Starting phenix.real_space_refine (version: 1.21rc1) on Fri May 12 15:00:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wve_6690/05_2023/5wve_6690_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wve_6690/05_2023/5wve_6690.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wve_6690/05_2023/5wve_6690.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wve_6690/05_2023/5wve_6690.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wve_6690/05_2023/5wve_6690_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wve_6690/05_2023/5wve_6690_updated.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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: 7 Type Number sf(0) Gaussians Fe 7 7.16 5 P 21 5.49 5 Mg 7 5.21 5 S 516 5.16 5 C 49679 2.51 5 N 13585 2.21 5 O 14790 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A GLU 283": "OE1" <-> "OE2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A GLU 316": "OE1" <-> "OE2" Residue "A GLU 339": "OE1" <-> "OE2" Residue "A GLU 366": "OE1" <-> "OE2" Residue "A GLU 373": "OE1" <-> "OE2" Residue "A GLU 377": "OE1" <-> "OE2" Residue "A GLU 409": "OE1" <-> "OE2" Residue "A GLU 412": "OE1" <-> "OE2" Residue "A ARG 434": "NH1" <-> "NH2" Residue "A GLU 528": "OE1" <-> "OE2" Residue "A GLU 546": "OE1" <-> "OE2" Residue "A GLU 570": "OE1" <-> "OE2" Residue "A GLU 575": "OE1" <-> "OE2" Residue "A GLU 648": "OE1" <-> "OE2" Residue "A GLU 652": "OE1" <-> "OE2" Residue "A GLU 934": "OE1" <-> "OE2" Residue "B ARG 38": "NH1" <-> "NH2" Residue "B TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 62": "OE1" <-> "OE2" Residue "C TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 166": "OE1" <-> "OE2" Residue "C ARG 228": "NH1" <-> "NH2" Residue "C GLU 283": "OE1" <-> "OE2" Residue "C GLU 308": "OE1" <-> "OE2" Residue "C GLU 316": "OE1" <-> "OE2" Residue "C GLU 339": "OE1" <-> "OE2" Residue "C GLU 366": "OE1" <-> "OE2" Residue "C GLU 373": "OE1" <-> "OE2" Residue "C GLU 377": "OE1" <-> "OE2" Residue "C GLU 409": "OE1" <-> "OE2" Residue "C GLU 412": "OE1" <-> "OE2" Residue "C ARG 434": "NH1" <-> "NH2" Residue "C GLU 528": "OE1" <-> "OE2" Residue "C GLU 546": "OE1" <-> "OE2" Residue "C GLU 570": "OE1" <-> "OE2" Residue "C GLU 575": "OE1" <-> "OE2" Residue "C GLU 648": "OE1" <-> "OE2" Residue "C GLU 652": "OE1" <-> "OE2" Residue "C GLU 934": "OE1" <-> "OE2" Residue "D ARG 38": "NH1" <-> "NH2" Residue "D TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 62": "OE1" <-> "OE2" Residue "E TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 166": "OE1" <-> "OE2" Residue "E ARG 228": "NH1" <-> "NH2" Residue "E GLU 283": "OE1" <-> "OE2" Residue "E GLU 308": "OE1" <-> "OE2" Residue "E GLU 316": "OE1" <-> "OE2" Residue "E GLU 339": "OE1" <-> "OE2" Residue "E GLU 366": "OE1" <-> "OE2" Residue "E GLU 373": "OE1" <-> "OE2" Residue "E GLU 377": "OE1" <-> "OE2" Residue "E GLU 409": "OE1" <-> "OE2" Residue "E GLU 412": "OE1" <-> "OE2" Residue "E ARG 434": "NH1" <-> "NH2" Residue "E GLU 528": "OE1" <-> "OE2" Residue "E GLU 546": "OE1" <-> "OE2" Residue "E GLU 570": "OE1" <-> "OE2" Residue "E GLU 575": "OE1" <-> "OE2" Residue "E GLU 648": "OE1" <-> "OE2" Residue "E GLU 652": "OE1" <-> "OE2" Residue "E GLU 934": "OE1" <-> "OE2" Residue "F ARG 38": "NH1" <-> "NH2" Residue "F TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 62": "OE1" <-> "OE2" Residue "G TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 166": "OE1" <-> "OE2" Residue "G ARG 228": "NH1" <-> "NH2" Residue "G GLU 283": "OE1" <-> "OE2" Residue "G GLU 308": "OE1" <-> "OE2" Residue "G GLU 316": "OE1" <-> "OE2" Residue "G GLU 339": "OE1" <-> "OE2" Residue "G GLU 366": "OE1" <-> "OE2" Residue "G GLU 373": "OE1" <-> "OE2" Residue "G GLU 377": "OE1" <-> "OE2" Residue "G GLU 409": "OE1" <-> "OE2" Residue "G GLU 412": "OE1" <-> "OE2" Residue "G ARG 434": "NH1" <-> "NH2" Residue "G GLU 528": "OE1" <-> "OE2" Residue "G GLU 546": "OE1" <-> "OE2" Residue "G GLU 570": "OE1" <-> "OE2" Residue "G GLU 575": "OE1" <-> "OE2" Residue "G GLU 648": "OE1" <-> "OE2" Residue "G GLU 652": "OE1" <-> "OE2" Residue "G GLU 934": "OE1" <-> "OE2" Residue "H ARG 38": "NH1" <-> "NH2" Residue "H TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 62": "OE1" <-> "OE2" Residue "I TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 166": "OE1" <-> "OE2" Residue "I ARG 228": "NH1" <-> "NH2" Residue "I GLU 283": "OE1" <-> "OE2" Residue "I GLU 308": "OE1" <-> "OE2" Residue "I GLU 316": "OE1" <-> "OE2" Residue "I GLU 339": "OE1" <-> "OE2" Residue "I GLU 366": "OE1" <-> "OE2" Residue "I GLU 373": "OE1" <-> "OE2" Residue "I GLU 377": "OE1" <-> "OE2" Residue "I GLU 409": "OE1" <-> "OE2" Residue "I GLU 412": "OE1" <-> "OE2" Residue "I ARG 434": "NH1" <-> "NH2" Residue "I GLU 528": "OE1" <-> "OE2" Residue "I GLU 546": "OE1" <-> "OE2" Residue "I GLU 570": "OE1" <-> "OE2" Residue "I GLU 575": "OE1" <-> "OE2" Residue "I GLU 648": "OE1" <-> "OE2" Residue "I GLU 652": "OE1" <-> "OE2" Residue "I GLU 934": "OE1" <-> "OE2" Residue "J ARG 38": "NH1" <-> "NH2" Residue "J TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 62": "OE1" <-> "OE2" Residue "K TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 166": "OE1" <-> "OE2" Residue "K GLU 175": "OE1" <-> "OE2" Residue "K ARG 228": "NH1" <-> "NH2" Residue "K GLU 283": "OE1" <-> "OE2" Residue "K GLU 308": "OE1" <-> "OE2" Residue "K GLU 316": "OE1" <-> "OE2" Residue "K GLU 339": "OE1" <-> "OE2" Residue "K GLU 366": "OE1" <-> "OE2" Residue "K GLU 373": "OE1" <-> "OE2" Residue "K GLU 377": "OE1" <-> "OE2" Residue "K GLU 409": "OE1" <-> "OE2" Residue "K GLU 412": "OE1" <-> "OE2" Residue "K ARG 434": "NH1" <-> "NH2" Residue "K GLU 528": "OE1" <-> "OE2" Residue "K GLU 546": "OE1" <-> "OE2" Residue "K GLU 570": "OE1" <-> "OE2" Residue "K GLU 575": "OE1" <-> "OE2" Residue "K GLU 648": "OE1" <-> "OE2" Residue "K GLU 652": "OE1" <-> "OE2" Residue "K GLU 934": "OE1" <-> "OE2" Residue "L ARG 38": "NH1" <-> "NH2" Residue "L TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 62": "OE1" <-> "OE2" Residue "M TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 166": "OE1" <-> "OE2" Residue "M ARG 228": "NH1" <-> "NH2" Residue "M GLU 283": "OE1" <-> "OE2" Residue "M GLU 308": "OE1" <-> "OE2" Residue "M GLU 316": "OE1" <-> "OE2" Residue "M GLU 339": "OE1" <-> "OE2" Residue "M GLU 366": "OE1" <-> "OE2" Residue "M GLU 373": "OE1" <-> "OE2" Residue "M GLU 377": "OE1" <-> "OE2" Residue "M GLU 409": "OE1" <-> "OE2" Residue "M GLU 412": "OE1" <-> "OE2" Residue "M ARG 434": "NH1" <-> "NH2" Residue "M GLU 528": "OE1" <-> "OE2" Residue "M GLU 546": "OE1" <-> "OE2" Residue "M GLU 570": "OE1" <-> "OE2" Residue "M GLU 575": "OE1" <-> "OE2" Residue "M GLU 648": "OE1" <-> "OE2" Residue "M GLU 652": "OE1" <-> "OE2" Residue "M GLU 934": "OE1" <-> "OE2" Residue "N ARG 38": "NH1" <-> "NH2" Residue "N TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 62": "OE1" <-> "OE2" Residue "S ARG 45": "NH1" <-> "NH2" Residue "T ARG 36": "NH1" <-> "NH2" Residue "W GLU 14": "OE1" <-> "OE2" Residue "W GLU 41": "OE1" <-> "OE2" Residue "X ARG 52": "NH1" <-> "NH2" Residue "Y GLU 3": "OE1" <-> "OE2" Residue "Y ARG 13": "NH1" <-> "NH2" Residue "Y GLU 33": "OE1" <-> "OE2" Residue "Y GLU 41": "OE1" <-> "OE2" Residue "Y ARG 90": "NH1" <-> "NH2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 78605 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 9139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1144, 9139 Classifications: {'peptide': 1144} Link IDs: {'PTRANS': 28, 'TRANS': 1115} Chain: "B" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 823 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "C" Number of atoms: 9139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1144, 9139 Classifications: {'peptide': 1144} Link IDs: {'PTRANS': 28, 'TRANS': 1115} Chain: "D" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 823 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "E" Number of atoms: 9139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1144, 9139 Classifications: {'peptide': 1144} Link IDs: {'PTRANS': 28, 'TRANS': 1115} Chain: "F" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 823 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "G" Number of atoms: 9139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1144, 9139 Classifications: {'peptide': 1144} Link IDs: {'PTRANS': 28, 'TRANS': 1115} Chain: "H" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 823 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "I" Number of atoms: 9139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1144, 9139 Classifications: {'peptide': 1144} Link IDs: {'PTRANS': 28, 'TRANS': 1115} Chain: "J" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 823 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "K" Number of atoms: 9139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1144, 9139 Classifications: {'peptide': 1144} Link IDs: {'PTRANS': 28, 'TRANS': 1115} Chain: "L" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 823 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "M" Number of atoms: 9139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1144, 9139 Classifications: {'peptide': 1144} Link IDs: {'PTRANS': 28, 'TRANS': 1115} Chain: "N" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 823 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "O" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 735 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 1, 'TRANS': 89} Chain: "P" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 735 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 1, 'TRANS': 89} Chain: "Q" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 735 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 1, 'TRANS': 89} Chain: "R" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 735 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 1, 'TRANS': 89} Chain: "S" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 783 Classifications: {'peptide': 96} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 783 Classifications: {'peptide': 96} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "U" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 783 Classifications: {'peptide': 96} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 783 Classifications: {'peptide': 96} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 762 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "X" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 742 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "Y" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 777 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' MG': 1, 'DTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' MG': 1, 'DTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' MG': 1, 'DTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' MG': 1, 'DTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' MG': 1, 'DTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' MG': 1, 'DTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' MG': 1, 'DTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 29.31, per 1000 atoms: 0.37 Number of scatterers: 78605 At special positions: 0 Unit cell: (302.84, 308.2, 148.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 7 26.01 S 516 16.00 P 21 15.00 Mg 7 11.99 O 14790 8.00 N 13585 7.00 C 49679 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS A 633 " - pdb=" SG CYS A 663 " distance=2.20 Simple disulfide: pdb=" SG CYS A 675 " - pdb=" SG CYS A 705 " distance=2.02 Simple disulfide: pdb=" SG CYS A 704 " - pdb=" SG CYS A 749 " distance=1.89 Simple disulfide: pdb=" SG CYS A 761 " - pdb=" SG CYS A 804 " distance=2.05 Simple disulfide: pdb=" SG CYS A 803 " - pdb=" SG CYS A 846 " distance=2.09 Simple disulfide: pdb=" SG CYS C 633 " - pdb=" SG CYS C 663 " distance=2.20 Simple disulfide: pdb=" SG CYS C 675 " - pdb=" SG CYS C 705 " distance=2.02 Simple disulfide: pdb=" SG CYS C 704 " - pdb=" SG CYS C 749 " distance=1.89 Simple disulfide: pdb=" SG CYS C 761 " - pdb=" SG CYS C 804 " distance=2.05 Simple disulfide: pdb=" SG CYS C 803 " - pdb=" SG CYS C 846 " distance=2.09 Simple disulfide: pdb=" SG CYS E 633 " - pdb=" SG CYS E 663 " distance=2.20 Simple disulfide: pdb=" SG CYS E 675 " - pdb=" SG CYS E 705 " distance=2.02 Simple disulfide: pdb=" SG CYS E 704 " - pdb=" SG CYS E 749 " distance=1.89 Simple disulfide: pdb=" SG CYS E 761 " - pdb=" SG CYS E 804 " distance=2.05 Simple disulfide: pdb=" SG CYS E 803 " - pdb=" SG CYS E 846 " distance=2.09 Simple disulfide: pdb=" SG CYS G 633 " - pdb=" SG CYS G 663 " distance=2.20 Simple disulfide: pdb=" SG CYS G 675 " - pdb=" SG CYS G 705 " distance=2.02 Simple disulfide: pdb=" SG CYS G 704 " - pdb=" SG CYS G 749 " distance=1.89 Simple disulfide: pdb=" SG CYS G 761 " - pdb=" SG CYS G 804 " distance=2.05 Simple disulfide: pdb=" SG CYS G 803 " - pdb=" SG CYS G 846 " distance=2.09 Simple disulfide: pdb=" SG CYS I 633 " - pdb=" SG CYS I 663 " distance=2.20 Simple disulfide: pdb=" SG CYS I 675 " - pdb=" SG CYS I 705 " distance=2.02 Simple disulfide: pdb=" SG CYS I 704 " - pdb=" SG CYS I 749 " distance=1.89 Simple disulfide: pdb=" SG CYS I 761 " - pdb=" SG CYS I 804 " distance=2.05 Simple disulfide: pdb=" SG CYS I 803 " - pdb=" SG CYS I 846 " distance=2.09 Simple disulfide: pdb=" SG CYS K 633 " - pdb=" SG CYS K 663 " distance=2.19 Simple disulfide: pdb=" SG CYS K 675 " - pdb=" SG CYS K 705 " distance=2.02 Simple disulfide: pdb=" SG CYS K 704 " - pdb=" SG CYS K 749 " distance=1.89 Simple disulfide: pdb=" SG CYS K 761 " - pdb=" SG CYS K 804 " distance=2.05 Simple disulfide: pdb=" SG CYS K 803 " - pdb=" SG CYS K 846 " distance=2.09 Simple disulfide: pdb=" SG CYS M 633 " - pdb=" SG CYS M 663 " distance=2.20 Simple disulfide: pdb=" SG CYS M 675 " - pdb=" SG CYS M 705 " distance=2.02 Simple disulfide: pdb=" SG CYS M 704 " - pdb=" SG CYS M 749 " distance=1.89 Simple disulfide: pdb=" SG CYS M 761 " - pdb=" SG CYS M 804 " distance=2.05 Simple disulfide: pdb=" SG CYS M 803 " - pdb=" SG CYS M 846 " distance=2.09 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=21, symmetry=0 Number of additional bonds: simple=21, symmetry=0 Coordination: Other bonds: Time building additional restraints: 26.55 Conformation dependent library (CDL) restraints added in 8.7 seconds 19432 Ramachandran restraints generated. 