier: 4.078A pdb=" N ILE K 84 " --> pdb=" O SER K 80 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS K 89 " --> pdb=" O ALA K 85 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG K 93 " --> pdb=" O LYS K 89 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLU K 96 " --> pdb=" O LEU K 92 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N MET K 97 " --> pdb=" O ARG K 93 " (cutoff:3.500A) Processing helix chain 'K' and resid 110 through 137 removed outlier: 3.510A pdb=" N LYS K 114 " --> pdb=" O LEU K 110 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU K 115 " --> pdb=" O GLU K 111 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP K 116 " --> pdb=" O SER K 112 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL K 117 " --> pdb=" O ALA K 113 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS K 118 " --> pdb=" O LYS K 114 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR K 120 " --> pdb=" O ASP K 116 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR K 131 " --> pdb=" O ARG K 127 " (cutoff:3.500A) Processing helix chain 'K' and resid 139 through 150 removed outlier: 3.513A pdb=" N ALA K 148 " --> pdb=" O ALA K 144 " (cutoff:3.500A) Processing helix chain 'K' and resid 151 through 174 removed outlier: 3.564A pdb=" N LEU K 155 " --> pdb=" O ASP K 151 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE K 160 " --> pdb=" O LEU K 156 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU K 161 " --> pdb=" O ALA K 157 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE K 162 " --> pdb=" O ARG K 158 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU K 168 " --> pdb=" O GLN K 164 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU K 169 " --> pdb=" O GLY K 165 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU K 170 " --> pdb=" O LYS K 166 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA K 171 " --> pdb=" O LYS K 167 " (cutoff:3.500A) Processing helix chain 'K' and resid 180 through 185 Processing helix chain 'L' and resid 24 through 45 removed outlier: 3.541A pdb=" N GLU L 29 " --> pdb=" O SER L 25 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER L 39 " --> pdb=" O ASP L 35 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY L 42 " --> pdb=" O THR L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 72 removed outlier: 3.760A pdb=" N GLY L 54 " --> pdb=" O GLU L 50 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE L 55 " --> pdb=" O GLU L 51 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU L 58 " --> pdb=" O GLY L 54 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN L 61 " --> pdb=" O GLU L 57 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER L 72 " --> pdb=" O GLY L 68 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 98 removed outlier: 4.077A pdb=" N ILE L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS L 89 " --> pdb=" O ALA L 85 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG L 93 " --> pdb=" O LYS L 89 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLU L 96 " --> pdb=" O LEU L 92 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N MET L 97 " --> pdb=" O ARG L 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 110 through 137 removed outlier: 3.510A pdb=" N LYS L 114 " --> pdb=" O LEU L 110 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU L 115 " --> pdb=" O GLU L 111 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP L 116 " --> pdb=" O SER L 112 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL L 117 " --> pdb=" O ALA L 113 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYS L 118 " --> pdb=" O LYS L 114 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR L 120 " --> pdb=" O ASP L 116 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR L 131 " --> pdb=" O ARG L 127 " (cutoff:3.500A) Processing helix chain 'L' and resid 139 through 150 removed outlier: 3.513A pdb=" N ALA L 148 " --> pdb=" O ALA L 144 " (cutoff:3.500A) Processing helix chain 'L' and resid 151 through 174 removed outlier: 3.563A pdb=" N LEU L 155 " --> pdb=" O ASP L 151 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE L 160 " --> pdb=" O LEU L 156 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU L 161 " --> pdb=" O ALA L 157 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE L 162 " --> pdb=" O ARG L 158 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU L 168 " --> pdb=" O GLN L 164 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU L 169 " --> pdb=" O GLY L 165 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU L 170 " --> pdb=" O LYS L 166 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA L 171 " --> pdb=" O LYS L 167 " (cutoff:3.500A) Processing helix chain 'L' and resid 180 through 185 Processing helix chain 'M' and resid 17 through 31 removed outlier: 3.860A pdb=" N LEU M 22 " --> pdb=" O PRO M 18 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN M 24 " --> pdb=" O GLU M 20 " (cutoff:3.500A) Processing helix chain 'M' and resid 73 through 89 removed outlier: 3.729A pdb=" N ALA M 86 " --> pdb=" O ALA M 82 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL M 87 " --> pdb=" O SER M 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 17 through 31 removed outlier: 3.860A pdb=" N LEU N 22 " --> pdb=" O PRO N 18 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN N 24 " --> pdb=" O GLU N 20 " (cutoff:3.500A) Processing helix chain 'N' and resid 73 through 89 removed outlier: 3.730A pdb=" N ALA N 86 " --> pdb=" O ALA N 82 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL N 87 " --> pdb=" O SER N 83 " (cutoff:3.500A) Processing helix chain 'O' and resid 17 through 31 removed outlier: 3.860A pdb=" N LEU O 22 " --> pdb=" O PRO O 18 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN O 24 " --> pdb=" O GLU O 20 " (cutoff:3.500A) Processing helix chain 'O' and resid 73 through 89 removed outlier: 3.730A pdb=" N ALA O 86 " --> pdb=" O ALA O 82 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL O 87 " --> pdb=" O SER O 83 " (cutoff:3.500A) Processing helix chain 'P' and resid 17 through 31 removed outlier: 3.859A pdb=" N LEU P 22 " --> pdb=" O PRO P 18 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN P 24 " --> pdb=" O GLU P 20 " (cutoff:3.500A) Processing helix chain 'P' and resid 73 through 89 removed outlier: 3.729A pdb=" N ALA P 86 " --> pdb=" O ALA P 82 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL P 87 " --> pdb=" O SER P 83 " (cutoff:3.500A) Processing helix chain 'Q' and resid 24 through 45 removed outlier: 3.542A pdb=" N GLU Q 29 " --> pdb=" O SER Q 25 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER Q 39 " --> pdb=" O ASP Q 35 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY Q 42 " --> pdb=" O THR Q 38 " (cutoff:3.500A) Processing helix chain 'Q' and resid 49 through 72 removed outlier: 3.760A pdb=" N GLY Q 54 " --> pdb=" O GLU Q 50 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE Q 55 " --> pdb=" O GLU Q 51 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU Q 58 " --> pdb=" O GLY Q 54 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN Q 61 " --> pdb=" O GLU Q 57 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER Q 72 " --> pdb=" O GLY Q 68 " (cutoff:3.500A) Processing helix chain 'Q' and resid 80 through 98 removed outlier: 4.078A pdb=" N ILE Q 84 " --> pdb=" O SER Q 80 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS Q 89 " --> pdb=" O ALA Q 85 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG Q 93 " --> pdb=" O LYS Q 89 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLU Q 96 " --> pdb=" O LEU Q 92 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N MET Q 97 " --> pdb=" O ARG Q 93 " (cutoff:3.500A) Processing helix chain 'Q' and resid 110 through 137 removed outlier: 3.510A pdb=" N LYS Q 114 " --> pdb=" O LEU Q 110 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU Q 115 " --> pdb=" O GLU Q 111 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP Q 116 " --> pdb=" O SER Q 112 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL Q 117 " --> pdb=" O ALA Q 113 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N CYS Q 118 " --> pdb=" O LYS Q 114 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR Q 120 " --> pdb=" O ASP Q 116 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR Q 131 " --> pdb=" O ARG Q 127 " (cutoff:3.500A) Processing helix chain 'Q' and resid 139 through 150 removed outlier: 3.513A pdb=" N ALA Q 148 " --> pdb=" O ALA Q 144 " (cutoff:3.500A) Processing helix chain 'Q' and resid 151 through 174 removed outlier: 3.563A pdb=" N LEU Q 155 " --> pdb=" O ASP Q 151 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE Q 160 " --> pdb=" O LEU Q 156 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU Q 161 " --> pdb=" O ALA Q 157 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE Q 162 " --> pdb=" O ARG Q 158 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU Q 168 " --> pdb=" O GLN Q 164 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU Q 169 " --> pdb=" O GLY Q 165 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU Q 170 " --> pdb=" O LYS Q 166 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA Q 171 " --> pdb=" O LYS Q 167 " (cutoff:3.500A) Processing helix chain 'Q' and resid 180 through 185 Processing helix chain 'R' and resid 24 through 45 removed outlier: 3.542A pdb=" N GLU R 29 " --> pdb=" O SER R 25 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER R 39 " --> pdb=" O ASP R 35 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY R 42 " --> pdb=" O THR R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 72 removed outlier: 3.760A pdb=" N GLY R 54 " --> pdb=" O GLU R 50 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE R 55 " --> pdb=" O GLU R 51 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU R 58 " --> pdb=" O GLY R 54 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN R 61 " --> pdb=" O GLU R 57 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER R 72 " --> pdb=" O GLY R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 80 through 98 removed outlier: 4.079A pdb=" N ILE R 84 " --> pdb=" O SER R 80 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS R 89 " --> pdb=" O ALA R 85 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG R 93 " --> pdb=" O LYS R 89 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLU R 96 " --> pdb=" O LEU R 92 