Starting phenix.real_space_refine on Wed Mar 20 09:11:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rw6_10033/03_2024/6rw6_10033.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rw6_10033/03_2024/6rw6_10033.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rw6_10033/03_2024/6rw6_10033.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rw6_10033/03_2024/6rw6_10033.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rw6_10033/03_2024/6rw6_10033.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rw6_10033/03_2024/6rw6_10033.pdb" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 305 5.16 5 C 62425 2.51 5 N 16785 2.21 5 O 19130 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 69": "NH1" <-> "NH2" Residue "A ARG 99": "NH1" <-> "NH2" Residue "A TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 124": "NH1" <-> "NH2" Residue "A ARG 142": "NH1" <-> "NH2" Residue "A ARG 208": "NH1" <-> "NH2" Residue "A TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 329": "NH1" <-> "NH2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "A ARG 354": "NH1" <-> "NH2" Residue "A ARG 412": "NH1" <-> "NH2" Residue "A ARG 462": "NH1" <-> "NH2" Residue "A ARG 487": "NH1" <-> "NH2" Residue "A ARG 553": "NH1" <-> "NH2" Residue "A PHE 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 952": "NH1" <-> "NH2" Residue "A ARG 1027": "NH1" <-> "NH2" Residue "A ARG 1050": "NH1" <-> "NH2" Residue "A TYR 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1195": "NH1" <-> "NH2" Residue "A ARG 1204": "NH1" <-> "NH2" Residue "A ARG 1287": "NH1" <-> "NH2" Residue "A ARG 1319": "NH1" <-> "NH2" Residue "A TYR 1410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1426": "NH1" <-> "NH2" Residue "A TYR 1430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1443": "NH1" <-> "NH2" Residue "A TYR 1530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1602": "NH1" <-> "NH2" Residue "A ARG 1659": "NH1" <-> "NH2" Residue "A TYR 1664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1727": "NH1" <-> "NH2" Residue "A PHE 1760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1855": "NH1" <-> "NH2" Residue "A TYR 1868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1873": "NH1" <-> "NH2" Residue "A ARG 1906": "NH1" <-> "NH2" Residue "A ARG 1927": "NH1" <-> "NH2" Residue "A ARG 2046": "NH1" <-> "NH2" Residue "A ARG 2189": "NH1" <-> "NH2" Residue "A ARG 2217": "NH1" <-> "NH2" Residue "A ARG 2255": "NH1" <-> "NH2" Residue "A ARG 2410": "NH1" <-> "NH2" Residue "A ARG 2411": "NH1" <-> "NH2" Residue "B ARG 69": "NH1" <-> "NH2" Residue "B ARG 99": "NH1" <-> "NH2" Residue "B TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 124": "NH1" <-> "NH2" Residue "B ARG 142": "NH1" <-> "NH2" Residue "B ARG 208": "NH1" <-> "NH2" Residue "B TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 329": "NH1" <-> "NH2" Residue "B ARG 332": "NH1" <-> "NH2" Residue "B ARG 354": "NH1" <-> "NH2" Residue "B ARG 412": "NH1" <-> "NH2" Residue "B ARG 462": "NH1" <-> "NH2" Residue "B ARG 487": "NH1" <-> "NH2" Residue "B ARG 553": "NH1" <-> "NH2" Residue "B PHE 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 952": "NH1" <-> "NH2" Residue "B ARG 1027": "NH1" <-> "NH2" Residue "B ARG 1050": "NH1" <-> "NH2" Residue "B TYR 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1195": "NH1" <-> "NH2" Residue "B ARG 1204": "NH1" <-> "NH2" Residue "B ARG 1287": "NH1" <-> "NH2" Residue "B ARG 1319": "NH1" <-> "NH2" Residue "B TYR 1410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1426": "NH1" <-> "NH2" Residue "B TYR 1430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1443": "NH1" <-> "NH2" Residue "B TYR 1530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1602": "NH1" <-> "NH2" Residue "B ARG 1659": "NH1" <-> "NH2" Residue "B TYR 1664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1727": "NH1" <-> "NH2" Residue "B PHE 1760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1855": "NH1" <-> "NH2" Residue "B TYR 1868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1873": "NH1" <-> "NH2" Residue "B ARG 1906": "NH1" <-> "NH2" Residue "B ARG 1927": "NH1" <-> "NH2" Residue "B ARG 2046": "NH1" <-> "NH2" Residue "B ARG 2189": "NH1" <-> "NH2" Residue "B ARG 2217": "NH1" <-> "NH2" Residue "B ARG 2255": "NH1" <-> "NH2" Residue "B ARG 2410": "NH1" <-> "NH2" Residue "B ARG 2411": "NH1" <-> "NH2" Residue "C ARG 69": "NH1" <-> "NH2" Residue "C ARG 99": "NH1" <-> "NH2" Residue "C TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 124": "NH1" <-> "NH2" Residue "C ARG 142": "NH1" <-> "NH2" Residue "C ARG 208": "NH1" <-> "NH2" Residue "C TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 329": "NH1" <-> "NH2" Residue "C ARG 332": "NH1" <-> "NH2" Residue "C ARG 354": "NH1" <-> "NH2" Residue "C ARG 412": "NH1" <-> "NH2" Residue "C ARG 462": "NH1" <-> "NH2" Residue "C ARG 487": "NH1" <-> "NH2" Residue "C ARG 553": "NH1" <-> "NH2" Residue "C PHE 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 952": "NH1" <-> "NH2" Residue "C ARG 1027": "NH1" <-> "NH2" Residue "C ARG 1050": "NH1" <-> "NH2" Residue "C TYR 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1195": "NH1" <-> "NH2" Residue "C ARG 1204": "NH1" <-> "NH2" Residue "C ARG 1287": "NH1" <-> "NH2" Residue "C ARG 1319": "NH1" <-> "NH2" Residue "C TYR 1410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1426": "NH1" <-> "NH2" Residue "C TYR 1430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1443": "NH1" <-> "NH2" Residue "C TYR 1530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1602": "NH1" <-> "NH2" Residue "C ARG 1659": "NH1" <-> "NH2" Residue "C TYR 1664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1727": "NH1" <-> "NH2" Residue "C PHE 1760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1855": "NH1" <-> "NH2" Residue "C TYR 1868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1873": "NH1" <-> "NH2" Residue "C ARG 1906": "NH1" <-> "NH2" Residue "C ARG 1927": "NH1" <-> "NH2" Residue "C ARG 2046": "NH1" <-> "NH2" Residue "C ARG 2189": "NH1" <-> "NH2" Residue "C ARG 2217": "NH1" <-> "NH2" Residue "C ARG 2255": "NH1" <-> "NH2" Residue "C ARG 2410": "NH1" <-> "NH2" Residue "C ARG 2411": "NH1" <-> "NH2" Residue "D ARG 69": "NH1" <-> "NH2" Residue "D ARG 99": "NH1" <-> "NH2" Residue "D TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 124": "NH1" <-> "NH2" Residue "D ARG 142": "NH1" <-> "NH2" Residue "D ARG 208": "NH1" <-> "NH2" Residue "D TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 329": "NH1" <-> "NH2" Residue "D ARG 332": "NH1" <-> "NH2" Residue "D ARG 354": "NH1" <-> "NH2" Residue "D ARG 412": "NH1" <-> "NH2" Residue "D ARG 462": "NH1" <-> "NH2" Residue "D ARG 487": "NH1" <-> "NH2" Residue "D ARG 553": "NH1" <-> "NH2" Residue "D PHE 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 952": "NH1" <-> "NH2" Residue "D ARG 1027": "NH1" <-> "NH2" Residue "D ARG 1050": "NH1" <-> "NH2" Residue "D TYR 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1195": "NH1" <-> "NH2" Residue "D ARG 1204": "NH1" <-> "NH2" Residue "D ARG 1287": "NH1" <-> "NH2" Residue "D ARG 1319": "NH1" <-> "NH2" Residue "D TYR 1410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1426": "NH1" <-> "NH2" Residue "D TYR 1430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1443": "NH1" <-> "NH2" Residue "D TYR 1530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1602": "NH1" <-> "NH2" Residue "D ARG 1659": "NH1" <-> "NH2" Residue "D TYR 1664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1727": "NH1" <-> "NH2" Residue "D PHE 1760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1855": "NH1" <-> "NH2" Residue "D TYR 1868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1873": "NH1" <-> "NH2" Residue "D ARG 1906": "NH1" <-> "NH2" Residue "D ARG 1927": "NH1" <-> "NH2" Residue "D ARG 2046": "NH1" <-> "NH2" Residue "D ARG 2189": "NH1" <-> "NH2" Residue "D ARG 2217": "NH1" <-> "NH2" Residue "D ARG 2255": "NH1" <-> "NH2" Residue "D ARG 2410": "NH1" <-> "NH2" Residue "D ARG 2411": "NH1" <-> "NH2" Residue "E ARG 69": "NH1" <-> "NH2" Residue "E ARG 99": "NH1" <-> "NH2" Residue "E TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 124": "NH1" <-> "NH2" Residue "E ARG 142": "NH1" <-> "NH2" Residue "E ARG 208": "NH1" <-> "NH2" Residue "E TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 329": "NH1" <-> "NH2" Residue "E ARG 332": "NH1" <-> "NH2" Residue "E ARG 354": "NH1" <-> "NH2" Residue "E ARG 412": "NH1" <-> "NH2" Residue "E ARG 462": "NH1" <-> "NH2" Residue "E ARG 487": "NH1" <-> "NH2" Residue "E ARG 553": "NH1" <-> "NH2" Residue "E PHE 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 952": "NH1" <-> "NH2" Residue "E ARG 1027": "NH1" <-> "NH2" Residue "E ARG 1050": "NH1" <-> "NH2" Residue "E TYR 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1195": "NH1" <-> "NH2" Residue "E ARG 1204": "NH1" <-> "NH2" Residue "E ARG 1287": "NH1" <-> "NH2" Residue "E ARG 1319": "NH1" <-> "NH2" Residue "E TYR 1410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1426": "NH1" <-> "NH2" Residue "E TYR 1430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1443": "NH1" <-> "NH2" Residue "E TYR 1530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1602": "NH1" <-> "NH2" Residue "E ARG 1659": "NH1" <-> "NH2" Residue "E TYR 1664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1727": "NH1" <-> "NH2" Residue "E PHE 1760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1855": "NH1" <-> "NH2" Residue "E TYR 1868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1873": "NH1" <-> "NH2" Residue "E ARG 1906": "NH1" <-> "NH2" Residue "E ARG 1927": "NH1" <-> "NH2" Residue "E ARG 2046": "NH1" <-> "NH2" Residue "E ARG 2189": "NH1" <-> "NH2" Residue "E ARG 2217": "NH1" <-> "NH2" Residue "E ARG 2255": "NH1" <-> "NH2" Residue "E ARG 2410": "NH1" <-> "NH2" Residue "E ARG 2411": "NH1" <-> "NH2" Time to flip residues: 0.22s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 98645 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 19729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2485, 19729 Classifications: {'peptide': 2485} Link IDs: {'PCIS': 3, 'PTRANS': 86, 'TRANS': 2395} Chain breaks: 2 Chain: "B" Number of atoms: 19729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2485, 19729 Classifications: {'peptide': 2485} Link IDs: {'PCIS': 3, 'PTRANS': 86, 'TRANS': 2395} Chain breaks: 2 Chain: "C" Number of atoms: 19729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2485, 19729 Classifications: {'peptide': 2485} Link IDs: {'PCIS': 3, 'PTRANS': 86, 'TRANS': 2395} Chain breaks: 2 Chain: "D" Number of atoms: 19729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2485, 19729 Classifications: {'peptide': 2485} Link IDs: {'PCIS': 3, 'PTRANS': 86, 'TRANS': 2395} Chain breaks: 2 Chain: "E" Number of atoms: 19729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2485, 19729 Classifications: {'peptide': 2485} Link IDs: {'PCIS': 3, 'PTRANS': 86, 'TRANS': 2395} Chain breaks: 2 Time building chain proxies: 38.55, per 1000 atoms: 0.39 Number of scatterers: 98645 At special positions: 0 Unit cell: (192.66, 191.52, 259.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 305 16.00 O 19130 8.00 N 16785 7.00 C 62425 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 29.30 Conformation dependent library (CDL) restraints added in 14.1 seconds 24790 Ramachandran restraints generated. 