Starting phenix.real_space_refine (version: dev) on Thu Feb 23 14:33:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rak_24363/02_2023/7rak_24363_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rak_24363/02_2023/7rak_24363.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rak_24363/02_2023/7rak_24363.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rak_24363/02_2023/7rak_24363.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rak_24363/02_2023/7rak_24363_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rak_24363/02_2023/7rak_24363_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 Process input model Symmetric amino acids flipped Residue "U TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 61296 Number of models: 1 Model: "" Number of chains: 32 Chain: "U" Number of atoms: 3800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3800 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 8, 'TRANS': 498} Chain: "A" Number of atoms: 3800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3800 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 8, 'TRANS': 498} Chain: "B" Number of atoms: 3800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3800 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 8, 'TRANS': 498} Chain: "C" Number of atoms: 3800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3800 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 8, 'TRANS': 498} Chain: "D" Number of atoms: 3800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3800 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 8, 'TRANS': 498} Chain: "E" Number of atoms: 3800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3800 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 8, 'TRANS': 498} Chain: "F" Number of atoms: 3800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3800 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 8, 'TRANS': 498} Chain: "G" Number of atoms: 3800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3800 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 8, 'TRANS': 498} Chain: "H" Number of atoms: 3800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3800 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 8, 'TRANS': 498} Chain: "I" Number of atoms: 3800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3800 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 8, 'TRANS': 498} Chain: "J" Number of atoms: 3800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3800 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 8, 'TRANS': 498} Chain: "K" Number of atoms: 3800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3800 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 8, 'TRANS': 498} Chain: "L" Number of atoms: 3800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3800 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 8, 'TRANS': 498} Chain: "M" Number of atoms: 3800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3800 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 8, 'TRANS': 498} Chain: "N" Number of atoms: 3800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3800 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 8, 'TRANS': 498} Chain: "O" Number of atoms: 3800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3800 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 8, 'TRANS': 498} Chain: "U" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 25.54, per 1000 atoms: 0.42 Number of scatterers: 61296 At special positions: 0 Unit cell: (178.2, 178.2, 212.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 384 16.00 P 48 15.00 O 12384 8.00 N 10592 7.00 C 37888 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: 17.88 Conformation dependent library (CDL) restraints added in 7.9 seconds 16160 Ramachandran restraints generated. 8080 Oldfield, 0 Emsley, 8080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15040 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 272 helices and 64 sheets defined 39.5% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.74 Creating SS restraints... Processing helix chain 'U' and resid 13 through 26 removed outlier: 3.745A pdb=" N MET U 17 " --> pdb=" O ASP U 13 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN U 18 " --> pdb=" O ALA U 14 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE U 24 " --> pdb=" O LEU U 20 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE U 25 " --> pdb=" O ALA U 21 " (cutoff:3.500A) Processing helix chain 'U' and resid 56 through 60 removed outlier: 3.578A pdb=" N ARG U 60 " --> pdb=" O VAL U 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 56 through 60' Processing helix chain 'U' and resid 67 through 80 removed outlier: 3.734A pdb=" N LYS U 70 " --> pdb=" O PRO U 67 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N MET U 71 " --> pdb=" O ALA U 68 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LEU U 72 " --> pdb=" O ALA U 69 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU U 80 " --> pdb=" O LYS U 77 " (cutoff:3.500A) Processing helix chain 'U' and resid 88 through 107 removed outlier: 3.767A pdb=" N GLU U 103 " --> pdb=" O ARG U 99 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU U 104 " --> pdb=" O LYS U 100 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU U 105 " --> pdb=" O ALA U 101 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ASP U 106 " --> pdb=" O GLU U 102 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N GLN U 107 " --> pdb=" O GLU U 103 " (cutoff:3.500A) Processing helix chain 'U' and resid 113 through 131 removed outlier: 3.644A pdb=" N GLN U 123 " --> pdb=" O GLN U 119 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS U 124 " --> pdb=" O ALA U 120 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS U 130 " --> pdb=" O GLN U 