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N MET R 97 " --> pdb=" O ARG R 93 " (cutoff:3.500A) Processing helix chain 'R' and resid 110 through 137 removed outlier: 3.511A pdb=" N LYS R 114 " --> pdb=" O LEU R 110 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU R 115 " --> pdb=" O GLU R 111 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP R 116 " --> pdb=" O SER R 112 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL R 117 " --> pdb=" O ALA R 113 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS R 118 " --> pdb=" O LYS R 114 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR R 120 " --> pdb=" O ASP R 116 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR R 131 " --> pdb=" O ARG R 127 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 150 removed outlier: 3.513A pdb=" N ALA R 148 " --> pdb=" O ALA R 144 " (cutoff:3.500A) Processing helix chain 'R' and resid 151 through 174 removed outlier: 3.562A pdb=" N LEU R 155 " --> pdb=" O ASP R 151 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE R 160 " --> pdb=" O LEU R 156 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU R 161 " --> pdb=" O ALA R 157 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE R 162 " --> pdb=" O ARG R 158 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU R 168 " --> pdb=" O GLN R 164 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU R 169 " --> pdb=" O GLY R 165 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU R 170 " --> pdb=" O LYS R 166 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA R 171 " --> pdb=" O LYS R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 180 through 185 Processing helix chain 'S' and resid 24 through 45 removed outlier: 3.542A pdb=" N GLU S 29 " --> pdb=" O SER S 25 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER S 39 " --> pdb=" O ASP S 35 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY S 42 " --> pdb=" O THR S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 49 through 72 removed outlier: 3.761A pdb=" N GLY S 54 " --> pdb=" O GLU S 50 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE S 55 " --> pdb=" O GLU S 51 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU S 58 " --> pdb=" O GLY S 54 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN S 61 " --> pdb=" O GLU S 57 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER S 72 " --> pdb=" O GLY S 68 " (cutoff:3.500A) Processing helix chain 'S' and resid 80 through 98 removed outlier: 4.077A pdb=" N ILE S 84 " --> pdb=" O SER S 80 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS S 89 " --> pdb=" O ALA S 85 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG S 93 " --> pdb=" O LYS S 89 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLU S 96 " --> pdb=" O LEU S 92 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N MET S 97 " --> pdb=" O ARG S 93 " (cutoff:3.500A) Processing helix chain 'S' and resid 110 through 137 removed outlier: 3.510A pdb=" N LYS S 114 " --> pdb=" O LEU S 110 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU S 115 " --> pdb=" O GLU S 111 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP S 116 " --> pdb=" O SER S 112 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL S 117 " --> pdb=" O ALA S 113 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N CYS S 118 " --> pdb=" O LYS S 114 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR S 120 " --> pdb=" O ASP S 116 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR S 131 " --> pdb=" O ARG S 127 " (cutoff:3.500A) Processing helix chain 'S' and resid 139 through 150 removed outlier: 3.513A pdb=" N ALA S 148 " --> pdb=" O ALA S 144 " (cutoff:3.500A) Processing helix chain 'S' and resid 151 through 174 removed outlier: 3.563A pdb=" N LEU S 155 " --> pdb=" O ASP S 151 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE S 160 " --> pdb=" O LEU S 156 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU S 161 " --> pdb=" O ALA S 157 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE S 162 " --> pdb=" O ARG S 158 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU S 168 " --> pdb=" O GLN S 164 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU S 169 " --> pdb=" O GLY S 165 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU S 170 " --> pdb=" O LYS S 166 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA S 171 " --> pdb=" O LYS S 167 " (cutoff:3.500A) Processing helix chain 'S' and resid 180 through 185 Processing helix chain 'T' and resid 24 through 45 removed outlier: 3.541A pdb=" N GLU T 29 " --> pdb=" O SER T 25 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER T 39 " --> pdb=" O ASP T 35 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY T 42 " --> pdb=" O THR T 38 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 72 removed outlier: 3.761A pdb=" N GLY T 54 " --> pdb=" O GLU T 50 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE T 55 " --> pdb=" O GLU T 51 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU T 58 " --> pdb=" O GLY T 54 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN T 61 " --> pdb=" O GLU T 57 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER T 72 " --> pdb=" O GLY T 68 " (cutoff:3.500A) Processing helix chain 'T' and resid 80 through 98 removed outlier: 4.079A pdb=" N ILE T 84 " --> pdb=" O SER T 80 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS T 89 " --> pdb=" O ALA T 85 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG T 93 " --> pdb=" O LYS T 89 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLU T 96 " --> pdb=" O LEU T 92 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N MET T 97 " --> pdb=" O ARG T 93 " (cutoff:3.500A) Processing helix chain 'T' and resid 110 through 137 removed outlier: 3.510A pdb=" N LYS T 114 " --> pdb=" O LEU T 110 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU T 115 " --> pdb=" O GLU T 111 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP T 116 " --> pdb=" O SER T 112 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL T 117 " --> pdb=" O ALA T 113 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N CYS T 118 " --> pdb=" O LYS T 114 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR T 120 " --> pdb=" O ASP T 116 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR T 131 " --> pdb=" O ARG T 127 " (cutoff:3.500A) Processing helix chain 'T' and resid 139 through 150 removed outlier: 3.514A pdb=" N ALA T 148 " --> pdb=" O ALA T 144 " (cutoff:3.500A) Processing helix chain 'T' and resid 151 through 174 removed outlier: 3.563A pdb=" N LEU T 155 " --> pdb=" O ASP T 151 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE T 160 " --> pdb=" O LEU T 156 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU T 161 " --> pdb=" O ALA T 157 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE T 162 " --> pdb=" O ARG T 158 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU T 168 " --> pdb=" O GLN T 164 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU T 169 " --> pdb=" O GLY T 165 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU T 170 " --> pdb=" O LYS T 166 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA T 171 " --> pdb=" O LYS T 167 " (cutoff:3.500A) Processing helix chain 'T' and resid 180 through 185 Processing helix chain 'U' and resid 17 through 31 removed outlier: 3.860A pdb=" N LEU U 22 " --> pdb=" O PRO U 18 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN U 24 " --> pdb=" O GLU U 20 " (cutoff:3.500A) Processing helix chain 'U' and resid 73 through 89 removed outlier: 3.729A pdb=" N ALA U 86 " --> pdb=" O ALA U 82 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL U 87 " --> pdb=" O SER U 83 " (cutoff:3.500A) Processing helix chain 'V' and resid 17 through 31 removed outlier: 3.861A pdb=" N LEU V 22 " --> pdb=" O PRO V 18 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN V 24 " --> pdb=" O GLU V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 73 through 89 removed outlier: 3.730A pdb=" N ALA V 86 " --> pdb=" O ALA V 82 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL V 87 " --> pdb=" O SER V 83 " (cutoff:3.500A) Processing helix chain 'W' and resid 17 through 31 removed outlier: 3.859A pdb=" N LEU W 22 " --> pdb=" O PRO W 18 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN W 24 " --> pdb=" O GLU W 20 " (cutoff:3.500A) Processing helix chain 'W' and resid 73 through 89 removed outlier: 3.730A pdb=" N ALA W 86 " --> pdb=" O ALA W 82 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL W 87 " --> pdb=" O SER W 83 " (cutoff:3.500A) Processing helix chain 'X' and resid 17 through 31 removed outlier: 3.861A pdb=" N LEU X 22 " --> pdb=" O PRO X 18 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN X 24 " --> pdb=" O GLU X 20 " (cutoff:3.500A) Processing helix chain 'X' and resid 73 through 89 removed outlier: 3.729A pdb=" N ALA X 86 " --> pdb=" O ALA X 82 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL X 87 " --> pdb=" O SER X 83 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'M' and resid 49 through 52 removed outlier: 4.426A pdb=" N ALA M 49 " --> pdb=" O PHE E 44 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU E 4 " --> pdb=" O ARG E 43 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N VAL E 45 " --> pdb=" O LEU E 4 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE E 6 " --> pdb=" O VAL E 45 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU E 47 " --> pdb=" O ILE E 6 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ALA E 8 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N TYR E 61 " --> pdb=" O THR E 9 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU E 62 " --> pdb=" O SER E 103 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N GLU E 105 " --> pdb=" O LEU E 62 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA E 64 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ARG E 107 " --> pdb=" O ALA E 64 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU E 66 " --> pdb=" O ARG E 107 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N MET E 109 " --> pdb=" O LEU E 66 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE E 68 " --> pdb=" O MET E 109 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL E 100 " --> pdb=" O VAL U 119 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 13 through 14 removed outlier: 6.833A pdb=" N ARG E 13 " --> pdb=" O ALA E 93 