12395 Oldfield, 0 Emsley, 12395 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 23560 Finding SS restraints... Secondary structure from input PDB file: 470 helices and 95 sheets defined 49.9% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 11.18 Creating SS restraints... Processing helix chain 'A' and resid 28 through 36 Processing helix chain 'A' and resid 41 through 70 Processing helix chain 'A' and resid 71 through 76 removed outlier: 3.922A pdb=" N ASN A 76 " --> pdb=" O PRO A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 81 removed outlier: 3.785A pdb=" N LEU A 80 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA A 81 " --> pdb=" O VAL A 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 77 through 81' Processing helix chain 'A' and resid 85 through 97 removed outlier: 3.624A pdb=" N LEU A 89 " --> pdb=" O PRO A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 102 Processing helix chain 'A' and resid 114 through 127 Processing helix chain 'A' and resid 137 through 142 Processing helix chain 'A' and resid 151 through 157 Processing helix chain 'A' and resid 161 through 178 Processing helix chain 'A' and resid 181 through 190 removed outlier: 3.576A pdb=" N VAL A 185 " --> pdb=" O ASN A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 215 removed outlier: 3.523A pdb=" N VAL A 210 " --> pdb=" O ASN A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 224 Processing helix chain 'A' and resid 224 through 231 removed outlier: 3.578A pdb=" N ALA A 228 " --> pdb=" O SER A 224 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET A 231 " --> pdb=" O ILE A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 241 removed outlier: 3.946A pdb=" N GLY A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE A 239 " --> pdb=" O SER A 235 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASN A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 253 removed outlier: 3.548A pdb=" N GLU A 253 " --> pdb=" O ASN A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 269 Processing helix chain 'A' and resid 272 through 277 Processing helix chain 'A' and resid 278 through 286 removed outlier: 3.555A pdb=" N ARG A 284 " --> pdb=" O GLU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 297 removed outlier: 3.718A pdb=" N SER A 294 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 403 Processing helix chain 'A' and resid 433 through 451 Processing helix chain 'A' and resid 453 through 465 Processing helix chain 'A' and resid 471 through 489 removed outlier: 3.524A pdb=" N LYS A 477 " --> pdb=" O ASP A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 499 removed outlier: 3.773A pdb=" N ILE A 497 " --> pdb=" O GLU A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 520 Processing helix chain 'A' and resid 523 through 527 removed outlier: 3.679A pdb=" N GLY A 526 " --> pdb=" O LEU A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 556 removed outlier: 3.671A pdb=" N THR A 549 " --> pdb=" O ASP A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 570 Processing helix chain 'A' and resid 581 through 597 Processing helix chain 'A' and resid 601 through 613 Processing helix chain 'A' and resid 623 through 645 Processing helix chain 'A' and resid 647 through 656 removed outlier: 3.664A pdb=" N MET A 654 " --> pdb=" O GLN A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 678 Processing helix chain 'A' and resid 687 through 700 Proline residue: A 694 - end of helix Processing helix chain 'A' and resid 704 through 719 removed outlier: 3.578A pdb=" N ALA A 708 " --> pdb=" O SER A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 738 removed outlier: 3.562A pdb=" N THR A 736 " --> pdb=" O ASP A 732 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR A 738 " --> pdb=" O LEU A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 770 removed outlier: 3.630A pdb=" N ILE A 752 " --> pdb=" O THR A 748 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A 770 " --> pdb=" O TYR A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 782 Processing helix chain 'A' and resid 783 through 787 Processing helix chain 'A' and resid 797 through 815 removed outlier: 3.683A pdb=" N MET A 803 " --> pdb=" O LEU A 799 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY A 815 " --> pdb=" O VAL A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 827 Processing helix chain 'A' and resid 831 through 840 Processing helix chain 'A' and resid 842 through 856 removed outlier: 3.582A pdb=" N LEU A 846 " --> pdb=" O ASP A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 888 Processing helix chain 'A' and resid 890 through 899 Processing helix chain 'A' and resid 911 through 924 removed outlier: 3.501A pdb=" N TRP A 915 " --> pdb=" O THR A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 954 removed outlier: 3.570A pdb=" N ALA A 944 " --> pdb=" O GLU A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 972 Processing helix chain 'A' and resid 984 through 1001 Processing helix chain 'A' and resid 1009 through 1014 Processing helix chain 'A' and resid 1015 through 1020 Processing helix chain 'A' and resid 1027 through 1040 removed outlier: 4.003A pdb=" N VAL A1038 " --> pdb=" O VAL A1034 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N TYR A1039 " --> pdb=" O SER A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1041 through 1044 Processing helix chain 'A' and resid 1054 through 1064 Processing helix chain 'A' and resid 1070 through 1090 removed outlier: 3.573A pdb=" N VAL A1088 " --> pdb=" O SER A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1131 No H-bonds generated for 'chain 'A' and resid 1129 through 1131' Processing helix chain 'A' and resid 1137 through 1141 removed outlier: 3.661A pdb=" N TRP A1141 " --> pdb=" O ALA A1138 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1224 Processing helix chain 'A' and resid 1255 through 1261 removed outlier: 3.515A pdb=" N LYS A1260 " --> pdb=" O ASP A1257 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASN A1261 " --> pdb=" O SER A1258 " (cutoff:3.500A) Processing helix chain 'A' and resid 1279 through 1289 removed outlier: 4.011A pdb=" N VAL A1285 " --> pdb=" O GLU A1281 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR A1286 " --> pdb=" O GLN A1282 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN A1289 " --> pdb=" O VAL A1285 " (cutoff:3.500A) Processing helix chain 'A' and resid 1290 through 1294 Processing helix chain 'A' and resid 1325 through 1329 removed outlier: 3.690A pdb=" N LEU A1329 " --> pdb=" O ASP A1326 " (cutoff:3.500A) Processing helix chain 'A' and resid 1366 through 1379 removed outlier: 3.531A pdb=" N MET A1375 " --> pdb=" O GLN A1371 " (cutoff:3.500A) Processing helix chain 'A' and resid 1463 through 1468 removed outlier: 3.650A pdb=" N LYS A1468 " --> pdb=" O ASP A1465 " (cutoff:3.500A) Processing helix chain 'A' and resid 1494 through 1496 No H-bonds generated for 'chain 'A' and resid 1494 through 1496' Processing helix chain 'A' and resid 1513 through 1517 Processing helix chain 'A' and resid 1608 through 1617 removed outlier: 4.078A pdb=" N VAL A1614 " --> pdb=" O ALA A1610 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ALA A1615 " --> pdb=" O ARG A1611 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG A1616 " --> pdb=" O GLN A1612 " (cutoff:3.500A) Processing helix chain 'A' and resid 1620 through 1625 Processing helix chain 'A' and resid 1628 through 1631 Processing helix chain 'A' and resid 1651 through 1656 removed outlier: 3.531A pdb=" N GLY A1656 " --> pdb=" O LEU A1652 " (cutoff:3.500A) Processing helix chain 'A' and resid 1764 through 1773 Processing helix chain 'A' and resid 1773 through 1786 Processing helix chain 'A' and resid 1788 through 1797 removed outlier: 3.541A pdb=" N ARG A1794 " --> pdb=" O ASP A1790 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TRP A1795 " --> pdb=" O GLU A1791 " (cutoff:3.500A) Processing helix chain 'A' and resid 1818 through 1823 Processing helix chain 'A' and resid 1836 through 1844 Processing helix chain 'A' and resid 1845 through 1870 removed outlier: 3.755A pdb=" N GLN A1870 " --> pdb=" O HIS A1866 " (cutoff:3.500A) Processing helix chain 'A' and resid 1872 through 1891 removed outlier: 3.546A pdb=" N ASN A1877 " --> pdb=" O ARG A1873 " (cutoff:3.500A) Processing helix chain 'A' and resid 1906 through 1911 Processing helix chain 'A' and resid 1912 through 1927 Processing helix chain 'A' and resid 1943 through 1947 removed outlier: 3.769A pdb=" N LEU A1947 " --> pdb=" O LEU A1944 " (cutoff:3.500A) Processing helix chain 'A' and resid 1953 through 1972 removed outlier: 3.557A pdb=" N TYR A1959 " --> pdb=" O VAL A1955 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TRP A1960 " --> pdb=" O MET A1956 " (cutoff:3.500A) Processing helix chain 'A' and resid 2018 through 2105 removed outlier: 4.052A pdb=" N LEU A2065 " --> pdb=" O ALA A2061 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N THR A2066 " --> pdb=" O GLU A2062 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN A2067 " --> pdb=" O LEU A2063 " (cutoff:3.500A) Processing helix chain 'A' and resid 2108 through 2122 Processing helix chain 'A' and resid 2124 through 2139 Processing helix chain 'A' and resid 2155 through 2244 Processing helix chain 'A' and resid 2247 through 2284 removed outlier: 3.576A pdb=" N TYR A2251 " --> pdb=" O ASN A2247 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A2268 " --> pdb=" O GLN A2264 " (cutoff:3.500A) Processing helix chain 'A' and resid 2298 through 2302 Processing helix chain 'A' and resid 2305 through 2325 Processing helix chain 'A' and resid 2337 through 2343 Processing helix chain 'A' and resid 2345 through 2349 Processing helix chain 'A' and resid 2352 through 2361 removed outlier: 3.746A pdb=" N ASP A2358 " --> pdb=" O ALA A2354 " (cutoff:3.500A) Processing helix chain 'A' and resid 2394 through 2402 removed outlier: 3.555A pdb=" N LYS A2397 " --> pdb=" O ALA A2394 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ILE A2398 " --> pdb=" O ASP A2395 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ARG A2399 " --> pdb=" O LEU A2396 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU A2400 " --> pdb=" O LYS A2397 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TYR A2402 " --> pdb=" O ARG A2399 " (cutoff:3.500A) Processing helix chain 'A' and resid 2497 through 2504 removed outlier: 3.574A pdb=" N LEU A2501 " --> pdb=" O GLN A2497 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR A2503 " --> pdb=" O THR A2499 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 36 Processing helix chain 'B' and resid 41 through 70 Processing helix chain 'B' and resid 71 through 76 removed outlier: 3.923A pdb=" N ASN B 76 " --> pdb=" O PRO B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 81 removed outlier: 3.787A pdb=" N LEU B 80 " --> pdb=" O ALA B 77 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA B 81 " --> pdb=" O VAL B 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 77 through 81' Processing helix chain 'B' and resid 85 through 97 removed outlier: 3.624A pdb=" N LEU B 89 " --> pdb=" O PRO B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 102 Processing helix chain 'B' and resid 114 through 127 Processing helix chain 'B' and resid 137 through 142 Processing helix chain 'B' and resid 151 through 157 Processing helix chain 'B' and resid 161 through 178 Processing helix chain 'B' and resid 181 through 190 removed outlier: 3.576A pdb=" N VAL B 185 " --> pdb=" O ASN B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 215 removed outlier: 3.524A pdb=" N VAL B 210 " --> pdb=" O ASN B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 224 Processing helix chain 'B' and resid 224 through 231 removed outlier: 3.578A pdb=" N ALA B 228 " --> pdb=" O SER B 224 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N MET B 231 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 241 removed outlier: 3.945A pdb=" N GLY B 238 " --> pdb=" O ALA B 234 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE B 239 " --> pdb=" O SER B 235 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASN B 240 " --> pdb=" O LEU B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 253 removed outlier: 3.550A pdb=" N GLU B 253 " --> pdb=" O ASN B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 269 Processing helix chain 'B' and resid 272 through 277 Processing helix chain 'B' and resid 278 through 286 removed outlier: 3.555A pdb=" N ARG B 284 " --> pdb=" O GLU B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 297 removed outlier: 3.718A pdb=" N SER B 294 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 403 Processing helix chain 'B' and resid 433 through 451 Processing helix chain 'B' and resid 453 through 465 Processing helix chain 'B' and resid 471 through 489 removed outlier: 3.526A pdb=" N LYS B 477 " --> pdb=" O ASP B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 499 removed outlier: 3.773A pdb=" N ILE B 497 " --> pdb=" O GLU B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 520 Processing helix chain 'B' and resid 523 through 527 removed outlier: 3.679A pdb=" N GLY B 526 " --> pdb=" O LEU B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 556 removed outlier: 3.669A pdb=" N THR B 549 " --> pdb=" O ASP B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 570 Processing helix chain 'B' and resid 581 through 597 Processing helix chain 'B' and resid 601 through 613 Processing helix chain 'B' and resid 623 through 645 Processing helix