9716 Oldfield, 0 Emsley, 9716 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 18440 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 297 helices and 126 sheets defined 31.6% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.27 Creating SS restraints... Processing helix chain 'A' and resid 108 through 117 Processing helix chain 'A' and resid 130 through 142 Processing helix chain 'A' and resid 160 through 169 removed outlier: 3.562A pdb=" N VAL A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 177 removed outlier: 3.528A pdb=" N GLY A 176 " --> pdb=" O SER A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 206 removed outlier: 3.627A pdb=" N MET A 197 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS A 198 " --> pdb=" O GLY A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 232 Processing helix chain 'A' and resid 248 through 253 Processing helix chain 'A' and resid 288 through 299 Processing helix chain 'A' and resid 308 through 317 removed outlier: 3.591A pdb=" N HIS A 311 " --> pdb=" O GLU A 308 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE A 314 " --> pdb=" O HIS A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 333 removed outlier: 3.831A pdb=" N ASP A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 347 removed outlier: 3.879A pdb=" N LEU A 342 " --> pdb=" O TRP A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 374 removed outlier: 3.532A pdb=" N MET A 368 " --> pdb=" O LEU A 364 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE A 370 " --> pdb=" O GLU A 366 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU A 373 " --> pdb=" O SER A 369 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N MET A 374 " --> pdb=" O ILE A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 388 removed outlier: 3.713A pdb=" N ASP A 381 " --> pdb=" O GLU A 377 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N TYR A 382 " --> pdb=" O ASP A 378 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR A 384 " --> pdb=" O LYS A 380 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP A 385 " --> pdb=" O ASP A 381 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE A 388 " --> pdb=" O THR A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 404 Processing helix chain 'A' and resid 408 through 420 removed outlier: 4.149A pdb=" N ASP A 413 " --> pdb=" O GLU A 409 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE A 414 " --> pdb=" O GLU A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 466 removed outlier: 7.004A pdb=" N SER A 451 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLN A 452 " --> pdb=" O LYS A 448 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN A 454 " --> pdb=" O CYS A 450 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASP A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LYS A 458 " --> pdb=" O GLN A 454 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS A 459 " --> pdb=" O ASP A 455 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN A 463 " --> pdb=" O LYS A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 494 removed outlier: 4.214A pdb=" N MET A 481 " --> pdb=" O GLU A 478 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR A 484 " --> pdb=" O MET A 481 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN A 485 " --> pdb=" O TYR A 482 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N PHE A 486 " --> pdb=" O TRP A 483 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA A 488 " --> pdb=" O ASN A 485 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET A 491 " --> pdb=" O ALA A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 503 Processing helix chain 'A' and resid 507 through 517 Processing helix chain 'A' and resid 521 through 532 removed outlier: 3.536A pdb=" N GLU A 528 " --> pdb=" O HIS A 524 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N HIS A 531 " --> pdb=" O VAL A 527 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE A 532 " --> pdb=" O GLU A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 549 removed outlier: 3.665A pdb=" N VAL A 540 " --> pdb=" O LYS A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 554 No H-bonds generated for 'chain 'A' and resid 551 through 554' Processing helix chain 'A' and resid 563 through 566 No H-bonds generated for 'chain 'A' and resid 563 through 566' Processing helix chain 'A' and resid 574 through 590 removed outlier: 3.555A pdb=" N LEU A 582 " --> pdb=" O GLN A 578 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP A 589 " --> pdb=" O LYS A 585 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASN A 590 " --> pdb=" O GLN A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 602 No H-bonds generated for 'chain 'A' and resid 600 through 602' Processing helix chain 'A' and resid 851 through 853 No H-bonds generated for 'chain 'A' and resid 851 through 853' Processing helix chain 'A' and resid 911 through 915 removed outlier: 4.139A pdb=" N CYS A 915 " --> pdb=" O THR A 911 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 911 through 915' Processing helix chain 'B' and resid 3 through 13 Processing helix chain 'B' and resid 50 through 54 Processing helix chain 'B' and resid 61 through 69 removed outlier: 3.523A pdb=" N GLU B 69 " --> pdb=" O MET B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 74 No H-bonds generated for 'chain 'B' and resid 71 through 74' Processing helix chain 'B' and resid 88 through 101 Processing helix chain 'C' and resid 108 through 117 Processing helix chain 'C' and resid 130 through 142 Processing helix chain 'C' and resid 160 through 169 removed outlier: 3.562A pdb=" N VAL C 168 " --> pdb=" O ALA C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 177 removed outlier: 3.526A pdb=" N GLY C 176 " --> pdb=" O SER C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 206 removed outlier: 3.627A pdb=" N MET C 197 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS C 198 " --> pdb=" O GLY C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 232 Processing helix chain 'C' and resid 248 through 253 Processing helix chain 'C' and resid 288 through 299 Processing helix chain 'C' and resid 308 through 317 removed outlier: 3.592A pdb=" N HIS C 311 " --> pdb=" O GLU C 308 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE C 314 " --> pdb=" O HIS C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 333 removed outlier: 3.829A pdb=" N ASP C 333 " --> pdb=" O ALA C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 347 removed outlier: 3.879A pdb=" N LEU C 342 " --> pdb=" O TRP C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 374 removed outlier: 3.530A pdb=" N MET C 368 " --> pdb=" O LEU C 364 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE C 370 " --> pdb=" O GLU C 366 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU C 373 " --> pdb=" O SER C 369 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N MET C 374 " --> pdb=" O ILE C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 388 removed outlier: 3.713A pdb=" N ASP C 381 " --> pdb=" O GLU C 377 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N TYR C 382 " --> pdb=" O ASP C 378 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR C 384 " --> pdb=" O LYS C 380 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP C 385 " --> pdb=" O ASP C 381 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE C 388 " --> pdb=" O THR C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 404 Processing helix chain 'C' and resid 408 through 420 removed outlier: 4.149A pdb=" N ASP C 413 " --> pdb=" O GLU C 409 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE C 414 " --> pdb=" O GLU C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 466 removed outlier: 7.003A pdb=" N SER C 451 " --> pdb=" O GLU C 447 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLN C 452 " --> pdb=" O LYS C 448 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN C 454 " --> pdb=" O CYS C 450 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASP C 455 " --> pdb=" O SER C 451 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LYS C 458 " --> pdb=" O GLN C 454 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS C 459 " --> pdb=" O ASP C 455 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN C 463 " --> pdb=" O LYS C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 494 removed outlier: 4.214A pdb=" N MET C 481 " --> pdb=" O GLU C 478 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR C 484 " --> pdb=" O MET C 481 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN C 485 " --> pdb=" O TYR C 482 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE C 486 " --> pdb=" O TRP C 483 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA C 488 " --> pdb=" O ASN C 485 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET C 491 " --> pdb=" O ALA C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 503 Processing helix chain 'C' and resid 507 through 517 Processing helix chain 'C' and resid 521 through 532 removed outlier: 3.538A pdb=" N GLU C 528 " --> pdb=" O HIS C 524 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N HIS C 531 " --> pdb=" O VAL C 527 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE C 532 " --> pdb=" O GLU C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 549 removed outlier: 3.667A pdb=" N VAL C 540 " --> pdb=" O LYS C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 554 No H-bonds generated for 'chain 'C' and resid 551 through 554' Processing helix chain 'C' and resid 563 through 566 No H-bonds generated for 'chain 'C' and resid 563 through 566' Processing helix chain 'C' and resid 574 through 590 removed outlier: 3.554A pdb=" N LEU C 582 " --> pdb=" O GLN C 578 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP C 589 " --> pdb=" O LYS C 585 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASN C 590 " --> pdb=" O GLN C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 602 No H-bonds generated for 'chain 'C' and resid 600 through 602' Processing helix chain 'C' and resid 851 through 853 No H-bonds generated for 'chain 'C' and resid 851 through 853' Processing helix chain 'C' and resid 911 through 915 removed outlier: 4.140A pdb=" N CYS C 915 " --> pdb=" O THR C 911 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 911 through 915' Processing helix chain 'D' and resid 3 through 13 Processing helix chain 'D' and resid 50 through 54 Processing helix chain 'D' and resid 61 through 69 removed outlier: 3.524A pdb=" N GLU D 69 " --> pdb=" O MET D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 74 No H-bonds generated for 'chain 'D' and resid 71 through 74' Processing helix chain 'D' and resid 88 through 101 Processing helix chain 'E' and resid 108 through 117 Processing helix chain 'E' and resid 130 through 142 Processing helix chain 'E' and resid 160 through 169 removed outlier: 3.561A pdb=" N VAL E 168 " --> pdb=" O ALA E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 177 removed outlier: 3.527A pdb=" N GLY E 176 " --> pdb=" O SER E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 206 removed outlier: 3.628A pdb=" N MET E 197 " --> pdb=" O SER E 193 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS E 198 " --> pdb=" O GLY E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 232 Processing helix chain 'E' and resid 248 through 253 Processing helix chain 'E' and resid 288 through 299 Processing helix chain 'E' and resid 308 through 317 removed outlier: 3.593A pdb=" N HIS E 311 " --> pdb=" O GLU E 308 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE E 314 " --> pdb=" O HIS E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 333 removed outlier: 3.831A pdb=" N ASP E 333 " --> pdb=" O ALA E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 347 removed outlier: 3.879A pdb=" N LEU E 342 " --> pdb=" O TRP E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 374 removed outlier: 3.532A pdb=" N MET E 368 " --> pdb=" O LEU E 364 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE E 370 " --> pdb=" O GLU E 366 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU E 373 " --> pdb=" O SER E 369 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N MET E 374 " --> pdb=" O ILE E 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 388 removed outlier: 3.712A pdb=" N ASP E 381 " --> pdb=" O GLU E 377 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N TYR E 382 " --> pdb=" O ASP E 378 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N THR E 384 " --> pdb=" O LYS E 380 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP E 385 " --> pdb=" O