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 49 through 52 removed outlier: 4.429A pdb=" N ALA E 49 " --> pdb=" O PHE U 44 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU U 4 " --> pdb=" O ARG U 43 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL U 45 " --> pdb=" O LEU U 4 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE U 6 " --> pdb=" O VAL U 45 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU U 47 " --> pdb=" O ILE U 6 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ALA U 8 " --> pdb=" O LEU U 47 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N TYR U 61 " --> pdb=" O THR U 9 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU U 62 " --> pdb=" O SER U 103 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N GLU U 105 " --> pdb=" O LEU U 62 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA U 64 " --> pdb=" O GLU U 105 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ARG U 107 " --> pdb=" O ALA U 64 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU U 66 " --> pdb=" O ARG U 107 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N MET U 109 " --> pdb=" O LEU U 66 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE U 68 " --> pdb=" O MET U 109 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL U 100 " --> pdb=" O VAL M 119 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 115 through 119 removed outlier: 3.577A pdb=" N VAL M 100 " --> pdb=" O VAL E 119 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU M 62 " --> pdb=" O SER M 103 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N GLU M 105 " --> pdb=" O LEU M 62 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ALA M 64 " --> pdb=" O GLU M 105 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ARG M 107 " --> pdb=" O ALA M 64 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU M 66 " --> pdb=" O ARG M 107 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N MET M 109 " --> pdb=" O LEU M 66 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE M 68 " --> pdb=" O MET M 109 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N TYR M 61 " --> pdb=" O THR M 9 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU M 4 " --> pdb=" O ARG M 43 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL M 45 " --> pdb=" O LEU M 4 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE M 6 " --> pdb=" O VAL M 45 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU M 47 " --> pdb=" O ILE M 6 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ALA M 8 " --> pdb=" O LEU M 47 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ALA U 49 " --> pdb=" O PHE M 44 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 49 through 52 removed outlier: 4.431A pdb=" N ALA G 49 " --> pdb=" O PHE F 44 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU F 4 " --> pdb=" O ARG F 43 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N VAL F 45 " --> pdb=" O LEU F 4 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE F 6 " --> pdb=" O VAL F 45 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU F 47 " --> pdb=" O ILE F 6 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ALA F 8 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N TYR F 61 " --> pdb=" O THR F 9 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU F 62 " --> pdb=" O SER F 103 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N GLU F 105 " --> pdb=" O LEU F 62 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ALA F 64 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ARG F 107 " --> pdb=" O ALA F 64 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU F 66 " --> pdb=" O ARG F 107 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N MET F 109 " --> pdb=" O LEU F 66 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE F 68 " --> pdb=" O MET F 109 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL F 100 " --> pdb=" O VAL P 119 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 13 through 14 removed outlier: 6.833A pdb=" N ARG F 13 " --> pdb=" O ALA F 93 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 49 through 52 removed outlier: 4.425A pdb=" N ALA F 49 " --> pdb=" O PHE P 44 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU P 4 " --> pdb=" O ARG P 43 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL P 45 " --> pdb=" O LEU P 4 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE P 6 " --> pdb=" O VAL P 45 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU P 47 " --> pdb=" O ILE P 6 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ALA P 8 " --> pdb=" O LEU P 47 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N TYR P 61 " --> pdb=" O THR P 9 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU P 62 " --> pdb=" O SER P 103 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N GLU P 105 " --> pdb=" O LEU P 62 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA P 64 " --> pdb=" O GLU P 105 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ARG P 107 " --> pdb=" O ALA P 64 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU P 66 " --> pdb=" O ARG P 107 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N MET P 109 " --> pdb=" O LEU P 66 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE P 68 " --> pdb=" O MET P 109 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL P 100 " --> pdb=" O VAL G 119 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 115 through 119 removed outlier: 3.592A pdb=" N VAL G 100 " --> pdb=" O VAL F 119 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU G 62 " --> pdb=" O SER G 103 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N GLU G 105 " --> pdb=" O LEU G 62 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ALA G 64 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ARG G 107 " --> pdb=" O ALA G 64 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU G 66 " --> pdb=" O ARG G 107 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N MET G 109 " --> pdb=" O LEU G 66 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE G 68 " --> pdb=" O MET G 109 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N TYR G 61 " --> pdb=" O THR G 9 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU G 4 " --> pdb=" O ARG G 43 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL G 45 " --> pdb=" O LEU G 4 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE G 6 " --> pdb=" O VAL G 45 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU G 47 " --> pdb=" O ILE G 6 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ALA G 8 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ALA P 49 " --> pdb=" O PHE G 44 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 13 through 14 removed outlier: 6.832A pdb=" N ARG G 13 " --> pdb=" O ALA G 93 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'V' and resid 49 through 52 removed outlier: 4.415A pdb=" N ALA V 49 " --> pdb=" O PHE H 44 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU H 4 " --> pdb=" O ARG H 43 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL H 45 " --> pdb=" O LEU H 4 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE H 6 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU H 47 " --> pdb=" O ILE H 6 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ALA H 8 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N TYR H 61 " --> pdb=" O THR H 9 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU H 62 " --> pdb=" O SER H 103 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N GLU H 105 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ALA H 64 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ARG H 107 " --> pdb=" O ALA H 64 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU H 66 " --> pdb=" O ARG H 107 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N MET H 109 " --> pdb=" O LEU H 66 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE H 68 " --> pdb=" O MET H 109 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL H 100 " --> pdb=" O VAL W 119 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 13 through 14 removed outlier: 6.832A pdb=" N ARG H 13 " --> pdb=" O ALA H 93 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 49 through 52 removed outlier: 4.431A pdb=" N ALA H 49 " --> pdb=" O PHE W 44 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU W 4 " --> pdb=" O ARG W 43 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL W 45 " --> pdb=" O LEU W 4 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ILE W 6 " --> pdb=" O VAL W 45 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU W 47 " --> pdb=" O ILE W 6 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ALA W 8 " --> pdb=" O LEU W 47 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N TYR W 61 " --> pdb=" O THR W 9 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU W 62 " --> pdb=" O SER W 103 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N GLU W 105 " --> pdb=" O LEU W 62 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA W 64 " --> pdb=" O GLU W 105 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ARG W 107 " --> pdb=" O ALA W 64 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU W 66 " --> pdb=" O ARG W 107 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N MET W 109 " --> pdb=" O LEU W 66 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE W 68 " --> pdb=" O MET W 109 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL W 100 " --> pdb=" O VAL V 119 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 115 through 119 removed outlier: 3.597A pdb=" N VAL V 100 " --> pdb=" O VAL H 119 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU V 62 " --> pdb=" O SER V 103 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N GLU V 105 " --> pdb=" O LEU V 62 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA V 64 " --> pdb=" O GLU V 105 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ARG V 107 " --> pdb=" O ALA V 64 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU V 66 " --> pdb=" O ARG V 107 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N MET V 109 " --> pdb=" O LEU V 66 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE V 68 " --> pdb=" O MET V 109 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N TYR V 61 " --> pdb=" O THR V 9 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU V 4 " --> pdb=" O ARG V 43 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL V 45 " --> pdb=" O LEU V 4 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE V 6 " --> pdb=" O VAL V 45 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU V 47 " --> pdb=" O ILE V 6 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ALA V 8 " --> pdb=" O LEU V 47 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ALA W 49 " --> pdb=" O PHE V 44 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 13 through 14 removed outlier: 6.832A pdb=" N ARG M 13 " --> pdb=" O ALA M 93 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'O' and resid 49 through 52 removed outlier: 4.394A pdb=" N ALA O 49 " --> pdb=" O PHE N 44 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU N 4 " --> pdb=" O ARG N 43 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL N 45 " --> pdb=" O LEU N 4 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE N 6 " --> pdb=" O VAL N 45 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU N 47 " --> pdb=" O ILE N 6 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ALA N 8 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N TYR N 61 " --> pdb=" O THR N 9 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU N 62 " --> pdb=" O SER N 103 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N GLU N 105 " --> pdb=" O LEU N 62 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ALA N 64 " --> pdb=" O GLU N 105 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ARG N 107 " --> pdb=" O ALA N 64 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU N 66 " --> pdb=" O ARG N 107 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N MET N 109 " --> pdb=" O LEU N 66 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE N 68 " --> pdb=" O MET N 109 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL N 100 " --> pdb=" O VAL X 119 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 13 through 14 removed outlier: 6.832A pdb=" N ARG N 13 " --> pdb=" O ALA N 93 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 49 through 52 removed outlier: 4.434A pdb=" N ALA N 49 " --> pdb=" O PHE X 44 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU X 4 " --> pdb=" O ARG X 43 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N VAL X 45 " --> pdb=" O LEU X 4 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE X 6 " --> pdb=" O VAL X 45 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU X 47 " --> pdb=" O ILE X 6 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ALA X 8 " --> pdb=" O LEU X 47 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N TYR X 61 " --> pdb=" O THR X 9 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU X 62 " --> pdb=" O SER X 103 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N GLU X 105 " --> pdb=" O LEU X 62 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA X 64 " --> pdb=" O GLU X 105 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ARG X 107 " --> pdb=" O ALA X 64 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU X 66 " --> pdb=" O ARG X 107 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N MET X 109 " --> pdb=" O LEU X 66 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE X 68 " --> pdb=" O MET X 109 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL X 100 " --> pdb=" O VAL O 119 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 115 through 119 removed outlier: 3.637A pdb=" N VAL O 100 " --> pdb=" O VAL N 119 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU O 62 " --> pdb=" O SER O 103 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N GLU O 105 " --> pdb=" O LEU O 62 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA O 64 " --> pdb=" O GLU O 105 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ARG O 107 " --> pdb=" O ALA O 64 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU O 66 " --> pdb=" O ARG O 107 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N MET O 109 " --> pdb=" O LEU O 66 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE O 68 " --> pdb=" O MET O 109 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N TYR O 61 " --> pdb=" O THR O 9 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU O 4 " --> pdb=" O ARG O 43 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL O 45 " --> pdb=" O LEU O 4 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE O 6 " --> pdb=" O VAL O 45 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N LEU O 47 " --> pdb=" O ILE O 6 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ALA O 8 " --> pdb=" O LEU O 47 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA X 49 " --> pdb=" O PHE O 44 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'O' and resid 13 through 14 removed outlier: 6.833A pdb=" N ARG O 13 " --> pdb=" O ALA O 93 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'P' and resid 13 through 14 removed outlier: 6.833A pdb=" N ARG P 13 " --> pdb=" O ALA P 93 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'U' and resid 13 through 14 removed outlier: 6.831A pdb=" N ARG U 13 " --> pdb=" O ALA U 93 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'V' and resid 13 through 14 removed outlier: 6.833A pdb=" N ARG V 13 " --> pdb=" O ALA V 93 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'W' and resid 13 through 14 removed outlier: 6.833A pdb=" N ARG W 13 " --> pdb=" O ALA W 93 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'X' and resid 13 through 14 removed outlier: 6.832A pdb=" N ARG X 13 " --> pdb=" O ALA X 93 " (cutoff:3.500A) 1368 hydrogen bonds defined for protein. 4032 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.11 Time building geometry restraints manager: 11.19 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: 8941 1.34 - 1.46: 2966 1.46 - 1.57: 14277 1.57 - 1.69: 12 1.69 - 1.80: 180 Bond restraints: 26376 Sorted by residual: bond pdb=" CB GLU O 48 " pdb=" CG GLU O 48 " ideal model delta sigma weight residual 1.520 1.574 -0.054 3.00e-02 1.11e+03 3.23e+00 bond pdb=" CB GLU W 48 " pdb=" CG GLU W 48 " ideal model delta sigma weight residual 1.520 1.574 -0.054 3.00e-02 1.11e+03 3.22e+00 bond pdb=" CB GLU G 48 " pdb=" CG GLU G 48 " ideal model delta sigma weight residual 1.520 1.573 -0.053 3.00e-02 1.11e+03 3.17e+00 bond pdb=" CB GLU F 48 " pdb=" CG GLU F 48 " ideal model delta sigma weight residual 1.520 1.573 -0.053 3.00e-02 1.11e+03 3.16e+00 bond pdb=" CB GLU X 48 " pdb=" CG GLU X 48 " ideal model delta sigma weight residual 1.520 1.573 -0.053 3.00e-02 1.11e+03 3.14e+00 ... (remaining 26371 not shown) Histogram of bond angle deviations from ideal: 100.28 - 107.02: 346 107.02 - 113.75: 15295 113.75 - 120.49: 10815 120.49 - 127.23: 8980 127.23 - 133.96: 84 Bond angle restraints: 35520 Sorted by residual: angle pdb=" CA GLU K 77 " pdb=" CB GLU K 77 " pdb=" CG GLU K 77 " ideal model delta sigma weight residual 114.10 122.28 -8.18 2.00e+00 2.50e-01 1.67e+01 angle pdb=" CA GLU D 77 " pdb=" CB GLU D 77 " pdb=" CG GLU D 77 " ideal model delta sigma weight residual 114.10 122.27 -8.17 2.00e+00 2.50e-01 1.67e+01 angle pdb=" CA GLU A 77 " pdb=" CB GLU A 77 " pdb=" CG GLU A 77 " ideal model delta sigma weight residual 114.10 122.26 -8.16 2.00e+00 2.50e-01 1.66e+01 angle pdb=" CA GLU C 77 " pdb=" CB GLU C 77 " pdb=" CG GLU C 77 " ideal model delta sigma weight residual 114.10 122.25 -8.15 2.00e+00 2.50e-01 1.66e+01 angle pdb=" CA GLU Q 77 " pdb=" CB GLU Q 77 " pdb=" CG GLU Q 77 " ideal model delta sigma weight residual 114.10 122.25 -8.15 2.00e+00 2.50e-01 1.66e+01 ... (remaining 35515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 14736 17.88 - 35.77: 1140 35.77 - 53.65: 168 53.65 - 71.54: 48 71.54 - 89.42: 96 Dihedral angle restraints: 16188 sinusoidal: 6408 harmonic: 9780 Sorted by residual: dihedral pdb=" CB GLU X 98 " pdb=" CG GLU X 98 " pdb=" CD GLU X 98 " pdb=" OE1 GLU X 98 " ideal model delta sinusoidal sigma weight residual 0.00 -89.42 89.42 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU M 98 " pdb=" CG GLU M 98 " pdb=" CD GLU M 98 " pdb=" OE1 GLU M 98 " ideal model delta sinusoidal sigma weight residual 0.00 -89.42 89.42 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU O 98 " pdb=" CG GLU O 98 " pdb=" CD GLU O 98 " pdb=" OE1 GLU O 98 " ideal model delta sinusoidal sigma weight residual 0.00 -89.40 89.40 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 16185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2298 0.031 - 0.063: 1364 0.063 - 0.094: 353 0.094 - 0.125: 184 0.125 - 0.156: 37 Chirality restraints: 4236 Sorted by residual: chirality pdb=" CB VAL E 57 " pdb=" CA VAL E 57 " pdb=" CG1 VAL E 57 " pdb=" CG2 VAL E 57 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.12e-01 chirality pdb=" CB VAL O 57 " pdb=" CA VAL O 57 " pdb=" CG1 VAL O 57 " pdb=" CG2 VAL O 57 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.09e-01 chirality pdb=" CB VAL V 57 " pdb=" CA VAL V 57 " pdb=" CG1 VAL V 57 " pdb=" CG2 VAL V 57 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.07e-01 ... (remaining 4233 not shown) Planarity restraints: 4560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU V 48 " -0.010 2.00e-02 2.50e+03 2.10e-02 4.39e+00 pdb=" CD GLU V 48 " 0.036 2.00e-02 2.50e+03 pdb=" OE1 GLU V 48 " -0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU V 48 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU P 48 " -0.010 2.00e-02 2.50e+03 2.07e-02 4.27e+00 pdb=" CD GLU P 48 " 0.036 2.00e-02 2.50e+03 pdb=" OE1 GLU P 48 " -0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU P 48 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU N 48 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.27e+00 pdb=" CD GLU N 48 " -0.036 2.00e-02 2.50e+03 pdb=" OE1 GLU N 48 " 0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU N 48 " 0.013 2.00e-02 2.50e+03 ... (remaining 4557 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.90: 9189 2.90 - 3.40: 22824 3.40 - 3.90: 40203 3.90 - 4.40: 48940 4.40 - 4.90: 83327 Nonbonded interactions: 204483 Sorted by model distance: nonbonded pdb=" O ILE N 74 " pdb=" OG1 THR N 78 " model vdw 2.394 2.440 nonbonded pdb=" O ILE W 74 " pdb=" OG1 THR W 78 " model vdw 2.394 2.440 nonbonded pdb=" O ILE G 74 " pdb=" OG1 THR G 78 " model vdw 2.394 2.440 nonbonded pdb=" O ILE P 74 " pdb=" OG1 THR P 78 " model vdw 2.395 2.440 nonbonded pdb=" O ILE V 74 " pdb=" OG1 THR V 78 " model vdw 2.395 2.440 ... (remaining 204478 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 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } 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: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.680 Check model and map are aligned: 0.380 Set scattering table: 0.250 Process input model: 66.990 Find NCS groups from input model: 1.610 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 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 0.054 26376 Z= 0.408 Angle : 0.747 8.176 35520 Z= 0.429 Chirality : 0.045 0.156 4236 Planarity : 0.005 0.049 4560 Dihedral : 15.208 89.423 9900 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.45 % Allowed : 4.99 % Favored : 94.