Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 27 21:04:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nht_9373/04_2023/6nht_9373.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nht_9373/04_2023/6nht_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_2023/6nht_9373.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nht_9373/04_2023/6nht_9373.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nht_9373/04_2023/6nht_9373.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nht_9373/04_2023/6nht_9373.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.014 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: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 13.26, per 1000 atoms: 0.51 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: 10.82 Conformation dependent library (CDL) restraints added in 4.1 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: 1.10 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: 7.60 Time building geometry restraints manager: 11.67 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: 1.960 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: 0.030 Extract box with map and model: 7.710 Check model and map are aligned: 0.420 Set scattering table: 0.220 Process input model: 63.680 Find NCS groups from input model: 1.830 Set up NCS constraints: 0.220 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: 0.000 Load rotamer database and sin/cos tables:12.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.040 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 3.331 Fit side-chains outliers start: 12 outliers final: 2 residues processed: 704 average time/residue: 1.9237 time to fit residues: 1501.6491 Evaluate side-chains 457 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 455 time to evaluate : 3.215 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 0.2657 time to fit residues: 5.1353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 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: 0.2140 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 : 0.525 5.837 35520 Z= 0.283 Chirality : 0.040 0.122 4236 Planarity : 0.005 0.039 4560 Dihedral : 4.225 13.155 3720 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer Outliers : 1.90 % 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: -3.45 (0.11), residues: 3384 helix: -2.91 (0.08), residues: 2028 sheet: 1.12 (0.25), residues: 420 loop : -1.91 (0.15), residues: 936 *********************** 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 518 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 467 time to evaluate : 3.197 Fit side-chains outliers start: 51 outliers final: 16 residues processed: 487 average time/residue: 1.7421 time to fit residues: 952.3632 Evaluate side-chains 445 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 429 time to evaluate : 2.969 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 7 residues processed: 9 average time/residue: 0.2733 time to fit residues: 8.4371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 81 optimal weight: 3.9990 chunk 294 optimal weight: 5.9990 chunk 318 optimal weight: 10.0000 chunk 262 optimal weight: 4.9990 chunk 292 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 chunk 236 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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: 0.8081 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 26376 Z= 0.289 Angle : 0.495 5.895 35520 Z= 0.261 Chirality : 0.040 0.123 4236 Planarity : 0.004 0.033 4560 Dihedral : 3.939 13.338 3720 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer Outliers : 2.12 % 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: -1.69 (0.13), residues: 3384 helix: -1.32 (0.10), residues: 2028 sheet: 1.65 (0.24), residues: 420 loop : -1.60 (0.16), residues: 936 *********************** 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 494 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 437 time to evaluate : 3.377 Fit side-chains outliers start: 57 outliers final: 35 residues processed: 465 average time/residue: 1.7340 time to fit residues: 905.5497 Evaluate side-chains 473 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 438 time to evaluate : 3.180 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 20 residues processed: 15 average time/residue: 0.4701 time to fit residues: 14.4871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 291 optimal weight: 5.9990 chunk 221 optimal weight: 6.9990 chunk 152 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 chunk 197 optimal weight: 5.9990 chunk 295 optimal weight: 3.9990 chunk 313 optimal weight: 2.9990 chunk 154 optimal weight: 6.9990 chunk 280 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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: 0.8072 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 26376 Z= 0.263 Angle : 0.469 6.025 35520 Z= 0.246 Chirality : 0.040 0.120 4236 Planarity : 0.003 0.033 4560 Dihedral : 3.769 11.924 3720 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer Outliers : 2.19 % 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: -0.72 (0.14), residues: 3384 helix: -0.47 (0.11), residues: 2004 sheet: 1.95 (0.23), residues: 420 loop : -1.36 (0.16), residues: 960 *********************** 