chain 'B' and resid 647 through 656 removed outlier: 3.663A pdb=" N MET B 654 " --> pdb=" O GLN B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 678 Processing helix chain 'B' and resid 687 through 700 Proline residue: B 694 - end of helix Processing helix chain 'B' and resid 704 through 719 removed outlier: 3.576A pdb=" N ALA B 708 " --> pdb=" O SER B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 726 through 738 removed outlier: 3.560A pdb=" N THR B 736 " --> pdb=" O ASP B 732 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR B 738 " --> pdb=" O LEU B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 770 removed outlier: 3.630A pdb=" N ILE B 752 " --> pdb=" O THR B 748 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY B 770 " --> pdb=" O TYR B 766 " (cutoff:3.500A) Processing helix chain 'B' and resid 772 through 782 Processing helix chain 'B' and resid 783 through 787 Processing helix chain 'B' and resid 797 through 815 removed outlier: 3.682A pdb=" N MET B 803 " --> pdb=" O LEU B 799 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY B 815 " --> pdb=" O VAL B 811 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 827 Processing helix chain 'B' and resid 831 through 840 Processing helix chain 'B' and resid 842 through 856 removed outlier: 3.583A pdb=" N LEU B 846 " --> pdb=" O ASP B 842 " (cutoff:3.500A) Processing helix chain 'B' and resid 870 through 888 Processing helix chain 'B' and resid 890 through 899 Processing helix chain 'B' and resid 911 through 924 removed outlier: 3.502A pdb=" N TRP B 915 " --> pdb=" O THR B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 954 removed outlier: 3.571A pdb=" N ALA B 944 " --> pdb=" O GLU B 940 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 972 Processing helix chain 'B' and resid 984 through 1001 Processing helix chain 'B' and resid 1009 through 1014 Processing helix chain 'B' and resid 1015 through 1020 Processing helix chain 'B' and resid 1027 through 1040 removed outlier: 4.003A pdb=" N VAL B1038 " --> pdb=" O VAL B1034 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N TYR B1039 " --> pdb=" O SER B1035 " (cutoff:3.500A) Processing helix chain 'B' and resid 1041 through 1044 Processing helix chain 'B' and resid 1054 through 1064 Processing helix chain 'B' and resid 1070 through 1090 removed outlier: 3.575A pdb=" N VAL B1088 " --> pdb=" O SER B1084 " (cutoff:3.500A) Processing helix chain 'B' and resid 1129 through 1131 No H-bonds generated for 'chain 'B' and resid 1129 through 1131' Processing helix chain 'B' and resid 1137 through 1141 removed outlier: 3.661A pdb=" N TRP B1141 " --> pdb=" O ALA B1138 " (cutoff:3.500A) Processing helix chain 'B' and resid 1217 through 1224 Processing helix chain 'B' and resid 1255 through 1261 removed outlier: 3.516A pdb=" N LYS B1260 " --> pdb=" O ASP B1257 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASN B1261 " --> pdb=" O SER B1258 " (cutoff:3.500A) Processing helix chain 'B' and resid 1279 through 1289 removed outlier: 4.009A pdb=" N VAL B1285 " --> pdb=" O GLU B1281 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR B1286 " --> pdb=" O GLN B1282 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN B1289 " --> pdb=" O VAL B1285 " (cutoff:3.500A) Processing helix chain 'B' and resid 1290 through 1294 Processing helix chain 'B' and resid 1325 through 1329 removed outlier: 3.688A pdb=" N LEU B1329 " --> pdb=" O ASP B1326 " (cutoff:3.500A) Processing helix chain 'B' and resid 1366 through 1379 removed outlier: 3.531A pdb=" N MET B1375 " --> pdb=" O GLN B1371 " (cutoff:3.500A) Processing helix chain 'B' and resid 1463 through 1468 removed outlier: 3.648A pdb=" N LYS B1468 " --> pdb=" O ASP B1465 " (cutoff:3.500A) Processing helix chain 'B' and resid 1494 through 1496 No H-bonds generated for 'chain 'B' and resid 1494 through 1496' Processing helix chain 'B' and resid 1513 through 1517 Processing helix chain 'B' and resid 1608 through 1617 removed outlier: 4.078A pdb=" N VAL B1614 " --> pdb=" O ALA B1610 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ALA B1615 " --> pdb=" O ARG B1611 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARG B1616 " --> pdb=" O GLN B1612 " (cutoff:3.500A) Processing helix chain 'B' and resid 1620 through 1625 Processing helix chain 'B' and resid 1628 through 1631 Processing helix chain 'B' and resid 1651 through 1656 removed outlier: 3.531A pdb=" N GLY B1656 " --> pdb=" O LEU B1652 " (cutoff:3.500A) Processing helix chain 'B' and resid 1764 through 1773 Processing helix chain 'B' and resid 1773 through 1786 Processing helix chain 'B' and resid 1788 through 1797 removed outlier: 3.542A pdb=" N ARG B1794 " --> pdb=" O ASP B1790 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TRP B1795 " --> pdb=" O GLU B1791 " (cutoff:3.500A) Processing helix chain 'B' and resid 1818 through 1823 Processing helix chain 'B' and resid 1836 through 1844 Processing helix chain 'B' and resid 1845 through 1870 removed outlier: 3.755A pdb=" N GLN B1870 " --> pdb=" O HIS B1866 " (cutoff:3.500A) Processing helix chain 'B' and resid 1872 through 1891 removed outlier: 3.547A pdb=" N ASN B1877 " --> pdb=" O ARG B1873 " (cutoff:3.500A) Processing helix chain 'B' and resid 1906 through 1911 Processing helix chain 'B' and resid 1912 through 1927 Processing helix chain 'B' and resid 1943 through 1947 removed outlier: 3.768A pdb=" N LEU B1947 " --> pdb=" O LEU B1944 " (cutoff:3.500A) Processing helix chain 'B' and resid 1953 through 1972 removed outlier: 3.556A pdb=" N TYR B1959 " --> pdb=" O VAL B1955 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TRP B1960 " --> pdb=" O MET B1956 " (cutoff:3.500A) Processing helix chain 'B' and resid 2018 through 2105 removed outlier: 4.054A pdb=" N LEU B2065 " --> pdb=" O ALA B2061 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N THR B2066 " --> pdb=" O GLU B2062 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN B2067 " --> pdb=" O LEU B2063 " (cutoff:3.500A) Processing helix chain 'B' and resid 2108 through 2122 Processing helix chain 'B' and resid 2124 through 2139 Processing helix chain 'B' and resid 2155 through 2244 Processing helix chain 'B' and resid 2247 through 2284 removed outlier: 3.576A pdb=" N TYR B2251 " --> pdb=" O ASN B2247 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B2268 " --> pdb=" O GLN B2264 " (cutoff:3.500A) Processing helix chain 'B' and resid 2298 through 2302 Processing helix chain 'B' and resid 2305 through 2325 Processing helix chain 'B' and resid 2337 through 2343 Processing helix chain 'B' and resid 2345 through 2349 Processing helix chain 'B' and resid 2352 through 2361 removed outlier: 3.746A pdb=" N ASP B2358 " --> pdb=" O ALA B2354 " (cutoff:3.500A) Processing helix chain 'B' and resid 2394 through 2402 removed outlier: 3.557A pdb=" N LYS B2397 " --> pdb=" O ALA B2394 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE B2398 " --> pdb=" O ASP B2395 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ARG B2399 " --> pdb=" O LEU B2396 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU B2400 " --> pdb=" O LYS B2397 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TYR B2402 " --> pdb=" O ARG B2399 " (cutoff:3.500A) Processing helix chain 'B' and resid 2497 through 2504 removed outlier: 3.573A pdb=" N LEU B2501 " --> pdb=" O GLN B2497 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR B2503 " --> pdb=" O THR B2499 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 36 Processing helix chain 'C' and resid 41 through 70 Processing helix chain 'C' and resid 71 through 76 removed outlier: 3.924A pdb=" N ASN C 76 " --> pdb=" O PRO C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 81 removed outlier: 3.787A pdb=" N LEU C 80 " --> pdb=" O ALA C 77 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA C 81 " --> pdb=" O VAL C 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 77 through 81' Processing helix chain 'C' and resid 85 through 97 removed outlier: 3.622A pdb=" N LEU C 89 " --> pdb=" O PRO C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 102 Processing helix chain 'C' and resid 114 through 127 Processing helix chain 'C' and resid 137 through 142 Processing helix chain 'C' and resid 151 through 157 Processing helix chain 'C' and resid 161 through 178 Processing helix chain 'C' and resid 181 through 190 removed outlier: 3.575A pdb=" N VAL C 185 " --> pdb=" O ASN C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 215 removed outlier: 3.524A pdb=" N VAL C 210 " --> pdb=" O ASN C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 224 Processing helix chain 'C' and resid 224 through 231 removed outlier: 3.579A pdb=" N ALA C 228 " --> pdb=" O SER C 224 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET C 231 " --> pdb=" O ILE C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 241 removed outlier: 3.947A pdb=" N GLY C 238 " --> pdb=" O ALA C 234 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE C 239 " --> pdb=" O SER C 235 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASN C 240 " --> pdb=" O LEU C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 253 removed outlier: 3.548A pdb=" N GLU C 253 " --> pdb=" O ASN C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 269 Processing helix chain 'C' and resid 272 through 277 Processing helix chain 'C' and resid 278 through 286 removed outlier: 3.555A pdb=" N ARG C 284 " --> pdb=" O GLU C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 297 removed outlier: 3.718A pdb=" N SER C 294 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE C 296 " --> pdb=" O GLU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 403 Processing helix chain 'C' and resid 433 through 451 Processing helix chain 'C' and resid 453 through 465 Processing helix chain 'C' and resid 471 through 489 removed outlier: 3.525A pdb=" N LYS C 477 " --> pdb=" O ASP C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 499 removed outlier: 3.774A pdb=" N ILE C 497 " --> pdb=" O GLU C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 520 Processing helix chain 'C' and resid 523 through 527 removed outlier: 3.679A pdb=" N GLY C 526 " --> pdb=" O LEU C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 556 removed outlier: 3.670A pdb=" N THR C 549 " --> pdb=" O ASP C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 570 Processing helix chain 'C' and resid 581 through 598 removed outlier: 3.851A pdb=" N HIS C 598 " --> pdb=" O LEU C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 613 Processing helix chain 'C' and resid 623 through 645 Processing helix chain 'C' and resid 647 through 656 removed outlier: 3.664A pdb=" N MET C 654 " --> pdb=" O GLN C 650 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 678 Processing helix chain 'C' and resid 687 through 700 Proline residue: C 694 - end of helix Processing helix chain 'C' and resid 704 through 719 removed outlier: 3.577A pdb=" N ALA C 708 " --> pdb=" O SER C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 726 through 738 removed outlier: 3.563A pdb=" N THR C 736 " --> pdb=" O ASP C 732 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR C 738 " --> pdb=" O LEU C 734 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 770 removed outlier: 3.631A pdb=" N ILE C 752 " --> pdb=" O THR C 748 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY C 770 " --> pdb=" O TYR C 766 " (cutoff:3.500A) Processing helix chain 'C' and resid 772 through 782 Processing helix chain 'C' and resid 783 through 787 Processing helix chain 'C' and resid 797 through 815 removed outlier: 3.681A pdb=" N MET C 803 " --> pdb=" O LEU C 799 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY C 815 " --> pdb=" O VAL C 811 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 827 Processing helix chain 'C' and resid 831 through 840 Processing helix chain 'C' and resid 842 through 856 removed outlier: 3.582A pdb=" N LEU C 846 " --> pdb=" O ASP C 842 " (cutoff:3.500A) Processing helix chain 'C' and resid 870 through 888 Processing helix chain 'C' and resid 890 through 899 Processing helix chain 'C' and resid 911 through 924 removed outlier: 3.501A pdb=" N TRP C 915 " --> pdb=" O THR C 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 954 removed outlier: 3.571A pdb=" N ALA C 944 " --> pdb=" O GLU C 940 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 972 Processing helix chain 'C' and resid 984 through 1001 Processing helix chain 'C' and resid 1009 