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.86 (0.09), residues: 3384 helix: -5.04 (0.03), residues: 2004 sheet: 0.27 (0.26), residues: 420 loop : -2.46 (0.13), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP C 86 HIS 0.003 0.001 HIS P 63 PHE 0.006 0.001 PHE W 44 TYR 0.014 0.002 TYR F 61 ARG 0.005 0.001 ARG W 43 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 704 time to evaluate : 3.022 Fit side-chains REVERT: A 51 GLU cc_start: 0.7791 (tp30) cc_final: 0.7514 (tp30) REVERT: A 75 LYS cc_start: 0.8285 (mttt) cc_final: 0.8025 (mttt) REVERT: C 51 GLU cc_start: 0.7785 (tp30) cc_final: 0.7501 (tp30) REVERT: C 53 LYS cc_start: 0.8965 (tttt) cc_final: 0.8656 (tttt) REVERT: D 65 LYS cc_start: 0.8365 (mmmt) cc_final: 0.8004 (mtpt) REVERT: H 70 ASP cc_start: 0.7936 (p0) cc_final: 0.7670 (p0) REVERT: I 67 MET cc_start: 0.8939 (mtp) cc_final: 0.8683 (mtm) REVERT: J 67 MET cc_start: 0.8998 (mtp) cc_final: 0.8631 (mtp) REVERT: J 158 ARG cc_start: 0.8204 (mmt-90) cc_final: 0.7968 (mmt180) REVERT: L 151 ASP cc_start: 0.7493 (m-30) cc_final: 0.7204 (m-30) REVERT: M 37 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7435 (tm-30) REVERT: R 123 ARG cc_start: 0.8262 (mmm-85) cc_final: 0.7897 (mmm160) REVERT: S 75 LYS cc_start: 0.8243 (mttt) cc_final: 0.7983 (mttt) REVERT: S 92 LEU cc_start: 0.8815 (mt) cc_final: 0.8602 (mm) REVERT: S 96 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7301 (mt-10) REVERT: S 97 MET cc_start: 0.8427 (mtp) cc_final: 0.8119 (mtp) REVERT: W 15 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7813 (mt-10) REVERT: W 24 GLN cc_start: 0.8053 (mt0) cc_final: 0.7792 (mt0) REVERT: X 37 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7542 (tm-30) outliers start: 12 outliers final: 2 residues processed: 704 average time/residue: 2.0444 time to fit residues: 1591.2093 Evaluate side-chains 460 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 458 time to evaluate : 3.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain L residue 162 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 273 optimal weight: 0.7980 chunk 245 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 165 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 253 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 154 optimal weight: 9.9990 chunk 189 optimal weight: 4.9990 chunk 294 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 34 GLN M 34 GLN O 34 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 26376 Z= 0.293 Angle : 0.524 5.868 35520 Z= 0.282 Chirality : 0.040 0.121 4236 Planarity : 0.005 0.038 4560 Dihedral : 4.248 21.882 3724 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.82 % Allowed : 18.19 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.44 (0.11), residues: 3384 helix: -2.90 (0.08), residues: 2028 sheet: 1.13 (0.25), residues: 420 loop : -1.91 (0.15), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP I 86 HIS 0.004 0.001 HIS H 63 PHE 0.005 0.001 PHE A 40 TYR 0.013 0.001 TYR O 61 ARG 0.003 0.000 ARG N 43 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 470 time to evaluate : 3.122 Fit side-chains REVERT: A 51 GLU cc_start: 0.7677 (tp30) cc_final: 0.7417 (tp30) REVERT: B 61 ASN cc_start: 0.8380 (m-40) cc_final: 0.8144 (m110) REVERT: C 51 GLU cc_start: 0.7717 (tp30) cc_final: 0.7449 (tp30) REVERT: C 67 MET cc_start: 0.8689 (mtp) cc_final: 0.8480 (mtm) REVERT: C 89 LYS cc_start: 0.8479 (ttpt) cc_final: 0.8242 (ttmp) REVERT: D 65 LYS cc_start: 0.8116 (mmmt) cc_final: 0.7721 (mtpt) REVERT: D 67 MET cc_start: 0.8721 (mtp) cc_final: 0.8413 (mtp) REVERT: E 20 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7519 (mt-10) REVERT: G 51 ARG cc_start: 0.8237 (tpp-160) cc_final: 0.8028 (tpp-160) REVERT: H 20 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7446 (mp0) REVERT: H 51 ARG cc_start: 0.8282 (tpp-160) cc_final: 0.8009 (tpp-160) REVERT: I 67 MET cc_start: 0.8462 (mtp) cc_final: 0.8252 (mtm) REVERT: J 51 GLU cc_start: 0.7713 (tp30) cc_final: 0.7463 (tp30) REVERT: J 167 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7270 (mttm) REVERT: J 184 MET cc_start: 0.7746 (OUTLIER) cc_final: 0.7510 (mmm) REVERT: K 151 ASP cc_start: 0.7504 (m-30) cc_final: 0.7293 (m-30) REVERT: L 184 MET cc_start: 0.7672 (OUTLIER) cc_final: 0.7025 (mmt) REVERT: N 51 ARG cc_start: 0.8197 (tpp-160) cc_final: 0.7967 (tpp-160) REVERT: R 184 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.7765 (ttp) REVERT: S 167 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7663 (mttm) REVERT: T 167 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7748 (mttm) outliers start: 49 outliers final: 17 residues processed: 491 average time/residue: 1.7952 time to fit residues: 989.5435 Evaluate side-chains 453 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 430 time to evaluate : 3.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain C residue 167 LYS Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain J residue 162 ILE Chi-restraints excluded: chain J residue 167 LYS Chi-restraints excluded: chain J residue 184 MET Chi-restraints excluded: chain L residue 184 MET Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain N residue 83 SER Chi-restraints excluded: chain O residue 70 ASP Chi-restraints excluded: chain R residue 162 ILE Chi-restraints excluded: chain R residue 184 MET Chi-restraints excluded: chain S residue 167 LYS Chi-restraints excluded: chain T residue 162 ILE Chi-restraints excluded: chain T residue 167 LYS Chi-restraints excluded: chain U residue 70 ASP Chi-restraints excluded: chain U residue 83 SER Chi-restraints excluded: chain W residue 83 SER Chi-restraints excluded: chain W residue 103 SER Chi-restraints excluded: chain X residue 70 ASP Chi-restraints excluded: chain X residue 103 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 163 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 chunk 244 optimal weight: 1.9990 chunk 200 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 294 optimal weight: 5.9990 chunk 318 optimal weight: 10.0000 chunk 262 optimal weight: 3.9990 chunk 292 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 236 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 26376 Z= 0.244 Angle : 0.470 5.894 35520 Z= 0.249 Chirality : 0.039 0.118 4236 Planarity : 0.003 0.032 4560 Dihedral : 3.844 12.466 3720 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.19 % Allowed : 20.05 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.13), residues: 3384 helix: -1.19 (0.11), residues: 2004 sheet: 1.67 (0.24), residues: 420 loop : -1.57 (0.15), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP A 86 HIS 0.003 0.001 HIS H 63 PHE 0.004 0.001 PHE T 40 TYR 0.012 0.001 TYR O 61 ARG 0.003 0.000 ARG I 158 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 465 time to evaluate : 3.333 Fit side-chains REVERT: A 51 GLU cc_start: 0.7624 (tp30) cc_final: 0.7360 (tp30) REVERT: B 51 GLU cc_start: 0.7559 (tp30) cc_final: 0.7249 (tp30) REVERT: B 61 ASN cc_start: 0.8378 (m-40) cc_final: 0.8148 (m110) REVERT: C 51 GLU cc_start: 0.7622 (tp30) cc_final: 0.7330 (tp30) REVERT: C 89 LYS cc_start: 0.8440 (ttpt) cc_final: 0.8185 (ttmp) REVERT: E 20 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7425 (mp0) REVERT: F 48 GLU cc_start: 0.7273 (mm-30) cc_final: 0.7064 (mp0) REVERT: H 20 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7476 (mp0) REVERT: H 97 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7501 (mm-30) REVERT: J 167 LYS cc_start: 0.7669 (OUTLIER) cc_final: 0.7314 (mttm) REVERT: J 184 MET cc_start: 0.7763 (OUTLIER) cc_final: 0.7543 (mmm) REVERT: K 123 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.6910 (mmm160) REVERT: L 184 MET cc_start: 0.7634 (OUTLIER) cc_final: 0.7021 (mmt) REVERT: R 93 ARG cc_start: 0.8441 (ttp80) cc_final: 0.8033 (ttt180) REVERT: R 184 MET cc_start: 0.7775 (OUTLIER) cc_final: 0.7540 (ttp) REVERT: S 167 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7595 (mttm) REVERT: T 167 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7680 (mttm) REVERT: W 15 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7605 (mt-10) outliers start: 59 outliers final: 30 residues processed: 493 average time/residue: 1.8605 time to fit residues: 1024.9871 Evaluate side-chains 471 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 433 time to evaluate : 3.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 167 LYS Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain C residue 167 LYS Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain H residue 20 GLU Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain J residue 141 GLU Chi-restraints excluded: chain J residue 162 ILE Chi-restraints excluded: chain J residue 167 LYS Chi-restraints excluded: chain J residue 184 MET Chi-restraints excluded: chain K residue 123 ARG Chi-restraints excluded: chain K residue 167 LYS Chi-restraints excluded: chain L residue 162 ILE Chi-restraints excluded: chain L residue 167 LYS Chi-restraints excluded: chain L residue 184 MET Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain N residue 42 SER Chi-restraints excluded: chain N residue 103 SER Chi-restraints excluded: chain O residue 70 ASP Chi-restraints excluded: chain O residue 103 SER Chi-restraints excluded: chain P residue 42 SER Chi-restraints excluded: chain P residue 103 SER Chi-restraints excluded: chain Q residue 162 ILE Chi-restraints excluded: chain R residue 162 ILE Chi-restraints excluded: chain R residue 184 MET Chi-restraints excluded: chain S residue 167 LYS Chi-restraints excluded: chain T residue 162 ILE Chi-restraints excluded: chain T residue 167 LYS Chi-restraints excluded: chain U residue 70 ASP Chi-restraints excluded: chain U residue 83 SER Chi-restraints excluded: chain U residue 103 SER Chi-restraints excluded: chain W residue 103 SER Chi-restraints excluded: chain X residue 70 ASP Chi-restraints excluded: chain X residue 103 SER Chi-restraints excluded: chain X residue 116 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 291 optimal weight: 2.9990 chunk 221 optimal weight: 7.9990 chunk 152 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 140 optimal weight: 0.7980 chunk 197 optimal weight: 5.9990 chunk 295 optimal weight: 0.7980 chunk 313 optimal weight: 2.9990 chunk 154 optimal weight: 0.3980 chunk 280 optimal weight: 0.9980 chunk 84 optimal weight: 8.