ASP E 381 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE E 388 " --> pdb=" O THR E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 404 Processing helix chain 'E' and resid 408 through 420 removed outlier: 4.149A pdb=" N ASP E 413 " --> pdb=" O GLU E 409 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE E 414 " --> pdb=" O GLU E 410 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 466 removed outlier: 7.003A pdb=" N SER E 451 " --> pdb=" O GLU E 447 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLN E 452 " --> pdb=" O LYS E 448 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN E 454 " --> pdb=" O CYS E 450 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASP E 455 " --> pdb=" O SER E 451 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LYS E 458 " --> pdb=" O GLN E 454 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS E 459 " --> pdb=" O ASP E 455 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN E 463 " --> pdb=" O LYS E 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 478 through 494 removed outlier: 4.216A pdb=" N MET E 481 " --> pdb=" O GLU E 478 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR E 484 " --> pdb=" O MET E 481 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN E 485 " --> pdb=" O TYR E 482 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE E 486 " --> pdb=" O TRP E 483 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA E 488 " --> pdb=" O ASN E 485 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N MET E 491 " --> pdb=" O ALA E 488 " (cutoff:3.500A) Processing helix chain 'E' and resid 497 through 503 Processing helix chain 'E' and resid 507 through 517 Processing helix chain 'E' and resid 521 through 532 removed outlier: 3.537A pdb=" N GLU E 528 " --> pdb=" O HIS E 524 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N HIS E 531 " --> pdb=" O VAL E 527 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE E 532 " --> pdb=" O GLU E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 535 through 549 removed outlier: 3.667A pdb=" N VAL E 540 " --> pdb=" O LYS E 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 551 through 554 No H-bonds generated for 'chain 'E' and resid 551 through 554' Processing helix chain 'E' and resid 563 through 566 No H-bonds generated for 'chain 'E' and resid 563 through 566' Processing helix chain 'E' and resid 574 through 590 removed outlier: 3.554A pdb=" N LEU E 582 " --> pdb=" O GLN E 578 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP E 589 " --> pdb=" O LYS E 585 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASN E 590 " --> pdb=" O GLN E 586 " (cutoff:3.500A) Processing helix chain 'E' and resid 600 through 602 No H-bonds generated for 'chain 'E' and resid 600 through 602' Processing helix chain 'E' and resid 851 through 853 No H-bonds generated for 'chain 'E' and resid 851 through 853' Processing helix chain 'E' and resid 911 through 915 removed outlier: 4.141A pdb=" N CYS E 915 " --> pdb=" O THR E 911 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 911 through 915' Processing helix chain 'F' and resid 3 through 13 Processing helix chain 'F' and resid 50 through 54 Processing helix chain 'F' and resid 61 through 69 removed outlier: 3.524A pdb=" N GLU F 69 " --> pdb=" O MET F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 74 No H-bonds generated for 'chain 'F' and resid 71 through 74' Processing helix chain 'F' and resid 88 through 101 Processing helix chain 'G' and resid 108 through 117 Processing helix chain 'G' and resid 130 through 142 Processing helix chain 'G' and resid 160 through 169 removed outlier: 3.562A pdb=" N VAL G 168 " --> pdb=" O ALA G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 177 removed outlier: 3.526A pdb=" N GLY G 176 " --> pdb=" O SER G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 192 through 206 removed outlier: 3.627A pdb=" N MET G 197 " --> pdb=" O SER G 193 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS G 198 " --> pdb=" O GLY G 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 220 through 232 Processing helix chain 'G' and resid 248 through 253 Processing helix chain 'G' and resid 288 through 299 Processing helix chain 'G' and resid 308 through 317 removed outlier: 3.593A pdb=" N HIS G 311 " --> pdb=" O GLU G 308 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE G 314 " --> pdb=" O HIS G 311 " (cutoff:3.500A) Processing helix chain 'G' and resid 321 through 333 removed outlier: 3.830A pdb=" N ASP G 333 " --> pdb=" O ALA G 329 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 347 removed outlier: 3.879A pdb=" N LEU G 342 " --> pdb=" O TRP G 338 " (cutoff:3.500A) Processing helix chain 'G' and resid 364 through 374 removed outlier: 3.532A pdb=" N MET G 368 " --> pdb=" O LEU G 364 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE G 370 " --> pdb=" O GLU G 366 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU G 373 " --> pdb=" O SER G 369 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N MET G 374 " --> pdb=" O ILE G 370 " (cutoff:3.500A) Processing helix chain 'G' and resid 377 through 388 removed outlier: 3.712A pdb=" N ASP G 381 " --> pdb=" O GLU G 377 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N TYR G 382 " --> pdb=" O ASP G 378 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N THR G 384 " --> pdb=" O LYS G 380 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP G 385 " --> pdb=" O ASP G 381 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE G 388 " --> pdb=" O THR G 384 " (cutoff:3.500A) Processing helix chain 'G' and resid 397 through 404 Processing helix chain 'G' and resid 408 through 420 removed outlier: 4.148A pdb=" N ASP G 413 " --> pdb=" O GLU G 409 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE G 414 " --> pdb=" O GLU G 410 " (cutoff:3.500A) Processing helix chain 'G' and resid 439 through 466 removed outlier: 7.003A pdb=" N SER G 451 " --> pdb=" O GLU G 447 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLN G 452 " --> pdb=" O LYS G 448 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN G 454 " --> pdb=" O CYS G 450 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASP G 455 " --> pdb=" O SER G 451 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LYS G 458 " --> pdb=" O GLN G 454 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS G 459 " --> pdb=" O ASP G 455 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN G 463 " --> pdb=" O LYS G 459 " (cutoff:3.500A) Processing helix chain 'G' and resid 478 through 494 removed outlier: 4.215A pdb=" N MET G 481 " --> pdb=" O GLU G 478 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR G 484 " --> pdb=" O MET G 481 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN G 485 " --> pdb=" O TYR G 482 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N PHE G 486 " --> pdb=" O TRP G 483 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA G 488 " --> pdb=" O ASN G 485 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N MET G 491 " --> pdb=" O ALA G 488 " (cutoff:3.500A) Processing helix chain 'G' and resid 497 through 503 Processing helix chain 'G' and resid 507 through 517 Processing helix chain 'G' and resid 521 through 532 removed outlier: 3.537A pdb=" N GLU G 528 " --> pdb=" O HIS G 524 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N HIS G 531 " --> pdb=" O VAL G 527 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE G 532 " --> pdb=" O GLU G 528 " (cutoff:3.500A) Processing helix chain 'G' and resid 535 through 549 removed outlier: 3.666A pdb=" N VAL G 540 " --> pdb=" O LYS G 536 " (cutoff:3.500A) Processing helix chain 'G' and resid 551 through 554 No H-bonds generated for 'chain 'G' and resid 551 through 554' Processing helix chain 'G' and resid 563 through 566 No H-bonds generated for 'chain 'G' and resid 563 through 566' Processing helix chain 'G' and resid 574 through 590 removed outlier: 3.553A pdb=" N LEU G 582 " --> pdb=" O GLN G 578 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP G 589 " --> pdb=" O LYS G 585 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASN G 590 " --> pdb=" O GLN G 586 " (cutoff:3.500A) Processing helix chain 'G' and resid 600 through 602 No H-bonds generated for 'chain 'G' and resid 600 through 602' Processing helix chain 'G' and resid 851 through 853 No H-bonds generated for 'chain 'G' and resid 851 through 853' Processing helix chain 'G' and resid 911 through 915 removed outlier: 4.140A pdb=" N CYS G 915 " --> pdb=" O THR G 911 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 911 through 915' Processing helix chain 'H' and resid 3 through 13 Processing helix chain 'H' and resid 50 through 54 Processing helix chain 'H' and resid 61 through 69 removed outlier: 3.523A pdb=" N GLU H 69 " --> pdb=" O MET H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 74 No H-bonds generated for 'chain 'H' and resid 71 through 74' Processing helix chain 'H' and resid 88 through 101 Processing helix chain 'I' and resid 108 through 117 Processing helix chain 'I' and resid 130 through 142 Processing helix chain 'I' and resid 160 through 169 removed outlier: 3.561A pdb=" N VAL I 168 " --> pdb=" O ALA I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 171 through 177 removed outlier: 3.526A pdb=" N GLY I 176 " --> pdb=" O SER I 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 192 through 206 removed outlier: 3.628A pdb=" N MET I 197 " --> pdb=" O SER I 193 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS I 198 " --> pdb=" O GLY I 194 " (cutoff:3.500A) Processing helix chain 'I' and resid 220 through 232 Processing helix chain 'I' and resid 248 through 253 Processing helix chain 'I' and resid 288 through 299 Processing helix chain 'I' and resid 308 through 317 removed outlier: 3.593A pdb=" N HIS I 311 " --> pdb=" O GLU I 308 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE I 314 " --> pdb=" O HIS I 311 " (cutoff:3.500A) Processing helix chain 'I' and resid 321 through 333 removed outlier: 3.832A pdb=" N ASP I 333 " --> pdb=" O ALA I 329 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 347 removed outlier: 3.879A pdb=" N LEU I 342 " --> pdb=" O TRP I 338 " (cutoff:3.500A) Processing helix chain 'I' and resid 364 through 374 removed outlier: 3.532A pdb=" N MET I 368 " --> pdb=" O LEU I 364 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE I 370 " --> pdb=" O GLU I 366 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU I 373 " --> pdb=" O SER I 369 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N MET I 374 " --> pdb=" O ILE I 370 " (cutoff:3.500A) Processing helix chain 'I' and resid 377 through 388 removed outlier: 3.713A pdb=" N ASP I 381 " --> pdb=" O GLU I 377 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N TYR I 382 " --> pdb=" O ASP I 378 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N THR I 384 " --> pdb=" O LYS I 380 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP I 385 " --> pdb=" O ASP I 381 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE I 388 " --> pdb=" O THR I 384 " (cutoff:3.500A) Processing helix chain 'I' and resid 397 through 404 Processing helix chain 'I' and resid 408 through 420 removed outlier: 4.149A pdb=" N ASP I 413 " --> pdb=" O GLU I 409 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE I 414 " --> pdb=" O GLU I 410 " (cutoff:3.500A) Processing helix chain 'I' and resid 439 through 466 removed outlier: 7.001A pdb=" N SER I 451 " --> pdb=" O GLU I 447 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLN I 452 " --> pdb=" O LYS I 448 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN I 454 " --> pdb=" O CYS I 450 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASP I 455 " --> pdb=" O SER I 451 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LYS I 458 " --> pdb=" O GLN I 454 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS I 459 " --> pdb=" O ASP I 455 " (cutoff:3.500A) Processing helix chain 'I' and resid 478 through 494 removed outlier: 4.213A pdb=" N MET I 481 " --> pdb=" O GLU I 478 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR I 484 " --> pdb=" O MET I 481 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN I 485 " --> pdb=" O TYR I 482 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE I 486 " --> pdb=" O TRP I 483 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA I 488 " --> pdb=" O ASN I 485 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET I 491 " --> pdb=" O ALA I 488 " (cutoff:3.500A) Processing helix chain 'I' and resid 497 through 503 Processing helix chain 'I' and resid 507 through 517 Processing helix chain 'I' and resid 521 through 532 removed outlier: 3.539A pdb=" N GLU I 528 " --> pdb=" O HIS I 524 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N HIS I 531 " --> pdb=" O VAL I 527 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE I 532 " --> pdb=" O GLU I 528 " (cutoff:3.500A) Processing helix chain 'I' and resid 535 through 549 removed outlier: 3.666A pdb=" N VAL I 540 " --> pdb=" O LYS I 536 " (cutoff:3.500A) Processing helix chain 'I' and resid 551 through 554 No H-bonds generated for 'chain 'I' and resid 551 through 554' Processing helix chain 'I' and resid 563 through 566 No H-bonds generated for 'chain 'I' and resid 563 through 566' Processing helix chain 'I' and resid 574 through 590 removed outlier: 3.553A pdb=" N LEU I 582 " --> pdb=" O GLN I 578 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP I 589 " --> pdb=" O