through 1014 Processing helix chain 'C' and resid 1015 through 1020 Processing helix chain 'C' and resid 1027 through 1040 removed outlier: 4.004A pdb=" N VAL C1038 " --> pdb=" O VAL C1034 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N TYR C1039 " --> pdb=" O SER C1035 " (cutoff:3.500A) Processing helix chain 'C' and resid 1041 through 1044 Processing helix chain 'C' and resid 1054 through 1064 Processing helix chain 'C' and resid 1070 through 1090 removed outlier: 3.575A pdb=" N VAL C1088 " --> pdb=" O SER C1084 " (cutoff:3.500A) Processing helix chain 'C' and resid 1129 through 1131 No H-bonds generated for 'chain 'C' and resid 1129 through 1131' Processing helix chain 'C' and resid 1137 through 1141 removed outlier: 3.662A pdb=" N TRP C1141 " --> pdb=" O ALA C1138 " (cutoff:3.500A) Processing helix chain 'C' and resid 1217 through 1224 Processing helix chain 'C' and resid 1255 through 1261 removed outlier: 3.514A pdb=" N LYS C1260 " --> pdb=" O ASP C1257 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASN C1261 " --> pdb=" O SER C1258 " (cutoff:3.500A) Processing helix chain 'C' and resid 1279 through 1289 removed outlier: 4.010A pdb=" N VAL C1285 " --> pdb=" O GLU C1281 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR C1286 " --> pdb=" O GLN C1282 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN C1289 " --> pdb=" O VAL C1285 " (cutoff:3.500A) Processing helix chain 'C' and resid 1290 through 1294 Processing helix chain 'C' and resid 1325 through 1329 removed outlier: 3.691A pdb=" N LEU C1329 " --> pdb=" O ASP C1326 " (cutoff:3.500A) Processing helix chain 'C' and resid 1366 through 1379 removed outlier: 3.531A pdb=" N MET C1375 " --> pdb=" O GLN C1371 " (cutoff:3.500A) Processing helix chain 'C' and resid 1463 through 1468 removed outlier: 3.647A pdb=" N LYS C1468 " --> pdb=" O ASP C1465 " (cutoff:3.500A) Processing helix chain 'C' and resid 1494 through 1496 No H-bonds generated for 'chain 'C' and resid 1494 through 1496' Processing helix chain 'C' and resid 1513 through 1517 Processing helix chain 'C' and resid 1608 through 1617 removed outlier: 4.079A pdb=" N VAL C1614 " --> pdb=" O ALA C1610 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ALA C1615 " --> pdb=" O ARG C1611 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG C1616 " --> pdb=" O GLN C1612 " (cutoff:3.500A) Processing helix chain 'C' and resid 1620 through 1625 Processing helix chain 'C' and resid 1628 through 1631 Processing helix chain 'C' and resid 1651 through 1656 removed outlier: 3.529A pdb=" N GLY C1656 " --> pdb=" O LEU C1652 " (cutoff:3.500A) Processing helix chain 'C' and resid 1764 through 1773 Processing helix chain 'C' and resid 1773 through 1786 Processing helix chain 'C' and resid 1788 through 1797 removed outlier: 3.540A pdb=" N ARG C1794 " --> pdb=" O ASP C1790 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TRP C1795 " --> pdb=" O GLU C1791 " (cutoff:3.500A) Processing helix chain 'C' and resid 1818 through 1823 Processing helix chain 'C' and resid 1836 through 1844 Processing helix chain 'C' and resid 1845 through 1870 removed outlier: 3.754A pdb=" N GLN C1870 " --> pdb=" O HIS C1866 " (cutoff:3.500A) Processing helix chain 'C' and resid 1872 through 1891 removed outlier: 3.546A pdb=" N ASN C1877 " --> pdb=" O ARG C1873 " (cutoff:3.500A) Processing helix chain 'C' and resid 1906 through 1911 Processing helix chain 'C' and resid 1912 through 1927 Processing helix chain 'C' and resid 1943 through 1947 removed outlier: 3.768A pdb=" N LEU C1947 " --> pdb=" O LEU C1944 " (cutoff:3.500A) Processing helix chain 'C' and resid 1953 through 1972 removed outlier: 3.557A pdb=" N TYR C1959 " --> pdb=" O VAL C1955 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N TRP C1960 " --> pdb=" O MET C1956 " (cutoff:3.500A) Processing helix chain 'C' and resid 2018 through 2105 removed outlier: 4.053A pdb=" N LEU C2065 " --> pdb=" O ALA C2061 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N THR C2066 " --> pdb=" O GLU C2062 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN C2067 " --> pdb=" O LEU C2063 " (cutoff:3.500A) Processing helix chain 'C' and resid 2108 through 2122 Processing helix chain 'C' and resid 2124 through 2139 Processing helix chain 'C' and resid 2155 through 2244 Processing helix chain 'C' and resid 2247 through 2284 removed outlier: 3.577A pdb=" N TYR C2251 " --> pdb=" O ASN C2247 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU C2268 " --> pdb=" O GLN C2264 " (cutoff:3.500A) Processing helix chain 'C' and resid 2298 through 2302 Processing helix chain 'C' and resid 2305 through 2325 Processing helix chain 'C' and resid 2337 through 2343 Processing helix chain 'C' and resid 2345 through 2349 Processing helix chain 'C' and resid 2352 through 2361 removed outlier: 3.745A pdb=" N ASP C2358 " --> pdb=" O ALA C2354 " (cutoff:3.500A) Processing helix chain 'C' and resid 2394 through 2402 removed outlier: 3.557A pdb=" N LYS C2397 " --> pdb=" O ALA C2394 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE C2398 " --> pdb=" O ASP C2395 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ARG C2399 " --> pdb=" O LEU C2396 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU C2400 " --> pdb=" O LYS C2397 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TYR C2402 " --> pdb=" O ARG C2399 " (cutoff:3.500A) Processing helix chain 'C' and resid 2497 through 2504 removed outlier: 3.573A pdb=" N LEU C2501 " --> pdb=" O GLN C2497 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR C2503 " --> pdb=" O THR C2499 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 36 Processing helix chain 'D' and resid 41 through 70 Processing helix chain 'D' and resid 71 through 76 removed outlier: 3.921A pdb=" N ASN D 76 " --> pdb=" O PRO D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 81 removed outlier: 3.785A pdb=" N LEU D 80 " --> pdb=" O ALA D 77 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA D 81 " --> pdb=" O VAL D 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 77 through 81' Processing helix chain 'D' and resid 85 through 97 removed outlier: 3.623A pdb=" N LEU D 89 " --> pdb=" O PRO D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 102 Processing helix chain 'D' and resid 114 through 127 Processing helix chain 'D' and resid 137 through 142 Processing helix chain 'D' and resid 151 through 157 Processing helix chain 'D' and resid 161 through 178 Processing helix chain 'D' and resid 181 through 190 removed outlier: 3.575A pdb=" N VAL D 185 " --> pdb=" O ASN D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 215 removed outlier: 3.525A pdb=" N VAL D 210 " --> pdb=" O ASN D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 224 Processing helix chain 'D' and resid 224 through 231 removed outlier: 3.580A pdb=" N ALA D 228 " --> pdb=" O SER D 224 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N MET D 231 " --> pdb=" O ILE D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 241 removed outlier: 3.947A pdb=" N GLY D 238 " --> pdb=" O ALA D 234 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE D 239 " --> pdb=" O SER D 235 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASN D 240 " --> pdb=" O LEU D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 253 removed outlier: 3.549A pdb=" N GLU D 253 " --> pdb=" O ASN D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 269 Processing helix chain 'D' and resid 272 through 277 Processing helix chain 'D' and resid 278 through 286 removed outlier: 3.555A pdb=" N ARG D 284 " --> pdb=" O GLU D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 297 removed outlier: 3.718A pdb=" N SER D 294 " --> pdb=" O ASP D 290 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN D 295 " --> pdb=" O GLU D 291 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 403 Processing helix chain 'D' and resid 433 through 451 Processing helix chain 'D' and resid 453 through 465 Processing helix chain 'D' and resid 471 through 489 removed outlier: 3.526A pdb=" N LYS D 477 " --> pdb=" O ASP D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 491 through 499 removed outlier: 3.773A pdb=" N ILE D 497 " --> pdb=" O GLU D 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 520 Processing helix chain 'D' and resid 523 through 527 removed outlier: 3.679A pdb=" N GLY D 526 " --> pdb=" O LEU D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 556 removed outlier: 3.669A pdb=" N THR D 549 " --> pdb=" O ASP D 545 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 570 Processing helix chain 'D' and resid 581 through 597 Processing helix chain 'D' and resid 601 through 613 Processing helix chain 'D' and resid 623 through 645 Processing helix chain 'D' and resid 647 through 656 removed outlier: 3.663A pdb=" N MET D 654 " --> pdb=" O GLN D 650 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 678 Processing helix chain 'D' and resid 687 through 700 Proline residue: D 694 - end of helix Processing helix chain 'D' and resid 704 through 719 removed outlier: 3.577A pdb=" N ALA D 708 " --> pdb=" O SER D 704 " (cutoff:3.500A) Processing helix chain 'D' and resid 726 through 738 removed outlier: 3.561A pdb=" N THR D 736 " --> pdb=" O ASP D 732 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR D 738 " --> pdb=" O LEU D 734 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 770 removed outlier: 3.631A pdb=" N ILE D 752 " --> pdb=" O THR D 748 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY D 770 " --> pdb=" O TYR D 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 772 through 782 Processing helix chain 'D' and resid 783 through 787 Processing helix chain 'D' and resid 797 through 815 removed outlier: 3.683A pdb=" N MET D 803 " --> pdb=" O LEU D 799 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY D 815 " --> pdb=" O VAL D 811 " (cutoff:3.500A) Processing helix chain 'D' and resid 817 through 827 Processing helix chain 'D' and resid 831 through 840 Processing helix chain 'D' and resid 842 through 856 removed outlier: 3.584A pdb=" N LEU D 846 " --> pdb=" O ASP D 842 " (cutoff:3.500A) Processing helix chain 'D' and resid 870 through 888 Processing helix chain 'D' and resid 890 through 899 Processing helix chain 'D' and resid 911 through 924 Processing helix chain 'D' and resid 927 through 954 removed outlier: 3.571A pdb=" N ALA D 944 " --> pdb=" O GLU D 940 " (cutoff:3.500A) Processing helix chain 'D' and resid 963 through 972 Processing helix chain 'D' and resid 984 through 1001 Processing helix chain 'D' and resid 1009 through 1014 Processing helix chain 'D' and resid 1015 through 1020 Processing helix chain 'D' and resid 1027 through 1040 removed outlier: 4.003A pdb=" N VAL D1038 " --> pdb=" O VAL D1034 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N TYR D1039 " --> pdb=" O SER D1035 " (cutoff:3.500A) Processing helix chain 'D' and resid 1041 through 1044 Processing helix chain 'D' and resid 1054 through 1064 Processing helix chain 'D' and resid 1070 through 1090 removed outlier: 3.573A pdb=" N VAL D1088 " --> pdb=" O SER D1084 " (cutoff:3.500A) Processing helix chain 'D' and resid 1129 through 1131 No H-bonds generated for 'chain 'D' and resid 1129 through 1131' Processing helix chain 'D' and resid 1137 through 1141 removed outlier: 3.661A pdb=" N TRP D1141 " --> pdb=" O ALA D1138 " (cutoff:3.500A) Processing helix chain 'D' and resid 1217 through 1224 Processing helix chain 'D' and resid 1255 through 1261 removed outlier: 3.514A pdb=" N LYS D1260 " --> pdb=" O ASP D1257 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASN D1261 " --> pdb=" O SER D1258 " (cutoff:3.500A) Processing helix chain 'D' and resid 1279 through 1289 removed outlier: 4.010A pdb=" N VAL D1285 " --> pdb=" O GLU D1281 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR D1286 " --> pdb=" O GLN D1282 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN D1289 " --> pdb=" O VAL D1285 " (cutoff:3.500A) Processing helix chain 'D' and resid 1290 through 1294 Processing helix chain 'D' and resid 1325 through 1329 removed outlier: 3.689A pdb=" N LEU D1329 " --> pdb=" O ASP D1326 " (cutoff:3.500A) Processing helix chain 'D' and resid 1366 through 1379 removed outlier: 3.532A pdb=" N MET D1375 " --> pdb=" O GLN D1371 " (cutoff:3.500A) Processing helix chain 'D' and resid 1463 through 1468 removed outlier: 3.649A pdb=" N LYS D1468 " --> pdb=" O ASP D1465 " (cutoff:3.500A) Processing helix chain 'D' and resid 1494 through 