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 493 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 434 time to evaluate : 3.509 Fit side-chains revert: symmetry clash outliers start: 59 outliers final: 41 residues processed: 466 average time/residue: 1.7267 time to fit residues: 904.9859 Evaluate side-chains 478 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 437 time to evaluate : 3.007 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 24 residues processed: 17 average time/residue: 0.4411 time to fit residues: 14.9700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 260 optimal weight: 0.6980 chunk 177 optimal weight: 8.9990 chunk 4 optimal weight: 0.9990 chunk 233 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 chunk 267 optimal weight: 0.9980 chunk 216 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 159 optimal weight: 5.9990 chunk 281 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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: 0.8041 moved from start: 0.2772 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= 0.173 Angle : 0.421 5.323 35520 Z= 0.223 Chirality : 0.038 0.115 4236 Planarity : 0.002 0.035 4560 Dihedral : 3.513 11.215 3720 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer Outliers : 2.38 % 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: 0.01 (0.14), residues: 3384 helix: 0.19 (0.12), residues: 2004 sheet: 2.21 (0.23), residues: 396 loop : -1.13 (0.16), residues: 984 *********************** 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 538 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 474 time to evaluate : 3.115 Fit side-chains revert: symmetry clash outliers start: 64 outliers final: 40 residues processed: 514 average time/residue: 1.7116 time to fit residues: 992.2103 Evaluate side-chains 473 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 433 time to evaluate : 3.164 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 24 residues processed: 16 average time/residue: 0.4551 time to fit residues: 14.9441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 105 optimal weight: 0.9980 chunk 282 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 183 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 313 optimal weight: 1.9990 chunk 260 optimal weight: 0.8980 chunk 145 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 164 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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: 0.8025 moved from start: 0.2911 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= 0.152 Angle : 0.413 7.930 35520 Z= 0.219 Chirality : 0.038 0.114 4236 Planarity : 0.002 0.034 4560 Dihedral : 3.375 10.842 3720 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer Outliers : 1.93 % 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: 0.64 (0.14), residues: 3384 helix: 0.71 (0.12), residues: 2004 sheet: 2.44 (0.23), residues: 396 loop : -0.90 (0.17), residues: 984 *********************** 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 512 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 460 time to evaluate : 3.195 Fit side-chains outliers start: 52 outliers final: 41 residues processed: 497 average time/residue: 1.6652 time to fit residues: 935.2642 Evaluate side-chains 475 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 434 time to evaluate : 3.126 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 31 residues processed: 10 average time/residue: 0.2562 time to fit residues: 8.8952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 302 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 178 optimal weight: 6.9990 chunk 228 optimal weight: 3.9990 chunk 177 optimal weight: 8.9990 chunk 263 optimal weight: 6.9990 chunk 175 optimal weight: 5.9990 chunk 312 optimal weight: 1.9990 chunk 195 optimal weight: 0.7980 chunk 190 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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: 0.8056 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 26376 Z= 0.236 Angle : 0.453 6.321 35520 Z= 0.237 Chirality : 0.040 0.116 4236 Planarity : 0.003 0.034 4560 Dihedral : 3.511 11.384 3720 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer Outliers : 2.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.14), residues: 3384 helix: 0.74 (0.11), residues: 2004 sheet: 2.47 (0.23), residues: 396 loop : -0.85 (0.17), residues: 984 *********************** 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 535 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 460 time to evaluate : 3.397 Fit side-chains outliers start: 75 outliers final: 54 residues processed: 510 average time/residue: 1.7107 time to fit residues: 984.9982 Evaluate side-chains 488 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 434 time to evaluate : 3.223 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 41 residues processed: 13 average time/residue: 0.5150 time to fit residues: 13.8516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 193 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 186 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 198 optimal weight: 0.7980 chunk 212 optimal weight: 0.9980 chunk 154 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 245 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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: 0.8024 moved from start: 0.3008 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= 0.158 Angle : 0.419 6.519 35520 Z= 0.222 Chirality : 0.038 0.116 4236 Planarity : 0.002 0.034 4560 Dihedral : 3.340 10.797 3720 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer Outliers : 2.