126 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR U 131 " --> pdb=" O GLU U 127 " (cutoff:3.500A) Processing helix chain 'U' and resid 146 through 150 Processing helix chain 'U' and resid 169 through 172 No H-bonds generated for 'chain 'U' and resid 169 through 172' Processing helix chain 'U' and resid 249 through 273 removed outlier: 3.975A pdb=" N MET U 253 " --> pdb=" O PRO U 249 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU U 254 " --> pdb=" O ALA U 250 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU U 263 " --> pdb=" O GLU U 259 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS U 264 " --> pdb=" O GLU U 260 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP U 265 " --> pdb=" O LYS U 261 " (cutoff:3.500A) Processing helix chain 'U' and resid 286 through 288 No H-bonds generated for 'chain 'U' and resid 286 through 288' Processing helix chain 'U' and resid 290 through 292 No H-bonds generated for 'chain 'U' and resid 290 through 292' Processing helix chain 'U' and resid 305 through 308 No H-bonds generated for 'chain 'U' and resid 305 through 308' Processing helix chain 'U' and resid 369 through 389 removed outlier: 3.787A pdb=" N ALA U 377 " --> pdb=" O GLU U 373 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASP U 379 " --> pdb=" O ALA U 375 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASP U 380 " --> pdb=" O ARG U 376 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY U 383 " --> pdb=" O ASP U 379 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL U 384 " --> pdb=" O ASP U 380 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL U 385 " --> pdb=" O ALA U 381 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N CYS U 387 " --> pdb=" O GLY U 383 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N THR U 388 " --> pdb=" O VAL U 384 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE U 389 " --> pdb=" O VAL U 385 " (cutoff:3.500A) Processing helix chain 'U' and resid 401 through 415 removed outlier: 3.555A pdb=" N LYS U 408 " --> pdb=" O GLU U 404 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU U 411 " --> pdb=" O MET U 407 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU U 414 " --> pdb=" O ARG U 410 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLY U 415 " --> pdb=" O GLU U 411 " (cutoff:3.500A) Processing helix chain 'U' and resid 420 through 440 removed outlier: 4.240A pdb=" N GLU U 432 " --> pdb=" O ALA U 428 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N VAL U 433 " --> pdb=" O ASP U 429 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ILE U 434 " --> pdb=" O ALA U 430 " (cutoff:3.500A) Proline residue: U 435 - end of helix Processing helix chain 'U' and resid 448 through 458 removed outlier: 3.572A pdb=" N ALA U 455 " --> pdb=" O VAL U 451 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA U 456 " --> pdb=" O LYS U 452 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N HIS U 457 " --> pdb=" O VAL U 453 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ALA U 458 " --> pdb=" O ARG U 454 " (cutoff:3.500A) Processing helix chain 'U' and resid 487 through 499 removed outlier: 3.557A pdb=" N ALA U 492 " --> pdb=" O VAL U 488 " (cutoff:3.500A) Processing helix chain 'U' and resid 501 through 504 No H-bonds generated for 'chain 'U' and resid 501 through 504' Processing helix chain 'A' and resid 13 through 26 removed outlier: 3.744A pdb=" N MET A 17 " --> pdb=" O ASP A 13 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN A 18 " --> pdb=" O ALA A 14 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE A 24 " --> pdb=" O LEU A 20 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 60 removed outlier: 3.578A pdb=" N ARG A 60 " --> pdb=" O VAL A 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 56 through 60' Processing helix chain 'A' and resid 67 through 80 removed outlier: 3.733A pdb=" N LYS A 70 " --> pdb=" O PRO A 67 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N MET A 71 " --> pdb=" O ALA A 68 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LEU A 72 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU A 80 " --> pdb=" O LYS A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 107 removed outlier: 3.765A pdb=" N GLU A 103 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A 104 " --> pdb=" O LYS A 100 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 105 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASP A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N GLN A 107 " --> pdb=" O GLU A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 131 removed outlier: 3.644A pdb=" N GLN A 123 " --> pdb=" O GLN A 119 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS A 124 " --> pdb=" O ALA A 120 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS A 130 " --> pdb=" O GLN A 126 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR A 131 " --> pdb=" O GLU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 150 Processing helix chain 'A' and resid 169 through 172 No H-bonds generated for 'chain 'A' and resid 169 through 172' Processing helix chain 'A' and resid 249 through 273 removed outlier: 3.975A pdb=" N MET A 253 " --> pdb=" O PRO A 249 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU A 254 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU A 263 " --> pdb=" O GLU A 259 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS A 264 " --> pdb=" O GLU A 260 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 290 through 292 No H-bonds generated for 'chain 'A' and resid 290 through 292' Processing helix chain 'A' and resid 305 through 308 No H-bonds generated for 'chain 'A' and resid 305 through 308' Processing helix chain 'A' and resid 369 through 389 removed outlier: 3.787A pdb=" N ALA A 377 " --> pdb=" O GLU A 373 