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 26376 Z= 0.140 Angle : 0.407 6.533 35520 Z= 0.218 Chirality : 0.038 0.117 4236 Planarity : 0.002 0.031 4560 Dihedral : 3.471 11.306 3720 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.82 % Allowed : 22.25 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.14), residues: 3384 helix: -0.12 (0.11), residues: 2004 sheet: 2.07 (0.24), residues: 420 loop : -1.21 (0.16), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 86 HIS 0.001 0.000 HIS P 63 PHE 0.003 0.000 PHE B 154 TYR 0.012 0.001 TYR O 61 ARG 0.003 0.000 ARG S 158 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 500 time to evaluate : 3.187 Fit side-chains REVERT: A 51 GLU cc_start: 0.7520 (tp30) cc_final: 0.7205 (tp30) REVERT: B 61 ASN cc_start: 0.8354 (m-40) cc_final: 0.8093 (m110) REVERT: B 89 LYS cc_start: 0.8237 (ttpt) cc_final: 0.8011 (tttt) REVERT: B 134 ARG cc_start: 0.8031 (mtm-85) cc_final: 0.7794 (mtt90) REVERT: C 36 GLU cc_start: 0.7964 (tt0) cc_final: 0.7736 (tt0) REVERT: C 51 GLU cc_start: 0.7383 (tp30) cc_final: 0.7058 (tp30) REVERT: C 89 LYS cc_start: 0.8370 (ttpt) cc_final: 0.8114 (ttmp) REVERT: D 65 LYS cc_start: 0.7904 (mtpt) cc_final: 0.7440 (mtpt) REVERT: H 20 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7382 (mp0) REVERT: H 51 ARG cc_start: 0.8230 (tpp-160) cc_final: 0.7947 (ttm110) REVERT: L 93 ARG cc_start: 0.8368 (ttp80) cc_final: 0.8085 (ttt180) REVERT: L 184 MET cc_start: 0.7690 (OUTLIER) cc_final: 0.7124 (mmt) REVERT: P 20 GLU cc_start: 0.7640 (mp0) cc_final: 0.7346 (mp0) REVERT: R 93 ARG cc_start: 0.8417 (ttp80) cc_final: 0.7959 (ttt180) REVERT: S 73 LYS cc_start: 0.8556 (mtpt) cc_final: 0.8274 (tttp) REVERT: T 167 LYS cc_start: 0.7770 (OUTLIER) cc_final: 0.7532 (mttm) REVERT: W 15 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7641 (mt-10) REVERT: W 20 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7361 (mp0) REVERT: W 51 ARG cc_start: 0.8310 (tpp-160) cc_final: 0.8051 (ttm110) outliers start: 49 outliers final: 25 residues processed: 521 average time/residue: 1.7090 time to fit residues: 1003.5288 Evaluate side-chains 482 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 454 time to evaluate : 3.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 103 SER Chi-restraints excluded: chain H residue 20 GLU Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain J residue 162 ILE Chi-restraints excluded: chain L residue 184 MET Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain O residue 70 ASP Chi-restraints excluded: chain O residue 103 SER Chi-restraints excluded: chain P residue 103 SER Chi-restraints excluded: chain Q residue 162 ILE Chi-restraints excluded: chain R residue 162 ILE Chi-restraints excluded: chain T residue 162 ILE Chi-restraints excluded: chain T residue 167 LYS Chi-restraints excluded: chain U residue 70 ASP Chi-restraints excluded: chain U residue 103 SER Chi-restraints excluded: chain V residue 103 SER Chi-restraints excluded: chain W residue 103 SER Chi-restraints excluded: chain X residue 70 ASP Chi-restraints excluded: chain X residue 103 SER Chi-restraints excluded: chain X residue 116 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 260 optimal weight: 0.5980 chunk 177 optimal weight: 0.0270 chunk 4 optimal weight: 1.9990 chunk 233 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 267 optimal weight: 0.9980 chunk 216 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 159 optimal weight: 0.9980 chunk 281 optimal weight: 0.0670 chunk 79 optimal weight: 0.0980 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 26376 Z= 0.104 Angle : 0.379 5.417 35520 Z= 0.203 Chirality : 0.037 0.113 4236 Planarity : 0.002 0.031 4560 Dihedral : 3.217 9.784 3720 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.75 % Allowed : 24.70 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.14), residues: 3384 helix: 0.84 (0.12), residues: 1932 sheet: 2.45 (0.24), residues: 396 loop : -0.77 (0.16), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 86 HIS 0.001 0.000 HIS H 63 PHE 0.005 0.000 PHE C 154 TYR 0.012 0.001 TYR O 61 ARG 0.003 0.000 ARG S 158 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 514 time to evaluate : 3.052 Fit side-chains REVERT: B 51 GLU cc_start: 0.7364 (tp30) cc_final: 0.6999 (tp30) REVERT: B 61 ASN cc_start: 0.8359 (m-40) cc_final: 0.8111 (m110) REVERT: B 89 LYS cc_start: 0.8079 (ttpt) cc_final: 0.7805 (tttt) REVERT: C 36 GLU cc_start: 0.7923 (tt0) cc_final: 0.7702 (tt0) REVERT: C 51 GLU cc_start: 0.7197 (tp30) cc_final: 0.6948 (tp30) REVERT: D 65 LYS cc_start: 0.7834 (mtpt) cc_final: 0.7375 (mtpt) REVERT: H 20 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7298 (mp0) REVERT: H 51 ARG cc_start: 0.8228 (tpp-160) cc_final: 0.7990 (ttm110) REVERT: I 36 GLU cc_start: 0.7962 (tt0) cc_final: 0.7700 (tt0) REVERT: K 47 TYR cc_start: 0.8868 (m-80) cc_final: 0.8561 (m-80) REVERT: L 36 GLU cc_start: 0.8035 (tt0) cc_final: 0.7798 (tt0) REVERT: L 93 ARG cc_start: 0.8429 (ttp80) cc_final: 0.8144 (ttt180) REVERT: L 184 MET cc_start: 0.7637 (OUTLIER) cc_final: 0.7092 (mmt) REVERT: P 20 GLU cc_start: 0.7543 (mp0) cc_final: 0.7257 (mp0) REVERT: R 93 ARG cc_start: 0.8404 (ttp80) cc_final: 0.8090 (ttt180) REVERT: R 184 MET cc_start: 0.7709 (mmm) cc_final: 0.7001 (mmm) REVERT: S 73 LYS cc_start: 0.8552 (mtpt) cc_final: 0.8310 (tttp) REVERT: S 162 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7957 (mp) REVERT: T 93 ARG cc_start: 0.8428 (ttp80) cc_final: 0.8202 (ttt180) REVERT: W 15 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7693 (mt-10) REVERT: W 51 ARG cc_start: 0.8290 (tpp-160) cc_final: 0.8045 (ttm110) outliers start: 47 outliers final: 17 residues processed: 542 average time/residue: 1.6952 time to fit residues: 1036.5783 Evaluate side-chains 499 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 479 time to evaluate : 3.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 167 LYS Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain H residue 20 GLU Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain J residue 162 ILE Chi-restraints excluded: chain L residue 184 MET Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain O residue 59 ARG Chi-restraints excluded: chain O residue 70 ASP Chi-restraints excluded: chain Q residue 162 ILE Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 150 SER Chi-restraints excluded: chain R residue 162 ILE Chi-restraints excluded: chain S residue 162 ILE Chi-restraints excluded: chain T residue 162 ILE Chi-restraints excluded: chain U residue 70 ASP Chi-restraints excluded: chain V residue 103 SER Chi-restraints excluded: chain X residue 70 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 105 optimal weight: 0.5980 chunk 282 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 77 optimal weight: 0.6980 chunk 313 optimal weight: 5.9990 chunk 260 optimal weight: 0.7980 chunk 145 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 164 optimal weight: 9.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 26376 Z= 0.199 Angle : 0.424 8.153 35520 Z= 0.223 Chirality : 0.039 0.116 4236 Planarity : 0.003 0.030 4560 Dihedral : 3.374 10.376 3720 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.79 % Allowed : 25.82 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.14), residues: 3384 helix: 0.89 (0.11), residues: 2004 sheet: 2.49 (0.23), residues: 420 loop : -0.80 (0.17), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP I 86 HIS 0.002 0.001 HIS H 63 PHE 0.004 0.001 PHE S 154 TYR 0.011 0.001 TYR S 94 ARG 0.003 0.000 ARG U 51 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 465 time to evaluate : 3.140 Fit side-chains REVERT: B 51 GLU cc_start: 0.7432 (tp30) cc_final: 0.7093 (tp30) REVERT: B 61 ASN cc_start: 0.8384 (m-40) cc_final: 0.8178 (m110) REVERT: B 89 LYS cc_start: 0.8154 (ttpt) cc_final: 0.7869 (tttt) REVERT: C 51 GLU cc_start: 0.7343 (tp30) cc_final: 0.7091 (tp30) REVERT: D 65 LYS cc_start: 0.7874 (mtpt) cc_final: 0.7410 (mtpt) REVERT: D 167 LYS cc_start: 0.7716 (OUTLIER) cc_final: 0.7511 (mtmm) REVERT: E 97 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7480 (mm-30) REVERT: G 20 GLU cc_start: 0.7720 (mp0) cc_final: 0.7224 (mp0) REVERT: H 20 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7408 (mp0) REVERT: L 93 ARG cc_start: 0.8429 (ttp80) cc_final: 0.8175 (ttt180) REVERT: L 184 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.6988 (mmt) REVERT: N 51 ARG cc_start: 0.8266 (ttm110) cc_final: 0.8066 (tpp-160) REVERT: O 20 GLU cc_start: 0.7602 (mp0) cc_final: 0.7208 (mp0) REVERT: P 20 GLU cc_start: 0.7637 (mp0) cc_final: 0.7297 (mp0) REVERT: R 184 MET cc_start: 0.7659 (mmm) cc_final: 0.6998 (mmm) REVERT: S 162 ILE cc_start: 0.8262 (OUTLIER) cc_final: 0.8031 (mp) REVERT: S 167 LYS cc_start: 0.7549 (OUTLIER) cc_final: 0.7268 (mttm) REVERT: T 93 ARG cc_start: 0.8465 (ttp80) cc_final: 0.8228 (ttt180) REVERT: W 15 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7721 (mt-10) REVERT: W 20 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7300 (mp0) REVERT: W 51 ARG cc_start: 0.8331 (tpp-160) cc_final: 0.7959 (ttm110) outliers start: 75 outliers final: 50 residues processed: 511 average time/residue: 1.7898 time to fit residues: 1029.4098 Evaluate side-chains 520 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 464 time to evaluate : 3.