LYS I 585 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASN I 590 " --> pdb=" O GLN I 586 " (cutoff:3.500A) Processing helix chain 'I' and resid 600 through 602 No H-bonds generated for 'chain 'I' and resid 600 through 602' Processing helix chain 'I' and resid 851 through 853 No H-bonds generated for 'chain 'I' and resid 851 through 853' Processing helix chain 'I' and resid 911 through 915 removed outlier: 4.141A pdb=" N CYS I 915 " --> pdb=" O THR I 911 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 911 through 915' Processing helix chain 'J' and resid 3 through 13 Processing helix chain 'J' and resid 50 through 54 Processing helix chain 'J' and resid 61 through 69 removed outlier: 3.522A pdb=" N GLU J 69 " --> pdb=" O MET J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 74 No H-bonds generated for 'chain 'J' and resid 71 through 74' Processing helix chain 'J' and resid 88 through 101 Processing helix chain 'K' and resid 108 through 117 Processing helix chain 'K' and resid 130 through 142 Processing helix chain 'K' and resid 160 through 169 removed outlier: 3.563A pdb=" N VAL K 168 " --> pdb=" O ALA K 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 177 removed outlier: 3.526A pdb=" N GLY K 176 " --> pdb=" O SER K 172 " (cutoff:3.500A) Processing helix chain 'K' and resid 192 through 206 removed outlier: 3.626A pdb=" N MET K 197 " --> pdb=" O SER K 193 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS K 198 " --> pdb=" O GLY K 194 " (cutoff:3.500A) Processing helix chain 'K' and resid 220 through 232 Processing helix chain 'K' and resid 248 through 253 Processing helix chain 'K' and resid 288 through 299 Processing helix chain 'K' and resid 308 through 317 removed outlier: 3.593A pdb=" N HIS K 311 " --> pdb=" O GLU K 308 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE K 314 " --> pdb=" O HIS K 311 " (cutoff:3.500A) Processing helix chain 'K' and resid 321 through 333 removed outlier: 3.832A pdb=" N ASP K 333 " --> pdb=" O ALA K 329 " (cutoff:3.500A) Processing helix chain 'K' and resid 338 through 347 removed outlier: 3.878A pdb=" N LEU K 342 " --> pdb=" O TRP K 338 " (cutoff:3.500A) Processing helix chain 'K' and resid 364 through 374 removed outlier: 3.532A pdb=" N MET K 368 " --> pdb=" O LEU K 364 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE K 370 " --> pdb=" O GLU K 366 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU K 373 " --> pdb=" O SER K 369 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N MET K 374 " --> pdb=" O ILE K 370 " (cutoff:3.500A) Processing helix chain 'K' and resid 377 through 388 removed outlier: 3.711A pdb=" N ASP K 381 " --> pdb=" O GLU K 377 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N TYR K 382 " --> pdb=" O ASP K 378 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR K 384 " --> pdb=" O LYS K 380 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP K 385 " --> pdb=" O ASP K 381 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE K 388 " --> pdb=" O THR K 384 " (cutoff:3.500A) Processing helix chain 'K' and resid 397 through 404 Processing helix chain 'K' and resid 408 through 420 removed outlier: 4.148A pdb=" N ASP K 413 " --> pdb=" O GLU K 409 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE K 414 " --> pdb=" O GLU K 410 " (cutoff:3.500A) Processing helix chain 'K' and resid 439 through 466 removed outlier: 7.004A pdb=" N SER K 451 " --> pdb=" O GLU K 447 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLN K 452 " --> pdb=" O LYS K 448 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN K 454 " --> pdb=" O CYS K 450 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASP K 455 " --> pdb=" O SER K 451 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LYS K 458 " --> pdb=" O GLN K 454 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS K 459 " --> pdb=" O ASP K 455 " (cutoff:3.500A) Processing helix chain 'K' and resid 478 through 494 removed outlier: 4.214A pdb=" N MET K 481 " --> pdb=" O GLU K 478 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR K 484 " --> pdb=" O MET K 481 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN K 485 " --> pdb=" O TYR K 482 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N PHE K 486 " --> pdb=" O TRP K 483 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA K 488 " --> pdb=" O ASN K 485 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N MET K 491 " --> pdb=" O ALA K 488 " (cutoff:3.500A) Processing helix chain 'K' and resid 497 through 503 Processing helix chain 'K' and resid 507 through 517 Processing helix chain 'K' and resid 521 through 532 removed outlier: 3.538A pdb=" N GLU K 528 " --> pdb=" O HIS K 524 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N HIS K 531 " --> pdb=" O VAL K 527 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE K 532 " --> pdb=" O GLU K 528 " (cutoff:3.500A) Processing helix chain 'K' and resid 535 through 549 removed outlier: 3.666A pdb=" N VAL K 540 " --> pdb=" O LYS K 536 " (cutoff:3.500A) Processing helix chain 'K' and resid 551 through 554 No H-bonds generated for 'chain 'K' and resid 551 through 554' Processing helix chain 'K' and resid 563 through 566 No H-bonds generated for 'chain 'K' and resid 563 through 566' Processing helix chain 'K' and resid 574 through 590 removed outlier: 3.553A pdb=" N LEU K 582 " --> pdb=" O GLN K 578 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP K 589 " --> pdb=" O LYS K 585 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASN K 590 " --> pdb=" O GLN K 586 " (cutoff:3.500A) Processing helix chain 'K' and resid 600 through 602 No H-bonds generated for 'chain 'K' and resid 600 through 602' Processing helix chain 'K' and resid 851 through 853 No H-bonds generated for 'chain 'K' and resid 851 through 853' Processing helix chain 'K' and resid 911 through 915 removed outlier: 4.141A pdb=" N CYS K 915 " --> pdb=" O THR K 911 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 911 through 915' Processing helix chain 'L' and resid 3 through 13 Processing helix chain 'L' and resid 50 through 54 Processing helix chain 'L' and resid 61 through 69 removed outlier: 3.523A pdb=" N GLU L 69 " --> pdb=" O MET L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 71 through 74 No H-bonds generated for 'chain 'L' and resid 71 through 74' Processing helix chain 'L' and resid 88 through 101 Processing helix chain 'M' and resid 108 through 117 Processing helix chain 'M' and resid 130 through 142 Processing helix chain 'M' and resid 160 through 167 Processing helix chain 'M' and resid 171 through 177 removed outlier: 3.526A pdb=" N GLY M 176 " --> pdb=" O SER M 172 " (cutoff:3.500A) Processing helix chain 'M' and resid 192 through 206 removed outlier: 3.628A pdb=" N MET M 197 " --> pdb=" O SER M 193 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS M 198 " --> pdb=" O GLY M 194 " (cutoff:3.500A) Processing helix chain 'M' and resid 220 through 232 Processing helix chain 'M' and resid 248 through 253 Processing helix chain 'M' and resid 288 through 299 Processing helix chain 'M' and resid 308 through 317 removed outlier: 3.590A pdb=" N HIS M 311 " --> pdb=" O GLU M 308 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE M 314 " --> pdb=" O HIS M 311 " (cutoff:3.500A) Processing helix chain 'M' and resid 321 through 333 removed outlier: 3.831A pdb=" N ASP M 333 " --> pdb=" O ALA M 329 " (cutoff:3.500A) Processing helix chain 'M' and resid 338 through 347 removed outlier: 3.878A pdb=" N LEU M 342 " --> pdb=" O TRP M 338 " (cutoff:3.500A) Processing helix chain 'M' and resid 364 through 374 removed outlier: 3.532A pdb=" N MET M 368 " --> pdb=" O LEU M 364 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE M 370 " --> pdb=" O GLU M 366 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU M 373 " --> pdb=" O SER M 369 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N MET M 374 " --> pdb=" O ILE M 370 " (cutoff:3.500A) Processing helix chain 'M' and resid 377 through 388 removed outlier: 3.714A pdb=" N ASP M 381 " --> pdb=" O GLU M 377 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N TYR M 382 " --> pdb=" O ASP M 378 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR M 384 " --> pdb=" O LYS M 380 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP M 385 " --> pdb=" O ASP M 381 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE M 388 " --> pdb=" O THR M 384 " (cutoff:3.500A) Processing helix chain 'M' and resid 397 through 404 Processing helix chain 'M' and resid 408 through 420 removed outlier: 4.151A pdb=" N ASP M 413 " --> pdb=" O GLU M 409 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE M 414 " --> pdb=" O GLU M 410 " (cutoff:3.500A) Processing helix chain 'M' and resid 439 through 466 removed outlier: 7.004A pdb=" N SER M 451 " --> pdb=" O GLU M 447 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLN M 452 " --> pdb=" O LYS M 448 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN M 454 " --> pdb=" O CYS M 450 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASP M 455 " --> pdb=" O SER M 451 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LYS M 458 " --> pdb=" O GLN M 454 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS M 459 " --> pdb=" O ASP M 455 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN M 463 " --> pdb=" O LYS M 459 " (cutoff:3.500A) Processing helix chain 'M' and resid 478 through 494 removed outlier: 4.215A pdb=" N MET M 481 " --> pdb=" O GLU M 478 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR M 484 " --> pdb=" O MET M 481 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN M 485 " --> pdb=" O TYR M 482 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE M 486 " --> pdb=" O TRP M 483 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA M 488 " --> pdb=" O ASN M 485 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N MET M 491 " --> pdb=" O ALA M 488 " (cutoff:3.500A) Processing helix chain 'M' and resid 497 through 503 Processing helix chain 'M' and resid 507 through 517 Processing helix chain 'M' and resid 521 through 532 removed outlier: 3.537A pdb=" N GLU M 528 " --> pdb=" O HIS M 524 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N HIS M 531 " --> pdb=" O VAL M 527 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE M 532 " --> pdb=" O GLU M 528 " (cutoff:3.500A) Processing helix chain 'M' and resid 535 through 549 removed outlier: 3.667A pdb=" N VAL M 540 " --> pdb=" O LYS M 536 " (cutoff:3.500A) Processing helix chain 'M' and resid 551 through 554 No H-bonds generated for 'chain 'M' and resid 551 through 554' Processing helix chain 'M' and resid 563 through 566 No H-bonds generated for 'chain 'M' and resid 563 through 566' Processing helix chain 'M' and resid 574 through 590 removed outlier: 3.552A pdb=" N LEU M 582 " --> pdb=" O GLN M 578 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP M 589 " --> pdb=" O LYS M 585 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASN M 590 " --> pdb=" O GLN M 586 " (cutoff:3.500A) Processing helix chain 'M' and resid 600 through 602 No H-bonds generated for 'chain 'M' and resid 600 through 602' Processing helix chain 'M' and resid 851 through 853 No H-bonds generated for 'chain 'M' and resid 851 through 853' Processing helix chain 'M' and resid 911 through 915 removed outlier: 4.140A pdb=" N CYS M 915 " --> pdb=" O THR M 911 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 911 through 915' Processing helix chain 'N' and resid 3 through 13 Processing helix chain 'N' and resid 50 through 54 Processing helix chain 'N' and resid 61 through 69 removed outlier: 3.521A pdb=" N GLU N 69 " --> pdb=" O MET N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 71 through 74 No H-bonds generated for 'chain 'N' and resid 71 through 74' Processing helix chain 'N' and resid 88 through 101 Processing helix chain 'O' and resid 3 through 17 removed outlier: 4.962A pdb=" N GLU O 14 " --> pdb=" O LEU O 10 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ALA O 15 " --> pdb=" O GLN O 11 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 32 Processing helix chain 'O' and resid 37 through 44 Processing helix chain 'O' and resid 49 through 62 removed outlier: 4.079A pdb=" N LYS O 62 " --> pdb=" O LYS O 58 " (cutoff:3.500A) Processing helix chain 'O' and resid 65 through 77 Processing helix chain 'O' and resid 81 through 90 removed outlier: 4.303A pdb=" N ASP O 89 " --> pdb=" O ALA O 85 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N GLY O 90 " --> pdb=" O LEU O 86 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 17 removed outlier: 4.962A pdb=" N GLU P 14 " --> pdb=" O LEU P 10 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ALA P 15 " --> pdb=" O GLN P 11 " (cutoff:3.500A) Processing helix chain 'P' and resid 22 through 32 Processing helix chain 'P' and resid 37 through 44 Processing helix chain 'P' and resid 49 through 62 removed outlier: 3.976A pdb=" N LYS P 62 " --> pdb=" O LYS P 58 " (cutoff:3.500A) Processing helix chain 'P' and resid 65 through 77 Processing helix chain 'P' and resid 81 through 90 removed outlier: 4.305A pdb=" N ASP P 89 " --> pdb=" O ALA P 85 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N GLY P 90 " --> pdb=" O LEU P 86 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 17 removed outlier: 4.962A pdb=" N GLU Q 14 " --> pdb=" O LEU Q 10 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ALA Q 15 " --> pdb=" O GLN Q 11 " (cutoff:3.500A) Processing