1496 No H-bonds generated for 'chain 'D' and resid 1494 through 1496' Processing helix chain 'D' and resid 1513 through 1517 Processing helix chain 'D' and resid 1608 through 1617 removed outlier: 4.080A pdb=" N VAL D1614 " --> pdb=" O ALA D1610 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ALA D1615 " --> pdb=" O ARG D1611 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG D1616 " --> pdb=" O GLN D1612 " (cutoff:3.500A) Processing helix chain 'D' and resid 1620 through 1625 Processing helix chain 'D' and resid 1628 through 1631 Processing helix chain 'D' and resid 1651 through 1656 removed outlier: 3.530A pdb=" N GLY D1656 " --> pdb=" O LEU D1652 " (cutoff:3.500A) Processing helix chain 'D' and resid 1764 through 1773 Processing helix chain 'D' and resid 1773 through 1786 Processing helix chain 'D' and resid 1788 through 1797 removed outlier: 3.540A pdb=" N ARG D1794 " --> pdb=" O ASP D1790 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TRP D1795 " --> pdb=" O GLU D1791 " (cutoff:3.500A) Processing helix chain 'D' and resid 1818 through 1823 Processing helix chain 'D' and resid 1836 through 1844 Processing helix chain 'D' and resid 1845 through 1870 removed outlier: 3.755A pdb=" N GLN D1870 " --> pdb=" O HIS D1866 " (cutoff:3.500A) Processing helix chain 'D' and resid 1872 through 1891 removed outlier: 3.546A pdb=" N ASN D1877 " --> pdb=" O ARG D1873 " (cutoff:3.500A) Processing helix chain 'D' and resid 1906 through 1911 Processing helix chain 'D' and resid 1912 through 1927 Processing helix chain 'D' and resid 1943 through 1947 removed outlier: 3.768A pdb=" N LEU D1947 " --> pdb=" O LEU D1944 " (cutoff:3.500A) Processing helix chain 'D' and resid 1953 through 1972 removed outlier: 3.559A pdb=" N TYR D1959 " --> pdb=" O VAL D1955 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N TRP D1960 " --> pdb=" O MET D1956 " (cutoff:3.500A) Processing helix chain 'D' and resid 2018 through 2105 removed outlier: 4.054A pdb=" N LEU D2065 " --> pdb=" O ALA D2061 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N THR D2066 " --> pdb=" O GLU D2062 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN D2067 " --> pdb=" O LEU D2063 " (cutoff:3.500A) Processing helix chain 'D' and resid 2108 through 2122 Processing helix chain 'D' and resid 2124 through 2139 Processing helix chain 'D' and resid 2155 through 2244 Processing helix chain 'D' and resid 2247 through 2284 removed outlier: 3.576A pdb=" N TYR D2251 " --> pdb=" O ASN D2247 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU D2268 " --> pdb=" O GLN D2264 " (cutoff:3.500A) Processing helix chain 'D' and resid 2298 through 2302 Processing helix chain 'D' and resid 2305 through 2325 Processing helix chain 'D' and resid 2337 through 2343 Processing helix chain 'D' and resid 2345 through 2349 Processing helix chain 'D' and resid 2352 through 2361 removed outlier: 3.745A pdb=" N ASP D2358 " --> pdb=" O ALA D2354 " (cutoff:3.500A) Processing helix chain 'D' and resid 2394 through 2402 removed outlier: 3.555A pdb=" N LYS D2397 " --> pdb=" O ALA D2394 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ILE D2398 " --> pdb=" O ASP D2395 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ARG D2399 " --> pdb=" O LEU D2396 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU D2400 " --> pdb=" O LYS D2397 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N TYR D2402 " --> pdb=" O ARG D2399 " (cutoff:3.500A) Processing helix chain 'D' and resid 2497 through 2504 removed outlier: 3.574A pdb=" N LEU D2501 " --> pdb=" O GLN D2497 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR D2503 " --> pdb=" O THR D2499 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 36 Processing helix chain 'E' and resid 41 through 70 Processing helix chain 'E' and resid 71 through 76 removed outlier: 3.924A pdb=" N ASN E 76 " --> pdb=" O PRO E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 81 removed outlier: 3.787A pdb=" N LEU E 80 " --> pdb=" O ALA E 77 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA E 81 " --> pdb=" O VAL E 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 77 through 81' Processing helix chain 'E' and resid 85 through 97 removed outlier: 3.623A pdb=" N LEU E 89 " --> pdb=" O PRO E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 102 Processing helix chain 'E' and resid 114 through 127 Processing helix chain 'E' and resid 137 through 142 Processing helix chain 'E' and resid 151 through 157 Processing helix chain 'E' and resid 161 through 178 Processing helix chain 'E' and resid 181 through 190 removed outlier: 3.575A pdb=" N VAL E 185 " --> pdb=" O ASN E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 215 removed outlier: 3.525A pdb=" N VAL E 210 " --> pdb=" O ASN E 206 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 224 Processing helix chain 'E' and resid 224 through 231 removed outlier: 3.578A pdb=" N ALA E 228 " --> pdb=" O SER E 224 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET E 231 " --> pdb=" O ILE E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 241 removed outlier: 3.945A pdb=" N GLY E 238 " --> pdb=" O ALA E 234 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE E 239 " --> pdb=" O SER E 235 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASN E 240 " --> pdb=" O LEU E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 253 removed outlier: 3.548A pdb=" N GLU E 253 " --> pdb=" O ASN E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 269 Processing helix chain 'E' and resid 272 through 277 Processing helix chain 'E' and resid 278 through 286 removed outlier: 3.555A pdb=" N ARG E 284 " --> pdb=" O GLU E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 297 removed outlier: 3.717A pdb=" N SER E 294 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN E 295 " --> pdb=" O GLU E 291 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE E 296 " --> pdb=" O GLU E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 403 Processing helix chain 'E' and resid 433 through 451 Processing helix chain 'E' and resid 453 through 465 Processing helix chain 'E' and resid 471 through 489 removed outlier: 3.526A pdb=" N LYS E 477 " --> pdb=" O ASP E 473 " (cutoff:3.500A) Processing helix chain 'E' and resid 491 through 499 removed outlier: 3.774A pdb=" N ILE E 497 " --> pdb=" O GLU E 493 " (cutoff:3.500A) Processing helix chain 'E' and resid 513 through 520 Processing helix chain 'E' and resid 523 through 527 removed outlier: 3.678A pdb=" N GLY E 526 " --> pdb=" O LEU E 523 " (cutoff:3.500A) Processing helix chain 'E' and resid 545 through 556 removed outlier: 3.670A pdb=" N THR E 549 " --> pdb=" O ASP E 545 " (cutoff:3.500A) Processing helix chain 'E' and resid 558 through 570 Processing helix chain 'E' and resid 581 through 597 Processing helix chain 'E' and resid 601 through 613 Processing helix chain 'E' and resid 623 through 645 Processing helix chain 'E' and resid 647 through 656 removed outlier: 3.662A pdb=" N MET E 654 " --> pdb=" O GLN E 650 " (cutoff:3.500A) Processing helix chain 'E' and resid 664 through 678 Processing helix chain 'E' and resid 687 through 700 Proline residue: E 694 - end of helix Processing helix chain 'E' and resid 704 through 719 removed outlier: 3.578A pdb=" N ALA E 708 " --> pdb=" O SER E 704 " (cutoff:3.500A) Processing helix chain 'E' and resid 726 through 738 removed outlier: 3.561A pdb=" N THR E 736 " --> pdb=" O ASP E 732 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR E 738 " --> pdb=" O LEU E 734 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 770 removed outlier: 3.631A pdb=" N ILE E 752 " --> pdb=" O THR E 748 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY E 770 " --> pdb=" O TYR E 766 " (cutoff:3.500A) Processing helix chain 'E' and resid 772 through 782 Processing helix chain 'E' and resid 783 through 787 Processing helix chain 'E' and resid 797 through 815 removed outlier: 3.682A pdb=" N MET E 803 " --> pdb=" O LEU E 799 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY E 815 " --> pdb=" O VAL E 811 " (cutoff:3.500A) Processing helix chain 'E' and resid 817 through 827 Processing helix chain 'E' and resid 831 through 840 Processing helix chain 'E' and resid 842 through 856 removed outlier: 3.583A pdb=" N LEU E 846 " --> pdb=" O ASP E 842 " (cutoff:3.500A) Processing helix chain 'E' and resid 870 through 888 Processing helix chain 'E' and resid 890 through 899 Processing helix chain 'E' and resid 911 through 924 removed outlier: 3.500A pdb=" N TRP E 915 " --> pdb=" O THR E 911 " (cutoff:3.500A) Processing helix chain 'E' and resid 927 through 954 removed outlier: 3.571A pdb=" N ALA E 944 " --> pdb=" O GLU E 940 " (cutoff:3.500A) Processing helix chain 'E' and resid 963 through 972 Processing helix chain 'E' and resid 984 through 1001 Processing helix chain 'E' and resid 1009 through 1014 Processing helix chain 'E' and resid 1015 through 1020 Processing helix chain 'E' and resid 1027 through 1040 removed outlier: 4.004A pdb=" N VAL E1038 " --> pdb=" O VAL E1034 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N TYR E1039 " --> pdb=" O SER E1035 " (cutoff:3.500A) Processing helix chain 'E' and resid 1041 through 1044 Processing helix chain 'E' and resid 1054 through 1064 Processing helix chain 'E' and resid 1070 through 1090 removed outlier: 3.575A pdb=" N VAL E1088 " --> pdb=" O SER E1084 " (cutoff:3.500A) Processing helix chain 'E' and resid 1129 through 1131 No H-bonds generated for 'chain 'E' and resid 1129 through 1131' Processing helix chain 'E' and resid 1137 through 1141 removed outlier: 3.662A pdb=" N TRP E1141 " --> pdb=" O ALA E1138 " (cutoff:3.500A) Processing helix chain 'E' and resid 1217 through 1224 Processing helix chain 'E' and resid 1255 through 1261 removed outlier: 3.514A pdb=" N LYS E1260 " --> pdb=" O ASP E1257 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASN E1261 " --> pdb=" O SER E1258 " (cutoff:3.500A) Processing helix chain 'E' and resid 1279 through 1289 removed outlier: 4.009A pdb=" N VAL E1285 " --> pdb=" O GLU E1281 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR E1286 " --> pdb=" O GLN E1282 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN E1289 " --> pdb=" O VAL E1285 " (cutoff:3.500A) Processing helix chain 'E' and resid 1290 through 1294 Processing helix chain 'E' and resid 1325 through 1329 removed outlier: 3.689A pdb=" N LEU E1329 " --> pdb=" O ASP E1326 " (cutoff:3.500A) Processing helix chain 'E' and resid 1366 through 1379 removed outlier: 3.530A pdb=" N MET E1375 " --> pdb=" O GLN E1371 " (cutoff:3.500A) Processing helix chain 'E' and resid 1463 through 1468 removed outlier: 3.649A pdb=" N LYS E1468 " --> pdb=" O ASP E1465 " (cutoff:3.500A) Processing helix chain 'E' and resid 1494 through 1496 No H-bonds generated for 'chain 'E' and resid 1494 through 1496' Processing helix chain 'E' and resid 1513 through 1517 Processing helix chain 'E' and resid 1608 through 1617 removed outlier: 4.078A pdb=" N VAL E1614 " --> pdb=" O ALA E1610 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ALA E1615 " --> pdb=" O ARG E1611 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG E1616 " --> pdb=" O GLN E1612 " (cutoff:3.500A) Processing helix chain 'E' and resid 1620 through 1625 Processing helix chain 'E' and resid 1628 through 1631 Processing helix chain 'E' and resid 1651 through 1656 removed outlier: 3.531A pdb=" N GLY E1656 " --> pdb=" O LEU E1652 " (cutoff:3.500A) Processing helix chain 'E' and resid 1764 through 1773 Processing helix chain 'E' and resid 1773 through 1786 Processing helix chain 'E' and resid 1788 through 1797 removed outlier: 3.542A pdb=" N ARG E1794 " --> pdb=" O ASP E1790 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TRP E1795 " --> pdb=" O GLU E1791 " (cutoff:3.500A) Processing helix chain 'E' and resid 1818 through 1823 Processing helix chain 'E' and resid 1836 through 1844 Processing helix chain 'E' and resid 1845 through 1870 removed outlier: 3.754A pdb=" N GLN E1870 " --> pdb=" O HIS E1866 " (cutoff:3.500A) Processing helix chain 'E' and resid 1872 through 1891 removed outlier: 3.547A pdb=" N ASN E1877 " --> pdb=" O ARG E1873 " (cutoff:3.500A) Processing helix chain 'E' and resid 1906 through 1911 Processing helix chain 'E' and resid 1912 through 1927 Processing helix chain 'E' and resid 1943 through 1947 removed outlier: 3.768A pdb=" N LEU E1947 " --> pdb=" O LEU E1944 " (cutoff:3.500A) Processing helix chain 'E' and resid 