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.14), residues: 3384 helix: 1.17 (0.12), residues: 2004 sheet: 2.60 (0.23), residues: 396 loop : -0.74 (0.17), residues: 984 *********************** 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 501 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 446 time to evaluate : 3.219 Fit side-chains outliers start: 55 outliers final: 47 residues processed: 490 average time/residue: 1.6722 time to fit residues: 926.5933 Evaluate side-chains 482 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 435 time to evaluate : 3.361 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 42 residues processed: 6 average time/residue: 0.8181 time to fit residues: 11.0378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 284 optimal weight: 5.9990 chunk 299 optimal weight: 6.9990 chunk 272 optimal weight: 10.0000 chunk 291 optimal weight: 4.9990 chunk 175 optimal weight: 5.9990 chunk 126 optimal weight: 8.9990 chunk 228 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 262 optimal weight: 7.9990 chunk 275 optimal weight: 0.9990 chunk 289 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.047 26376 Z= 0.518 Angle : 0.593 7.018 35520 Z= 0.301 Chirality : 0.046 0.126 4236 Planarity : 0.005 0.057 4560 Dihedral : 3.950 12.695 3720 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer Outliers : 2.60 % 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: 0.27 (0.14), residues: 3384 helix: 0.33 (0.11), residues: 2004 sheet: 2.64 (0.24), residues: 396 loop : -1.02 (0.17), residues: 984 *********************** 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 505 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 435 time to evaluate : 3.408 Fit side-chains outliers start: 70 outliers final: 51 residues processed: 484 average time/residue: 1.7641 time to fit residues: 966.1144 Evaluate side-chains 478 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 427 time to evaluate : 3.366 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 36 residues processed: 16 average time/residue: 0.7565 time to fit residues: 20.3985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 191 optimal weight: 0.7980 chunk 307 optimal weight: 2.9990 chunk 187 optimal weight: 0.9980 chunk 145 optimal weight: 0.0010 chunk 213 optimal weight: 1.9990 chunk 322 optimal weight: 8.9990 chunk 297 optimal weight: 3.9990 chunk 257 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 198 optimal weight: 1.9990 chunk 157 optimal weight: 0.7980 overall best weight: 0.6986 ------------------------------------------------------------------------------- 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: 0.8026 moved from start: 0.3058 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= 0.143 Angle : 0.436 7.101 35520 Z= 0.231 Chirality : 0.038 0.115 4236 Planarity : 0.003 0.044 4560 Dihedral : 3.410 11.516 3720 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer Outliers : 1.41 % 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: 1.08 (0.14), residues: 3384 helix: 1.09 (0.12), residues: 2004 sheet: 2.63 (0.23), residues: 396 loop : -0.82 (0.17), residues: 984 ********************** 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 486 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 448 time to evaluate : 3.278 Fit side-chains outliers start: 38 outliers final: 35 residues processed: 483 average time/residue: 1.6629 time to fit residues: 906.7760 Evaluate side-chains 468 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 433 time to evaluate : 3.150 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 33 residues processed: 3 average time/residue: 0.5558 time to fit residues: 6.5323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 237 optimal weight: 0.0670 chunk 37 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 257 optimal weight: 0.7980 chunk 107 optimal weight: 6.9990 chunk 264 optimal weight: 0.0570 chunk 32 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 overall best weight: 0.5436 ------------------------------------------------------------------------------- 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 = 0.3651 r_free = 0.3651 target = 0.143472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.107006 restraints weight = 28275.261| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.09 r_work: 0.3043 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 26376 Z= 0.133 Angle : 0.417 6.838 35520 Z= 0.221 Chirality : 0.037 0.114 4236 Planarity : 0.002 0.045 4560 Dihedral : 3.210 10.161 3720 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.14), residues: 3384 helix: 1.60 (0.12), residues: 2004 sheet: 2.71 (0.23), residues: 396 loop : -0.63 (0.17), residues: 984 =============================================================================== Job complete usr+sys time: 12889.64 seconds wall clock time: 227 minutes 17.10 seconds (13637.10 seconds total)