Starting phenix.real_space_refine on Sat Mar 23 16:14:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rvr_10010/03_2024/6rvr_10010.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rvr_10010/03_2024/6rvr_10010.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rvr_10010/03_2024/6rvr_10010.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rvr_10010/03_2024/6rvr_10010.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rvr_10010/03_2024/6rvr_10010.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rvr_10010/03_2024/6rvr_10010.pdb" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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 120 5.16 5 C 24312 2.51 5 N 6408 2.21 5 O 6876 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 108": "OE1" <-> "OE2" Residue "A ASP 120": "OD1" <-> "OD2" Residue "A TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 139": "OE1" <-> "OE2" Residue "A GLU 190": "OE1" <-> "OE2" Residue "A GLU 200": "OE1" <-> "OE2" Residue "A GLU 212": "OE1" <-> "OE2" Residue "A GLU 223": "OE1" <-> "OE2" Residue "A TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 251": "OD1" <-> "OD2" Residue "A GLU 487": "OE1" <-> "OE2" Residue "A ASP 517": "OD1" <-> "OD2" Residue "A GLU 550": "OE1" <-> "OE2" Residue "A ASP 553": "OD1" <-> "OD2" Residue "A GLU 566": "OE1" <-> "OE2" Residue "A ASP 567": "OD1" <-> "OD2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 108": "OE1" <-> "OE2" Residue "B ASP 120": "OD1" <-> "OD2" Residue "B TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 139": "OE1" <-> "OE2" Residue "B GLU 190": "OE1" <-> "OE2" Residue "B GLU 200": "OE1" <-> "OE2" Residue "B GLU 212": "OE1" <-> "OE2" Residue "B GLU 223": "OE1" <-> "OE2" Residue "B TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 251": "OD1" <-> "OD2" Residue "B GLU 487": "OE1" <-> "OE2" Residue "B ASP 517": "OD1" <-> "OD2" Residue "B GLU 550": "OE1" <-> "OE2" Residue "B ASP 553": "OD1" <-> "OD2" Residue "B GLU 566": "OE1" <-> "OE2" Residue "B ASP 567": "OD1" <-> "OD2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 108": "OE1" <-> "OE2" Residue "C ASP 120": "OD1" <-> "OD2" Residue "C TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 139": "OE1" <-> "OE2" Residue "C GLU 190": "OE1" <-> "OE2" Residue "C GLU 200": "OE1" <-> "OE2" Residue "C GLU 212": "OE1" <-> "OE2" Residue "C GLU 223": "OE1" <-> "OE2" Residue "C TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 251": "OD1" <-> "OD2" Residue "C GLU 487": "OE1" <-> "OE2" Residue "C ASP 517": "OD1" <-> "OD2" Residue "C GLU 550": "OE1" <-> "OE2" Residue "C ASP 553": "OD1" <-> "OD2" Residue "C GLU 566": "OE1" <-> "OE2" Residue "C ASP 567": "OD1" <-> "OD2" Residue "D PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 108": "OE1" <-> "OE2" Residue "D ASP 120": "OD1" <-> "OD2" Residue "D TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 139": "OE1" <-> "OE2" Residue "D GLU 190": "OE1" <-> "OE2" Residue "D GLU 200": "OE1" <-> "OE2" Residue "D GLU 212": "OE1" <-> "OE2" Residue "D GLU 223": "OE1" <-> "OE2" Residue "D TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 251": "OD1" <-> "OD2" Residue "D GLU 487": "OE1" <-> "OE2" Residue "D ASP 517": "OD1" <-> "OD2" Residue "D GLU 550": "OE1" <-> "OE2" Residue "D ASP 553": "OD1" <-> "OD2" Residue "D GLU 566": "OE1" <-> "OE2" Residue "D ASP 567": "OD1" <-> "OD2" Residue "E PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 108": "OE1" <-> "OE2" Residue "E ASP 120": "OD1" <-> "OD2" Residue "E TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 139": "OE1" <-> "OE2" Residue "E GLU 190": "OE1" <-> "OE2" Residue "E GLU 200": "OE1" <-> "OE2" Residue "E GLU 212": "OE1" <-> "OE2" Residue "E GLU 223": "OE1" <-> "OE2" Residue "E TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 251": "OD1" <-> "OD2" Residue "E GLU 487": "OE1" <-> "OE2" Residue "E ASP 517": "OD1" <-> "OD2" Residue "E GLU 550": "OE1" <-> "OE2" Residue "E ASP 553": "OD1" <-> "OD2" Residue "E GLU 566": "OE1" <-> "OE2" Residue "E ASP 567": "OD1" <-> "OD2" Residue "F PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 108": "OE1" <-> "OE2" Residue "F ASP 120": "OD1" <-> "OD2" Residue "F TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 139": "OE1" <-> "OE2" Residue "F GLU 190": "OE1" <-> "OE2" Residue "F GLU 200": "OE1" <-> "OE2" Residue "F GLU 212": "OE1" <-> "OE2" Residue "F GLU 223": "OE1" <-> "OE2" Residue "F TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 251": "OD1" <-> "OD2" Residue "F GLU 487": "OE1" <-> "OE2" Residue "F ASP 517": "OD1" <-> "OD2" Residue "F GLU 550": "OE1" <-> "OE2" Residue "F ASP 553": "OD1" <-> "OD2" Residue "F GLU 566": "OE1" <-> "OE2" Residue "F ASP 567": "OD1" <-> "OD2" Residue "G PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 108": "OE1" <-> "OE2" Residue "G ASP 120": "OD1" <-> "OD2" Residue "G TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 139": "OE1" <-> "OE2" Residue "G GLU 190": "OE1" <-> "OE2" Residue "G GLU 200": "OE1" <-> "OE2" Residue "G GLU 212": "OE1" <-> "OE2" Residue "G GLU 223": "OE1" <-> "OE2" Residue "G TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 251": "OD1" <-> "OD2" Residue "G GLU 487": "OE1" <-> "OE2" Residue "G ASP 517": "OD1" <-> "OD2" Residue "G GLU 550": "OE1" <-> "OE2" Residue "G ASP 553": "OD1" <-> "OD2" Residue "G GLU 566": "OE1" <-> "OE2" Residue "G ASP 567": "OD1" <-> "OD2" Residue "H PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 108": "OE1" <-> "OE2" Residue "H ASP 120": "OD1" <-> "OD2" Residue "H TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 139": "OE1" <-> "OE2" Residue "H GLU 190": "OE1" <-> "OE2" Residue "H GLU 200": "OE1" <-> "OE2" Residue "H GLU 212": "OE1" <-> "OE2" Residue "H GLU 223": "OE1" <-> "OE2" Residue "H TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 251": "OD1" <-> "OD2" Residue "H GLU 487": "OE1" <-> "OE2" Residue "H ASP 517": "OD1" <-> "OD2" Residue "H GLU 550": "OE1" <-> "OE2" Residue "H ASP 553": "OD1" <-> "OD2" Residue "H GLU 566": "OE1" <-> "OE2" Residue "H ASP 567": "OD1" <-> "OD2" Residue "I PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 108": "OE1" <-> "OE2" Residue "I ASP 120": "OD1" <-> "OD2" Residue "I TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 139": "OE1" <-> "OE2" Residue "I GLU 190": "OE1" <-> "OE2" Residue "I GLU 200": "OE1" <-> "OE2" Residue "I GLU 212": "OE1" <-> "OE2" Residue "I GLU 223": "OE1" <-> "OE2" Residue "I TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 251": "OD1" <-> "OD2" Residue "I GLU 487": "OE1" <-> "OE2" Residue "I ASP 517": "OD1" <-> "OD2" Residue "I GLU 550": "OE1" <-> "OE2" Residue "I ASP 553": "OD1" <-> "OD2" Residue "I GLU 566": "OE1" <-> "OE2" Residue "I ASP 567": "OD1" <-> "OD2" Residue "J PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 108": "OE1" <-> "OE2" Residue "J ASP 120": "OD1" <-> "OD2" Residue "J TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 139": "OE1" <-> "OE2" Residue "J GLU 190": "OE1" <-> "OE2" Residue "J GLU 200": "OE1" <-> "OE2" Residue "J GLU 212": "OE1" <-> "OE2" Residue "J GLU 223": "OE1" <-> "OE2" Residue "J TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 251": "OD1" <-> "OD2" Residue "J GLU 487": "OE1" <-> "OE2" Residue "J ASP 517": "OD1" <-> "OD2" Residue "J GLU 550": "OE1" <-> "OE2" Residue "J ASP 553": "OD1" <-> "OD2" Residue "J GLU 566": "OE1" <-> "OE2" Residue "J ASP 567": "OD1" <-> "OD2" Residue "K PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 108": "OE1" <-> "OE2" Residue "K ASP 120": "OD1" <-> "OD2" Residue "K TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 139": "OE1" <-> "OE2" Residue "K GLU 190": "OE1" <-> "OE2" Residue "K GLU 200": "OE1" <-> "OE2" Residue "K GLU 212": "OE1" <-> "OE2" Residue "K GLU 223": "OE1" <-> "OE2" Residue "K TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 251": "OD1" <-> "OD2" Residue "K GLU 487": "OE1" <-> "OE2" Residue "K ASP 517": "OD1" <-> "OD2" Residue "K GLU 550": "OE1" <-> "OE2" Residue "K ASP 553": "OD1" <-> "OD2" Residue "K GLU 566": "OE1" <-> "OE2" Residue "K ASP 567": "OD1" <-> "OD2" Residue "L PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 108": "OE1" <-> "OE2" Residue "L ASP 120": "OD1" <-> "OD2" Residue "L TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 139": "OE1" <-> "OE2" Residue "L GLU 190": "OE1" <-> "OE2" Residue "L GLU 200": "OE1" <-> "OE2" Residue "L GLU 212": "OE1" <-> "OE2" Residue "L GLU 223": "OE1" <-> "OE2" Residue "L TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 251": "OD1" <-> "OD2" Residue "L GLU 487": "OE1" <-> "OE2" Residue "L ASP 517": "OD1" <-> "OD2" Residue "L GLU 550": "OE1" <-> "OE2" Residue "L ASP 553": "OD1" <-> "OD2" Residue "L GLU 566": "OE1" <-> "OE2" Residue "L ASP 567": "OD1" <-> "OD2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 37716 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3143 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 371} Chain breaks: 4 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 3143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3143 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 371} Chain breaks: 4 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 3143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3143 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 371} Chain breaks: 4 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 3143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3143 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 371} Chain breaks: 4 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "E" Number of atoms: 3143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3143 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 371} Chain breaks: 4 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 3143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3143 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 371} Chain breaks: 4 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 3143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3143 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 371} Chain breaks: 4 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "H" Number of atoms: 3143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3143 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 371} Chain breaks: 4 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "I" Number of atoms: 3143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3143 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 371} Chain breaks: 4 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "J" Number of atoms: 3143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3143 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 371} Chain breaks: 4 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "K" Number of atoms: 3143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3143 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 371} Chain breaks: 4 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "L" Number of atoms: 3143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3143 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 371} Chain breaks: 4 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 19.32, per 1000 atoms: 0.51 Number of scatterers: 37716 At special positions: 0 Unit cell: (159.5, 159.5, 136.4, 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 120 16.00 O 6876 8.00 N 6408 7.00 C 24312 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: 14.63 Conformation dependent library (CDL) restraints added in 6.6 seconds 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9024 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 48 sheets defined 59.2% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.18 Creating SS restraints... Processing helix chain 'A' and resid 24 through 36 removed outlier: 4.224A pdb=" N LEU A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLN A 35 " --> pdb=" O PHE A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 50 removed outlier: 4.469A pdb=" N ALA A 48 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 50 " --> pdb=" O TYR A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 70 removed outlier: 3.937A pdb=" N THR A 62 " --> pdb=" O ARG A 58 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE A 65 " --> pdb=" O PHE A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 92 removed outlier: 3.720A pdb=" N TRP A 92 " --> pdb=" O ILE A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 132 removed outlier: 4.584A pdb=" N GLU A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU A 108 " --> pdb=" O GLU A 104 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N SER A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP A 110 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR A 112 " --> pdb=" O GLU A 108 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR A 123 " --> pdb=" O ARG A 119 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR A 124 " --> pdb=" O ASP A 120 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ASN A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG A 128 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL A 129 " --> pdb=" O ASN A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 149 removed outlier: 3.625A pdb=" N VAL A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP A 143 " --> pdb=" O GLU A 139 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N TRP A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ALA A 147 " --> pdb=" O ASP A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 164 removed outlier: 3.526A pdb=" N HIS A 163 " --> pdb=" O THR A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 171 removed outlier: 3.754A pdb=" N SER A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 203 removed outlier: 4.551A pdb=" N ILE A 187 " --> pdb=" O THR A 183 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR A 189 " --> pdb=" O ARG A 185 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS A 196 " --> pdb=" O TYR A 192 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU A 197 " --> pdb=" O GLU A 193 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE A 198 " --> pdb=" O ALA A 194 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE A 199 " --> pdb=" O THR A 195 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU A 200 " --> pdb=" O LYS A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 276 removed outlier: 3.571A pdb=" N ARG A 256 " --> pdb=" O SER A 252 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU A 257 " --> pdb=" O PRO A 253 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N GLN A 259 " --> pdb=" O GLN A 255 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ASN A 260 " --> pdb=" O ARG A 256 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE A 262 " --> pdb=" O TYR A 258 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR A 267 " --> pdb=" O MET A 263 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU A 269 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N HIS A 270 " --> pdb=" O ARG A 266 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE A 273 " --> pdb=" O GLU A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 448 removed outlier: 3.756A pdb=" N GLU A 445 " --> pdb=" O ALA A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 496 removed outlier: 4.210A pdb=" N THR A 486 " --> pdb=" O THR A 482 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLU A 487 " --> pdb=" O LYS A 483 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR A 496 " --> pdb=" O GLU A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 528 removed outlier: 3.851A pdb=" N SER A 520 " --> pdb=" O SER A 516 " (cutoff:3.500A) Proline residue: A 525 - end of helix Processing helix chain 'A' and resid 541 through 545 removed outlier: 3.771A pdb=" N ALA A 544 " --> pdb=" O ASP A 541 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR A 545 " --> pdb=" O VAL A 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 541 through 545' Processing helix chain 'A' and resid 547 through 558 removed outlier: 3.637A pdb=" N ASP A 553 " --> pdb=" O VAL A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 570 removed outlier: 3.536A pdb=" N TYR A 564 " --> pdb=" O ARG A 560 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE A 565 " --> pdb=" O LEU A 561 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU A 566 " --> pdb=" O ALA A 562 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP A 567 " --> pdb=" O ILE A 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 36 removed outlier: 4.224A pdb=" N LEU B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN B 35 " --> pdb=" O PHE B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 50 removed outlier: 4.469A pdb=" N ALA B 48 " --> pdb=" O THR B 45 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 50 " --> pdb=" O TYR B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 70 removed outlier: 3.936A pdb=" N THR B 62 " --> pdb=" O ARG B 58 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE B 65 " --> pdb=" O PHE B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 92 removed outlier: 3.718A pdb=" N TRP B 92 " --> pdb=" O ILE B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 132 removed outlier: 4.584A pdb=" N GLU B 104 " --> pdb=" O SER B 100 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLU B 108 " --> pdb=" O GLU B 104 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N SER B 109 " --> pdb=" O SER B 105 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR B 123 " --> pdb=" O ARG B 119 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR B 124 " --> pdb=" O ASP B 120 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASN B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG B 128 " --> pdb=" O THR B 124 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL B 129 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 149 removed outlier: 3.625A pdb=" N VAL B 142 " --> pdb=" O TYR B 138 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP B 143 " --> pdb=" O GLU B 139 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N TRP B 144 " --> pdb=" O ARG B 140 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ALA B 147 " --> pdb=" O ASP B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 164 removed outlier: 3.526A pdb=" N HIS B 163 " --> pdb=" O THR B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 171 removed outlier: 3.754A pdb=" N SER B 168 " --> pdb=" O SER B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 203 removed outlier: 4.551A pdb=" N ILE B 187 " --> pdb=" O THR B 183 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR B 189 " --> pdb=" O ARG B 185 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS B 196 " --> pdb=" O TYR B 192 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU B 197 " --> pdb=" O GLU B 193 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE B 198 " --> pdb=" O ALA B 194 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE B 199 " --> pdb=" O THR B 195 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 276 removed outlier: 3.571A pdb=" N ARG B 256 " --> pdb=" O SER B 252 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU B 257 " --> pdb=" O PRO B 253 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N GLN B 259 " --> pdb=" O GLN B 255 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ASN B 260 " --> pdb=" O ARG B 256 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE B 262 " --> pdb=" O TYR B 258 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR B 267 " --> pdb=" O MET B 263 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU B 269 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N HIS B 270 " --> pdb=" O ARG B 266 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE B 273 " --> pdb=" O GLU B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 448 removed outlier: 3.756A pdb=" N GLU B 445 " --> pdb=" O ALA B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 496 removed outlier: 4.210A pdb=" N THR B 486 " --> pdb=" O THR B 482 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLU B 487 " --> pdb=" O LYS B 483 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR B 496 " --> pdb=" O GLU B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 528 removed outlier: 3.851A pdb=" N SER B 520 " --> pdb=" O SER B 516 " (cutoff:3.500A) Proline residue: B 525 - end of helix Processing helix chain 'B' and resid 541 through 545 removed outlier: 3.771A pdb=" N ALA B 544 " --> pdb=" O ASP B 541 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR B 545 " --> pdb=" O VAL B 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 541 through 545' Processing helix chain 'B' and resid 547 through 558 removed outlier: 3.637A pdb=" N ASP B 553 " --> pdb=" O VAL B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 570 removed outlier: 3.536A pdb=" N TYR B 564 " --> pdb=" O ARG B 560 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE B 565 " --> pdb=" O LEU B 561 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU B 566 " --> pdb=" O ALA B 562 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP B 567 " --> pdb=" O ILE B 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 36 removed outlier: 4.224A pdb=" N LEU C 34 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN C 35 " --> pdb=" O PHE C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 50 removed outlier: 4.469A pdb=" N ALA C 48 " --> pdb=" O THR C 45 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU C 50 " --> pdb=" O TYR C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 70 removed outlier: 3.937A pdb=" N THR C 62 " --> pdb=" O ARG C 58 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE C 65 " --> pdb=" O PHE C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 92 removed outlier: 3.718A pdb=" N TRP C 92 " --> pdb=" O ILE C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 132 removed outlier: 4.584A pdb=" N GLU C 104 " --> pdb=" O SER C 100 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU C 108 " --> pdb=" O GLU C 104 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N SER C 109 " --> pdb=" O SER C 105 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP C 110 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR C 112 " --> pdb=" O GLU C 108 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR C 123 " --> pdb=" O ARG C 119 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR C 124 " --> pdb=" O ASP C 120 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASN C 125 " --> pdb=" O LEU C 121 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG C 128 " --> pdb=" O THR C 124 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL C 129 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 149 removed outlier: 3.625A pdb=" N VAL C 142 " --> pdb=" O TYR C 138 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP C 143 " --> pdb=" O GLU C 139 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N TRP C 144 " --> pdb=" O ARG C 140 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ALA C 147 " --> pdb=" O ASP C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 164 removed outlier: 3.526A pdb=" N HIS C 163 " --> pdb=" O THR C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 171 removed outlier: 3.755A pdb=" N SER C 168 " --> pdb=" O SER C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 203 removed outlier: 4.551A pdb=" N ILE C 187 " --> pdb=" O THR C 183 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR C 189 " --> pdb=" O ARG C 185 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS C 196 " --> pdb=" O TYR C 192 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU C 197 " --> pdb=" O GLU C 193 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE C 198 " --> pdb=" O ALA C 194 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE C 199 " --> pdb=" O THR C 195 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU C 200 " --> pdb=" O LYS C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 276 removed outlier: 3.571A pdb=" N ARG C 256 " --> pdb=" O SER C 252 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU C 257 " --> pdb=" O PRO C 253 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N GLN C 259 " --> pdb=" O GLN C 255 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ASN C 260 " --> pdb=" O ARG C 256 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE C 262 " --> pdb=" O TYR C 258 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR C 267 " --> pdb=" O MET C 263 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU C 269 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N HIS C 270 " --> pdb=" O ARG C 266 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE C 273 " --> pdb=" O GLU C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 448 removed outlier: 3.757A pdb=" N GLU C 445 " --> pdb=" O ALA C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 496 removed outlier: 4.210A pdb=" N THR C 486 " --> pdb=" O THR C 482 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLU C 487 " --> pdb=" O LYS C 483 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR C 496 " --> pdb=" O GLU C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 528 removed outlier: 3.852A pdb=" N SER C 520 " --> pdb=" O SER C 516 " (cutoff:3.500A) Proline residue: C 525 - end of helix Processing helix chain 'C' and resid 541 through 545 removed outlier: 3.771A pdb=" N ALA C 544 " --> pdb=" O ASP C 541 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR C 545 " --> pdb=" O VAL C 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 541 through 545' Processing helix chain 'C' and resid 547 through 558 removed outlier: 3.637A pdb=" N ASP C 553 " --> pdb=" O VAL C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 570 removed outlier: 3.536A pdb=" N TYR C 564 " --> pdb=" O ARG C 560 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE C 565 " --> pdb=" O LEU C 561 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU C 566 " --> pdb=" O ALA C 562 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP C 567 " --> pdb=" O ILE C 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 36 removed outlier: 4.223A pdb=" N LEU D 34 " --> pdb=" O LEU D 30 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN D 35 " --> pdb=" O PHE D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 50 removed outlier: 4.469A pdb=" N ALA D 48 " --> pdb=" O THR D 45 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU D 50 " --> pdb=" O TYR D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 70 removed outlier: 3.936A pdb=" N THR D 62 " --> pdb=" O ARG D 58 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE D 65 " --> pdb=" O PHE D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 92 removed outlier: 3.719A pdb=" N TRP D 92 " --> pdb=" O ILE D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 132 removed outlier: 4.585A pdb=" N GLU D 104 " --> pdb=" O SER D 100 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU D 108 " --> pdb=" O GLU D 104 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N SER D 109 " --> pdb=" O SER D 105 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N THR D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR D 123 " --> pdb=" O ARG D 119 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR D 124 " --> pdb=" O ASP D 120 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASN D 125 " --> pdb=" O LEU D 121 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG D 128 " --> pdb=" O THR D 124 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL D 129 " --> pdb=" O ASN D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 149 removed outlier: 3.625A pdb=" N VAL D 142 " --> pdb=" O TYR D 138 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP D 143 " --> pdb=" O GLU D 139 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N TRP D 144 " --> pdb=" O ARG D 140 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ALA D 147 " --> pdb=" O ASP D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 164 removed outlier: 3.526A pdb=" N HIS D 163 " --> pdb=" O THR D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 171 removed outlier: 3.754A pdb=" N SER D 168 " --> pdb=" O SER D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 203 removed outlier: 4.551A pdb=" N ILE D 187 " --> pdb=" O THR D 183 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR D 189 " --> pdb=" O ARG D 185 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS D 196 " --> pdb=" O TYR D 192 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU D 197 " --> pdb=" O GLU D 193 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE D 198 " --> pdb=" O ALA D 194 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE D 199 " --> pdb=" O THR D 195 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU D 200 " --> pdb=" O LYS D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 276 removed outlier: 3.571A pdb=" N ARG D 256 " --> pdb=" O SER D 252 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU D 257 " --> pdb=" O PRO D 253 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N GLN D 259 " --> pdb=" O GLN D 255 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ASN D 260 " --> pdb=" O ARG D 256 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE D 262 " --> pdb=" O TYR D 258 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR D 267 " --> pdb=" O MET D 263 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU D 269 " --> pdb=" O TYR D 265 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N HIS D 270 " --> pdb=" O ARG D 266 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS D 272 " --> pdb=" O LEU D 268 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE D 273 " --> pdb=" O GLU D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 448 removed outlier: 3.756A pdb=" N GLU D 445 " --> pdb=" O ALA D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 496 removed outlier: 4.210A pdb=" N THR D 486 " --> pdb=" O THR D 482 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLU D 487 " --> pdb=" O LYS D 483 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR D 496 " --> pdb=" O GLU D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 528 removed outlier: 3.852A pdb=" N SER D 520 " --> pdb=" O SER D 516 " (cutoff:3.500A) Proline residue: D 525 - end of helix Processing helix chain 'D' and resid 541 through 545 removed outlier: 3.772A pdb=" N ALA D 544 " --> pdb=" O ASP D 541 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR D 545 " --> pdb=" O VAL D 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 541 through 545' Processing helix chain 'D' and resid 547 through 558 removed outlier: 3.636A pdb=" N ASP D 553 " --> pdb=" O VAL D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 570 removed outlier: 3.537A pdb=" N TYR D 564 " --> pdb=" O ARG D 560 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE D 565 " --> pdb=" O LEU D 561 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU D 566 " --> pdb=" O ALA D 562 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP D 567 " --> pdb=" O ILE D 563 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 36 removed outlier: 4.223A pdb=" N LEU E 34 " --> pdb=" O LEU E 30 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN E 35 " --> pdb=" O PHE E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 50 removed outlier: 4.468A pdb=" N ALA E 48 " --> pdb=" O THR E 45 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU E 50 " --> pdb=" O TYR E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 70 removed outlier: 3.937A pdb=" N THR E 62 " --> pdb=" O ARG E 58 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE E 65 " --> pdb=" O PHE E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 92 removed outlier: 3.718A pdb=" N TRP E 92 " --> pdb=" O ILE E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 132 removed outlier: 4.584A pdb=" N GLU E 104 " --> pdb=" O SER E 100 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU E 108 " --> pdb=" O GLU E 104 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N SER E 109 " --> pdb=" O SER E 105 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP E 110 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N THR E 112 " --> pdb=" O GLU E 108 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR E 123 " --> pdb=" O ARG E 119 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N THR E 124 " --> pdb=" O ASP E 120 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASN E 125 " --> pdb=" O LEU E 121 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ARG E 128 " --> pdb=" O THR E 124 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL E 129 " --> pdb=" O ASN