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 167 LYS Chi-restraints excluded: chain C residue 167 LYS Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 167 LYS Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 103 SER Chi-restraints excluded: chain H residue 20 GLU Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain I residue 150 SER Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain J residue 150 SER Chi-restraints excluded: chain J residue 162 ILE Chi-restraints excluded: chain K residue 150 SER Chi-restraints excluded: chain L residue 49 ASP Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 162 ILE Chi-restraints excluded: chain L residue 184 MET Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain O residue 42 SER Chi-restraints excluded: chain O residue 70 ASP Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain O residue 103 SER Chi-restraints excluded: chain P residue 42 SER Chi-restraints excluded: chain Q residue 67 MET Chi-restraints excluded: chain Q residue 162 ILE Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 150 SER Chi-restraints excluded: chain R residue 162 ILE Chi-restraints excluded: chain S residue 92 LEU Chi-restraints excluded: chain S residue 150 SER Chi-restraints excluded: chain S residue 162 ILE Chi-restraints excluded: chain S residue 167 LYS Chi-restraints excluded: chain T residue 150 SER Chi-restraints excluded: chain T residue 162 ILE Chi-restraints excluded: chain U residue 42 SER Chi-restraints excluded: chain U residue 70 ASP Chi-restraints excluded: chain U residue 73 ASP Chi-restraints excluded: chain U residue 83 SER Chi-restraints excluded: chain U residue 103 SER Chi-restraints excluded: chain V residue 42 SER Chi-restraints excluded: chain V residue 103 SER Chi-restraints excluded: chain W residue 20 GLU Chi-restraints excluded: chain W residue 103 SER Chi-restraints excluded: chain X residue 42 SER Chi-restraints excluded: chain X residue 70 ASP Chi-restraints excluded: chain X residue 103 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 302 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 178 optimal weight: 6.9990 chunk 228 optimal weight: 2.9990 chunk 177 optimal weight: 0.0870 chunk 263 optimal weight: 0.0060 chunk 175 optimal weight: 0.8980 chunk 312 optimal weight: 5.9990 chunk 195 optimal weight: 5.9990 chunk 190 optimal weight: 2.9990 chunk 144 optimal weight: 0.2980 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 26376 Z= 0.114 Angle : 0.389 7.325 35520 Z= 0.206 Chirality : 0.037 0.109 4236 Planarity : 0.002 0.031 4560 Dihedral : 3.163 9.646 3720 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.79 % Allowed : 27.31 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.14), residues: 3384 helix: 1.53 (0.12), residues: 1992 sheet: 2.67 (0.24), residues: 420 loop : -0.69 (0.17), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP Q 86 HIS 0.001 0.000 HIS W 3 PHE 0.005 0.000 PHE S 154 TYR 0.010 0.001 TYR O 61 ARG 0.003 0.000 ARG I 158 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 457 time to evaluate : 2.941 Fit side-chains REVERT: B 61 ASN cc_start: 0.8363 (m-40) cc_final: 0.8138 (m110) REVERT: C 51 GLU cc_start: 0.7184 (tp30) cc_final: 0.6914 (tp30) REVERT: D 65 LYS cc_start: 0.7827 (mtpt) cc_final: 0.7369 (mtpt) REVERT: E 7 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6844 (mt-10) REVERT: G 20 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7122 (mp0) REVERT: H 20 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7306 (mp0) REVERT: J 92 LEU cc_start: 0.8533 (mm) cc_final: 0.8323 (mp) REVERT: K 47 TYR cc_start: 0.8900 (m-80) cc_final: 0.8595 (m-80) REVERT: L 93 ARG cc_start: 0.8361 (ttp80) cc_final: 0.8135 (ttt180) REVERT: L 184 MET cc_start: 0.7546 (OUTLIER) cc_final: 0.6966 (mmt) REVERT: R 184 MET cc_start: 0.7676 (mmm) cc_final: 0.7078 (mmm) REVERT: T 93 ARG cc_start: 0.8382 (ttp80) cc_final: 0.8155 (ttt180) REVERT: W 15 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7642 (mt-10) REVERT: W 20 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7201 (mp0) REVERT: W 51 ARG cc_start: 0.8247 (tpp-160) cc_final: 0.7981 (ttm110) outliers start: 48 outliers final: 33 residues processed: 488 average time/residue: 1.7083 time to fit residues: 939.5396 Evaluate side-chains 465 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 427 time to evaluate : 2.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 167 LYS Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain C residue 167 LYS Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain E residue 7 GLU Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain G residue 20 GLU Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 103 SER Chi-restraints excluded: chain H residue 20 GLU Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain I residue 150 SER Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain J residue 162 ILE Chi-restraints excluded: chain K residue 150 SER Chi-restraints excluded: chain L residue 49 ASP Chi-restraints excluded: chain L residue 184 MET Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain O residue 70 ASP Chi-restraints excluded: chain O residue 103 SER Chi-restraints excluded: chain Q residue 95 MET Chi-restraints excluded: chain Q residue 150 SER Chi-restraints excluded: chain Q residue 162 ILE Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 150 SER Chi-restraints excluded: chain R residue 162 ILE Chi-restraints excluded: chain T residue 162 ILE Chi-restraints excluded: chain U residue 70 ASP Chi-restraints excluded: chain V residue 103 SER Chi-restraints excluded: chain W residue 20 GLU Chi-restraints excluded: chain W residue 103 SER Chi-restraints excluded: chain X residue 70 ASP Chi-restraints excluded: chain X residue 103 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 193 optimal weight: 0.5980 chunk 124 optimal weight: 7.9990 chunk 186 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 60 optimal weight: 0.5980 chunk 198 optimal weight: 0.9990 chunk 212 optimal weight: 0.6980 chunk 154 optimal weight: 5.9990 chunk 29 optimal weight: 0.5980 chunk 245 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 26376 Z= 0.131 Angle : 0.396 7.020 35520 Z= 0.209 Chirality : 0.037 0.114 4236 Planarity : 0.002 0.032 4560 Dihedral : 3.166 9.652 3720 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 2.01 % Allowed : 27.42 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.14), residues: 3384 helix: 1.78 (0.12), residues: 1992 sheet: 2.74 (0.23), residues: 420 loop : -0.61 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP I 86 HIS 0.001 0.000 HIS B 46 PHE 0.004 0.000 PHE L 154 TYR 0.010 0.001 TYR J 94 ARG 0.007 0.000 ARG U 51 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 431 time to evaluate : 3.086 Fit side-chains REVERT: B 61 ASN cc_start: 0.8345 (m-40) cc_final: 0.8144 (m110) REVERT: B 89 LYS cc_start: 0.8060 (ttpt) cc_final: 0.7842 (tttt) REVERT: C 51 GLU cc_start: 0.7183 (tp30) cc_final: 0.6905 (tp30) REVERT: D 65 LYS cc_start: 0.7838 (mtpt) cc_final: 0.7378 (mtpt) REVERT: E 7 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6860 (mt-10) REVERT: G 20 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7019 (mp0) REVERT: H 20 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7305 (mp0) REVERT: H 51 ARG cc_start: 0.7990 (ttm170) cc_final: 0.7744 (ttm170) REVERT: I 77 GLU cc_start: 0.7736 (pm20) cc_final: 0.7422 (pm20) REVERT: J 28 ILE cc_start: 0.8540 (mm) cc_final: 0.8327 (mm) REVERT: J 51 GLU cc_start: 0.7269 (mm-30) cc_final: 0.7037 (tp30) REVERT: K 47 TYR cc_start: 0.8889 (m-80) cc_final: 0.8584 (m-80) REVERT: L 93 ARG cc_start: 0.8318 (ttp80) cc_final: 0.8081 (ttt180) REVERT: L 184 MET cc_start: 0.7591 (OUTLIER) cc_final: 0.7009 (mmt) REVERT: M 7 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7077 (mt-10) REVERT: O 20 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7233 (mp0) REVERT: R 75 LYS cc_start: 0.8247 (mttt) cc_final: 0.8009 (mppt) REVERT: R 184 MET cc_start: 0.7651 (mmm) cc_final: 0.7074 (mmm) REVERT: S 167 LYS cc_start: 0.7563 (OUTLIER) cc_final: 0.7297 (mttm) REVERT: T 93 ARG cc_start: 0.8397 (ttp80) cc_final: 0.8171 (ttt180) REVERT: W 15 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7737 (mt-10) REVERT: W 20 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7229 (mp0) REVERT: W 51 ARG cc_start: 0.8295 (tpp-160) cc_final: 0.7962 (ttm110) outliers start: 54 outliers final: 34 residues processed: 472 average time/residue: 1.6666 time to fit residues: 892.1961 Evaluate side-chains 465 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 423 time to evaluate : 3.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 167 LYS Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain E residue 7 GLU Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain G residue 20 GLU Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 103 SER Chi-restraints excluded: chain H residue 20 GLU Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain J residue 162 ILE Chi-restraints excluded: chain K residue 150 SER Chi-restraints excluded: chain L residue 49 ASP Chi-restraints excluded: chain L residue 184 MET Chi-restraints excluded: chain M residue 7 GLU Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain O residue 70 ASP Chi-restraints excluded: chain O residue 103 SER Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain Q residue 150 SER Chi-restraints excluded: chain Q residue 162 ILE Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 150 SER Chi-restraints excluded: chain R residue 162 ILE Chi-restraints excluded: chain S residue 49 ASP Chi-restraints excluded: chain S residue 167 LYS Chi-restraints excluded: chain T residue 162 ILE Chi-restraints excluded: chain U residue 70 ASP Chi-restraints excluded: chain U residue 73 ASP Chi-restraints excluded: chain U residue 103 SER Chi-restraints excluded: chain V residue 103 SER Chi-restraints excluded: chain W residue 20 GLU Chi-restraints excluded: chain W residue 103 SER Chi-restraints excluded: chain X residue 70 ASP Chi-restraints excluded: chain X residue 73 ASP Chi-restraints excluded: chain X residue 103 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 284 optimal weight: 0.9980 chunk 299 optimal weight: 0.5980 chunk 272 optimal weight: 0.4980 chunk 291 optimal weight: 4.9990 chunk 175 optimal weight: 6.9990 chunk 126 optimal weight: 8.9990 chunk 228 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 262 optimal weight: 3.9990 chunk 275 optimal weight: 0.8980 chunk 289 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 26376 Z= 0.138 Angle : 0.397 6.878 35520 Z= 0.209 Chirality : 0.038 0.112 4236 Planarity : 0.002 0.034 4560 Dihedral : 3.156 9.286 3720 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.05 % Allowed : 27.34 