helix chain 'Q' and resid 22 through 32 Processing helix chain 'Q' and resid 37 through 45 Processing helix chain 'Q' and resid 49 through 62 removed outlier: 3.977A pdb=" N LYS Q 62 " --> pdb=" O LYS Q 58 " (cutoff:3.500A) Processing helix chain 'Q' and resid 65 through 77 Processing helix chain 'Q' and resid 81 through 90 removed outlier: 4.305A pdb=" N ASP Q 89 " --> pdb=" O ALA Q 85 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N GLY Q 90 " --> pdb=" O LEU Q 86 " (cutoff:3.500A) Processing helix chain 'R' and resid 3 through 17 removed outlier: 4.962A pdb=" N GLU R 14 " --> pdb=" O LEU R 10 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ALA R 15 " --> pdb=" O GLN R 11 " (cutoff:3.500A) Processing helix chain 'R' and resid 22 through 32 Processing helix chain 'R' and resid 37 through 44 Processing helix chain 'R' and resid 49 through 62 removed outlier: 3.977A pdb=" N LYS R 62 " --> pdb=" O LYS R 58 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 77 Processing helix chain 'R' and resid 81 through 90 removed outlier: 4.304A pdb=" N ASP R 89 " --> pdb=" O ALA R 85 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N GLY R 90 " --> pdb=" O LEU R 86 " (cutoff:3.500A) Processing helix chain 'S' and resid 3 through 11 Processing helix chain 'S' and resid 13 through 19 Processing helix chain 'S' and resid 26 through 31 Processing helix chain 'S' and resid 37 through 44 Processing helix chain 'S' and resid 51 through 64 removed outlier: 4.019A pdb=" N GLU S 63 " --> pdb=" O ILE S 59 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR S 64 " --> pdb=" O ILE S 60 " (cutoff:3.500A) Processing helix chain 'S' and resid 69 through 80 Processing helix chain 'S' and resid 83 through 94 Processing helix chain 'T' and resid 3 through 11 Processing helix chain 'T' and resid 13 through 19 Processing helix chain 'T' and resid 26 through 31 Processing helix chain 'T' and resid 37 through 44 Processing helix chain 'T' and resid 51 through 64 removed outlier: 4.020A pdb=" N GLU T 63 " --> pdb=" O ILE T 59 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR T 64 " --> pdb=" O ILE T 60 " (cutoff:3.500A) Processing helix chain 'T' and resid 69 through 80 Processing helix chain 'T' and resid 83 through 94 Processing helix chain 'U' and resid 3 through 11 removed outlier: 3.842A pdb=" N ARG U 10 " --> pdb=" O ARG U 6 " (cutoff:3.500A) Processing helix chain 'U' and resid 13 through 17 Processing helix chain 'U' and resid 26 through 31 Processing helix chain 'U' and resid 37 through 44 Processing helix chain 'U' and resid 51 through 64 removed outlier: 4.019A pdb=" N GLU U 63 " --> pdb=" O ILE U 59 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR U 64 " --> pdb=" O ILE U 60 " (cutoff:3.500A) Processing helix chain 'U' and resid 69 through 80 Processing helix chain 'U' and resid 83 through 94 Processing helix chain 'V' and resid 3 through 11 Processing helix chain 'V' and resid 13 through 19 Processing helix chain 'V' and resid 26 through 31 Processing helix chain 'V' and resid 37 through 44 Processing helix chain 'V' and resid 51 through 64 removed outlier: 4.020A pdb=" N GLU V 63 " --> pdb=" O ILE V 59 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR V 64 " --> pdb=" O ILE V 60 " (cutoff:3.500A) Processing helix chain 'V' and resid 69 through 80 Processing helix chain 'V' and resid 83 through 94 Processing helix chain 'W' and resid 3 through 11 Processing helix chain 'W' and resid 13 through 19 Processing helix chain 'W' and resid 22 through 24 No H-bonds generated for 'chain 'W' and resid 22 through 24' Processing helix chain 'W' and resid 26 through 31 Processing helix chain 'W' and resid 37 through 44 Processing helix chain 'W' and resid 49 through 62 removed outlier: 4.001A pdb=" N LYS W 62 " --> pdb=" O LYS W 58 " (cutoff:3.500A) Processing helix chain 'W' and resid 65 through 77 Processing helix chain 'W' and resid 81 through 90 removed outlier: 4.651A pdb=" N ASP W 89 " --> pdb=" O ALA W 85 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N GLY W 90 " --> pdb=" O LEU W 86 " (cutoff:3.500A) Processing helix chain 'X' and resid 3 through 19 removed outlier: 5.133A pdb=" N GLU X 14 " --> pdb=" O LEU X 10 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ALA X 15 " --> pdb=" O GLN X 11 " (cutoff:3.500A) Processing helix chain 'X' and resid 22 through 32 Processing helix chain 'X' and resid 37 through 45 Processing helix chain 'X' and resid 49 through 62 removed outlier: 3.633A pdb=" N LYS X 62 " --> pdb=" O LYS X 58 " (cutoff:3.500A) Processing helix chain 'X' and resid 65 through 77 Processing helix chain 'X' and resid 81 through 90 removed outlier: 4.115A pdb=" N ASP X 89 " --> pdb=" O ALA X 85 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N GLY X 90 " --> pdb=" O LEU X 86 " (cutoff:3.500A) Processing helix chain 'Y' and resid 3 through 11 Processing helix chain 'Y' and resid 13 through 19 Processing helix chain 'Y' and resid 26 through 31 Processing helix chain 'Y' and resid 37 through 44 Processing helix chain 'Y' and resid 51 through 64 removed outlier: 3.719A pdb=" N GLU Y 63 " --> pdb=" O ILE Y 59 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N THR Y 64 " --> pdb=" O ILE Y 60 " (cutoff:3.500A) Processing helix chain 'Y' and resid 69 through 80 Processing helix chain 'Y' and resid 83 through 93 removed outlier: 3.755A pdb=" N ASN Y 92 " --> pdb=" O PHE Y 88 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 277 through 281 removed outlier: 6.770A pdb=" N TRP A 149 " --> pdb=" O TYR A 278 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N VAL A 280 " --> pdb=" O TRP A 149 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N THR A 151 " --> pdb=" O VAL A 280 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ILE A 260 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 9.100A pdb=" N ILE A 152 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N LEU A 262 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU A 240 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N THR A 263 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU A 242 " --> pdb=" O THR A 263 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 609 through 611 removed outlier: 3.902A pdb=" N LEU A 609 " --> pdb=" O LEU A 908 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 621 through 623 removed outlier: 6.330A pdb=" N LYS A 643 " --> pdb=" O LYS A 649 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LYS A 649 " --> pdb=" O LYS A 643 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 702 through 707 removed outlier: 6.217A pdb=" N GLY A 719 " --> pdb=" O ASN A 703 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N CYS A 705 " --> pdb=" O ALA A 717 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ALA A 717 " --> pdb=" O CYS A 705 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N PHE A 707 " --> pdb=" O LEU A 715 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU A 715 " --> pdb=" O PHE A 707 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ASP A 729 " --> pdb=" O CYS A 735 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N CYS A 735 " --> pdb=" O ASP A 729 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 768 through 771 removed outlier: 3.847A pdb=" N HIS A 748 " --> pdb=" O CYS A 761 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 804 through 806 removed outlier: 5.463A pdb=" N ASP A 825 " --> pdb=" O LEU A 831 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N LEU A 831 " --> pdb=" O ASP A 825 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 854 through 858 removed outlier: 5.505A pdb=" N ASN A 868 " --> pdb=" O LYS A 874 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N LYS A 874 " --> pdb=" O ASN A 868 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 928 through 930 removed outlier: 3.790A pdb=" N MET A 936 " --> pdb=" O VAL A 929 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 967 through 969 Processing sheet with id= J, first strand: chain 'A' and resid 1009 through 1011 Processing sheet with id= K, first strand: chain 'A' and resid 1079 through 1081 Processing sheet with id= L, first strand: chain 'A' and resid 1090 through 1093 removed outlier: 3.515A pdb=" N SER A1090 " --> pdb=" O SER A1104 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 1132 through 1135 Processing sheet with id= N, first strand: chain 'A' and resid 1182 through 1185 removed outlier: 4.000A pdb=" N ASP A1182 " --> pdb=" O ALA A1195 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA A1195 " --> pdb=" O ASP A1182 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 1233 through 1235 Processing sheet with id= P, first strand: chain 'A' and resid 660 through 665 removed outlier: 6.642A pdb=" N CYS A 675 " --> pdb=" O LEU A 661 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N CYS A 663 " --> pdb=" O ALA A 673 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ALA A 673 " --> pdb=" O CYS A 663 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'A' and resid 681 through 684 Processing sheet with id= R, first strand: chain 'A' and resid 885 through 890 removed outlier: 6.366A pdb=" N SER A 900 " --> pdb=" O HIS A 886 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL A 888 " --> pdb=" O LEU A 898 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU A 898 " --> pdb=" O VAL A 888 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 277 through 281 removed outlier: 6.770A pdb=" N TRP C 149 " --> pdb=" O TYR C 278 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N VAL C 280 " --> pdb=" O TRP C 149 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N THR C 151 " --> pdb=" O VAL C 280 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ILE C 260 " --> pdb=" O VAL C 150 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N ILE C 152 " --> pdb=" O ILE C 260 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N LEU C 262 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU C 240 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N THR C 263 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU C 242 " --> pdb=" O THR C 263 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 609 through 611 removed outlier: 3.902A pdb=" N LEU C 609 " --> pdb=" O LEU C 908 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 621 through 623 removed outlier: 6.328A pdb=" N LYS C 643 " --> pdb=" O LYS C 649 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LYS C 649 " --> pdb=" O LYS C 643 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 702 through 707 removed outlier: 6.217A pdb=" N GLY C 719 " --> pdb=" O ASN C 703 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N CYS C 705 " --> pdb=" O ALA C 717 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ALA C 717 " --> pdb=" O CYS C 705 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N PHE C 707 " --> pdb=" O LEU C 715 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU C 715 " --> pdb=" O PHE C 707 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ASP C 729 " --> pdb=" O CYS C 735 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N CYS C 735 " --> pdb=" O ASP C 729 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 768 through 771 removed outlier: 3.845A pdb=" N HIS C 748 " --> pdb=" O CYS C 761 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 804 through 806 removed outlier: 5.463A pdb=" N ASP C 825 " --> pdb=" O LEU C 831 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N LEU C 831 " --> pdb=" O ASP C 825 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 854 through 858 removed outlier: 5.505A pdb=" N ASN C 868 " --> pdb=" O LYS C 874 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N LYS C 874 " --> pdb=" O ASN C 868 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 928 through 930 removed outlier: 3.792A pdb=" N MET C 936 " --> pdb=" O VAL C 929 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'C' and resid 967 through 969 Processing sheet with id= AB, first strand: chain 'C' and resid 1009 through 1011 Processing sheet with id= AC, first strand: chain 'C' and resid 1079 through 1081 Processing sheet with id= AD, first strand: chain 'C' and resid 1090 through 1093 removed outlier: 3.516A pdb=" N SER C1090 " --> pdb=" O SER C1104 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'C' and resid 1132 through 1135 Processing sheet with id= AF, first strand: chain 'C' and resid 1182 through 1185 removed outlier: 4.002A pdb=" N ASP C1182 " --> pdb=" O ALA C1195 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA C1195 " --> pdb=" O ASP C1182 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'C' and resid 1233 through 1235 Processing sheet with id= AH, first strand: chain 'C' and resid 660 through 665 removed outlier: 6.642A pdb=" N CYS C 675 " --> pdb=" O LEU C 661 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N CYS C 663 " --> pdb=" O ALA C 673 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ALA C 673 " --> pdb=" O CYS C 663 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'C' and resid 681 through 684 Processing sheet with id= AJ, first strand: chain 'C' and resid 885 through 890 removed outlier: 6.367A pdb=" N SER C 900 " --> pdb=" O HIS C 886 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL C 888 " --> pdb=" O LEU C 898 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU C 898 " --> pdb=" O VAL C 888 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'E' and