E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 149 removed outlier: 3.625A pdb=" N VAL E 142 " --> pdb=" O TYR E 138 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP E 143 " --> pdb=" O GLU E 139 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N TRP E 144 " --> pdb=" O ARG E 140 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ALA E 147 " --> pdb=" O ASP E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 164 removed outlier: 3.526A pdb=" N HIS E 163 " --> pdb=" O THR E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 171 removed outlier: 3.754A pdb=" N SER E 168 " --> pdb=" O SER E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 203 removed outlier: 4.551A pdb=" N ILE E 187 " --> pdb=" O THR E 183 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR E 189 " --> pdb=" O ARG E 185 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS E 196 " --> pdb=" O TYR E 192 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU E 197 " --> pdb=" O GLU E 193 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE E 198 " --> pdb=" O ALA E 194 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE E 199 " --> pdb=" O THR E 195 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU E 200 " --> pdb=" O LYS E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 276 removed outlier: 3.571A pdb=" N ARG E 256 " --> pdb=" O SER E 252 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU E 257 " --> pdb=" O PRO E 253 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N GLN E 259 " --> pdb=" O GLN E 255 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ASN E 260 " --> pdb=" O ARG E 256 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE E 262 " --> pdb=" O TYR E 258 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR E 267 " --> pdb=" O MET E 263 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU E 269 " --> pdb=" O TYR E 265 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N HIS E 270 " --> pdb=" O ARG E 266 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS E 272 " --> pdb=" O LEU E 268 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE E 273 " --> pdb=" O GLU E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 448 removed outlier: 3.756A pdb=" N GLU E 445 " --> pdb=" O ALA E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 480 through 496 removed outlier: 4.210A pdb=" N THR E 486 " --> pdb=" O THR E 482 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLU E 487 " --> pdb=" O LYS E 483 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR E 496 " --> pdb=" O GLU E 492 " (cutoff:3.500A) Processing helix chain 'E' and resid 515 through 528 removed outlier: 3.852A pdb=" N SER E 520 " --> pdb=" O SER E 516 " (cutoff:3.500A) Proline residue: E 525 - end of helix Processing helix chain 'E' and resid 541 through 545 removed outlier: 3.771A pdb=" N ALA E 544 " --> pdb=" O ASP E 541 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR E 545 " --> pdb=" O VAL E 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 541 through 545' Processing helix chain 'E' and resid 547 through 558 removed outlier: 3.638A pdb=" N ASP E 553 " --> pdb=" O VAL E 549 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 570 removed outlier: 3.536A pdb=" N TYR E 564 " --> pdb=" O ARG E 560 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE E 565 " --> pdb=" O LEU E 561 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU E 566 " --> pdb=" O ALA E 562 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP E 567 " --> pdb=" O ILE E 563 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 36 removed outlier: 4.224A pdb=" N LEU F 34 " --> pdb=" O LEU F 30 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN F 35 " --> pdb=" O PHE F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 50 removed outlier: 4.469A pdb=" N ALA F 48 " --> pdb=" O THR F 45 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU F 50 " --> pdb=" O TYR F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 70 removed outlier: 3.936A pdb=" N THR F 62 " --> pdb=" O ARG F 58 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE F 65 " --> pdb=" O PHE F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 92 removed outlier: 3.719A pdb=" N TRP F 92 " --> pdb=" O ILE F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 132 removed outlier: 4.584A pdb=" N GLU F 104 " --> pdb=" O SER F 100 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLU F 108 " --> pdb=" O GLU F 104 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N SER F 109 " --> pdb=" O SER F 105 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP F 110 " --> pdb=" O THR F 106 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N THR F 112 " --> pdb=" O GLU F 108 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR F 123 " --> pdb=" O ARG F 119 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR F 124 " --> pdb=" O ASP F 120 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASN F 125 " --> pdb=" O LEU F 121 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG F 128 " --> pdb=" O THR F 124 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL F 129 " --> pdb=" O ASN F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 149 removed outlier: 3.625A pdb=" N VAL F 142 " --> pdb=" O TYR F 138 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP F 143 " --> pdb=" O GLU F 139 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N TRP F 144 " --> pdb=" O ARG F 140 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ALA F 147 " --> pdb=" O ASP F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 164 removed outlier: 3.526A pdb=" N HIS F 163 " --> pdb=" O THR F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 171 removed outlier: 3.755A pdb=" N SER F 168 " --> pdb=" O SER F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 203 removed outlier: 4.551A pdb=" N ILE F 187 " --> pdb=" O THR F 183 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N THR F 189 " --> pdb=" O ARG F 185 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS F 196 " --> pdb=" O TYR F 192 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU F 197 " --> pdb=" O GLU F 193 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE F 198 " --> pdb=" O ALA F 194 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE F 199 " --> pdb=" O THR F 195 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU F 200 " --> pdb=" O LYS F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 276 removed outlier: 3.571A pdb=" N ARG F 256 " --> pdb=" O SER F 252 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU F 257 " --> pdb=" O PRO F 253 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N GLN F 259 " --> pdb=" O GLN F 255 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ASN F 260 " --> pdb=" O ARG F 256 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE F 262 " --> pdb=" O TYR F 258 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR F 267 " --> pdb=" O MET F 263 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU F 269 " --> pdb=" O TYR F 265 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N HIS F 270 " --> pdb=" O ARG F 266 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS F 272 " --> pdb=" O LEU F 268 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE F 273 " --> pdb=" O GLU F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 441 through 448 removed outlier: 3.756A pdb=" N GLU F 445 " --> pdb=" O ALA F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 480 through 496 removed outlier: 4.210A pdb=" N THR F 486 " --> pdb=" O THR F 482 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLU F 487 " --> pdb=" O LYS F 483 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR F 496 " --> pdb=" O GLU F 492 " (cutoff:3.500A) Processing helix chain 'F' and resid 515 through 528 removed outlier: 3.851A pdb=" N SER F 520 " --> pdb=" O SER F 516 " (cutoff:3.500A) Proline residue: F 525 - end of helix Processing helix chain 'F' and resid 541 through 545 removed outlier: 3.771A pdb=" N ALA F 544 " --> pdb=" O ASP F 541 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR F 545 " --> pdb=" O VAL F 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 541 through 545' Processing helix chain 'F' and resid 547 through 558 removed outlier: 3.637A pdb=" N ASP F 553 " --> pdb=" O VAL F 549 " (cutoff:3.500A) Processing helix chain 'F' and resid 559 through 570 removed outlier: 3.536A pdb=" N TYR F 564 " --> pdb=" O ARG F 560 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE F 565 " --> pdb=" O LEU F 561 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU F 566 " --> pdb=" O ALA F 562 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP F 567 " --> pdb=" O ILE F 563 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 36 removed outlier: 4.224A pdb=" N LEU G 34 " --> pdb=" O LEU G 30 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN G 35 " --> pdb=" O PHE G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 50 removed outlier: 4.468A pdb=" N ALA G 48 " --> pdb=" O THR G 45 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU G 50 " --> pdb=" O TYR G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 70 removed outlier: 3.936A pdb=" N THR G 62 " --> pdb=" O ARG G 58 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE G 65 " --> pdb=" O PHE G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 92 removed outlier: 3.718A pdb=" N TRP G 92 " --> pdb=" O ILE G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 132 removed outlier: 4.584A pdb=" N GLU G 104 " --> pdb=" O SER G 100 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU G 108 " --> pdb=" O GLU G 104 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N SER G 109 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP G 110 " --> pdb=" O THR G 106 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N THR G 112 " --> pdb=" O GLU G 108 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR G 123 " --> pdb=" O ARG G 119 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR G 124 " --> pdb=" O ASP G 120 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASN G 125 " --> pdb=" O LEU G 121 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ARG G 128 " --> pdb=" O THR G 124 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL G 129 " --> pdb=" O ASN G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 149 removed outlier: 3.625A pdb=" N VAL G 142 " --> pdb=" O TYR G 138 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP G 143 " --> pdb=" O GLU G 139 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N TRP G 144 " --> pdb=" O ARG G 140 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ALA G 147 " --> pdb=" O ASP G 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 164 removed outlier: 3.527A pdb=" N HIS G 163 " --> pdb=" O THR G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 171 removed outlier: 3.755A pdb=" N SER G 168 " --> pdb=" O SER G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 203 removed outlier: 4.551A pdb=" N ILE G 187 " --> pdb=" O THR G 183 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR G 189 " --> pdb=" O ARG G 185 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS G 196 " --> pdb=" O TYR G 192 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU G 197 " --> pdb=" O GLU G 193 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE G 198 " --> pdb=" O ALA G 194 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE G 199 " --> pdb=" O THR G 195 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU G 200 " --> pdb=" O LYS G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 276 removed outlier: 3.571A pdb=" N ARG G 256 " --> pdb=" O SER G 252 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU G 257 " --> pdb=" O PRO G 253 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N GLN G 259 " --> pdb=" O GLN G 255 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ASN G 260 " --> pdb=" O ARG G 256 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE G 262 " --> pdb=" O TYR G 258 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR G 267 " --> pdb=" O MET G 263 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU G 269 " --> pdb=" O TYR G 265 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N HIS G 270 " --> pdb=" O ARG G 266 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS G 272 " --> pdb=" O LEU G 268 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE G 273 " --> pdb=" O GLU G 269 " (cutoff:3.500A) Processing helix chain 'G' and resid 441 through 448 removed outlier: 3.756A pdb=" N GLU G 445 " --> pdb=" O ALA G 441 " (cutoff:3.500A) Processing helix chain 'G' and resid 480 through 496 removed outlier: 4.210A pdb=" N THR G 486 " --> pdb=" O THR G 482 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLU G 487 " --> pdb=" O LYS G 483 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR G 496 " --> pdb=" O GLU G 492 " (cutoff:3.500A) Processing helix chain 'G' and resid 515 through 528 removed outlier: 3.851A pdb=" N SER G 520 " --> pdb=" O SER G 516 " (cutoff:3.500A) Proline residue: G 525 - end of helix Processing helix chain 'G' and resid 541 through 545 removed outlier: 3.772A pdb=" N ALA G 544 " --> pdb=" O ASP G 541 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR G 545 " --> pdb=" O VAL G 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 541 through 545' Processing helix chain 'G' and resid 547 through 558 removed outlier: 3.637A pdb=" N ASP G 553 " --> pdb=" O VAL G 549 " (cutoff:3.500A) Processing helix chain 'G' and resid 559 through 570 removed outlier: 3.536A pdb=" N TYR G 564 " --> pdb=" O ARG G 560 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE G 565 " --> pdb=" O LEU G 561 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU G 566 " --> pdb=" O ALA G 562 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP G 567 " --> pdb=" O ILE G 563 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 36 removed outlier: 4.224A pdb=" N LEU H 34 " --> pdb=" O LEU H 30 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN H 35 " --> pdb=" O PHE H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 50 removed outlier: 4.468A pdb=" N ALA H 48 " --> pdb=" O THR H 45 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU H 50 " --> pdb=" O TYR H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 70 removed outlier: 3.937A pdb=" N THR H 62 " --> pdb=" O ARG H 58 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE H 65 " --> pdb=" O PHE H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 92 removed outlier: 3.718A pdb=" N TRP H 92 " --> pdb=" O ILE H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 132 removed outlier: 4.584A pdb=" N GLU H 104 " --> pdb=" O SER H 100 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU H 108 " --> pdb=" O GLU H 104 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N SER H 109 " --> pdb=" O SER H 105 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP H 110 " --> pdb=" O THR H 106 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR H 112 " --> pdb=" O GLU H 108 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR H 123 " --> pdb=" O ARG H 119 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N THR H 124 " --> pdb=" O ASP H 120 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ASN H 125 " --> pdb=" O LEU H 121 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG H 128 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL H 129 " --> pdb=" O ASN H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 149 removed outlier: 3.625A pdb=" N VAL H 142 " --> pdb=" O TYR H 138 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP H 143 " --> pdb=" O GLU H 139 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N TRP H 144 " --> pdb=" O ARG H 140 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ALA H 147 " --> pdb=" O ASP H 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 164 removed outlier: 3.527A pdb=" N HIS H 163 " --> pdb=" O THR H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 171 removed outlier: 3.755A pdb=" N SER H 168 " --> pdb=" O SER H 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 203 removed outlier: 4.551A pdb=" N ILE H 187 " --> pdb=" O THR H 183 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N THR H 189 " --> pdb=" O ARG H 185 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS H 196 " --> pdb=" O TYR H 192 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU H 197 " --> pdb=" O GLU H 193 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE H 198 " --> pdb=" O ALA H 194 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE H 199 " --> pdb=" O THR H 195 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU H 200 " --> pdb=" O LYS H 196 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 276 removed outlier: 3.571A pdb=" N ARG H 256 " --> pdb=" O SER H 252 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU H 257 " --> pdb=" O PRO H 253 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N GLN H 259 " --> pdb=" O GLN H 255 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ASN H 260 " --> pdb=" O ARG H 256 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE H 262 " --> pdb=" O TYR H 258 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR H 267 " --> pdb=" O MET H 263 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU H 269 " --> pdb=" O TYR H 265 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N HIS H 270 " --> pdb=" O ARG H 266 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS H 272 " --> pdb=" O LEU H 268 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE H 273 " --> pdb=" O GLU H 269 " (cutoff:3.500A) Processing helix chain 'H' and resid 441 through 448 removed outlier: 3.756A pdb=" N GLU H 445 " --> pdb=" O ALA H 441 " (cutoff:3.500A) Processing helix chain 'H' and resid 480 through 496 removed outlier: 4.210A pdb=" N THR H 486 " --> pdb=" O THR H 482 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLU H 487 " --> pdb=" O LYS H 483 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR H 496 " --> pdb=" O GLU H 492 " (cutoff:3.500A) Processing helix chain 'H' and resid 515 through 528 removed outlier: 3.852A pdb=" N SER H 520 " --> pdb=" O SER H 516 " (cutoff:3.500A) Proline residue: H 525 - end of helix Processing helix chain 'H' and resid 541 through 545 removed outlier: 3.772A pdb=" N ALA H 544 " --> pdb=" O ASP H 541 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR H 545 " --> pdb=" O VAL H 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 541 through 545' Processing helix chain 'H' and resid 547 through 558 removed outlier: 3.637A pdb=" N ASP H 553 " --> pdb=" O VAL H 549 " (cutoff:3.500A) Processing helix chain 'H' and resid 559 through 570 removed outlier: 3.536A pdb=" N TYR H 564 " --> pdb=" O ARG H 560 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE H 565 " --> pdb=" O LEU H 561 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU H 566 " --> pdb=" O ALA H 562 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP H 567 " --> pdb=" O ILE H 563 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 36 removed outlier: 4.224A pdb=" N LEU I 34 " --> pdb=" O LEU I 30 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN I 35 " --> pdb=" O PHE I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 43 through 50 removed outlier: 4.469A pdb=" N ALA I 48 " --> pdb=" O THR I 45 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU I 50 " --> pdb=" O TYR I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 54 through 70 removed outlier: 3.936A pdb=" N THR I 62 " --> pdb=" O ARG I 58 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE I 65 " --> pdb=" O PHE I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 92 removed outlier: 3.718A pdb=" N TRP I 92 " --> pdb=" O ILE I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 132 removed outlier: 4.584A pdb=" N GLU I 104 " --> pdb=" O SER I 100 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLU I 108 " --> pdb=" O GLU I 104 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N SER I 109 " --> pdb=" O SER I 105 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP I 110 " --> pdb=" O THR I 106 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N THR I 112 " --> pdb=" O GLU I 108 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR I 123 " --> pdb=" O ARG I 119 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N THR I 124 " --> pdb=" O ASP I 120 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASN I 125 " --> pdb=" O LEU I 121 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ARG I 128 " --> pdb=" O THR I 124 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL I 129 " --> pdb=" O ASN I 125 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 149 removed outlier: 3.625A pdb=" N VAL I 142 " --> pdb=" O TYR I 138 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP I 143 " --> pdb=" O GLU I 139 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N TRP I 144 " --> pdb=" O ARG I 140 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ALA I 147 " --> pdb=" O ASP I 143 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 164 removed outlier: 3.527A pdb=" N HIS I 163 " --> pdb=" O THR I 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 164 through 171 removed outlier: 3.754A pdb=" N SER I 168 " --> pdb=" O SER I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 203 removed outlier: 4.551A pdb=" N ILE I 187 " --> pdb=" O THR I 183 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR I 189 " --> pdb=" O ARG I 185 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS I 196 " --> pdb=" O TYR I 192 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU I 197 " --> pdb=" O GLU I 193 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE I 198 " --> pdb=" O ALA I 194 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE I 199 " --> pdb=" O THR I 195 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU I 200 " --> pdb=" O LYS I 196 " (cutoff:3.500A) Processing helix chain 'I' and resid 252 through 276 removed outlier: 3.571A pdb=" N ARG I 256 " --> pdb=" O SER I 252 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU I 257 " --> pdb=" O PRO I 253 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N GLN I 259 " --> pdb=" O GLN I 255 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ASN I 260 " --> pdb=" O ARG I 256 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE I 262 " --> pdb=" O TYR I 258 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR I 267 " --> pdb=" O MET I 263 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU I 269 " --> pdb=" O TYR I 265 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N HIS I 270 " --> pdb=" O ARG I 266 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS I 272 " --> pdb=" O LEU I 268 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE I 273 " --> pdb=" O GLU I 269 " (cutoff:3.500A) Processing helix chain 'I' and resid 441 through 448 removed outlier: 3.756A pdb=" N GLU I 445 " --> pdb=" O ALA I 441 " (cutoff:3.500A) Processing helix chain 'I' and resid 480 through 496 removed outlier: 4.210A pdb=" N THR I 486 " --> pdb=" O THR I 482 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLU I 487 " --> pdb=" O LYS I 483 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR I 496 " --> pdb=" O GLU I 492 " (cutoff:3.500A) Processing helix chain 'I' and resid 515 through 528 removed outlier: 3.851A pdb=" N SER I 520 " --> pdb=" O SER I 516 " (cutoff:3.500A) Proline residue: I 525 - end of helix Processing helix chain 'I' and resid 541 through 545 removed outlier: 3.773A pdb=" N ALA I 544 " --> pdb=" O ASP I 541 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR I 545 " --> pdb=" O VAL I 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 541 through 545' Processing helix chain 'I' and resid 547 through 558 removed outlier: 3.637A pdb=" N ASP I 553 " --> pdb=" O VAL I 549 " (cutoff:3.500A) Processing helix chain 'I' and resid 559 through 570 removed outlier: 3.535A pdb=" N TYR I 564 " --> pdb=" O ARG I 560 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE I 565 " --> pdb=" O LEU I 561 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU I 566 " --> pdb=" O ALA I 562 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP I 567 " --> pdb=" O ILE I 563 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 36 removed outlier: 4.224A pdb=" N LEU J 34 " --> pdb=" O LEU J 30 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN J 35 " --> pdb=" O PHE J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 50 removed outlier: 4.469A pdb=" N ALA J 48 " --> pdb=" O THR J 45 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU J 50 " --> pdb=" O TYR J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 70 removed outlier: 3.937A pdb=" N THR J 62 " --> pdb=" O ARG J 58 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE J 65 " --> pdb=" O PHE J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 75 through 92 removed outlier: 3.718A pdb=" N TRP J 92 " --> pdb=" O ILE J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 132 removed outlier: 4.584A pdb=" N GLU J 104 " --> pdb=" O SER J 100 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLU J 108 " --> pdb=" O GLU J 104 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N SER J 109 " --> pdb=" O SER J 105 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP J 110 " --> pdb=" O THR J 106 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR J 112 " --> pdb=" O GLU J 108 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR J 123 " --> pdb=" O ARG J 119 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR J 124 " --> pdb=" O ASP J 120 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASN J 125 " --> pdb=" O LEU J 121 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ARG J 128 " --> pdb=" O THR J 124 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL J 129 " --> pdb=" O ASN J 125 " (cutoff:3.500A) Processing helix chain 'J' and resid 138 through 149 removed outlier: 3.625A pdb=" N VAL J 142 " --> pdb=" O TYR J 138 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP J 143 " --> pdb=" O GLU J 139 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N TRP J 144 " --> pdb=" O ARG J 140 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ALA J 147 " --> pdb=" O ASP J 143 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 164 removed outlier: 3.526A pdb=" N HIS J 163 " --> pdb=" O THR J 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 164 through 171 removed outlier: 3.755A pdb=" N SER J 168 " --> pdb=" O SER J 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 203 removed outlier: 4.551A pdb=" N ILE J 187 " --> pdb=" O THR J 183 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N THR J 189 " --> pdb=" O ARG J 185 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS J 196 " --> pdb=" O TYR J 192 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU J 197 " --> pdb=" O GLU J 193 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE J 198 " --> pdb=" O ALA J 194 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE J 199 " --> pdb=" O THR J 195 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU J 200 " --> pdb=" O LYS J 196 " (cutoff:3.500A) Processing helix chain 'J' and resid 252 through 276 removed outlier: 3.571A pdb=" N ARG J 256 " --> pdb=" O SER J 252 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU J 257 " --> pdb=" O PRO J 253 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N GLN J 259 " --> pdb=" O GLN J 255 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ASN J 260 " --> pdb=" O ARG J 256 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE J 262 " --> pdb=" O TYR J 258 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR J 267 " --> pdb=" O MET J 263 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU J 269 " --> pdb=" O TYR J 265 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N HIS J 270 " --> pdb=" O ARG J 266 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS J 272 " --> pdb=" O LEU J 268 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE J 273 " --> pdb=" O GLU J 269 " (cutoff:3.500A) Processing helix chain 'J' and resid 441 through 448 removed outlier: 3.756A pdb=" N GLU J 445 " --> pdb=" O ALA J 441 " (cutoff:3.500A) Processing helix chain 'J' and resid 480 through 496 removed outlier: 4.210A pdb=" N THR J 486 " --> pdb=" O THR J 482 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLU J 487 " --> pdb=" O LYS J 483 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR J 496 " --> pdb=" O GLU J 492 " (cutoff:3.500A) Processing helix chain 'J' and resid 515 through 528 removed outlier: 3.851A pdb=" N SER J 520 " --> pdb=" O SER J 516 " (cutoff:3.500A) Proline residue: J 525 - end of helix Processing helix chain 'J' and resid 541 through 545 removed outlier: 3.771A pdb=" N ALA J 544 " --> pdb=" O ASP J 541 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR J 545 " --> pdb=" O VAL J 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 541 through 545' Processing helix chain 'J' and resid 547 through 558 removed outlier: 3.638A pdb=" N ASP J 553 " --> pdb=" O VAL J 549 " (cutoff:3.500A) Processing helix chain 'J' and resid 559 through 570 removed outlier: 3.535A pdb=" N TYR J 564 " --> pdb=" O ARG J 560 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE J 565 " --> pdb=" O LEU J 561 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU J 566 " --> pdb=" O ALA J 562 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP J 567 " --> pdb=" O ILE J 563 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 36 removed outlier: 4.224A pdb=" N LEU K 34 " --> pdb=" O LEU K 30 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN K 35 " --> pdb=" O PHE K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 50 removed outlier: 4.468A pdb=" N ALA K 48 " --> pdb=" O THR K 45 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU K 50 " --> pdb=" O TYR K 47 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 70 removed outlier: 3.937A pdb=" N THR K 62 " --> pdb=" O ARG K 58 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE K 65 " --> pdb=" O PHE K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 75 through 92 removed outlier: 3.718A pdb=" N TRP K 92 " --> pdb=" O ILE K 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 100 through 132 removed outlier: 4.584A pdb=" N GLU K 104 " --> pdb=" O SER K 100 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLU K 108 " --> pdb=" O GLU K 104 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N SER K 109 " --> pdb=" O SER K 105 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP K 110 " --> pdb=" O THR K 106 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N THR K 112 " --> pdb=" O GLU K 108 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR K 123 " --> pdb=" O ARG K 119 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR K 124 " --> pdb=" O ASP K 120 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASN K 125 " --> pdb=" O LEU K 121 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG K 128 " --> pdb=" O THR K 124 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL K 129 " --> pdb=" O ASN K 125 " (cutoff:3.500A) Processing helix chain 'K' and resid 138 through 149 removed outlier: 3.625A pdb=" N VAL K 142 " --> pdb=" O TYR K 138 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP K 143 " --> pdb=" O GLU K 139 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N TRP K 144 " --> pdb=" O ARG K 140 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ALA K 147 " --> pdb=" O ASP K 143 " (cutoff:3.500A) Processing helix chain 'K' and resid 159 through 164 removed outlier: 3.526A pdb=" N HIS K 163 " --> pdb=" O THR K 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 164 through 171 removed outlier: 3.755A pdb=" N SER K 168 " --> pdb=" O SER K 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 181 through 203 removed outlier: 4.551A pdb=" N ILE K 187 " --> pdb=" O THR K 183 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR K 189 " --> pdb=" O ARG K 185 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS K 196 " --> pdb=" O TYR K 192 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU K 197 " --> pdb=" O GLU K 193 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE K 198 " --> pdb=" O ALA K 194 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE K 199 " --> pdb=" O THR K 195 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU K 200 " --> pdb=" O LYS K 196 " (cutoff:3.500A) Processing helix chain 'K' and resid 252 through 276 removed outlier: 3.571A pdb=" N ARG K 256 " --> pdb=" O SER K 252 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU K 257 " --> pdb=" O PRO K 253 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N GLN K 259 " --> pdb=" O GLN K 255 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ASN K 260 " --> pdb=" O ARG K 256 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE K 262 " --> pdb=" O TYR K 258 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR K 267 " --> pdb=" O MET K 263 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU K 269 " --> pdb=" O TYR K 265 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N HIS K 270 " --> pdb=" O ARG K 266 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS K 272 " --> pdb=" O LEU K 268 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE K 273 " --> pdb=" O GLU K 269 " (cutoff:3.500A) Processing helix chain 'K' and resid 441 through 448 removed outlier: 3.756A pdb=" N GLU K 445 " --> pdb=" O ALA K 441 " (cutoff:3.500A) Processing helix chain 'K' and resid 480 through 496 removed outlier: 4.210A pdb=" N THR K 486 " --> pdb=" O THR K 482 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLU K 487 " --> pdb=" O LYS K 483 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR K 496 " --> pdb=" O GLU K 492 " (cutoff:3.500A) Processing helix chain 'K' and resid 515 through 528 removed outlier: 3.852A pdb=" N SER K 520 " --> pdb=" O SER K 516 " (cutoff:3.500A) Proline residue: K 525 - end of helix Processing helix chain 'K' and resid 541 through 545 removed outlier: 3.771A pdb=" N ALA K 544 " --> pdb=" O ASP K 541 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR K 545 " --> pdb=" O VAL K 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 541 through 545' Processing helix chain 'K' and resid 547 through 558 removed outlier: 3.637A pdb=" N ASP K 553 " --> pdb=" O VAL K 549 " (cutoff:3.500A) Processing helix chain 'K' and resid 559 through 570 removed outlier: 3.536A pdb=" N TYR K 564 " --> pdb=" O ARG K 560 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE K 565 " --> pdb=" O LEU K 561 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU K 566 " --> pdb=" O ALA K 562 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP K 567 " --> pdb=" O ILE K 563 " (cutoff:3.500A) Processing helix chain 'L' and resid 24 through 36 removed outlier: 4.224A pdb=" N LEU L 34 " --> pdb=" O LEU L 30 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN L 35 " --> pdb=" O PHE L 31 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 50 removed outlier: 4.468A pdb=" N ALA L 48 " --> pdb=" O THR L 45 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU L 50 " --> pdb=" O TYR L 47 " (cutoff:3.500A) Processing helix chain 'L' and resid 54 through 70 removed outlier: 3.937A pdb=" N THR L 62 " --> pdb=" O ARG L 58 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE L 65 " --> pdb=" O PHE L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 92 removed outlier: 3.719A pdb=" N TRP L 92 " --> pdb=" O ILE L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 100 through 132 removed outlier: 4.584A pdb=" N GLU L 104 " --> pdb=" O SER L 100 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU L 108 " --> pdb=" O GLU L 104 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N SER L 109 " --> pdb=" O SER L 105 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP L 110 " --> pdb=" O THR L 106 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N THR L 112 " --> pdb=" O GLU L 108 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR L 123 " --> pdb=" O ARG L 119 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR L 124 " --> pdb=" O ASP L 120 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASN L 125 " --> pdb=" O LEU L 121 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ARG L 128 " --> pdb=" O THR L 124 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL L 129 " --> pdb=" O ASN L 125 " (cutoff:3.500A) Processing helix chain 'L' and resid 138 through 149 removed outlier: 3.625A pdb=" N VAL L 142 " --> pdb=" O TYR L 138 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP L 143 " --> pdb=" O GLU L 139 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N TRP L 144 " --> pdb=" O ARG L 140 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ALA L 147 " --> pdb=" O ASP L 143 " (cutoff:3.500A) Processing helix chain 'L' and resid 159 through 164 removed outlier: 3.527A pdb=" N HIS L 163 " --> pdb=" O THR L 159 " (cutoff:3.500A) Processing helix chain 'L' and resid 164 through 171 removed outlier: 3.753A pdb=" N SER L 168 " --> pdb=" O SER L 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 181 through 203 removed outlier: 4.551A pdb=" N ILE L 187 " --> pdb=" O THR L 183 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR L 189 " --> pdb=" O ARG L 185 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS L 196 " --> pdb=" O TYR L 192 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU L 197 " --> pdb=" O GLU L 193 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE L 198 " --> pdb=" O ALA L 194 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE L 199 " --> pdb=" O THR L 195 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU L 200 " --> pdb=" O LYS L 196 " (cutoff:3.500A) Processing helix chain 'L' and resid 252 through 276 removed outlier: 3.571A pdb=" N ARG L 256 " --> pdb=" O SER L 252 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU L 257 " --> pdb=" O PRO L 253 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N GLN L 259 " --> pdb=" O GLN L 255 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ASN L 260 " --> pdb=" O ARG L 256 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE L 262 " --> pdb=" O TYR L 258 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR L 267 " --> pdb=" O MET L 263 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU L 269 " --> pdb=" O TYR L 265 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N HIS L 270 " --> pdb=" O ARG L 266 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS L 272 " --> pdb=" O LEU L 268 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE L 273 " --> pdb=" O GLU L 269 " (cutoff:3.500A) Processing helix chain 'L' and resid 441 through 448 removed outlier: 3.756A pdb=" N GLU L 445 " --> pdb=" O ALA L 441 " (cutoff:3.500A) Processing helix chain 'L' and resid 480 through 496 removed outlier: 4.211A pdb=" N THR L 486 " --> pdb=" O THR L 482 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLU L 487 " --> pdb=" O LYS L 483 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR L 496 " --> pdb=" O GLU L 492 " (cutoff:3.500A) Processing helix chain 'L' and resid 515 through 528 removed outlier: 3.852A pdb=" N SER L 520 " --> pdb=" O SER L 516 " (cutoff:3.500A) Proline residue: L 525 - end of helix Processing helix chain 'L' and resid 541 through 545 removed outlier: 3.772A pdb=" N ALA L 544 " --> pdb=" O ASP L 541 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR L 545 " --> pdb=" O VAL L 542 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 541 through 545' Processing helix chain 'L' and resid 547 through 558 removed outlier: 3.637A pdb=" N ASP L 553 " --> pdb=" O VAL L 549 " (cutoff:3.500A) Processing helix chain 'L' and resid 559 through 570 removed outlier: 3.535A pdb=" N TYR L 564 " --> pdb=" O ARG L 560 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE L 565 " --> pdb=" O LEU L 561 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU L 566 " --> pdb=" O ALA L 562 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP L 567 " --> pdb=" O ILE L 563 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 removed outlier: 3.674A pdb=" N GLU A 223 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 205 through 206 removed outlier: 3.815A pdb=" N ALA A 153 " --> pdb=" O ARG A 234 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG A 234 " --> pdb=" O ALA A 153 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 456 through 458 removed outlier: 4.009A pdb=" N ALA A 457 " --> pdb=" O ALA A 284 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE A 285 " --> pdb=" O LEU L 467 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 466 through 469 removed outlier: 6.502A pdb=" N ILE B 285 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA B 457 " --> pdb=" O ALA B 284 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 500 through 502 removed outlier: 3.592A pdb=" N THR A 500 " --> pdb=" O ARG A 513 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG A 513 " --> pdb=" O THR A 500 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR A 511 " --> pdb=" O VAL A 502 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 19 through 20 removed outlier: 3.674A pdb=" N GLU B 223 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 205 through 206 removed outlier: 3.815A pdb=" N ALA B 153 " --> pdb=" O ARG B 234 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG B 234 " --> pdb=" O ALA B 153 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 466 through 469 removed outlier: 6.505A pdb=" N ILE C 285 " --> pdb=" O LEU B 467 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA C 457 " --> pdb=" O ALA C 284 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 500 through 502 removed outlier: 3.591A pdb=" N THR B 500 " --> pdb=" O ARG B 513 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG B 513 " --> pdb=" O THR B 500 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR B 511 " --> pdb=" O VAL B 502 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 19 through 20 removed outlier: 3.674A pdb=" N GLU C 223 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 205 through 206 removed outlier: 3.814A pdb=" N ALA C 153 " --> pdb=" O ARG C 234 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG C 234 " --> pdb=" O ALA C 153 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 466 through 469 removed outlier: 6.507A pdb=" N ILE D 285 " --> pdb=" O LEU C 467 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA D 457 " --> pdb=" O ALA D 284 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 500 through 502 removed outlier: 3.592A pdb=" N THR C 500 " --> pdb=" O ARG C 513 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG C 513 " --> pdb=" O THR C 500 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR C 511 " --> pdb=" O VAL C 502 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 19 through 20 removed outlier: 3.674A pdb=" N GLU D 223 " --> pdb=" O LEU D 218 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 205 through 206 removed outlier: 3.815A pdb=" N ALA D 153 " --> pdb=" O ARG D 234 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG D 234 " --> pdb=" O ALA D 153 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 466 through 469 removed outlier: 6.505A pdb=" N ILE E 285 " --> pdb=" O LEU D 467 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA E 457 " --> pdb=" O ALA E 284 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 500 through 502 removed outlier: 3.592A pdb=" N THR D 500 " --> pdb=" O ARG D 513 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG D 513 " --> pdb=" O THR D 500 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR D 511 " --> pdb=" O VAL D 502 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 19 through 20 removed outlier: 3.673A pdb=" N GLU E 223 " --> pdb=" O LEU E 218 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 205 through 206 removed outlier: 3.815A pdb=" N ALA E 153 " --> pdb=" O ARG E 234 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG E 234 " --> pdb=" O ALA E 153 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 466 through 469 removed outlier: 6.504A pdb=" N ILE F 285 " --> pdb=" O LEU E 467 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA F 457 " --> pdb=" O ALA F 284 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 500 through 502 removed outlier: 3.592A pdb=" N THR E 500 " --> pdb=" O ARG E 513 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG E 513 " --> pdb=" O THR E 500 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR E 511 " --> pdb=" O VAL E 502 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 19 through 20 removed outlier: 3.673A pdb=" N GLU F 223 " --> pdb=" O LEU F 218 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 205 through 206 removed outlier: 3.815A pdb=" N ALA F 153 " --> pdb=" O ARG F 234 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG F 234 " --> pdb=" O ALA F 153 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 466 through 469 removed outlier: 6.505A pdb=" N ILE G 285 " --> pdb=" O LEU F 467 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA G 457 " --> pdb=" O ALA G 284 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 500 through 502 removed outlier: 3.592A pdb=" N THR F 500 " --> pdb=" O ARG F 513 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG F 513 " --> pdb=" O THR F 500 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR F 511 " --> pdb=" O VAL F 502 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 19 through 20 removed outlier: 3.673A pdb=" N GLU G 223 " --> pdb=" O LEU G 218 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 205 through 206 removed outlier: 3.815A pdb=" N ALA G 153 " --> pdb=" O ARG G 234 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG G 234 " --> pdb=" O ALA G 153 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 466 through 469 removed outlier: 6.504A pdb=" N ILE H 285 " --> pdb=" O LEU G 467 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA H 457 " --> pdb=" O ALA H 284 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 500 through 502 removed outlier: 3.592A pdb=" N THR G 500 " --> pdb=" O ARG G 513 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG G 513 " --> pdb=" O THR G 500 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR G 511 " --> pdb=" O VAL G 502 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 19 through 20 removed outlier: 3.673A pdb=" N GLU H 223 " --> pdb=" O LEU H 218 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 205 through 206 removed outlier: 3.814A pdb=" N ALA H 153 " --> pdb=" O ARG H 234 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG H 234 " --> pdb=" O ALA H 153 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 466 through 469 removed outlier: 6.498A pdb=" N ILE I 285 " --> pdb=" O LEU H 467 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA I 457 " --> pdb=" O ALA I 284 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 500 through 502 removed outlier: 3.592A pdb=" N THR H 500 " --> pdb=" O ARG H 513 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG H 513 " --> pdb=" O THR H 500 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR H 511 " --> pdb=" O VAL H 502 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 19 through 20 removed outlier: 3.673A pdb=" N GLU I 223 " --> pdb=" O LEU I 218 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 205 through 206 removed outlier: 3.815A pdb=" N ALA I 153 " --> pdb=" O ARG I 234 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG I 234 " --> pdb=" O ALA I 153 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 466 through 469 removed outlier: 6.518A pdb=" N ILE J 285 " --> pdb=" O LEU I 467 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA J 457 " --> pdb=" O ALA J 284 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 500 through 502 removed outlier: 3.592A pdb=" N THR I 500 " --> pdb=" O ARG I 513 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG I 513 " --> pdb=" O THR I 500 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR I 511 " --> pdb=" O VAL I 502 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 19 through 20 removed outlier: 3.673A pdb=" N GLU J 223 " --> pdb=" O LEU J 218 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 205 through 206 removed outlier: 3.815A pdb=" N ALA J 153 " --> pdb=" O ARG J 234 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG J 234 " --> pdb=" O ALA J 153 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 466 through 469 removed outlier: 6.501A pdb=" N ILE K 285 " --> pdb=" O LEU J 467 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA K 457 " --> pdb=" O ALA K 284 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 500 through 502 removed outlier: 3.593A pdb=" N THR J 500 " --> pdb=" O ARG J 513 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG J 513 " --> pdb=" O THR J 500 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR J 511 " --> pdb=" O VAL J 502 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 19 through 20 removed outlier: 3.672A pdb=" N GLU K 223 " --> pdb=" O LEU K 218 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 205 through 206 removed outlier: 3.815A pdb=" N ALA K 153 " --> pdb=" O ARG K 234 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG K 234 " --> pdb=" O ALA K 153 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 466 through 469 removed outlier: 6.502A pdb=" N ILE L 285 " --> pdb=" O LEU K 467 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA L 457 " --> pdb=" O ALA L 284 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 500 through 502 removed outlier: 3.593A pdb=" N THR K 500 " --> pdb=" O ARG K 513 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG K 513 " --> pdb=" O THR K 500 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR K 511 " --> pdb=" O VAL K 502 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 19 through 20 removed outlier: 3.674A pdb=" N GLU L 223 " --> pdb=" O LEU L 218 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 205 through 206 removed outlier: 3.815A pdb=" N ALA L 153 " --> pdb=" O ARG L 234 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG L 234 " --> pdb=" O ALA L 153 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 500 through 502 removed outlier: 3.592A pdb=" N THR L 500 " --> pdb=" O ARG L 513 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG L 513 " --> pdb=" O THR L 500 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR L 511 " --> pdb=" O VAL L 502 " (cutoff:3.500A) 1536 hydrogen bonds defined for protein. 