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.14), residues: 3384 helix: 1.92 (0.12), residues: 1992 sheet: 2.73 (0.23), residues: 420 loop : -0.51 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP S 86 HIS 0.001 0.000 HIS B 46 PHE 0.005 0.000 PHE K 136 TYR 0.011 0.001 TYR R 94 ARG 0.008 0.000 ARG U 51 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 449 time to evaluate : 2.824 Fit side-chains REVERT: B 89 LYS cc_start: 0.8073 (ttpt) cc_final: 0.7843 (tttt) REVERT: C 51 GLU cc_start: 0.7175 (tp30) cc_final: 0.6890 (tp30) REVERT: D 65 LYS cc_start: 0.7837 (mtpt) cc_final: 0.7377 (mtpt) REVERT: E 43 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.8756 (ptt-90) REVERT: E 97 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7594 (mm-30) REVERT: E 105 GLU cc_start: 0.8031 (tt0) cc_final: 0.7736 (tm-30) REVERT: G 20 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7095 (mp0) REVERT: H 20 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7298 (mp0) REVERT: H 51 ARG cc_start: 0.8003 (ttm170) cc_final: 0.7787 (ttm170) REVERT: H 110 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7805 (tt0) REVERT: I 77 GLU cc_start: 0.7707 (pm20) cc_final: 0.7465 (pm20) REVERT: J 51 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6950 (tp30) REVERT: K 47 TYR cc_start: 0.8908 (m-80) cc_final: 0.8594 (m-80) REVERT: L 93 ARG cc_start: 0.8312 (ttp80) cc_final: 0.8076 (ttt180) REVERT: L 151 ASP cc_start: 0.7482 (m-30) cc_final: 0.7150 (m-30) REVERT: L 184 MET cc_start: 0.7613 (OUTLIER) cc_final: 0.7040 (mmt) REVERT: M 7 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7213 (mt-10) REVERT: O 20 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7150 (mp0) REVERT: R 75 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.8005 (mppt) REVERT: R 184 MET cc_start: 0.7618 (OUTLIER) cc_final: 0.7413 (mmm) REVERT: S 167 LYS cc_start: 0.7529 (OUTLIER) cc_final: 0.7239 (mttm) REVERT: T 93 ARG cc_start: 0.8395 (ttp80) cc_final: 0.8157 (ttt180) REVERT: W 15 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7735 (mt-10) REVERT: W 20 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.7134 (mp0) REVERT: W 51 ARG cc_start: 0.8299 (tpp-160) cc_final: 0.7950 (ttm110) outliers start: 55 outliers final: 38 residues processed: 487 average time/residue: 1.6828 time to fit residues: 927.9808 Evaluate side-chains 479 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 430 time to evaluate : 2.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 167 LYS Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain E residue 43 ARG Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain G residue 20 GLU Chi-restraints excluded: chain G residue 42 SER Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 103 SER Chi-restraints excluded: chain H residue 20 GLU Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain J residue 162 ILE Chi-restraints excluded: chain K residue 49 ASP Chi-restraints excluded: chain K residue 150 SER Chi-restraints excluded: chain L residue 49 ASP Chi-restraints excluded: chain L residue 184 MET Chi-restraints excluded: chain M residue 7 GLU Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain N residue 42 SER Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain O residue 70 ASP Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain O residue 103 SER Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain Q residue 150 SER Chi-restraints excluded: chain Q residue 162 ILE Chi-restraints excluded: chain R residue 75 LYS Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 150 SER Chi-restraints excluded: chain R residue 162 ILE Chi-restraints excluded: chain R residue 184 MET Chi-restraints excluded: chain S residue 167 LYS Chi-restraints excluded: chain T residue 162 ILE Chi-restraints excluded: chain U residue 70 ASP Chi-restraints excluded: chain U residue 73 ASP Chi-restraints excluded: chain U residue 103 SER Chi-restraints excluded: chain V residue 103 SER Chi-restraints excluded: chain W residue 20 GLU Chi-restraints excluded: chain W residue 103 SER Chi-restraints excluded: chain X residue 70 ASP Chi-restraints excluded: chain X residue 73 ASP Chi-restraints excluded: chain X residue 103 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 191 optimal weight: 5.9990 chunk 307 optimal weight: 6.9990 chunk 187 optimal weight: 6.9990 chunk 145 optimal weight: 0.0060 chunk 213 optimal weight: 6.9990 chunk 322 optimal weight: 0.1980 chunk 297 optimal weight: 0.4980 chunk 257 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 chunk 157 optimal weight: 0.5980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 26376 Z= 0.128 Angle : 0.397 7.199 35520 Z= 0.209 Chirality : 0.037 0.113 4236 Planarity : 0.002 0.032 4560 Dihedral : 3.113 8.802 3720 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.90 % Allowed : 27.75 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.14), residues: 3384 helix: 2.08 (0.12), residues: 1992 sheet: 2.77 (0.23), residues: 420 loop : -0.44 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP Q 86 HIS 0.001 0.000 HIS H 63 PHE 0.006 0.000 PHE K 136 TYR 0.010 0.001 TYR L 94 ARG 0.008 0.000 ARG U 51 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6768 Ramachandran restraints generated. 3384 Oldfield, 0 Emsley, 3384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 437 time to evaluate : 3.007 Fit side-chains REVERT: C 51 GLU cc_start: 0.7161 (tp30) cc_final: 0.6864 (tp30) REVERT: D 65 LYS cc_start: 0.7899 (mtpt) cc_final: 0.7448 (mtpt) REVERT: E 43 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.8771 (ptt-90) REVERT: G 20 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7078 (mp0) REVERT: G 51 ARG cc_start: 0.8208 (ttm110) cc_final: 0.7794 (ttm170) REVERT: H 20 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.7255 (mp0) REVERT: H 51 ARG cc_start: 0.8033 (ttm170) cc_final: 0.7799 (ttm170) REVERT: H 110 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7813 (tt0) REVERT: I 36 GLU cc_start: 0.7987 (tt0) cc_final: 0.7744 (tt0) REVERT: J 51 GLU cc_start: 0.7127 (mm-30) cc_final: 0.6867 (tp30) REVERT: K 47 TYR cc_start: 0.8906 (m-80) cc_final: 0.8584 (m-80) REVERT: L 151 ASP cc_start: 0.7472 (m-30) cc_final: 0.7170 (m-30) REVERT: L 184 MET cc_start: 0.7567 (OUTLIER) cc_final: 0.7100 (mmt) REVERT: M 7 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.7011 (mt-10) REVERT: O 20 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7146 (mp0) REVERT: R 75 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7979 (mppt) REVERT: R 184 MET cc_start: 0.7648 (OUTLIER) cc_final: 0.7308 (mmm) REVERT: S 167 LYS cc_start: 0.7473 (OUTLIER) cc_final: 0.7192 (mttm) REVERT: T 93 ARG cc_start: 0.8375 (ttp80) cc_final: 0.8152 (ttt180) REVERT: W 15 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7638 (mt-10) REVERT: W 20 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.7146 (mp0) REVERT: W 51 ARG cc_start: 0.8290 (tpp-160) cc_final: 0.7945 (ttm110) outliers start: 51 outliers final: 37 residues processed: 473 average time/residue: 1.6795 time to fit residues: 898.6381 Evaluate side-chains 489 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 441 time to evaluate : 3.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 167 LYS Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain E residue 43 ARG Chi-restraints excluded: chain E residue 103 SER Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain G residue 20 GLU Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 103 SER Chi-restraints excluded: chain H residue 20 GLU Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain I residue 167 LYS Chi-restraints excluded: chain J residue 162 ILE Chi-restraints excluded: chain K residue 150 SER Chi-restraints excluded: chain L residue 49 ASP Chi-restraints excluded: chain L residue 184 MET Chi-restraints excluded: chain M residue 7 GLU Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain M residue 103 SER Chi-restraints excluded: chain N residue 42 SER Chi-restraints excluded: chain O residue 7 GLU Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain O residue 70 ASP Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain Q residue 52 MET Chi-restraints excluded: chain Q residue 150 SER Chi-restraints excluded: chain Q residue 162 ILE Chi-restraints excluded: chain R residue 75 LYS Chi-restraints excluded: chain R residue 150 SER Chi-restraints excluded: chain R residue 162 ILE Chi-restraints excluded: chain R residue 184 MET Chi-restraints excluded: chain S residue 49 ASP Chi-restraints excluded: chain S residue 167 LYS Chi-restraints excluded: chain T residue 162 ILE Chi-restraints excluded: chain U residue 70 ASP Chi-restraints excluded: chain U residue 73 ASP Chi-restraints excluded: chain U residue 103 SER Chi-restraints excluded: chain V residue 103 SER Chi-restraints excluded: chain W residue 20 GLU Chi-restraints excluded: chain W residue 103 SER Chi-restraints excluded: chain X residue 70 ASP Chi-restraints excluded: chain X residue 73 ASP Chi-restraints excluded: chain X residue 103 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 204 optimal weight: 3.9990 chunk 273 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 237 optimal weight: 0.0470 chunk 37 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 257 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 264 optimal weight: 0.3980 chunk 32 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 overall best weight: 1.4282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.141013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.103915 restraints weight = 28435.592| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.12 r_work: 0.3012 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26376 Z= 0.203 Angle : 0.434 7.065 35520 Z= 0.227 Chirality : 0.039 0.116 4236 Planarity : 0.003 0.045 4560 Dihedral : 3.293 9.826 3720 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.19 % Allowed : 27.60 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.14), residues: 3384 helix: 1.82 (0.11), residues: 1992 sheet: 2.68 (0.23), residues: 420 loop : -0.48 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP S 86 HIS 0.002 0.001 HIS H 63 PHE 0.008 0.001 PHE K 136 TYR 0.012 0.001 TYR S 94 ARG 0.012 0.000 ARG U 51 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13318.39 seconds wall clock time: 238 minutes 4.32 seconds (14284.32 seconds total)