resid 277 through 281 removed outlier: 6.771A pdb=" N TRP E 149 " --> pdb=" O TYR E 278 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N VAL E 280 " --> pdb=" O TRP E 149 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N THR E 151 " --> pdb=" O VAL E 280 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ILE E 260 " --> pdb=" O VAL E 150 " (cutoff:3.500A) removed outlier: 9.099A pdb=" N ILE E 152 " --> pdb=" O ILE E 260 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N LEU E 262 " --> pdb=" O ILE E 152 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU E 240 " --> pdb=" O LEU E 261 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N THR E 263 " --> pdb=" O LEU E 240 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU E 242 " --> pdb=" O THR E 263 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'E' and resid 609 through 611 removed outlier: 3.903A pdb=" N LEU E 609 " --> pdb=" O LEU E 908 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'E' and resid 621 through 623 removed outlier: 6.327A pdb=" N LYS E 643 " --> pdb=" O LYS E 649 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LYS E 649 " --> pdb=" O LYS E 643 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'E' and resid 702 through 707 removed outlier: 6.217A pdb=" N GLY E 719 " --> pdb=" O ASN E 703 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N CYS E 705 " --> pdb=" O ALA E 717 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ALA E 717 " --> pdb=" O CYS E 705 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N PHE E 707 " --> pdb=" O LEU E 715 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU E 715 " --> pdb=" O PHE E 707 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ASP E 729 " --> pdb=" O CYS E 735 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N CYS E 735 " --> pdb=" O ASP E 729 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'E' and resid 768 through 771 removed outlier: 3.846A pdb=" N HIS E 748 " --> pdb=" O CYS E 761 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'E' and resid 804 through 806 removed outlier: 5.463A pdb=" N ASP E 825 " --> pdb=" O LEU E 831 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N LEU E 831 " --> pdb=" O ASP E 825 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'E' and resid 854 through 858 removed outlier: 5.506A pdb=" N ASN E 868 " --> pdb=" O LYS E 874 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N LYS E 874 " --> pdb=" O ASN E 868 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'E' and resid 928 through 930 removed outlier: 3.791A pdb=" N MET E 936 " --> pdb=" O VAL E 929 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'E' and resid 967 through 969 Processing sheet with id= AT, first strand: chain 'E' and resid 1009 through 1011 Processing sheet with id= AU, first strand: chain 'E' and resid 1079 through 1081 Processing sheet with id= AV, first strand: chain 'E' and resid 1090 through 1093 removed outlier: 3.517A pdb=" N SER E1090 " --> pdb=" O SER E1104 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'E' and resid 1132 through 1135 Processing sheet with id= AX, first strand: chain 'E' and resid 1182 through 1185 removed outlier: 4.002A pdb=" N ASP E1182 " --> pdb=" O ALA E1195 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA E1195 " --> pdb=" O ASP E1182 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'E' and resid 1233 through 1235 Processing sheet with id= AZ, first strand: chain 'E' and resid 660 through 665 removed outlier: 6.643A pdb=" N CYS E 675 " --> pdb=" O LEU E 661 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N CYS E 663 " --> pdb=" O ALA E 673 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ALA E 673 " --> pdb=" O CYS E 663 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'E' and resid 681 through 684 Processing sheet with id= BB, first strand: chain 'E' and resid 885 through 890 removed outlier: 6.368A pdb=" N SER E 900 " --> pdb=" O HIS E 886 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL E 888 " --> pdb=" O LEU E 898 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU E 898 " --> pdb=" O VAL E 888 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'G' and resid 277 through 281 removed outlier: 6.770A pdb=" N TRP G 149 " --> pdb=" O TYR G 278 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N VAL G 280 " --> pdb=" O TRP G 149 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N THR G 151 " --> pdb=" O VAL G 280 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ILE G 260 " --> pdb=" O VAL G 150 " (cutoff:3.500A) removed outlier: 9.098A pdb=" N ILE G 152 " --> pdb=" O ILE G 260 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LEU G 262 " --> pdb=" O ILE G 152 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU G 240 " --> pdb=" O LEU G 261 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N THR G 263 " --> pdb=" O LEU G 240 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU G 242 " --> pdb=" O THR G 263 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'G' and resid 609 through 611 removed outlier: 3.901A pdb=" N LEU G 609 " --> pdb=" O LEU G 908 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'G' and resid 621 through 623 removed outlier: 6.330A pdb=" N LYS G 643 " --> pdb=" O LYS G 649 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LYS G 649 " --> pdb=" O LYS G 643 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'G' and resid 702 through 707 removed outlier: 6.216A pdb=" N GLY G 719 " --> pdb=" O ASN G 703 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N CYS G 705 " --> pdb=" O ALA G 717 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ALA G 717 " --> pdb=" O CYS G 705 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N PHE G 707 " --> pdb=" O LEU G 715 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU G 715 " --> pdb=" O PHE G 707 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ASP G 729 " --> pdb=" O CYS G 735 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N CYS G 735 " --> pdb=" O ASP G 729 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'G' and resid 768 through 771 removed outlier: 3.846A pdb=" N HIS G 748 " --> pdb=" O CYS G 761 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'G' and resid 804 through 806 removed outlier: 5.462A pdb=" N ASP G 825 " --> pdb=" O LEU G 831 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N LEU G 831 " --> pdb=" O ASP G 825 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'G' and resid 854 through 858 removed outlier: 5.505A pdb=" N ASN G 868 " --> pdb=" O LYS G 874 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N LYS G 874 " --> pdb=" O ASN G 868 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'G' and resid 928 through 930 removed outlier: 3.791A pdb=" N MET G 936 " --> pdb=" O VAL G 929 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'G' and resid 967 through 969 Processing sheet with id= BL, first strand: chain 'G' and resid 1009 through 1011 Processing sheet with id= BM, first strand: chain 'G' and resid 1079 through 1081 Processing sheet with id= BN, first strand: chain 'G' and resid 1090 through 1093 removed outlier: 3.517A pdb=" N SER G1090 " --> pdb=" O SER G1104 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'G' and resid 1132 through 1135 Processing sheet with id= BP, first strand: chain 'G' and resid 1182 through 1185 removed outlier: 4.002A pdb=" N ASP G1182 " --> pdb=" O ALA G1195 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA G1195 " --> pdb=" O ASP G1182 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'G' and resid 1233 through 1235 Processing sheet with id= BR, first strand: chain 'G' and resid 660 through 665 removed outlier: 6.641A pdb=" N CYS G 675 " --> pdb=" O LEU G 661 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N CYS G 663 " --> pdb=" O ALA G 673 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ALA G 673 " --> pdb=" O CYS G 663 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'G' and resid 681 through 684 Processing sheet with id= BT, first strand: chain 'G' and resid 885 through 890 removed outlier: 6.368A pdb=" N SER G 900 " --> pdb=" O HIS G 886 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL G 888 " --> pdb=" O LEU G 898 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU G 898 " --> pdb=" O VAL G 888 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'I' and resid 277 through 281 removed outlier: 6.770A pdb=" N TRP I 149 " --> pdb=" O TYR I 278 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N VAL I 280 " --> pdb=" O TRP I 149 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N THR I 151 " --> pdb=" O VAL I 280 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ILE I 260 " --> pdb=" O VAL I 150 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N ILE I 152 " --> pdb=" O ILE I 260 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N LEU I 262 " --> pdb=" O ILE I 152 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU I 240 " --> pdb=" O LEU I 261 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N THR I 263 " --> pdb=" O LEU I 240 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU I 242 " --> pdb=" O THR I 263 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'I' and resid 609 through 611 removed outlier: 3.901A pdb=" N LEU I 609 " --> pdb=" O LEU I 908 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'I' and resid 621 through 623 removed outlier: 6.327A pdb=" N LYS I 643 " --> pdb=" O LYS I 649 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LYS I 649 " --> pdb=" O LYS I 643 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'I' and resid 702 through 707 removed outlier: 6.217A pdb=" N GLY I 719 " --> pdb=" O ASN I 703 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N CYS I 705 " --> pdb=" O ALA I 717 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ALA I 717 " --> pdb=" O CYS I 705 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N PHE I 707 " --> pdb=" O LEU I 715 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU I 715 " --> pdb=" O PHE I 707 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ASP I 729 " --> pdb=" O CYS I 735 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N CYS I 735 " --> pdb=" O ASP I 729 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'I' and resid 768 through 771 removed outlier: 3.847A pdb=" N HIS I 748 " --> pdb=" O CYS I 761 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'I' and resid 804 through 806 removed outlier: 5.462A pdb=" N ASP I 825 " --> pdb=" O LEU I 831 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N LEU I 831 " --> pdb=" O ASP I 825 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'I' and resid 854 through 858 removed outlier: 5.505A pdb=" N ASN I 868 " --> pdb=" O LYS I 874 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N LYS I 874 " --> pdb=" O ASN I 868 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'I' and resid 928 through 930 removed outlier: 3.790A pdb=" N MET I 936 " --> pdb=" O VAL I 929 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'I' and resid 967 through 969 Processing sheet with id= CD, first strand: chain 'I' and resid 1009 through 1011 Processing sheet with id= CE, first strand: chain 'I' and resid 1079 through 1081 Processing sheet with id= CF, first strand: chain 'I' and resid 1090 through 1093 removed outlier: 3.515A pdb=" N SER I1090 " --> pdb=" O SER I1104 " (cutoff:3.500A) Processing sheet with id= CG, first strand: chain 'I' and resid 1132 through 1135 Processing sheet with id= CH, first strand: chain 'I' and resid 1182 through 1185 removed outlier: 4.001A pdb=" N ASP I1182 " --> pdb=" O ALA I1195 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA I1195 " --> pdb=" O ASP I1182 " (cutoff:3.500A) Processing sheet with id= CI, first strand: chain 'I' and resid 1233 through 1235 Processing sheet with id= CJ, first strand: chain 'I' and resid 660 through 665 removed outlier: 6.643A pdb=" N CYS I 675 " --> pdb=" O LEU I 661 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N CYS I 663 " --> pdb=" O ALA I 673 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ALA I 673 " --> pdb=" O CYS I 663 " (cutoff:3.500A) Processing sheet with id= CK, first strand: chain 'I' and resid 681 through 684 Processing sheet with id= CL, first strand: chain 'I' and resid 885 through 890 removed outlier: 6.367A pdb=" N SER I 900 " --> pdb=" O HIS I 886 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL I 888 " --> pdb=" O LEU I 898 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU I 898 " --> pdb=" O VAL I 888 " (cutoff:3.500A) Processing sheet with id= CM, first strand: chain 'K' and resid 277 through 281 removed outlier: 6.769A pdb=" N TRP K 149 " --> pdb=" O TYR K 278 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N VAL K 280 " --> pdb=" O TRP K 149 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N THR K 151 " --> pdb=" O VAL K 280 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ILE K 260 " --> pdb=" O VAL K 150 " (cutoff:3.500A) removed outlier: 9.099A pdb=" N ILE K 152 " --> pdb=" O ILE K 260 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N LEU K 262 " --> pdb=" O ILE K 152 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU K 240 " --> pdb=" O LEU K 261 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N THR K 263 " --> pdb=" O LEU K 240 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU K 242 " --> pdb=" O THR K 263 " (cutoff:3.500A) Processing sheet with id= CN, first strand: chain 'K' and resid 609 through 611 removed outlier: 3.902A pdb=" N LEU K 609 " --> pdb=" O LEU K 908 " (cutoff:3.500A) Processing sheet with id= CO, first strand: chain 'K' and resid 621 through 623 removed outlier: 6.328A pdb=" N LYS K 643 " --> pdb=" O LYS K 649 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N LYS K 649 " --> pdb=" O LYS K 643 " (cutoff:3.500A) Processing sheet with id= CP, first strand: chain 'K' and resid 702 through 707 removed outlier: 6.217A pdb=" N GLY K 719 " --> pdb=" O ASN K 703 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N CYS K 705 " --> pdb=" O ALA K 717 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ALA K 717 " --> pdb=" O CYS K 705 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N PHE K 707 " --> pdb=" O LEU K 715 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU K 715 " --> pdb=" O PHE K 707 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ASP K 729 " --> pdb=" O CYS K 735 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N CYS K 735 " --> pdb=" O ASP K 729 " (cutoff:3.500A) Processing sheet with id= CQ, first strand: chain 'K' and resid 768 through 771 removed outlier: 3.846A pdb=" N HIS K 748 " --> pdb=" O CYS K 761 " (cutoff:3.500A) Processing sheet with id= CR, first strand: chain 'K' and resid 804 through 806 removed outlier: 5.463A pdb=" N ASP K 825 " --> pdb=" O LEU K 831 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LEU K 831 " --> pdb=" O ASP K 825 " (cutoff:3.500A) Processing sheet with id= CS, first strand: chain 'K' and resid 854 through 858 removed outlier: 5.504A pdb=" N ASN K 868 " --> pdb=" O LYS K 874 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N LYS K 874 " --> pdb=" O ASN K 868 " (cutoff:3.500A) Processing sheet with id= CT, first strand: chain 'K' and resid 928 through 930 removed outlier: 3.792A pdb=" N MET K 936 " --> pdb=" O VAL K 929 " (cutoff:3.500A) Processing sheet with id= CU, first strand: chain 'K' and resid 967 through 969 Processing sheet with id= CV, first strand: chain 'K' and resid 1009 through 1011 Processing sheet with id= CW, first strand: chain 'K' and resid 1079 through 1081 Processing sheet with id= CX, first strand: chain 'K' and resid 1090 through 1093 removed outlier: 3.517A pdb=" N SER K1090 " --> pdb=" O SER K1104 " (cutoff:3.500A) Processing sheet with id= CY, first strand: chain 'K' and resid 1132 through 1135 Processing sheet with id= CZ, first strand: chain 'K' and resid 1182 through 1185 removed outlier: 4.002A pdb=" N ASP K1182 " --> pdb=" O ALA K1195 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA K1195 " --> pdb=" O ASP K1182 " (cutoff:3.500A) Processing sheet with id= DA, first strand: chain 'K' and resid 1233 through 1235 Processing sheet with id= DB, first strand: chain 'K' and resid 660 through 665 removed outlier: 6.641A pdb=" N CYS K 675 " --> pdb=" O LEU K 661 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N CYS K 663 " --> pdb=" O ALA K 673 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ALA K 673 " --> pdb=" O CYS K 663 " (cutoff:3.500A) Processing sheet with id= DC, first strand: chain 'K' and resid 681 through 684 Processing sheet with id= DD, first strand: chain 'K' and resid 885 through 890 removed outlier: 6.367A pdb=" N SER K 900 " --> pdb=" O HIS K 886 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL K 888 " --> pdb=" O LEU K 898 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU K 898 " --> pdb=" O VAL K 888 " (cutoff:3.500A) Processing sheet with id= DE, first strand: chain 'M' and resid 277 through 281 removed outlier: 6.770A pdb=" N TRP M 149 " --> pdb=" O TYR M 278 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N VAL M 280 " --> pdb=" O TRP M 149 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N THR M 151 " --> pdb=" O VAL M 280 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ILE M 260 " --> pdb=" O VAL M 150 " (cutoff:3.500A) removed outlier: 9.099A pdb=" N ILE M 152 " --> pdb=" O ILE M 260 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LEU M 262 " --> pdb=" O ILE M 152 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU M 240 " --> pdb=" O LEU M 261 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N THR M 263 " --> pdb=" O LEU M 240 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU M 242 " --> pdb=" O THR M 263 " (cutoff:3.500A) Processing sheet with id= DF, first strand: chain 'M' and resid 609 through 611 removed outlier: 3.902A pdb=" N LEU M 609 " --> pdb=" O LEU M 908 " (cutoff:3.500A) Processing sheet with id= DG, first strand: chain 'M' and resid 621 through 623 removed outlier: 6.329A pdb=" N LYS M 643 " --> pdb=" O LYS M 649 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LYS M 649 " --> pdb=" O LYS M 643 " (cutoff:3.500A) Processing sheet with id= DH, first strand: chain 'M' and resid 702 through 707 removed outlier: 6.217A pdb=" N GLY M 719 " --> pdb=" O ASN M 703 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N CYS M 705 " --> pdb=" O ALA M 717 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ALA M 717 " --> pdb=" O CYS M 705 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N PHE M 707 " --> pdb=" O LEU M 715 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU M 715 " --> pdb=" O PHE M 707 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ASP M 729 " --> pdb=" O CYS M 735 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N CYS M 735 " --> pdb=" O ASP M 729 " (cutoff:3.500A) Processing sheet with id= DI, first strand: chain 'M' and resid 768 through 771 removed outlier: 3.844A pdb=" N HIS M 748 " --> pdb=" O CYS M 761 " (cutoff:3.500A) Processing sheet with id= DJ, first strand: chain 'M' and resid 804 through 806 removed outlier: 5.462A pdb=" N ASP M 825 " --> pdb=" O LEU M 831 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N LEU M 831 " --> pdb=" O ASP M 825 " (cutoff:3.500A) Processing sheet with id= DK, first strand: chain 'M' and resid 854 through 858 removed outlier: 5.505A pdb=" N ASN M 868 " --> pdb=" O LYS M 874 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N LYS M 874 " --> pdb=" O ASN M 868 " (cutoff:3.500A) Processing sheet with id= DL, first strand: chain 'M' and resid 928 through 930 removed outlier: 3.790A pdb=" N MET M 936 " --> pdb=" O VAL M 929 " (cutoff:3.500A) Processing sheet with id= DM, first strand: chain 'M' and resid 967 through 969 Processing sheet with id= DN, first strand: chain 'M' and resid 1009 through 1011 Processing sheet with id= DO, first strand: chain 'M' and resid 1079 through 1081 Processing sheet with id= DP, first strand: chain 'M' and resid 1090 through 1093 removed outlier: 3.516A pdb=" N SER M1090 " --> pdb=" O SER M1104 " (cutoff:3.500A) Processing sheet with id= DQ, first strand: chain 'M' and resid 1132 through 1135 Processing sheet with id= DR, first strand: chain 'M' and resid 1182 through 1185 removed outlier: 4.001A pdb=" N ASP M1182 " --> pdb=" O ALA M1195 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA M1195 " --> pdb=" O ASP M1182 " (cutoff:3.500A) Processing sheet with id= DS, first strand: chain 'M' and resid 1233 through 1235 Processing sheet with id= DT, first strand: chain 'M' and resid 660 through 665 removed outlier: 6.642A pdb=" N CYS M 675 " --> pdb=" O LEU M 661 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N CYS M 663 " --> pdb=" O ALA M 673 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ALA M 673 " --> pdb=" O CYS M 663 " (cutoff:3.500A) Processing sheet with id= DU, first strand: chain 'M' and resid 681 through 684 Processing sheet with id= DV, first strand: chain 'M' and resid 885 through 890 removed outlier: 6.366A pdb=" N SER M 900 " --> pdb=" O HIS M 886 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL M 888 " --> pdb=" O LEU M 898 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU M 898 " --> pdb=" O VAL M 888 " (cutoff:3.500A) 2326 hydrogen bonds defined for protein. 6348 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: 33.43 Time building geometry restraints manager: 28.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.37: 26796 1.37 - 1.55: 52476 1.55 - 1.73: 235 1.73 - 1.92: 728 1.92 - 2.10: 21 Bond restraints: 80256 Sorted by residual: bond pdb=" C TRP K1179 " pdb=" N VAL K1180 " ideal model delta sigma weight residual 1.332 1.190 0.142 1.36e-02 5.41e+03 1.09e+02 bond pdb=" C4 DTP E1301 " pdb=" C5 DTP E1301 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.94e+01 bond pdb=" C4 DTP A1301 " pdb=" C5 DTP A1301 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.87e+01 bond pdb=" C4 DTP G1301 " pdb=" C5 DTP G1301 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.86e+01 bond pdb=" C4 DTP I1301 " pdb=" C5 DTP I1301 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.84e+01 ... (remaining 80251 not shown) Histogram of bond angle deviations from ideal: 85.94 - 104.38: 990 104.38 - 122.82: 97071 122.82 - 141.26: 10468 141.26 - 159.70: 0 159.70 - 178.14: 14 Bond angle restraints: 108543 Sorted by residual: angle pdb=" PB DTP E1301 " pdb=" O3B DTP E1301 " pdb=" PG DTP E1301 " ideal model delta sigma weight residual 139.87 120.39 19.48 1.00e+00 1.00e+00 3.80e+02 angle pdb=" PB DTP A1301 " pdb=" O3B DTP A1301 " pdb=" PG DTP A1301 " ideal model delta sigma weight residual 139.87 120.41 19.46 1.00e+00 1.00e+00 3.79e+02 angle pdb=" PB DTP I1301 " pdb=" O3B DTP I1301 " pdb=" PG DTP I1301 " ideal model delta sigma weight residual 139.87 120.49 19.38 1.00e+00 1.00e+00 3.75e+02 angle pdb=" PB DTP C1301 " pdb=" O3B DTP C1301 " pdb=" PG DTP C1301 " ideal model delta sigma weight residual 139.87 120.52 19.35 1.00e+00 1.00e+00 3.74e+02 angle pdb=" PB DTP M1301 " pdb=" O3B DTP M1301 " pdb=" PG DTP M1301 " ideal model delta sigma weight residual 139.87 120.53 19.34 1.00e+00 1.00e+00 3.74e+02 ... (remaining 108538 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.25: 43758 26.25 - 52.49: 3312 52.49 - 78.74: 935 78.74 - 104.98: 117 104.98 - 131.23: 7 Dihedral angle restraints: 48129 sinusoidal: 19707 harmonic: 28422 Sorted by residual: dihedral pdb=" CB CYS M 761 " pdb=" SG CYS M 761 " pdb=" SG CYS M 804 " pdb=" CB CYS M 804 " ideal model delta sinusoidal sigma weight residual 93.00 174.18 -81.18 1 1.00e+01 1.00e-02 8.13e+01 dihedral pdb=" CB CYS A 761 " pdb=" SG CYS A 761 " pdb=" SG CYS A 804 " pdb=" CB CYS A 804 " ideal model delta sinusoidal sigma weight residual 93.00 174.14 -81.14 1 1.00e+01 1.00e-02 8.12e+01 dihedral pdb=" CB CYS E 761 " pdb=" SG CYS E 761 " pdb=" SG CYS E 804 " pdb=" CB CYS E 804 " ideal model delta sinusoidal sigma weight residual 93.00 174.13 -81.13 1 1.00e+01 1.00e-02 8.12e+01 ... (remaining 48126 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 9998 0.096 - 0.192: 1594 0.192 - 0.288: 338 0.288 - 0.383: 49 0.383 - 0.479: 14 Chirality restraints: 11993 Sorted by residual: chirality pdb=" CA HIS A 153 " pdb=" N HIS A 153 " pdb=" C HIS A 153 " pdb=" CB HIS A 153 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.74e+00 chirality pdb=" CA HIS E 153 " pdb=" N HIS E 153 " pdb=" C HIS E 153 " pdb=" CB HIS E 153 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.74e+00 chirality pdb=" CA HIS G 153 " pdb=" N HIS G 153 " pdb=" C HIS G 153 " pdb=" CB HIS G 153 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.73e+00 ... (remaining 11990 not shown) Planarity restraints: 13790 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG T 52 " -0.677 9.50e-02 1.11e+02 3.04e-01 5.62e+01 pdb=" NE ARG T 52 " 0.040 2.00e-02 2.50e+03 pdb=" CZ ARG T 52 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG T 52 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG T 52 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE M 560 " -0.102 5.00e-02 4.00e+02 1.60e-01 4.09e+01 pdb=" N PRO M 561 " 0.277 5.00e-02 4.00e+02 pdb=" CA PRO M 561 " -0.096 5.00e-02 4.00e+02 pdb=" CD PRO M 561 " -0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 560 " 0.102 5.00e-02 4.00e+02 1.60e-01 4.08e+01 pdb=" N PRO C 561 " -0.276 5.00e-02 4.00e+02 pdb=" CA PRO C 561 " 0.096 5.00e-02 4.00e+02 pdb=" CD PRO C 561 " 0.079 5.00e-02 4.00e+02 ... (remaining 13787 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.17: 245 2.17 - 2.86: 31574 2.86 - 3.54: 114044 3.54 - 4.22: 189357 4.22 - 4.90: 312739 Nonbonded interactions: 647959 Sorted by model distance: nonbonded pdb=" OG SER A 141 " pdb=" CD1 LEU W 10 " model vdw 1.493 3.460 nonbonded pdb=" O TRP E 483 " pdb=" CB LEU E 487 " model vdw 1.816 3.440 nonbonded pdb=" O TRP C 483 " pdb=" CB LEU C 487 " model vdw 1.816 3.440 nonbonded pdb=" O TRP G 483 " pdb=" CB LEU G 487 " model vdw 1.816 3.440 nonbonded pdb=" O TRP A 483 " pdb=" CB LEU A 487 " model vdw 1.816 3.440 ... (remaining 647954 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 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = (chain 'W' and resid 1 through 91) selection = (chain 'X' and resid 1 through 91) } ncs_group { reference = (chain 'S' and (resid 1 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB )) or resid 29 through 95)) selection = (chain 'T' and (resid 1 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB )) or resid 29 through 95)) selection = (chain 'U' and (resid 1 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB )) or resid 29 through 95)) selection = (chain 'V' and (resid 1 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB )) or resid 29 through 95)) selection = chain 'Y' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.500 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: 0.050 Extract box with map and model: 12.700 Check model and map are aligned: 0.860 Set scattering table: 0.550 Process input model: 157.130 Find NCS groups from input model: 4.180 Set up NCS constraints: 0.680 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 180.