4464 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: 13.35 Time building geometry restraints manager: 15.84 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: 11847 1.34 - 1.45: 6190 1.45 - 1.57: 20375 1.57 - 1.69: 0 1.69 - 1.81: 168 Bond restraints: 38580 Sorted by residual: bond pdb=" C GLY L 524 " pdb=" N PRO L 525 " ideal model delta sigma weight residual 1.337 1.317 0.020 9.80e-03 1.04e+04 3.97e+00 bond pdb=" C GLY F 524 " pdb=" N PRO F 525 " ideal model delta sigma weight residual 1.337 1.317 0.019 9.80e-03 1.04e+04 3.95e+00 bond pdb=" C GLY I 524 " pdb=" N PRO I 525 " ideal model delta sigma weight residual 1.337 1.317 0.019 9.80e-03 1.04e+04 3.86e+00 bond pdb=" C GLY B 524 " pdb=" N PRO B 525 " ideal model delta sigma weight residual 1.337 1.317 0.019 9.80e-03 1.04e+04 3.85e+00 bond pdb=" C GLY E 524 " pdb=" N PRO E 525 " ideal model delta sigma weight residual 1.337 1.317 0.019 9.80e-03 1.04e+04 3.85e+00 ... (remaining 38575 not shown) Histogram of bond angle deviations from ideal: 99.55 - 106.43: 972 106.43 - 113.32: 21565 113.32 - 120.20: 14660 120.20 - 127.08: 14754 127.08 - 133.96: 453 Bond angle restraints: 52404 Sorted by residual: angle pdb=" N HIS H 22 " pdb=" CA HIS H 22 " pdb=" C HIS H 22 " ideal model delta sigma weight residual 109.81 116.97 -7.16 2.21e+00 2.05e-01 1.05e+01 angle pdb=" N HIS J 22 " pdb=" CA HIS J 22 " pdb=" C HIS J 22 " ideal model delta sigma weight residual 109.81 116.96 -7.15 2.21e+00 2.05e-01 1.05e+01 angle pdb=" N HIS I 22 " pdb=" CA HIS I 22 " pdb=" C HIS I 22 " ideal model delta sigma weight residual 109.81 116.94 -7.13 2.21e+00 2.05e-01 1.04e+01 angle pdb=" N HIS A 22 " pdb=" CA HIS A 22 " pdb=" C HIS A 22 " ideal model delta sigma weight residual 109.81 116.94 -7.13 2.21e+00 2.05e-01 1.04e+01 angle pdb=" N HIS B 22 " pdb=" CA HIS B 22 " pdb=" C HIS B 22 " ideal model delta sigma weight residual 109.81 116.93 -7.12 2.21e+00 2.05e-01 1.04e+01 ... (remaining 52399 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 20592 17.24 - 34.48: 1944 34.48 - 51.72: 420 51.72 - 68.96: 96 68.96 - 86.21: 48 Dihedral angle restraints: 23100 sinusoidal: 9204 harmonic: 13896 Sorted by residual: dihedral pdb=" CA PRO D 53 " pdb=" C PRO D 53 " pdb=" N GLY D 54 " pdb=" CA GLY D 54 " ideal model delta harmonic sigma weight residual 180.00 156.73 23.27 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA PRO A 53 " pdb=" C PRO A 53 " pdb=" N GLY A 54 " pdb=" CA GLY A 54 " ideal model delta harmonic sigma weight residual 180.00 156.74 23.26 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA PRO L 53 " pdb=" C PRO L 53 " pdb=" N GLY L 54 " pdb=" CA GLY L 54 " ideal model delta harmonic sigma weight residual 180.00 156.74 23.26 0 5.00e+00 4.00e-02 2.16e+01 ... (remaining 23097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 3198 0.036 - 0.072: 2008 0.072 - 0.109: 647 0.109 - 0.145: 180 0.145 - 0.181: 39 Chirality restraints: 6072 Sorted by residual: chirality pdb=" CA GLN B 209 " pdb=" N GLN B 209 " pdb=" C GLN B 209 " pdb=" CB GLN B 209 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.18e-01 chirality pdb=" CA GLN H 209 " pdb=" N GLN H 209 " pdb=" C GLN H 209 " pdb=" CB GLN H 209 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.18e-01 chirality pdb=" CA GLN J 209 " pdb=" N GLN J 209 " pdb=" C GLN J 209 " pdb=" CB GLN J 209 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.13e-01 ... (remaining 6069 not shown) Planarity restraints: 6516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 439 " 0.009 2.00e-02 2.50e+03 1.83e-02 3.34e+00 pdb=" C SER D 439 " -0.032 2.00e-02 2.50e+03 pdb=" O SER D 439 " 0.012 2.00e-02 2.50e+03 pdb=" N THR D 440 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 439 " 0.009 2.00e-02 2.50e+03 1.83e-02 3.34e+00 pdb=" C SER B 439 " -0.032 2.00e-02 2.50e+03 pdb=" O SER B 439 " 0.012 2.00e-02 2.50e+03 pdb=" N THR B 440 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER L 439 " 0.009 2.00e-02 2.50e+03 1.83e-02 3.34e+00 pdb=" C SER L 439 " -0.032 2.00e-02 2.50e+03 pdb=" O SER L 439 " 0.012 2.00e-02 2.50e+03 pdb=" N THR L 440 " 0.011 2.00e-02 2.50e+03 ... (remaining 6513 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 684 2.65 - 3.21: 36221 3.21 - 3.77: 50484 3.77 - 4.34: 68856 4.34 - 4.90: 115929 Nonbonded interactions: 272174 Sorted by model distance: nonbonded pdb=" O LYS H 498 " pdb=" OG SER H 515 " model vdw 2.082 2.440 nonbonded pdb=" O LYS E 498 " pdb=" OG SER E 515 " model vdw 2.082 2.440 nonbonded pdb=" O LYS F 498 " pdb=" OG SER F 515 " model vdw 2.082 2.440 nonbonded pdb=" O LYS C 498 " pdb=" OG SER C 515 " model vdw 2.082 2.440 nonbonded pdb=" O LYS B 498 " pdb=" OG SER B 515 " model vdw 2.082 2.440 ... (remaining 272169 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.530 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: 4.690 Check model and map are aligned: 0.600 Set scattering table: 0.400 Process input model: 97.640 Find NCS groups from input model: 2.470 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 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 : 0.008 0.054 38580 Z= 0.541 Angle : 0.750 7.157 52404 Z= 0.423 Chirality : 0.051 0.181 6072 Planarity : 0.005 0.034 6516 Dihedral : 14.894 86.205 14076 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % Rotamer: Outliers : 0.57 % Allowed : 9.10 % Favored : 90.33 % 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: -4.34 (0.10), residues: 4560 helix: -2.69 (0.08), residues: 2196 sheet: -1.96 (0.26), residues: 360 loop : -3.21 (0.13), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 110 HIS 0.007 0.001 HIS K 22 PHE 0.027 0.003 PHE D 210 TYR 0.023 0.002 TYR F 141 ARG 0.003 0.000 ARG E 256 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 4236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 386 time to evaluate : 4.728 Fit side-chains revert: symmetry clash REVERT: A 161 GLU cc_start: 0.7047 (mp0) cc_final: 0.6840 (mp0) REVERT: D 161 GLU cc_start: 0.7011 (mp0) cc_final: 0.6798 (mp0) outliers start: 24 outliers final: 1 residues processed: 402 average time/residue: 0.5926 time to fit residues: 363.5442 Evaluate side-chains 264 residues out of total 4236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 263 time to evaluate : 5.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 223 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 395 optimal weight: 20.0000 chunk 354 optimal weight: 0.9980 chunk 196 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 239 optimal weight: 20.0000 chunk 189 optimal weight: 0.6980 chunk 366 optimal weight: 7.9990 chunk 141 optimal weight: 1.9990 chunk 223 optimal weight: 8.9990 chunk 273 optimal weight: 7.9990 chunk 424 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 ASN A 463 ASN B 260 ASN B 463 ASN C 260 ASN C 463 ASN D 49 ASN D 260 ASN D 463 ASN E 260 ASN E 463 ASN F 49 ASN F 260 ASN F 463 ASN G 49 ASN G 260 ASN G 463 ASN H 260 ASN H 463 ASN I 260 ASN I 463 ASN J 260 ASN J 463 ASN K 260 ASN K 463 ASN L 260 ASN L 463 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 38580 Z= 0.173 Angle : 0.572 6.051 52404 Z= 0.306 Chirality : 0.043 0.142 6072 Planarity : 0.004 0.040 6516 Dihedral : 4.474 43.588 5199 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 1.70 % Allowed : 10.03 % Favored : 88.28 % 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: -3.16 (0.11), residues: 4560 helix: -1.62 (0.09), residues: 2328 sheet: -1.45 (0.26), residues: 360 loop : -2.77 (0.13), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 110 HIS 0.003 0.001 HIS L 131 PHE 0.017 0.001 PHE A 262 TYR 0.012 0.001 TYR L 141 ARG 0.005 0.000 ARG H 220 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 4236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 371 time to evaluate : 4.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 20 residues processed: 417 average time/residue: 0.4664 time to fit residues: 322.0194 Evaluate side-chains 316 residues out of total 4236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 296 time to evaluate : 4.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 222 ASP Chi-restraints excluded: chain F residue 222 ASP Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 222 ASP Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 568 LEU Chi-restraints excluded: chain J residue 502 VAL Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 222 ASP Chi-restraints excluded: chain L residue 222 ASP Chi-restraints excluded: chain L residue 568 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 236 optimal weight: 7.9990 chunk 131 optimal weight: 9.9990 chunk 353 optimal weight: 7.9990 chunk 289 optimal weight: 3.9990 chunk 117 optimal weight: 10.0000 chunk 425 optimal weight: 6.9990 chunk 459 optimal weight: 1.9990 chunk 379 optimal weight: 8.9990 chunk 422 optimal weight: 9.9990 chunk 145 optimal weight: 7.9990 chunk 341 optimal weight: 0.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN B 49 ASN B 278 ASN C 49 ASN D 49 ASN E 49 ASN E 278 ASN G 49 ASN H 49 ASN H 278 ASN I 49 ASN J 49 ASN K 49 ASN K 278 ASN L 49 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 38580 Z= 0.320 Angle : 0.604 6.546 52404 Z= 0.325 Chirality : 0.045 0.148 6072 Planarity : 0.005 0.048 6516 Dihedral : 4.520 19.257 5196 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 2.63 % Allowed : 12.01 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.12), residues: 4560 helix: -0.81 (0.11), residues: 2256 sheet: -1.12 (0.27), residues: 360 loop : -2.74 (0.13), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 110 HIS 0.004 0.001 HIS I 22 PHE 0.021 0.002 PHE J 262 TYR 0.015 0.001 TYR L 141 ARG 0.007 0.000 ARG A 557 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 4236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 315 time to evaluate : 4.934 Fit side-chains revert: symmetry clash REVERT: A 161 GLU cc_start: 0.6772 (mp0) cc_final: 0.6528 (mp0) REVERT: C 566 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7484 (mp0) REVERT: F 566 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7543 (mp0) REVERT: L 566 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7534 (mp0) outliers start: 110 outliers final: 49 residues processed: 389 average time/residue: 0.4904 time to fit residues: 311.9764 Evaluate side-chains 343 residues out of total 4236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 291 time to evaluate : 4.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 71 HIS Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 566 GLU Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 472 SER Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 71 HIS Chi-restraints excluded: chain E residue 502 VAL Chi-restraints excluded: chain E residue 549 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 263 MET Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 566 GLU Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 71 HIS Chi-restraints excluded: chain H residue 502 VAL Chi-restraints excluded: chain H residue 549 VAL Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 211 THR Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 263 MET Chi-restraints excluded: chain I residue 549 VAL Chi-restraints excluded: chain I residue 568 LEU Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 472 SER Chi-restraints excluded: chain J residue 502 VAL Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 71 HIS Chi-restraints excluded: chain K residue 502 VAL Chi-restraints excluded: chain K residue 549 VAL Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 211 THR Chi-restraints excluded: chain L residue 549 VAL Chi-restraints excluded: chain L residue 566 GLU Chi-restraints excluded: chain L residue 568 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 420 optimal weight: 7.9990 chunk 320 optimal weight: 5.9990 chunk 220 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 203 optimal weight: 5.9990 chunk 285 optimal weight: 1.9990 chunk 427 optimal weight: 10.0000 chunk 452 optimal weight: 0.9980 chunk 223 optimal weight: 6.9990 chunk 404 optimal weight: 9.9990 chunk 121 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN B 49 ASN E 49 ASN G 49 ASN H 49 ASN J 49 ASN K 49 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 38580 Z= 0.298 Angle : 0.573 6.605 52404 Z= 0.309 Chirality : 0.045 0.147 6072 Planarity : 0.005 0.047 6516 Dihedral : 4.479 18.634 5196 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 3.37 % Allowed : 13.16 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.12), residues: 4560 helix: -0.50 (0.11), residues: 2280 sheet: -0.56 (0.24), residues: 468 loop : -2.83 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 110 HIS 0.003 0.001 HIS G 22 PHE 0.018 0.002 PHE J 262 TYR 0.014 0.001 TYR H 141 ARG 0.008 0.000 ARG I 557 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 4236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 312 time to evaluate : 4.728 Fit side-chains revert: symmetry clash REVERT: A 150 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7953 (mtm) REVERT: A 459 VAL cc_start: 0.8334 (OUTLIER) cc_final: 0.8102 (m) REVERT: B 459 VAL cc_start: 0.8428 (OUTLIER) cc_final: 0.8203 (m) REVERT: B 566 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7634 (mp0) REVERT: C 459 VAL cc_start: 0.8603 (OUTLIER) cc_final: 0.8388 (m) REVERT: C 566 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7528 (mp0) REVERT: D 459 VAL cc_start: 0.8335 (OUTLIER) cc_final: 0.8103 (m) REVERT: E 459 VAL cc_start: 0.8431 (OUTLIER) cc_final: 0.8205 (m) REVERT: F 459 VAL cc_start: 0.8544 (OUTLIER) cc_final: 0.8301 (m) REVERT: F 566 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7552 (mp0) REVERT: G 459 VAL cc_start: 0.8328 (OUTLIER) cc_final: 0.8097 (m) REVERT: H 459 VAL cc_start: 0.8427 (OUTLIER) cc_final: 0.8203 (m) REVERT: H 566 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7635 (mp0) REVERT: I 459 VAL cc_start: 0.8598 (OUTLIER) cc_final: 0.8382 (m) REVERT: J 150 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.7952 (mtm) REVERT: J 459 VAL cc_start: 0.8293 (OUTLIER) cc_final: 0.8055 (m) REVERT: K 459 VAL cc_start: 0.8433 (OUTLIER) cc_final: 0.8208 (m) REVERT: K 566 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7645 (mp0) REVERT: L 459 VAL cc_start: 0.8571 (OUTLIER) cc_final: 0.8338 (m) REVERT: L 566 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7545 (mp0) outliers start: 141 outliers final: 75 residues processed: 406 average time/residue: 0.4739 time to fit residues: 318.5744 Evaluate side-chains 370 residues out of total 4236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 275 time to evaluate : 4.