1953 through 1972 removed outlier: 3.559A pdb=" N TYR E1959 " --> pdb=" O VAL E1955 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N TRP E1960 " --> pdb=" O MET E1956 " (cutoff:3.500A) Processing helix chain 'E' and resid 2018 through 2105 removed outlier: 4.052A pdb=" N LEU E2065 " --> pdb=" O ALA E2061 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N THR E2066 " --> pdb=" O GLU E2062 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN E2067 " --> pdb=" O LEU E2063 " (cutoff:3.500A) Processing helix chain 'E' and resid 2108 through 2122 Processing helix chain 'E' and resid 2124 through 2139 Processing helix chain 'E' and resid 2155 through 2244 Processing helix chain 'E' and resid 2247 through 2284 removed outlier: 3.574A pdb=" N TYR E2251 " --> pdb=" O ASN E2247 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU E2268 " --> pdb=" O GLN E2264 " (cutoff:3.500A) Processing helix chain 'E' and resid 2298 through 2302 Processing helix chain 'E' and resid 2305 through 2325 Processing helix chain 'E' and resid 2337 through 2343 Processing helix chain 'E' and resid 2345 through 2349 Processing helix chain 'E' and resid 2352 through 2361 removed outlier: 3.745A pdb=" N ASP E2358 " --> pdb=" O ALA E2354 " (cutoff:3.500A) Processing helix chain 'E' and resid 2394 through 2402 removed outlier: 3.555A pdb=" N LYS E2397 " --> pdb=" O ALA E2394 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ILE E2398 " --> pdb=" O ASP E2395 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ARG E2399 " --> pdb=" O LEU E2396 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU E2400 " --> pdb=" O LYS E2397 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TYR E2402 " --> pdb=" O ARG E2399 " (cutoff:3.500A) Processing helix chain 'E' and resid 2497 through 2504 removed outlier: 3.573A pdb=" N LEU E2501 " --> pdb=" O GLN E2497 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR E2503 " --> pdb=" O THR E2499 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 159 through 160 Processing sheet with id=AA2, first strand: chain 'A' and resid 312 through 318 removed outlier: 3.552A pdb=" N TYR A 367 " --> pdb=" O VAL A 413 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU A 372 " --> pdb=" O GLU A 377 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N GLU A 377 " --> pdb=" O LEU A 372 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 341 through 349 removed outlier: 6.405A pdb=" N ASN A 352 " --> pdb=" O PHE A 348 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 535 through 537 Processing sheet with id=AA5, first strand: chain 'A' and resid 1092 through 1098 removed outlier: 5.760A pdb=" N VAL A1093 " --> pdb=" O LEU A1113 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU A1113 " --> pdb=" O VAL A1093 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER A1095 " --> pdb=" O ILE A1111 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N TYR A1121 " --> pdb=" O ILE A1147 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1158 through 1163 Processing sheet with id=AA7, first strand: chain 'A' and resid 1233 through 1239 removed outlier: 3.649A pdb=" N TYR A1239 " --> pdb=" O THR A1244 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR A1244 " --> pdb=" O TYR A1239 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1300 through 1301 removed outlier: 4.081A pdb=" N ARG A1300 " --> pdb=" O LEU A1586 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1310 through 1311 removed outlier: 3.530A pdb=" N THR A1575 " --> pdb=" O GLU A1311 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1310 through 1311 removed outlier: 3.530A pdb=" N THR A1575 " --> pdb=" O GLU A1311 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLY A1566 " --> pdb=" O ALA A1557 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA A1557 " --> pdb=" O GLY A1566 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1331 through 1332 Processing sheet with id=AB3, first strand: chain 'A' and resid 1340 through 1345 removed outlier: 3.766A pdb=" N ASP A1348 " --> pdb=" O ALA A1345 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1443 through 1450 removed outlier: 3.598A pdb=" N ASN A1449 " --> pdb=" O SER A1432 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N SER A1432 " --> pdb=" O ASN A1449 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TYR A1388 " --> pdb=" O PRO A1486 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLU A1488 " --> pdb=" O ILE A1386 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE A1386 " --> pdb=" O GLU A1488 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ASN A1490 " --> pdb=" O LYS A1384 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LYS A1384 " --> pdb=" O ASN A1490 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N TYR A1388 " --> pdb=" O PRO A1406 " (cutoff:3.500A) removed outlier: 9.080A pdb=" N SER A1390 " --> pdb=" O PHE A1404 " (cutoff:3.500A) removed outlier: 9.470A pdb=" N PHE A1404 " --> pdb=" O SER A1390 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1633 through 1635 Processing sheet with id=AB6, first strand: chain 'A' and resid 1686 through 1693 removed outlier: 4.437A pdb=" N TYR A1642 " --> pdb=" O LEU A1750 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER A1746 " --> pdb=" O VAL A1646 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1673 through 1680 removed outlier: 5.568A pdb=" N ILE A1675 " --> pdb=" O ILE A1665 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ILE A1665 " --> pdb=" O ILE A1675 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 2144 through 2146 Processing sheet with id=AB9, first strand: chain 'A' and resid 2148 through 2150 Processing sheet with id=AC1, first strand: chain 'A' and resid 2329 through 2336 removed outlier: 5.692A pdb=" N THR A2514 " --> pdb=" O ILE A2412 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N ILE A2412 " --> pdb=" O THR A2514 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N LYS A2516 " --> pdb=" O ARG A2410 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ARG A2410 " --> pdb=" O LYS A2516 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 2367 through 2368 Processing sheet with id=AC3, first strand: chain 'B' and resid 159 through 160 Processing sheet with id=AC4, first strand: chain 'B' and resid 312 through 318 removed outlier: 3.551A pdb=" N TYR B 367 " --> pdb=" O VAL B 413 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU B 372 " --> pdb=" O GLU B 377 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N GLU B 377 " --> pdb=" O LEU B 372 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 341 through 349 removed outlier: 6.407A pdb=" N ASN B 352 " --> pdb=" O PHE B 348 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 535 through 537 Processing sheet with id=AC7, first strand: chain 'B' and resid 1092 through 1098 removed outlier: 5.759A pdb=" N VAL B1093 " --> pdb=" O LEU B1113 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU B1113 " --> pdb=" O VAL B1093 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER B1095 " --> pdb=" O ILE B1111 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N TYR B1121 " --> pdb=" O ILE B1147 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=AC9, first strand: chain 'B' and resid 1233 through 1239 removed outlier: 3.648A pdb=" N TYR B1239 " --> pdb=" O THR B1244 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR B1244 " --> pdb=" O TYR B1239 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1300 through 1301 removed outlier: 4.081A pdb=" N ARG B1300 " --> pdb=" O LEU B1586 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1310 through 1311 removed outlier: 3.530A pdb=" N THR B1575 " --> pdb=" O GLU B1311 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1310 through 1311 removed outlier: 3.530A pdb=" N THR B1575 " --> pdb=" O GLU B1311 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLY B1566 " --> pdb=" O ALA B1557 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA B1557 " --> pdb=" O GLY B1566 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1331 through 1332 Processing sheet with id=AD5, first strand: chain 'B' and resid 1340 through 1345 removed outlier: 3.766A pdb=" N ASP B1348 " --> pdb=" O ALA B1345 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1443 through 1450 removed outlier: 3.596A pdb=" N ASN B1449 " --> pdb=" O SER B1432 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N SER B1432 " --> pdb=" O ASN B1449 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TYR B1388 " --> pdb=" O PRO B1486 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLU B1488 " --> pdb=" O ILE B1386 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE B1386 " --> pdb=" O GLU B1488 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ASN B1490 " --> pdb=" O LYS B1384 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LYS B1384 " --> pdb=" O ASN B1490 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TYR B1388 " --> pdb=" O PRO B1406 " (cutoff:3.500A) removed outlier: 9.080A pdb=" N SER B1390 " --> pdb=" O PHE B1404 " (cutoff:3.500A) removed outlier: 9.467A pdb=" N PHE B1404 " --> pdb=" O SER B1390 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1633 through 1635 Processing sheet with id=AD8, first strand: chain 'B' and resid 1686 through 1693 removed outlier: 4.437A pdb=" N TYR B1642 " --> pdb=" O LEU B1750 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER B1746 " --> pdb=" O VAL B1646 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1673 through 1680 removed outlier: 5.567A pdb=" N ILE B1675 " --> pdb=" O ILE B1665 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ILE B1665 " --> pdb=" O ILE B1675 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 2148 through 2150 Processing sheet with id=AE2, first strand: chain 'B' and resid 2329 through 2336 removed outlier: 5.691A pdb=" N THR B2514 " --> pdb=" O ILE B2412 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ILE B2412 " --> pdb=" O THR B2514 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N LYS B2516 " --> pdb=" O ARG B2410 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ARG B2410 " --> pdb=" O LYS B2516 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 2367 through 2368 Processing sheet with id=AE4, first strand: chain 'C' and resid 159 through 160 Processing sheet with id=AE5, first strand: chain 'C' and resid 312 through 318 removed outlier: 3.552A pdb=" N TYR C 367 " --> pdb=" O VAL C 413 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU C 372 " --> pdb=" O GLU C 377 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N GLU C 377 " --> pdb=" O LEU C 372 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 341 through 349 removed outlier: 6.404A pdb=" N ASN C 352 " --> pdb=" O PHE C 348 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 535 through 537 Processing sheet with id=AE8, first strand: chain 'C' and resid 1092 through 1098 removed outlier: 5.760A pdb=" N VAL C1093 " --> pdb=" O LEU C1113 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU C1113 " --> pdb=" O VAL C1093 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER C1095 " --> pdb=" O ILE C1111 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N TYR C1121 " --> pdb=" O ILE C1147 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1158 through 1163 Processing sheet with id=AF1, first strand: chain 'C' and resid 1233 through 1239 removed outlier: 3.649A pdb=" N TYR C1239 " --> pdb=" O THR C1244 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR C1244 " --> pdb=" O TYR C1239 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1300 through 1301 removed outlier: 4.081A pdb=" N ARG C1300 " --> pdb=" O LEU C1586 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1310 through 1311 removed outlier: 3.531A pdb=" N THR C1575 " --> pdb=" O GLU C1311 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1310 through 1311 removed outlier: 3.531A pdb=" N THR C1575 " --> pdb=" O GLU C1311 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLY C1566 " --> pdb=" O ALA C1557 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA C1557 " --> pdb=" O GLY C1566 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 1331 through 1332 Processing sheet with id=AF6, first strand: chain 'C' and resid 1340 through 1345 removed outlier: 3.765A pdb=" N ASP C1348 " --> pdb=" O ALA C1345 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 1443 through 1450 removed outlier: 3.596A pdb=" N ASN C1449 " --> pdb=" O SER C1432 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N SER C1432 " --> pdb=" O ASN C1449 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TYR C1388 " --> pdb=" O PRO C1486 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLU C1488 " --> pdb=" O ILE C1386 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE C1386 " --> pdb=" O GLU C1488 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ASN C1490 " --> pdb=" O LYS C1384 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LYS C1384 " --> pdb=" O ASN C1490 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N TYR C1388 " --> pdb=" O PRO C1406 " (cutoff:3.500A) removed outlier: 9.080A pdb=" N SER C1390 " --> pdb=" O PHE C1404 " (cutoff:3.500A) removed outlier: 9.469A pdb=" N PHE C1404 " --> pdb=" O SER C1390 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 1633 through 1635 Processing sheet with id=AF9, first strand: chain 'C' and resid 1686 through 1693 removed outlier: 4.437A pdb=" N TYR C1642 " --> pdb=" O LEU C1750 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER C1746 " --> pdb=" O VAL C1646 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 1673 through 1680 removed outlier: 5.567A pdb=" N ILE C1675 " --> pdb=" O ILE C1665 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ILE C1665 " --> pdb=" O ILE C1675 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 2148 through 2150 Processing sheet with id=AG3, first strand: chain 'C' and resid 2329 through 2336 removed outlier: 5.693A pdb=" N THR C2514 " --> pdb=" O ILE C2412 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ILE C2412 " --> pdb=" O THR C2514 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N LYS C2516 " --> pdb=" O ARG C2410 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ARG C2410 " --> pdb=" O LYS C2516 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 2367 through 2368 Processing sheet with id=AG5, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AG6, first strand: chain 'D' and resid 312 through 318 removed outlier: 3.552A pdb=" N TYR D 367 " --> pdb=" O VAL D 413 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU D 372 " --> pdb=" O GLU D 377 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N GLU D 377 " --> pdb=" O LEU D 372 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'D' and resid 341 through 349 removed outlier: 6.406A pdb=" N ASN D 352 " --> pdb=" O PHE D 348 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'D' and resid 535 through 537 Processing sheet with id=AG9, first strand: chain 'D' and resid 1092 through 1098 removed outlier: 5.758A pdb=" N VAL D1093 " --> pdb=" O LEU D1113 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU D1113 " --> pdb=" O VAL D1093 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER D1095 " --> pdb=" O ILE D1111 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N TYR D1121 " --> pdb=" O ILE D1147 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'D' and resid 1158 through 1163 Processing sheet with id=AH2, first strand: chain 'D' and resid 1233 through 1239 removed outlier: 3.650A pdb=" N TYR D1239 " --> pdb=" O THR D1244 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR D1244 " --> pdb=" O TYR D1239 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'D' and resid 1300 through 1301 removed outlier: 4.080A pdb=" N ARG D1300 " --> pdb=" O LEU D1586 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'D' and resid 1310 through 1311 removed outlier: 3.531A pdb=" N THR D1575 " --> pdb=" O GLU D1311 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'D' and resid 1310 through 1311 removed outlier: 3.531A pdb=" N THR D1575 " --> pdb=" O GLU D1311 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLY D1566 " --> pdb=" O ALA D1557 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA D1557 " --> pdb=" O GLY D1566 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'D' and resid 1331 through 1332 Processing sheet with id=AH7, first strand: chain 'D' and resid 1340 through 1345 removed outlier: 3.764A pdb=" N ASP D1348 " --> pdb=" O ALA D1345 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'D' and resid 1443 through 1450 removed outlier: 3.597A pdb=" N ASN D1449 " --> pdb=" O SER D1432 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N SER D1432 " --> pdb=" O ASN D1449 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TYR D1388 " --> pdb=" O PRO D1486 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLU D1488 " --> pdb=" O ILE D1386 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE D1386 " --> pdb=" O GLU D1488 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ASN D1490 " --> pdb=" O LYS D1384 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LYS D1384 " --> pdb=" O ASN D1490 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N TYR D1388 " --> pdb=" O PRO D1406 " (cutoff:3.500A) removed outlier: 9.080A pdb=" N SER D1390 " --> pdb=" O PHE D1404 " (cutoff:3.500A) removed outlier: 9.470A pdb=" N PHE D1404 " --> pdb=" O SER D1390 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'D' and resid 1633 through 1635 Processing sheet with id=AI1, first strand: chain 'D' and resid 1686 through 1693 removed outlier: 4.437A pdb=" N TYR D1642 " --> pdb=" O LEU D1750 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER D1746 " --> pdb=" O VAL D1646 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'D' and resid 1673 through 1680 removed outlier: 5.567A pdb=" N ILE D1675 " --> pdb=" O ILE D1665 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ILE D1665 " --> pdb=" O ILE D1675 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'D' and resid 2148 through 2150 Processing sheet with id=AI4, first strand: chain 'D' and resid 2329 through 2336 removed outlier: 5.691A pdb=" N THR D2514 " --> pdb=" O ILE D2412 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ILE D2412 " --> pdb=" O THR D2514 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N LYS D2516 " --> pdb=" O ARG D2410 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ARG D2410 " --> pdb=" O LYS D2516 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'D' and resid 2367 through 2368 Processing sheet with id=AI6, first strand: chain 'E' and resid 159 through 160 Processing sheet with id=AI7, first strand: chain 'E' and resid 312 through 318 removed outlier: 3.550A pdb=" N TYR E 367 " --> pdb=" O VAL E 413 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU E 372 " --> pdb=" O GLU E 377 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N GLU E 377 " --> pdb=" O LEU E 372 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'E' and resid 341 through 349 removed outlier: 6.406A pdb=" N ASN E 352 " --> pdb=" O PHE E 348 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'E' and resid 535 through 537 Processing sheet with id=AJ1, first strand: chain 'E' and resid 1092 through 1098 removed outlier: 5.761A pdb=" N VAL E1093 " --> pdb=" O LEU E1113 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU E1113 " --> pdb=" O VAL E1093 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER E1095 " --> pdb=" O ILE E1111 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N TYR E1121 " --> pdb=" O ILE E1147 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'E' and resid 1158 through 1163 Processing sheet with id=AJ3, first strand: chain 'E' and resid 1233 through 1239 removed outlier: 3.649A pdb=" N TYR E1239 " --> pdb=" O THR E1244 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR E1244 " --> pdb=" O TYR E1239 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'E' and resid 1300 through 1301 removed outlier: 4.080A pdb=" N ARG E1300 " --> pdb=" O LEU E1586 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'E' and resid 1310 through 1311 removed outlier: 3.531A pdb=" N THR E1575 " --> pdb=" O GLU E1311 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'E' and resid 1310 through 1311 removed outlier: 3.531A pdb=" N THR E1575 " --> pdb=" O GLU E1311 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLY E1566 " --> pdb=" O ALA E1557 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA E1557 " --> pdb=" O GLY E1566 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'E' and resid 1331 through 1332 Processing sheet with id=AJ8, first strand: chain 'E' and resid 1340 through 1345 removed outlier: 3.764A pdb=" N ASP E1348 " --> pdb=" O ALA E1345 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'E' and resid 1443 through 1450 removed outlier: 3.597A pdb=" N ASN E1449 " --> pdb=" O SER E1432 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N SER E1432 " --> pdb=" O ASN E1449 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TYR E1388 " --> pdb=" O PRO E1486 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLU E1488 " --> pdb=" O ILE E1386 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE E1386 " --> pdb=" O GLU E1488 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ASN E1490 " --> pdb=" O LYS E1384 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LYS E1384 " --> pdb=" O ASN E1490 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N TYR E1388 " --> pdb=" O PRO E1406 " (cutoff:3.500A) removed outlier: 9.078A pdb=" N SER E1390 " --> pdb=" O PHE E1404 " (cutoff:3.500A) removed outlier: 9.469A pdb=" N PHE E1404 " --> pdb=" O SER E1390 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'E' and resid 1633 through 1635 Processing sheet with id=AK2, first strand: chain 'E' and resid 1686 through 1693 removed outlier: 4.437A pdb=" N TYR E1642 " --> pdb=" O LEU E1750 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER E1746 " --> pdb=" O VAL E1646 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'E' and resid 1673 through 1680 removed outlier: 5.568A pdb=" N ILE E1675 " --> pdb=" O ILE E1665 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ILE E1665 " --> pdb=" O ILE E1675 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'E' and resid 2329 through 2336 removed outlier: 5.691A pdb=" N THR E2514 " --> pdb=" O ILE E2412 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ILE E2412 " --> pdb=" O THR E2514 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N LYS E2516 " --> pdb=" O ARG E2410 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ARG E2410 " --> pdb=" O LYS E2516 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'E' and resid 2367 through 2368 5226 hydrogen bonds defined for protein. 15003 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: 65.35 Time building geometry restraints manager: 32.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 29098 1.33 - 1.45: 16490 1.45 - 1.57: 54612 1.57 - 1.68: 0 1.68 - 1.80: 570 Bond restraints: 100770 Sorted by residual: bond pdb=" CB VAL C2270 " pdb=" CG2 VAL C2270 " ideal model delta sigma weight residual 1.521 1.440 0.081 3.30e-02 9.18e+02 5.96e+00 bond pdb=" CB VAL D2270 " pdb=" CG2 VAL D2270 " ideal model delta sigma weight residual 1.521 1.440 0.081 3.30e-02 9.18e+02 5.96e+00 bond pdb=" CB VAL E2270 " pdb=" CG2 VAL E2270 " ideal model delta sigma weight residual 1.521 1.441 0.080 3.30e-02 9.18e+02 5.93e+00 bond pdb=" CB VAL A2270 " pdb=" CG2 VAL A2270 " ideal model delta sigma weight residual 1.521 1.441 0.080 3.30e-02 9.18e+02 5.92e+00 bond pdb=" CB VAL B2270 " pdb=" CG2 VAL B2270 " ideal model delta sigma weight residual 1.521 1.441 0.080 3.30e-02 9.18e+02 5.89e+00 ... (remaining 100765 not shown) Histogram of bond angle deviations from ideal: 95.02 - 103.73: 1219 103.73 - 112.44: 52223 112.44 - 121.15: 57390 121.15 - 129.86: 25349 129.86 - 138.57: 689 Bond angle restraints: 136870 Sorted by residual: angle pdb=" N VAL A1668 " pdb=" CA VAL A1668 " pdb=" C VAL A1668 " ideal model delta sigma weight residual 109.46 101.03 8.43 1.38e+00 5.25e-01 3.73e+01 angle pdb=" N VAL D1668 " pdb=" CA VAL D1668 " pdb=" C VAL D1668 " ideal model delta sigma weight residual 109.46 101.09 8.37 1.38e+00 5.25e-01 3.68e+01 angle pdb=" N VAL C1668 " pdb=" CA VAL C1668 " pdb=" C VAL C1668 " ideal model delta sigma weight residual 109.46 101.12 8.34 1.38e+00 5.25e-01 3.66e+01 angle pdb=" N VAL B1668 " pdb=" CA VAL B1668 " pdb=" C VAL B1668 " ideal model delta sigma weight residual 109.46 101.12 8.34 1.38e+00 5.25e-01 3.65e+01 angle pdb=" N VAL E1668 " pdb=" CA VAL E1668 " pdb=" C VAL E1668 " ideal model delta sigma weight residual 109.46 101.12 8.34 1.38e+00 5.25e-01 3.65e+01 ... (remaining 136865 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.75: 57671 15.75 - 31.51: 