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1510 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 0.217 80256 Z= 0.537 Angle : 1.345 19.482 108543 Z= 0.941 Chirality : 0.076 0.479 11993 Planarity : 0.010 0.304 13790 Dihedral : 19.341 131.230 29584 Min Nonbonded Distance : 1.493 Molprobity Statistics. All-atom Clashscore : 69.05 Ramachandran Plot: Outliers : 3.39 % Allowed : 7.12 % Favored : 89.49 % Rotamer Outliers : 16.86 % Cbeta Deviations : 0.08 % 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: -0.75 (0.09), residues: 9716 helix: 0.00 (0.09), residues: 3194 sheet: -1.64 (0.16), residues: 1148 loop : -0.43 (0.09), residues: 5374 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19432 Ramachandran restraints generated. 9716 Oldfield, 0 Emsley, 9716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19432 Ramachandran restraints generated. 9716 Oldfield, 0 Emsley, 9716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2773 residues out of total 8701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1467 poor density : 1306 time to evaluate : 7.108 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 1467 outliers final: 255 residues processed: 2444 average time/residue: 0.7988 time to fit residues: 3239.4574 Evaluate side-chains 1112 residues out of total 8701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 857 time to evaluate : 7.141 Switching outliers to nearest non-outliers 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: 255 outliers final: 8 residues processed: 255 average time/residue: 0.7124 time to fit residues: 324.2108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 816 optimal weight: 7.9990 chunk 732 optimal weight: 9.9990 chunk 406 optimal weight: 5.9990 chunk 250 optimal weight: 0.8980 chunk 494 optimal weight: 8.9990 chunk 391 optimal weight: 7.9990 chunk 757 optimal weight: 0.8980 chunk 293 optimal weight: 0.7980 chunk 460 optimal weight: 8.9990 chunk 564 optimal weight: 7.9990 chunk 878 optimal weight: 3.9990 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN ** A 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 257 GLN ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 ASN ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 583 GLN A 709 ASN A1163 HIS ** A1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 HIS B 52 ASN C 235 HIS ** C 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 420 ASN C 463 GLN ** C 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 545 GLN C 562 ASN ** C 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 583 GLN ** C 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 709 ASN ** C 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 933 ASN ** C1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 ASN E 134 ASN ** E 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 347 ASN E 429 ASN ** E 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 454 GLN E 463 GLN E 477 GLN E 545 GLN ** E 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 565 GLN E 583 GLN E 599 ASN E 709 ASN ** E 840 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 933 ASN ** E1044 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN G 183 HIS G 235 HIS G 311 HIS G 347 ASN ** G 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 449 ASN G 463 GLN ** G 490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 531 HIS ** G 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 933 ASN ** G1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 42 GLN I 183 HIS I 201 ASN I 235 HIS I 347 ASN I 429 ASN I 438 HIS I 457 HIS I 463 GLN I 477 GLN I 531 HIS I 545 GLN I 553 HIS ** I 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 583 GLN ** I 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 709 ASN ** I 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 933 ASN ** I1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1219 ASN ** I1237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 33 HIS K 153 HIS ** K 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 311 HIS K 347 ASN ** K 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 457 HIS K 463 GLN K 468 HIS K 477 GLN K 545 GLN ** K 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 583 GLN ** K 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 709 ASN K 840 HIS ** K 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 933 ASN K1001 GLN ** K1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 183 HIS ** M 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 347 ASN M 429 ASN ** M 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 454 GLN M 477 GLN M 553 HIS M 562 ASN M 565 GLN M 578 GLN M 583 GLN ** M 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 709 ASN M 737 ASN ** M 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 933 ASN M 942 HIS ** M 992 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 HIS O 45 ASN O 65 ASN P 45 ASN P 65 ASN ** P 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 45 ASN ** Q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 65 ASN Q 88 HIS R 11 GLN R 28 HIS R 45 ASN R 50 GLN R 65 ASN S 24 GLN S 44 GLN S 82 GLN T 44 GLN T 82 GLN U 21 GLN U 82 GLN V 44 GLN V 82 GLN W 7 ASN W 11 GLN W 45 ASN W 51 GLN X 7 ASN X 11 GLN X 51 GLN Y 44 GLN Total number of N/Q/H flips: 113 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1975 moved from start: 0.4856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 80256 Z= 0.280 Angle : 0.848 12.592 108543 Z= 0.437 Chirality : 0.048 0.308 11993 Planarity : 0.006 0.091 13790 Dihedral : 7.603 130.117 10480 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 24.81 Ramachandran Plot: Outliers : 0.81 % Allowed : 6.33 % Favored : 92.86 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.25 (0.08), residues: 9716 helix: -0.03 (0.08), residues: 3196 sheet: -1.59 (0.13), residues: 1512 loop : -1.04 (0.09), residues: 5008 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19432 Ramachandran restraints generated. 9716 Oldfield, 0 Emsley, 9716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19432 Ramachandran restraints generated. 9716 Oldfield, 0 Emsley, 9716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1030 residues out of total 8701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 995 time to evaluate : 7.101 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 35 outliers final: 3 residues processed: 1026 average time/residue: 0.7853 time to fit residues: 1361.8577 Evaluate side-chains 684 residues out of total 8701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 681 time to evaluate : 7.134 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.6985 time to fit residues: 13.6840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 488 optimal weight: 0.7980 chunk 272 optimal weight: 0.1980 chunk 730 optimal weight: 20.0000 chunk 597 optimal weight: 0.2980 chunk 242 optimal weight: 0.5980 chunk 879 optimal weight: 0.8980 chunk 950 optimal weight: 8.9990 chunk 783 optimal weight: 6.9990 chunk 872 optimal weight: 4.9990 chunk 299 optimal weight: 0.2980 chunk 705 optimal weight: 5.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN ** A 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 ASN ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 GLN A 477 GLN A 531 HIS A 974 GLN ** A1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1237 ASN B 12 GLN C 336 ASN C 347 ASN C 477 GLN C 521 HIS C 543 ASN C 562 ASN C 565 GLN C 640 GLN C 737 ASN C 748 HIS C 881 HIS ** C1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1237 ASN ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 ASN ** E 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 416 GLN E 420 ASN E 562 ASN E 706 HIS E 840 HIS E 881 HIS ** E1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 531 HIS ** G 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 545 GLN ** G 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 565 GLN ** G 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 881 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 336 ASN ** I 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 420 ASN I 452 GLN I 477 GLN I 583 GLN ** I 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 904 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 942 HIS I1095 HIS ** I1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1237 ASN ** K 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 201 ASN ** K 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 420 ASN K 438 HIS ** K 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 840 HIS K 904 GLN ** K1126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1237 ASN L 42 GLN M 235 HIS ** M 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 429 ASN ** M 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 452 GLN M 463 GLN M 477 GLN M 545 GLN M 562 ASN M 737 ASN M 904 GLN M1095 HIS ** M1176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M1237 ASN N 42 GLN P 51 GLN ** Q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 38 HIS ** U 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 12 HIS Total number of N/Q/H flips: 61 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1927 moved from start: 0.5570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 80256 Z= 0.198 Angle : 0.705 11.665 108543 Z= 0.360 Chirality : 0.043 0.234 11993 Planarity : 0.004 0.072 13790 Dihedral : 7.014 112.747 10480 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 19.86 Ramachandran Plot: Outliers : 0.67 % Allowed : 6.55 % Favored : 92.79 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.22 (0.08), residues: 9716 helix: 0.13 (0.09), residues: 3163 sheet: -1.65 (0.12), residues: 1589 loop : -1.08 (0.09), residues: 4964 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19432 Ramachandran restraints generated. 9716 Oldfield, 0 Emsley, 9716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19432 Ramachandran restraints generated. 9716 Oldfield, 0 Emsley, 9716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 888 residues out of total 8701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 879 time to evaluate : 7.169 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 9 outliers final: 2 residues processed: 886 average time/residue: 0.7645 time to fit residues: 1161.7556 Evaluate side-chains 660 residues out of total 8701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 658 time to evaluate : 7.143 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.5638 time to fit residues: 12.1705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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-1.21rc1-4953/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: 72.887 > 50: distance: 34 - 52: 33.250 distance: 38 - 60: 31.962 distance: 47 - 52: 33.657 distance: 53 - 54: 40.543 distance: 53 - 56: 54.083 distance: 54 - 55: 41.461 distance: 54 - 60: 66.338 distance: 56 - 57: 53.968 distance: 57 - 58: 58.075 distance: 57 - 59: 55.292 distance: 60 - 61: 35.452 distance: 61 - 64: 40.778 distance: 62 - 63: 57.513 distance: 62 - 66: 40.813 distance: 64 - 65: 63.439 distance: 67 - 68: 41.482 distance: 67 - 70: 6.670 distance: 68 - 69: 44.401 distance: 68 - 77: 42.103 distance: 70 - 71: 55.107 distance: 71 - 72: 38.861 distance: 72 - 73: 42.561 distance: 73 - 74: 43.251 distance: 74 - 75: 40.892 distance: 74 - 76: 18.587 distance: 77 - 78: 40.623 distance: 78 - 79: 54.165 distance: 78 - 81: 53.799 distance: 79 - 80: 45.466 distance: 79 - 86: 70.032 distance: 81 - 82: 34.666 distance: 82 - 83: 47.974 distance: 83 - 84: 45.615 distance: 83 - 85: 46.505 distance: 87 - 90: 49.961 distance: 88 - 89: 67.406 distance: 90 - 91: 16.364 distance: 91 - 92: 56.191 distance: 91 - 93: 39.386 distance: 94 - 95: 57.308 distance: 95 - 96: 40.512 distance: 95 - 98: 48.053 distance: 96 - 97: 57.339 distance: 96 - 105: 34.963 distance: 98 - 99: 27.748 distance: 99 - 100: 49.832 distance: 99 - 101: 38.236 distance: 100 - 102: 27.535 distance: 101 - 103: 35.086 distance: 102 - 104: 41.091 distance: 103 - 104: 56.926 distance: 105 - 106: 47.772 distance: 106 - 107: 49.800 distance: 106 - 109: 35.646 distance: 107 - 108: 68.506 distance: 109 - 110: 60.576 distance: 110 - 111: 43.082 distance: 111 - 112: 16.696 distance: 112 - 113: 47.741 distance: 113 - 114: 40.478 distance: 113 - 115: 27.161 distance: 116 - 122: 44.743 distance: 117 - 118: 43.894 distance: 117 - 120: 56.763 distance: 118 - 119: 51.847 distance: 118 - 123: 42.821 distance: 119 - 149: 30.792 distance: 120 - 121: 57.557 distance: 121 - 122: 48.969 distance: 123 - 124: 5.661 distance: 124 - 125: 47.337 distance: 124 - 127: 51.832 distance: 125 - 126: 35.162 distance: 125 - 133: 12.006 distance: 126 - 158: 19.376 distance: 127 - 128: 56.102 distance: 128 - 129: 68.945 distance: 128 - 130: 56.796 distance: 129 - 131: 56.619 distance: 130 - 132: 50.278 distance: 131 - 132: 39.337 distance: 133 - 134: 28.428 distance: 134 - 135: 49.419 distance: 134 - 137: 41.687 distance: 135 - 136: 38.524 distance: 135 - 141: 26.636 distance: 136 - 165: 31.255 distance: 137 - 138: 35.690 distance: 138 - 139: 23.082 distance: 139 - 140: 18.311