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 71 HIS Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 566 GLU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 566 GLU Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 472 SER Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 222 ASP Chi-restraints excluded: chain E residue 263 MET Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 502 VAL Chi-restraints excluded: chain E residue 549 VAL Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 222 ASP Chi-restraints excluded: chain F residue 263 MET Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 566 GLU Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 279 THR Chi-restraints excluded: chain G residue 459 VAL Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 71 HIS Chi-restraints excluded: chain H residue 222 ASP Chi-restraints excluded: chain H residue 263 MET Chi-restraints excluded: chain H residue 279 THR Chi-restraints excluded: chain H residue 459 VAL Chi-restraints excluded: chain H residue 502 VAL Chi-restraints excluded: chain H residue 549 VAL Chi-restraints excluded: chain H residue 566 GLU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 211 THR Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 263 MET Chi-restraints excluded: chain I residue 279 THR Chi-restraints excluded: chain I residue 459 VAL Chi-restraints excluded: chain I residue 549 VAL Chi-restraints excluded: chain I residue 568 LEU Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 150 MET Chi-restraints excluded: chain J residue 279 THR Chi-restraints excluded: chain J residue 459 VAL Chi-restraints excluded: chain J residue 472 SER Chi-restraints excluded: chain J residue 502 VAL Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 71 HIS Chi-restraints excluded: chain K residue 222 ASP Chi-restraints excluded: chain K residue 263 MET Chi-restraints excluded: chain K residue 279 THR Chi-restraints excluded: chain K residue 459 VAL Chi-restraints excluded: chain K residue 502 VAL Chi-restraints excluded: chain K residue 549 VAL Chi-restraints excluded: chain K residue 566 GLU Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 211 THR Chi-restraints excluded: chain L residue 222 ASP Chi-restraints excluded: chain L residue 263 MET Chi-restraints excluded: chain L residue 279 THR Chi-restraints excluded: chain L residue 459 VAL Chi-restraints excluded: chain L residue 549 VAL Chi-restraints excluded: chain L residue 566 GLU Chi-restraints excluded: chain L residue 568 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 376 optimal weight: 0.1980 chunk 256 optimal weight: 4.9990 chunk 6 optimal weight: 20.0000 chunk 336 optimal weight: 2.9990 chunk 186 optimal weight: 0.9990 chunk 386 optimal weight: 9.9990 chunk 312 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 230 optimal weight: 8.9990 chunk 406 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN G 49 ASN J 49 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 38580 Z= 0.167 Angle : 0.508 5.767 52404 Z= 0.272 Chirality : 0.042 0.144 6072 Planarity : 0.005 0.044 6516 Dihedral : 4.159 19.758 5196 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 2.60 % Allowed : 15.21 % Favored : 82.19 % 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: -1.74 (0.12), residues: 4560 helix: -0.42 (0.11), residues: 2352 sheet: -0.24 (0.25), residues: 468 loop : -2.41 (0.15), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 110 HIS 0.002 0.001 HIS D 22 PHE 0.012 0.001 PHE A 262 TYR 0.009 0.001 TYR C 141 ARG 0.009 0.000 ARG E 557 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 4236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 353 time to evaluate : 4.667 Fit side-chains revert: symmetry clash REVERT: A 150 MET cc_start: 0.8125 (ptp) cc_final: 0.7890 (mtm) REVERT: A 459 VAL cc_start: 0.8332 (OUTLIER) cc_final: 0.8101 (m) REVERT: B 459 VAL cc_start: 0.8420 (OUTLIER) cc_final: 0.8205 (m) REVERT: B 566 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7592 (mp0) REVERT: C 459 VAL cc_start: 0.8586 (OUTLIER) cc_final: 0.8370 (m) REVERT: C 566 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7486 (mp0) REVERT: D 150 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7885 (mtm) REVERT: D 459 VAL cc_start: 0.8330 (OUTLIER) cc_final: 0.8105 (m) REVERT: E 459 VAL cc_start: 0.8423 (OUTLIER) cc_final: 0.8201 (m) REVERT: F 459 VAL cc_start: 0.8541 (OUTLIER) cc_final: 0.8281 (m) REVERT: F 566 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7527 (mp0) REVERT: G 150 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7880 (mtm) REVERT: G 459 VAL cc_start: 0.8322 (OUTLIER) cc_final: 0.8095 (m) REVERT: H 459 VAL cc_start: 0.8420 (OUTLIER) cc_final: 0.8200 (m) REVERT: H 550 GLU cc_start: 0.7946 (pm20) cc_final: 0.7623 (pm20) REVERT: H 566 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7596 (mp0) REVERT: I 459 VAL cc_start: 0.8580 (OUTLIER) cc_final: 0.8360 (m) REVERT: J 150 MET cc_start: 0.8126 (ptp) cc_final: 0.7891 (mtm) REVERT: J 459 VAL cc_start: 0.8293 (OUTLIER) cc_final: 0.8053 (m) REVERT: K 459 VAL cc_start: 0.8424 (OUTLIER) cc_final: 0.8203 (m) REVERT: L 459 VAL cc_start: 0.8531 (OUTLIER) cc_final: 0.8283 (m) REVERT: L 566 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7543 (mp0) outliers start: 109 outliers final: 52 residues processed: 416 average time/residue: 0.4614 time to fit residues: 319.4723 Evaluate side-chains 362 residues out of total 4236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 291 time to evaluate : 4.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 71 HIS Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 491 SER Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 566 GLU Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 566 GLU Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 491 SER Chi-restraints excluded: chain E residue 502 VAL Chi-restraints excluded: chain E residue 549 VAL Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 222 ASP Chi-restraints excluded: chain F residue 263 MET Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 566 GLU Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 49 ASN Chi-restraints excluded: chain G residue 150 MET Chi-restraints excluded: chain G residue 279 THR Chi-restraints excluded: chain G residue 459 VAL Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain H residue 71 HIS Chi-restraints excluded: chain H residue 279 THR Chi-restraints excluded: chain H residue 459 VAL Chi-restraints excluded: chain H residue 491 SER Chi-restraints excluded: chain H residue 502 VAL Chi-restraints excluded: chain H residue 549 VAL Chi-restraints excluded: chain H residue 566 GLU Chi-restraints excluded: chain I residue 211 THR Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 263 MET Chi-restraints excluded: chain I residue 459 VAL Chi-restraints excluded: chain I residue 549 VAL Chi-restraints excluded: chain I residue 568 LEU Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 279 THR Chi-restraints excluded: chain J residue 459 VAL Chi-restraints excluded: chain J residue 502 VAL Chi-restraints excluded: chain K residue 263 MET Chi-restraints excluded: chain K residue 279 THR Chi-restraints excluded: chain K residue 459 VAL Chi-restraints excluded: chain K residue 491 SER Chi-restraints excluded: chain K residue 502 VAL Chi-restraints excluded: chain K residue 549 VAL Chi-restraints excluded: chain L residue 211 THR Chi-restraints excluded: chain L residue 222 ASP Chi-restraints excluded: chain L residue 263 MET Chi-restraints excluded: chain L residue 459 VAL Chi-restraints excluded: chain L residue 549 VAL Chi-restraints excluded: chain L residue 566 GLU Chi-restraints excluded: chain L residue 568 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 152 optimal weight: 9.9990 chunk 407 optimal weight: 0.9980 chunk 89 optimal weight: 7.9990 chunk 265 optimal weight: 1.9990 chunk 111 optimal weight: 7.9990 chunk 452 optimal weight: 3.9990 chunk 375 optimal weight: 0.8980 chunk 209 optimal weight: 6.9990 chunk 37 optimal weight: 8.9990 chunk 149 optimal weight: 2.9990 chunk 237 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 49 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 38580 Z= 0.186 Angle : 0.513 5.731 52404 Z= 0.272 Chirality : 0.042 0.143 6072 Planarity : 0.005 0.050 6516 Dihedral : 4.089 19.593 5196 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 2.98 % Allowed : 16.36 % Favored : 80.66 % 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: -1.42 (0.13), residues: 4560 helix: -0.06 (0.11), residues: 2268 sheet: -0.08 (0.24), residues: 492 loop : -2.35 (0.15), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 110 HIS 0.002 0.001 HIS D 22 PHE 0.013 0.001 PHE D 262 TYR 0.009 0.001 TYR H 141 ARG 0.011 0.000 ARG I 557 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 4236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 307 time to evaluate : 4.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 VAL cc_start: 0.8309 (OUTLIER) cc_final: 0.8087 (m) REVERT: B 459 VAL cc_start: 0.8438 (OUTLIER) cc_final: 0.8208 (m) REVERT: B 566 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7546 (mp0) REVERT: C 459 VAL cc_start: 0.8590 (OUTLIER) cc_final: 0.8371 (m) REVERT: C 566 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7526 (mp0) REVERT: D 459 VAL cc_start: 0.8345 (OUTLIER) cc_final: 0.8134 (m) REVERT: E 459 VAL cc_start: 0.8439 (OUTLIER) cc_final: 0.8209 (m) REVERT: F 459 VAL cc_start: 0.8550 (OUTLIER) cc_final: 0.8291 (m) REVERT: F 566 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7535 (mp0) REVERT: G 459 VAL cc_start: 0.8340 (OUTLIER) cc_final: 0.8122 (m) REVERT: H 459 VAL cc_start: 0.8439 (OUTLIER) cc_final: 0.8210 (m) REVERT: H 566 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7550 (mp0) REVERT: I 459 VAL cc_start: 0.8588 (OUTLIER) cc_final: 0.8366 (m) REVERT: J 459 VAL cc_start: 0.8305 (OUTLIER) cc_final: 0.8088 (m) REVERT: K 459 VAL cc_start: 0.8441 (OUTLIER) cc_final: 0.8212 (m) REVERT: L 459 VAL cc_start: 0.8554 (OUTLIER) cc_final: 0.8312 (m) REVERT: L 566 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7520 (mp0) outliers start: 125 outliers final: 81 residues processed: 386 average time/residue: 0.4746 time to fit residues: 302.8034 Evaluate side-chains 391 residues out of total 4236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 293 time to evaluate : 4.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 71 HIS Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 263 MET Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 491 SER Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 566 GLU Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 552 ILE Chi-restraints excluded: chain C residue 566 GLU Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 222 ASP Chi-restraints excluded: chain E residue 263 MET Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 491 SER Chi-restraints excluded: chain E residue 502 VAL Chi-restraints excluded: chain E residue 549 VAL Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 222 ASP Chi-restraints excluded: chain F residue 263 MET Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain F residue 491 SER Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 552 ILE Chi-restraints excluded: chain F residue 566 GLU Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 279 THR Chi-restraints excluded: chain G residue 459 VAL Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 71 HIS Chi-restraints excluded: chain H residue 222 ASP Chi-restraints excluded: chain H residue 263 MET Chi-restraints excluded: chain H residue 279 THR Chi-restraints excluded: chain H residue 459 VAL Chi-restraints excluded: chain H residue 491 SER Chi-restraints excluded: chain H residue 502 VAL Chi-restraints excluded: chain H residue 549 VAL Chi-restraints excluded: chain H residue 566 GLU Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 211 THR Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 263 MET Chi-restraints excluded: chain I residue 459 VAL Chi-restraints excluded: chain I residue 491 SER Chi-restraints excluded: chain I residue 549 VAL Chi-restraints excluded: chain I residue 568 LEU Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 222 ASP Chi-restraints excluded: chain J residue 279 THR Chi-restraints excluded: chain J residue 459 VAL Chi-restraints excluded: chain J residue 502 VAL Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 71 HIS Chi-restraints excluded: chain K residue 222 ASP Chi-restraints excluded: chain K residue 263 MET Chi-restraints excluded: chain K residue 279 THR Chi-restraints excluded: chain K residue 459 VAL Chi-restraints excluded: chain K residue 491 SER Chi-restraints excluded: chain K residue 502 VAL Chi-restraints excluded: chain K residue 549 VAL Chi-restraints excluded: chain L residue 33 ILE Chi-restraints excluded: chain L residue 211 THR Chi-restraints excluded: chain L residue 222 ASP Chi-restraints excluded: chain L residue 263 MET Chi-restraints excluded: chain L residue 459 VAL Chi-restraints excluded: chain L residue 491 SER Chi-restraints excluded: chain L residue 549 VAL Chi-restraints excluded: chain L residue 566 GLU Chi-restraints excluded: chain L residue 568 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 436 optimal weight: 30.0000 chunk 51 optimal weight: 5.9990 chunk 257 optimal weight: 0.9980 chunk 330 optimal weight: 4.9990 chunk 256 optimal weight: 2.9990 chunk 381 optimal weight: 0.0970 chunk 252 optimal weight: 2.9990 chunk 451 optimal weight: 3.9990 chunk 282 optimal weight: 9.9990 chunk 275 optimal weight: 7.9990 chunk 208 optimal weight: 2.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 49 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 38580 Z= 0.176 Angle : 0.507 5.625 52404 Z= 0.268 Chirality : 0.041 0.144 6072 Planarity : 0.004 0.051 6516 Dihedral : 4.016 19.550 5196 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 3.10 % Allowed : 16.95 % Favored : 79.94 % 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: -1.20 (0.13), residues: 4560 helix: 0.09 (0.11), residues: 2268 sheet: 0.10 (0.25), residues: 492 loop : -2.22 (0.15), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 110 HIS 0.002 0.001 HIS B 163 PHE 0.012 0.001 PHE D 262 TYR 0.008 0.001 TYR A 141 ARG 0.013 0.000 ARG C 557 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 4236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 311 time to evaluate : 4.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 VAL cc_start: 0.8306 (OUTLIER) cc_final: 0.8082 (m) REVERT: B 459 VAL cc_start: 0.8440 (OUTLIER) cc_final: 0.8227 (m) REVERT: B 566 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7524 (mp0) REVERT: C 459 VAL cc_start: 0.8533 (OUTLIER) cc_final: 0.8310 (m) REVERT: C 566 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7507 (mp0) REVERT: D 459 VAL cc_start: 0.8385 (OUTLIER) cc_final: 0.8145 (m) REVERT: E 459 VAL cc_start: 0.8442 (OUTLIER) cc_final: 0.8239 (m) REVERT: F 459 VAL cc_start: 0.8556 (OUTLIER) cc_final: 0.8308 (m) REVERT: F 566 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7507 (mp0) REVERT: G 459 VAL cc_start: 0.8376 (OUTLIER) cc_final: 0.8139 (m) REVERT: H 459 VAL cc_start: 0.8442 (OUTLIER) cc_final: 0.8229 (m) REVERT: H 566 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7528 (mp0) REVERT: I 459 VAL cc_start: 0.8530 (OUTLIER) cc_final: 0.8302 (m) REVERT: J 459 VAL cc_start: 0.8304 (OUTLIER) cc_final: 0.8084 (m) REVERT: K 459 VAL cc_start: 0.8451 (OUTLIER) cc_final: 0.8238 (m) REVERT: L 459 VAL cc_start: 0.8548 (OUTLIER) cc_final: 0.8310 (m) REVERT: L 566 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7500 (mp0) outliers start: 130 outliers final: 91 residues processed: 397 average time/residue: 0.4679 time to fit residues: 307.9919 Evaluate side-chains 400 residues out of total 4236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 292 time to evaluate : 4.