2144 31.51 - 47.26: 480 47.26 - 63.01: 25 63.01 - 78.77: 85 Dihedral angle restraints: 60405 sinusoidal: 23810 harmonic: 36595 Sorted by residual: dihedral pdb=" CA VAL B1668 " pdb=" C VAL B1668 " pdb=" N VAL B1669 " pdb=" CA VAL B1669 " ideal model delta harmonic sigma weight residual -180.00 -130.09 -49.91 0 5.00e+00 4.00e-02 9.97e+01 dihedral pdb=" CA VAL A1668 " pdb=" C VAL A1668 " pdb=" N VAL A1669 " pdb=" CA VAL A1669 " ideal model delta harmonic sigma weight residual -180.00 -130.15 -49.85 0 5.00e+00 4.00e-02 9.94e+01 dihedral pdb=" CA VAL E1668 " pdb=" C VAL E1668 " pdb=" N VAL E1669 " pdb=" CA VAL E1669 " ideal model delta harmonic sigma weight residual -180.00 -130.17 -49.83 0 5.00e+00 4.00e-02 9.93e+01 ... (remaining 60402 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 9966 0.050 - 0.099: 4052 0.099 - 0.149: 957 0.149 - 0.199: 126 0.199 - 0.248: 44 Chirality restraints: 15145 Sorted by residual: chirality pdb=" CG LEU E 762 " pdb=" CB LEU E 762 " pdb=" CD1 LEU E 762 " pdb=" CD2 LEU E 762 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CG LEU D 762 " pdb=" CB LEU D 762 " pdb=" CD1 LEU D 762 " pdb=" CD2 LEU D 762 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CG LEU A 762 " pdb=" CB LEU A 762 " pdb=" CD1 LEU A 762 " pdb=" CD2 LEU A 762 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 15142 not shown) Planarity restraints: 17815 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B1532 " 0.025 2.00e-02 2.50e+03 2.74e-02 1.31e+01 pdb=" CG PHE B1532 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 PHE B1532 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 PHE B1532 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B1532 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE B1532 " 0.017 2.00e-02 2.50e+03 pdb=" CZ PHE B1532 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D1532 " -0.025 2.00e-02 2.50e+03 2.73e-02 1.31e+01 pdb=" CG PHE D1532 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE D1532 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 PHE D1532 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE D1532 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE D1532 " -0.017 2.00e-02 2.50e+03 pdb=" CZ PHE D1532 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C1532 " -0.026 2.00e-02 2.50e+03 2.73e-02 1.30e+01 pdb=" CG PHE C1532 " 0.061 2.00e-02 2.50e+03 pdb=" CD1 PHE C1532 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE C1532 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE C1532 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE C1532 " -0.017 2.00e-02 2.50e+03 pdb=" CZ PHE C1532 " 0.000 2.00e-02 2.50e+03 ... (remaining 17812 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 3526 2.70 - 3.25: 95205 3.25 - 3.80: 166290 3.80 - 4.35: 214498 4.35 - 4.90: 363559 Nonbonded interactions: 843078 Sorted by model distance: nonbonded pdb=" O LEU A 67 " pdb=" OH TYR A 103 " model vdw 2.148 2.440 nonbonded pdb=" O LEU E 67 " pdb=" OH TYR E 103 " model vdw 2.149 2.440 nonbonded pdb=" O LEU D 67 " pdb=" OH TYR D 103 " model vdw 2.149 2.440 nonbonded pdb=" O LEU C 67 " pdb=" OH TYR C 103 " model vdw 2.151 2.440 nonbonded pdb=" O LEU B 67 " pdb=" OH TYR B 103 " model vdw 2.151 2.440 ... (remaining 843073 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.090 Extract box with map and model: 15.550 Check model and map are aligned: 1.110 Set scattering table: 0.740 Process input model: 233.040 Find NCS groups from input model: 4.920 Set up NCS constraints: 0.470 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: 0.030 Load rotamer database and sin/cos tables:11.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 270.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 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 : 0.011 0.081 100770 Z= 0.728 Angle : 0.956 13.798 136870 Z= 0.538 Chirality : 0.056 0.248 15145 Planarity : 0.006 0.055 17815 Dihedral : 9.754 78.765 36845 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.20 % Favored : 97.76 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.68 (0.06), residues: 12395 helix: -3.48 (0.04), residues: 5585 sheet: -0.81 (0.10), residues: 2175 loop : -1.54 (0.08), residues: 4635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.004 TRP A 714 HIS 0.019 0.005 HIS E1704 PHE 0.061 0.004 PHE B1532 TYR 0.056 0.004 TYR A1239 ARG 0.024 0.002 ARG B1863 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24790 Ramachandran restraints generated. 12395 Oldfield, 0 Emsley, 12395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24790 Ramachandran restraints generated. 12395 Oldfield, 0 Emsley, 12395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1892 residues out of total 10645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1892 time to evaluate : 8.665 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: A 215 ASP cc_start: 0.8376 (t0) cc_final: 0.8010 (t0) REVERT: A 218 LEU cc_start: 0.8882 (mp) cc_final: 0.8611 (mp) REVERT: A 287 ASN cc_start: 0.8955 (t0) cc_final: 0.8323 (t0) REVERT: A 291 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7660 (tm-30) REVERT: A 292 GLU cc_start: 0.8403 (mt-10) cc_final: 0.8138 (mt-10) REVERT: A 660 ASN cc_start: 0.8598 (t0) cc_final: 0.8360 (p0) REVERT: A 983 THR cc_start: 0.8703 (p) cc_final: 0.8477 (t) REVERT: A 1010 SER cc_start: 0.8800 (m) cc_final: 0.8535 (p) REVERT: A 1072 ASP cc_start: 0.7990 (m-30) cc_final: 0.7690 (m-30) REVERT: A 1087 GLN cc_start: 0.9034 (tt0) cc_final: 0.8814 (tt0) REVERT: A 1195 ARG cc_start: 0.8420 (ptm-80) cc_final: 0.8095 (ptp90) REVERT: A 1273 MET cc_start: 0.7039 (mmt) cc_final: 0.6709 (mmm) REVERT: A 1437 TRP cc_start: 0.8425 (t60) cc_final: 0.8211 (t-100) REVERT: A 1528 MET cc_start: 0.8794 (mtp) cc_final: 0.8367 (mtm) REVERT: A 1892 ASP cc_start: 0.8213 (m-30) cc_final: 0.7948 (m-30) REVERT: A 1895 TYR cc_start: 0.8616 (t80) cc_final: 0.8323 (t80) REVERT: B 164 LEU cc_start: 0.9425 (tt) cc_final: 0.9156 (tt) REVERT: B 176 GLU cc_start: 0.8830 (tp30) cc_final: 0.8583 (tm-30) REVERT: B 186 MET cc_start: 0.8656 (mmt) cc_final: 0.8391 (mmt) REVERT: B 215 ASP cc_start: 0.8095 (t0) cc_final: 0.7702 (t70) REVERT: B 287 ASN cc_start: 0.8959 (t0) cc_final: 0.8698 (t0) REVERT: B 468 LEU cc_start: 0.8503 (mp) cc_final: 0.8302 (mt) REVERT: B 654 MET cc_start: 0.8398 (mtm) cc_final: 0.7926 (mtm) REVERT: B 983 THR cc_start: 0.8599 (p) cc_final: 0.8353 (t) REVERT: B 1195 ARG cc_start: 0.8319 (ptm-80) cc_final: 0.7969 (ptm160) REVERT: B 1401 LYS cc_start: 0.8741 (mtpp) cc_final: 0.8323 (mmmm) REVERT: B 1454 ASP cc_start: 0.8421 (p0) cc_final: 0.8180 (p0) REVERT: B 1758 MET cc_start: 0.8489 (ptp) cc_final: 0.7984 (ptm) REVERT: B 1895 TYR cc_start: 0.8423 (t80) cc_final: 0.8143 (t80) REVERT: B 2101 LYS cc_start: 0.9217 (tttm) cc_final: 0.9001 (ttpp) REVERT: B 2204 LYS cc_start: 0.8825 (mttp) cc_final: 0.8543 (mtmm) REVERT: C 215 ASP cc_start: 0.8259 (t0) cc_final: 0.7484 (t70) REVERT: C 287 ASN cc_start: 0.9022 (t0) cc_final: 0.8626 (t0) REVERT: C 363 TYR cc_start: 0.8486 (m-80) cc_final: 0.8267 (m-80) REVERT: C 654 MET cc_start: 0.8308 (mtm) cc_final: 0.7985 (mtm) REVERT: C 1003 ASN cc_start: 0.8401 (t0) cc_final: 0.8083 (t0) REVERT: C 1010 SER cc_start: 0.8760 (m) cc_final: 0.8498 (p) REVERT: C 1072 ASP cc_start: 0.7985 (m-30) cc_final: 0.7708 (m-30) REVERT: C 1087 GLN cc_start: 0.8954 (tt0) cc_final: 0.8715 (tt0) REVERT: C 1148 ASP cc_start: 0.8252 (m-30) cc_final: 0.8010 (m-30) REVERT: C 1264 MET cc_start: 0.8792 (mmt) cc_final: 0.8562 (mmm) REVERT: C 1543 ASN cc_start: 0.8293 (p0) cc_final: 0.7782 (p0) REVERT: C 1892 ASP cc_start: 0.8300 (m-30) cc_final: 0.8052 (m-30) REVERT: C 2101 LYS cc_start: 0.9271 (tttm) cc_final: 0.8746 (tmmt) REVERT: C 2165 MET cc_start: 0.8761 (mtt) cc_final: 0.8551 (mtt) REVERT: D 112 MET cc_start: 0.8727 (ptp) cc_final: 0.8511 (ptm) REVERT: D 176 GLU cc_start: 0.8804 (tp30) cc_final: 0.8589 (tm-30) REVERT: D 215 ASP cc_start: 0.8015 (t0) cc_final: 0.7470 (t70) REVERT: D 218 LEU cc_start: 0.8913 (mp) cc_final: 0.8647 (mp) REVERT: D 291 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7748 (tm-30) REVERT: D 469 ASP cc_start: 0.7671 (m-30) cc_final: 0.7466 (m-30) REVERT: D 660 ASN cc_start: 0.8519 (t0) cc_final: 0.8310 (p0) REVERT: D 983 THR cc_start: 0.8563 (p) cc_final: 0.8336 (t) REVERT: D 1010 SER cc_start: 0.8870 (m) cc_final: 0.8584 (p) REVERT: D 1072 ASP cc_start: 0.8115 (m-30) cc_final: 0.7914 (m-30) REVERT: D 1143 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7864 (mt-10) REVERT: D 1148 ASP cc_start: 0.8315 (m-30) cc_final: 0.8008 (p0) REVERT: D 1273 MET cc_start: 0.7000 (mmt) cc_final: 0.6606 (mmp) REVERT: D 1403 MET cc_start: 0.9244 (mtt) cc_final: 0.9044 (mtp) REVERT: D 1596 MET cc_start: 0.8643 (ttp) cc_final: 0.8235 (ttp) REVERT: D 2101 LYS cc_start: 0.9289 (tttm) cc_final: 0.8813 (ttpp) REVERT: D 2232 GLU cc_start: 0.8286 (tt0) cc_final: 0.8039 (tp30) REVERT: E 186 MET cc_start: 0.8673 (mmt) cc_final: 0.8008 (mmt) REVERT: E 215 ASP cc_start: 0.8333 (t0) cc_final: 0.7544 (t0) REVERT: E 218 LEU cc_start: 0.9026 (mp) cc_final: 0.8742 (mp) REVERT: E 290 ASP cc_start: 0.7401 (t0) cc_final: 0.7094 (t0) REVERT: E 983 THR cc_start: 0.8678 (p) cc_final: 0.8405 (t) REVERT: E 1007 ASN cc_start: 0.8364 (m-40) cc_final: 0.8152 (m110) REVERT: E 1056 MET cc_start: 0.9298 (mtp) cc_final: 0.9019 (mtp) REVERT: E 1195 ARG cc_start: 0.8260 (ptm-80) cc_final: 0.7886 (ptt180) REVERT: E 1273 MET cc_start: 0.7035 (mmt) cc_final: 0.6672 (mmp) REVERT: E 1543 ASN cc_start: 0.8397 (p0) cc_final: 0.7766 (p0) REVERT: E 1884 MET cc_start: 0.8517 (mmm) cc_final: 0.8091 (mmm) REVERT: E 1895 TYR cc_start: 0.8256 (t80) cc_final: 0.7979 (t80) REVERT: E 2165 MET cc_start: 0.8821 (mtt) cc_final: 0.8522 (mtt) REVERT: E 2204 LYS cc_start: 0.8890 (mttp) cc_final: 0.8619 (mttp) outliers start: 0 outliers final: 6 residues processed: 1892 average time/residue: 1.9900 time to fit residues: 4996.7790 Evaluate side-chains 1069 residues out of total 10645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1063 time to evaluate : 8.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1683 ASP Chi-restraints excluded: chain B residue 2479 GLN Chi-restraints excluded: chain C residue 2409 ILE Chi-restraints excluded: chain D residue 1622 ASP Chi-restraints excluded: chain D residue 1790 ASP Chi-restraints excluded: chain E residue 1790 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.2332 > 50: distance: 27 - 32: 12.870 distance: 32 - 33: 6.350 distance: 33 - 34: 4.556 distance: 33 - 36: 6.407 distance: 34 - 35: 5.823 distance: 34 - 40: 9.088 distance: 36 - 37: 8.025 distance: 37 - 38: 5.317 distance: 37 - 39: 13.565 distance: 40 - 41: 11.351 distance: 41 - 42: 7.870 distance: 41 - 44: 4.506 distance: 42 - 43: 10.895 distance: 42 - 52: 22.623 distance: 44 - 45: 3.830 distance: 45 - 46: 8.885 distance: 45 - 47: 3.103 distance: 46 - 48: 4.333 distance: 47 - 49: 3.661 distance: 48 - 50: 5.616 distance: 49 - 50: 6.343 distance: 52 - 53: 13.979 distance: 53 - 54: 9.200 distance: 53 - 56: 18.434 distance: 54 - 55: 31.500 distance: 54 - 60: 9.170 distance: 56 - 57: 14.534 distance: 57 - 58: 23.773 distance: 57 - 59: 25.077 distance: 60 - 61: 19.557 distance: 60 - 66: 22.350 distance: 61 - 62: 30.610 distance: 61 - 64: 14.412 distance: 62 - 67: 32.540 distance: 65 - 66: 7.359 distance: 67 - 68: 16.079 distance: 68 - 69: 11.461 distance: 68 - 71: 12.470 distance: 69 - 70: 15.852 distance: 69 - 75: 12.189 distance: 71 - 72: 5.088 distance: 71 - 73: 18.069 distance: 72 - 74: 14.546 distance: 75 - 76: 19.703 distance: 76 - 77: 10.608 distance: 76 - 79: 5.041 distance: 77 - 78: 6.777 distance: 77 - 87: 11.821 distance: 79 - 80: 3.060 distance: 80 - 81: 16.404 distance: 80 - 82: 24.173 distance: 81 - 83: 4.482 distance: 82 - 84: 6.453 distance: 83 - 85: 24.407 distance: 84 - 85: 21.298 distance: 85 - 86: 9.630 distance: 87 - 88: 8.858 distance: 88 - 89: 11.998 distance: 88 - 91: 5.997 distance: 89 - 90: 22.932 distance: 89 - 92: 18.220 distance: 92 - 93: 6.709 distance: 93 - 94: 11.296 distance: 93 - 96: 6.324 distance: 94 - 95: 6.415 distance: 94 - 99: 7.126 distance: 96 - 98: 14.758 distance: 99 - 100: 5.467 distance: 99 - 105: 19.617 distance: 100 - 101: 14.211 distance: 100 - 103: 4.942 distance: 101 - 102: 7.430 distance: 101 - 106: 10.729 distance: 103 - 104: 14.735 distance: 104 - 105: 14.765 distance: 106 - 107: 13.910 distance: 107 - 108: 20.863 distance: 107 - 110: 15.844 distance: 108 - 111: 28.633