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 71 HIS Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 491 SER Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 566 GLU Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 552 ILE Chi-restraints excluded: chain C residue 566 GLU Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 71 HIS Chi-restraints excluded: chain E residue 222 ASP Chi-restraints excluded: chain E residue 263 MET Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 491 SER Chi-restraints excluded: chain E residue 502 VAL Chi-restraints excluded: chain E residue 549 VAL Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 222 ASP Chi-restraints excluded: chain F residue 263 MET Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain F residue 491 SER Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 552 ILE Chi-restraints excluded: chain F residue 566 GLU Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 49 ASN Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 150 MET Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 279 THR Chi-restraints excluded: chain G residue 282 LEU Chi-restraints excluded: chain G residue 459 VAL Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain G residue 552 ILE Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 71 HIS Chi-restraints excluded: chain H residue 222 ASP Chi-restraints excluded: chain H residue 263 MET Chi-restraints excluded: chain H residue 279 THR Chi-restraints excluded: chain H residue 459 VAL Chi-restraints excluded: chain H residue 491 SER Chi-restraints excluded: chain H residue 502 VAL Chi-restraints excluded: chain H residue 549 VAL Chi-restraints excluded: chain H residue 566 GLU Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 211 THR Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 263 MET Chi-restraints excluded: chain I residue 459 VAL Chi-restraints excluded: chain I residue 491 SER Chi-restraints excluded: chain I residue 549 VAL Chi-restraints excluded: chain I residue 568 LEU Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 222 ASP Chi-restraints excluded: chain J residue 279 THR Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 286 VAL Chi-restraints excluded: chain J residue 459 VAL Chi-restraints excluded: chain J residue 502 VAL Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 71 HIS Chi-restraints excluded: chain K residue 222 ASP Chi-restraints excluded: chain K residue 279 THR Chi-restraints excluded: chain K residue 459 VAL Chi-restraints excluded: chain K residue 502 VAL Chi-restraints excluded: chain K residue 549 VAL Chi-restraints excluded: chain L residue 33 ILE Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 211 THR Chi-restraints excluded: chain L residue 222 ASP Chi-restraints excluded: chain L residue 263 MET Chi-restraints excluded: chain L residue 459 VAL Chi-restraints excluded: chain L residue 491 SER Chi-restraints excluded: chain L residue 549 VAL Chi-restraints excluded: chain L residue 566 GLU Chi-restraints excluded: chain L residue 568 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 279 optimal weight: 20.0000 chunk 180 optimal weight: 6.9990 chunk 269 optimal weight: 10.0000 chunk 135 optimal weight: 4.9990 chunk 88 optimal weight: 7.9990 chunk 87 optimal weight: 9.9990 chunk 286 optimal weight: 2.9990 chunk 307 optimal weight: 0.2980 chunk 223 optimal weight: 5.9990 chunk 42 optimal weight: 0.0060 chunk 354 optimal weight: 0.8980 overall best weight: 1.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 49 ASN I 495 ASN L 495 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 38580 Z= 0.167 Angle : 0.507 6.707 52404 Z= 0.267 Chirality : 0.041 0.146 6072 Planarity : 0.004 0.059 6516 Dihedral : 3.948 19.879 5196 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 3.06 % Allowed : 17.07 % Favored : 79.87 % 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: -1.02 (0.13), residues: 4560 helix: 0.20 (0.11), residues: 2268 sheet: 0.21 (0.25), residues: 492 loop : -2.09 (0.15), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 110 HIS 0.002 0.000 HIS B 163 PHE 0.012 0.001 PHE J 262 TYR 0.008 0.001 TYR E 141 ARG 0.013 0.000 ARG J 557 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 4236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 313 time to evaluate : 4.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 VAL cc_start: 0.8307 (OUTLIER) cc_final: 0.8085 (m) REVERT: B 459 VAL cc_start: 0.8453 (OUTLIER) cc_final: 0.8243 (m) REVERT: C 459 VAL cc_start: 0.8540 (OUTLIER) cc_final: 0.8310 (m) REVERT: C 566 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7488 (mp0) REVERT: D 459 VAL cc_start: 0.8383 (OUTLIER) cc_final: 0.8148 (m) REVERT: E 459 VAL cc_start: 0.8446 (OUTLIER) cc_final: 0.8228 (m) REVERT: F 459 VAL cc_start: 0.8561 (OUTLIER) cc_final: 0.8311 (m) REVERT: F 566 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7487 (mp0) REVERT: G 459 VAL cc_start: 0.8379 (OUTLIER) cc_final: 0.8139 (m) REVERT: H 459 VAL cc_start: 0.8451 (OUTLIER) cc_final: 0.8241 (m) REVERT: I 459 VAL cc_start: 0.8532 (OUTLIER) cc_final: 0.8299 (m) REVERT: J 459 VAL cc_start: 0.8306 (OUTLIER) cc_final: 0.8086 (m) REVERT: K 459 VAL cc_start: 0.8454 (OUTLIER) cc_final: 0.8242 (m) REVERT: L 459 VAL cc_start: 0.8563 (OUTLIER) cc_final: 0.8314 (m) REVERT: L 566 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7462 (mp0) outliers start: 128 outliers final: 94 residues processed: 397 average time/residue: 0.4772 time to fit residues: 315.4718 Evaluate side-chains 419 residues out of total 4236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 310 time to evaluate : 4.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 72 CYS Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 71 HIS Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 491 SER Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 566 GLU Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 71 HIS Chi-restraints excluded: chain E residue 222 ASP Chi-restraints excluded: chain E residue 263 MET Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 491 SER Chi-restraints excluded: chain E residue 502 VAL Chi-restraints excluded: chain E residue 549 VAL Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 222 ASP Chi-restraints excluded: chain F residue 263 MET Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain F residue 491 SER Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 566 GLU Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 150 MET Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 279 THR Chi-restraints excluded: chain G residue 282 LEU Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 459 VAL Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 71 HIS Chi-restraints excluded: chain H residue 222 ASP Chi-restraints excluded: chain H residue 263 MET Chi-restraints excluded: chain H residue 279 THR Chi-restraints excluded: chain H residue 459 VAL Chi-restraints excluded: chain H residue 491 SER Chi-restraints excluded: chain H residue 502 VAL Chi-restraints excluded: chain H residue 549 VAL Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 211 THR Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 263 MET Chi-restraints excluded: chain I residue 279 THR Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain I residue 459 VAL Chi-restraints excluded: chain I residue 491 SER Chi-restraints excluded: chain I residue 549 VAL Chi-restraints excluded: chain I residue 568 LEU Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 222 ASP Chi-restraints excluded: chain J residue 279 THR Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 459 VAL Chi-restraints excluded: chain J residue 502 VAL Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 71 HIS Chi-restraints excluded: chain K residue 222 ASP Chi-restraints excluded: chain K residue 279 THR Chi-restraints excluded: chain K residue 459 VAL Chi-restraints excluded: chain K residue 491 SER Chi-restraints excluded: chain K residue 502 VAL Chi-restraints excluded: chain K residue 549 VAL Chi-restraints excluded: chain L residue 33 ILE Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 211 THR Chi-restraints excluded: chain L residue 222 ASP Chi-restraints excluded: chain L residue 263 MET Chi-restraints excluded: chain L residue 279 THR Chi-restraints excluded: chain L residue 282 LEU Chi-restraints excluded: chain L residue 459 VAL Chi-restraints excluded: chain L residue 491 SER Chi-restraints excluded: chain L residue 549 VAL Chi-restraints excluded: chain L residue 566 GLU Chi-restraints excluded: chain L residue 568 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 410 optimal weight: 6.9990 chunk 432 optimal weight: 0.0470 chunk 394 optimal weight: 3.9990 chunk 420 optimal weight: 0.0970 chunk 253 optimal weight: 20.0000 chunk 183 optimal weight: 4.9990 chunk 330 optimal weight: 7.9990 chunk 128 optimal weight: 7.9990 chunk 379 optimal weight: 10.0000 chunk 397 optimal weight: 8.9990 chunk 418 optimal weight: 1.9990 overall best weight: 2.2282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 49 ASN I 495 ASN L 495 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 38580 Z= 0.187 Angle : 0.515 5.799 52404 Z= 0.272 Chirality : 0.042 0.148 6072 Planarity : 0.005 0.059 6516 Dihedral : 3.988 20.231 5196 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 2.98 % Allowed : 17.31 % Favored : 79.70 % 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: -0.92 (0.13), residues: 4560 helix: 0.27 (0.11), residues: 2268 sheet: 0.26 (0.25), residues: 492 loop : -2.02 (0.15), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 110 HIS 0.002 0.001 HIS G 22 PHE 0.013 0.001 PHE A 262 TYR 0.009 0.001 TYR H 141 ARG 0.013 0.000 ARG I 557 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 4236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 309 time to evaluate : 4.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 459 VAL cc_start: 0.8324 (OUTLIER) cc_final: 0.8109 (m) REVERT: B 459 VAL cc_start: 0.8459 (OUTLIER) cc_final: 0.8251 (m) REVERT: C 459 VAL cc_start: 0.8548 (OUTLIER) cc_final: 0.8319 (m) REVERT: C 566 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7465 (mp0) REVERT: D 459 VAL cc_start: 0.8404 (OUTLIER) cc_final: 0.8171 (m) REVERT: E 459 VAL cc_start: 0.8448 (OUTLIER) cc_final: 0.8242 (m) REVERT: F 459 VAL cc_start: 0.8567 (OUTLIER) cc_final: 0.8323 (m) REVERT: F 566 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7463 (mp0) REVERT: G 459 VAL cc_start: 0.8398 (OUTLIER) cc_final: 0.8165 (m) REVERT: I 459 VAL cc_start: 0.8542 (OUTLIER) cc_final: 0.8310 (m) REVERT: J 459 VAL cc_start: 0.8323 (OUTLIER) cc_final: 0.8109 (m) REVERT: K 459 VAL cc_start: 0.8462 (OUTLIER) cc_final: 0.8262 (m) REVERT: L 459 VAL cc_start: 0.8573 (OUTLIER) cc_final: 0.8327 (m) REVERT: L 566 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7464 (mp0) outliers start: 125 outliers final: 104 residues processed: 396 average time/residue: 0.4806 time to fit residues: 314.3626 Evaluate side-chains 415 residues out of total 4236 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 297 time to evaluate : 4.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 72 CYS Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 222 ASP Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 71 HIS Chi-restraints excluded: chain B residue 222 ASP Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 491 SER Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 71 HIS Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 491 SER Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 552 ILE Chi-restraints excluded: chain C residue 566 GLU Chi-restraints excluded: chain C residue 568 LEU Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 222 ASP Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 71 HIS Chi-restraints excluded: chain E residue 222 ASP Chi-restraints excluded: chain E residue 263 MET Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 491 SER Chi-restraints excluded: chain E residue 502 VAL Chi-restraints excluded: chain E residue 549 VAL Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 222 ASP Chi-restraints excluded: chain F residue 263 MET Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain F residue 491 SER Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 552 ILE Chi-restraints excluded: chain F residue 566 GLU Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 49 ASN Chi-restraints excluded: chain G residue 150 MET Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 279 THR Chi-restraints excluded: chain G residue 282 LEU Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 459 VAL Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 71 HIS Chi-restraints excluded: chain H residue 222 ASP Chi-restraints excluded: chain H residue 263 MET Chi-restraints excluded: chain H residue 279 THR Chi-restraints excluded: chain H residue 491 SER Chi-restraints excluded: chain H residue 502 VAL Chi-restraints excluded: chain H residue 549 VAL Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 211 THR Chi-restraints excluded: chain I residue 222 ASP Chi-restraints excluded: chain I residue 263 MET Chi-restraints excluded: chain I residue 279 THR Chi-restraints excluded: chain I residue 459 VAL Chi-restraints excluded: chain I residue 491 SER Chi-restraints excluded: chain I residue 549 VAL Chi-restraints excluded: chain I residue 568 LEU Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 72 CYS Chi-restraints excluded: chain J residue 222 ASP Chi-restraints excluded: chain J residue 279 THR Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 286 VAL Chi-restraints excluded: chain J residue 459 VAL Chi-restraints excluded: chain J residue 502 VAL Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 71 HIS Chi-restraints excluded: chain K residue 222 ASP Chi-restraints excluded: chain K residue 279 THR Chi-restraints excluded: chain K residue 459 VAL Chi-restraints excluded: chain K residue 491 SER Chi-restraints excluded: chain K residue 502 VAL Chi-restraints excluded: chain K residue 549 VAL Chi-restraints excluded: chain L residue 33 ILE Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 211 THR Chi-restraints excluded: chain L residue 222 ASP Chi-restraints excluded: chain L residue 263 MET Chi-restraints excluded: chain L residue 279 THR Chi-restraints excluded: chain L residue 459 VAL Chi-restraints excluded: chain L residue 491 SER Chi-restraints excluded: chain L residue 549 VAL Chi-restraints excluded: chain L residue 566 GLU Chi-restraints excluded: chain L residue 568 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.366 > 50: distance: 34 - 51: 24.901 distance: 38 - 43: 4.141 distance: 43 - 44: 19.277 distance: 44 - 45: 9.472 distance: 44 - 47: 16.221 distance: 45 - 46: 28.066 distance: 45 - 51: 15.200 distance: 46 - 68: 25.515 distance: 47 - 48: 13.313 distance: 47 - 49: 5.103 distance: 48 - 50: 8.489 distance: 51 - 52: 3.385 distance: 52 - 53: 12.139 distance: 52 - 55: 12.414 distance: 53 - 54: 25.469 distance: 53 - 63: 15.224 distance: 55 - 56: 12.603 distance: 56 - 57: 11.266 distance: 56 - 58: 6.207 distance: 57 - 59: 8.748 distance: 58 - 60: 6.613 distance: 59 - 61: 8.456 distance: 60 - 61: 9.489 distance: 61 - 62: 6.543 distance: 63 - 64: 14.526 distance: 64 - 65: 47.928 distance: 64 - 67: 15.369 distance: 65 - 66: 12.447 distance: 65 - 68: 41.700 distance: 68 - 69: 6.529 distance: 69 - 70: 8.261 distance: 69 - 72: 46.561 distance: 70 - 71: 20.275 distance: 70 - 76: 9.893 distance: 72 - 73: 39.326 distance: 76 - 77: 3.789 distance: 77 - 78: 30.679 distance: 77 - 80: 24.506 distance: 78 - 79: 39.891 distance: 81 - 83: 39.066 distance: 85 - 86: 20.999 distance: 85 - 88: 27.475 distance: 86 - 87: 23.434 distance: 86 - 95: 33.526 distance: 88 - 89: 14.128 distance: 89 - 90: 27.914 distance: 90 - 91: 23.041 distance: 91 - 92: 11.721 distance: 92 - 93: 6.688 distance: 95 - 96: 33.008 distance: 96 - 97: 44.711 distance: 96 - 99: 7.189 distance: 97 - 98: 4.633 distance: 97 - 103: 34.057 distance: 99 - 100: 30.597 distance: 100 - 101: 4.530 distance: 100 - 102: 16.064 distance: 103 - 104: 15.137 distance: 103 - 109: 27.532 distance: 104 - 105: 35.104 distance: 104 - 107: 27.012 distance: 105 - 106: 6.356 distance: 105 - 110: 19.463 distance: 107 - 108: 18.835 distance: 108 - 109: 20.301 distance: 110 - 111: 3.428 distance: 111 - 112: 20.038 distance: 112 - 113: 18.590 distance: 112 - 114: 13.424 distance: 113 - 133: 37.206 distance: 114 - 115: 22.314 distance: 115 - 116: 14.597 distance: 115 - 118: 14.510 distance: 116 - 117: 13.773 distance: 116 - 121: 11.835 distance: 117 - 138: 16.091 distance: 118 - 119: 33.654 distance: 118 - 120: 25.421