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ASP A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASP A 380 " --> pdb=" O ARG A 376 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY A 383 " --> pdb=" O ASP A 379 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL A 384 " --> pdb=" O ASP A 380 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N CYS A 387 " --> pdb=" O GLY A 383 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N THR A 388 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE A 389 " --> pdb=" O VAL A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 415 removed outlier: 3.554A pdb=" N LYS A 408 " --> pdb=" O GLU A 404 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU A 411 " --> pdb=" O MET A 407 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU A 414 " --> pdb=" O ARG A 410 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLY A 415 " --> pdb=" O GLU A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 440 removed outlier: 4.246A pdb=" N GLU A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N VAL A 433 " --> pdb=" O ASP A 429 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ILE A 434 " --> pdb=" O ALA A 430 " (cutoff:3.500A) Proline residue: A 435 - end of helix Processing helix chain 'A' and resid 448 through 458 removed outlier: 3.562A pdb=" N ALA A 455 " --> pdb=" O VAL A 451 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 456 " --> pdb=" O LYS A 452 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N HIS A 457 " --> pdb=" O VAL A 453 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ALA A 458 " --> pdb=" O ARG A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 499 removed outlier: 3.558A pdb=" N ALA A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 504 No H-bonds generated for 'chain 'A' and resid 501 through 504' Processing helix chain 'B' and resid 13 through 26 removed outlier: 3.744A pdb=" N MET B 17 " --> pdb=" O ASP B 13 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN B 18 " --> pdb=" O ALA B 14 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE B 24 " --> pdb=" O LEU B 20 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 60 removed outlier: 3.577A pdb=" N ARG B 60 " --> pdb=" O VAL B 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 56 through 60' Processing helix chain 'B' and resid 67 through 80 removed outlier: 3.734A pdb=" N LYS B 70 " --> pdb=" O PRO B 67 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N MET B 71 " --> pdb=" O ALA B 68 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU B 72 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU B 80 " --> pdb=" O LYS B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 107 removed outlier: 3.766A pdb=" N GLU B 103 " --> pdb=" O ARG B 99 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU B 104 " --> pdb=" O LYS B 100 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 105 " --> pdb=" O ALA B 101 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASP B 106 " --> pdb=" O GLU B 102 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N GLN B 107 " --> pdb=" O GLU B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 131 removed outlier: 3.644A pdb=" N GLN B 123 " --> pdb=" O GLN B 119 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS B 124 " --> pdb=" O ALA B 120 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS B 130 " --> pdb=" O GLN B 126 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR B 131 " --> pdb=" O GLU B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 150 Processing helix chain 'B' and resid 169 through 172 No H-bonds generated for 'chain 'B' and resid 169 through 172' Processing helix chain 'B' and resid 249 through 273 removed outlier: 3.975A pdb=" N MET B 253 " --> pdb=" O PRO B 249 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU B 254 " --> pdb=" O ALA B 250 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU B 263 " --> pdb=" O GLU B 259 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS B 264 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASP B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 290 through 292 No H-bonds generated for 'chain 'B' and resid 290 through 292' Processing helix chain 'B' and resid 305 through 308 No H-bonds generated for 'chain 'B' and resid 305 through 308' Processing helix chain 'B' and resid 369 through 389 removed outlier: 3.788A pdb=" N ALA B 377 " --> pdb=" O GLU B 373 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASP B 379 " --> pdb=" O ALA B 375 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASP B 380 " --> pdb=" O ARG B 376 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY B 383 " --> pdb=" O ASP B 379 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL B 384 " --> pdb=" O ASP B 380 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N CYS B 387 " --> pdb=" O GLY B 383 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N THR B 388 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE B 389 " --> pdb=" O VAL B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 415 removed outlier: 3.553A pdb=" N LYS B 408 " --> pdb=" O GLU B 404 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU B 411 " --> pdb=" O MET B 407 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU B 414 " --> pdb=" O ARG B 410 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLY B 415 " --> pdb=" O GLU B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 440 removed outlier: 4.240A pdb=" N GLU B 432 " --> pdb=" O ALA B 428 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N VAL B 433 " --> pdb=" O ASP B 429 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ILE B 434 " --> pdb=" O ALA B 430 " (cutoff:3.500A) Proline residue: B 435 - end of helix Processing helix chain 'B' and resid 448 through 458 removed outlier: 3.577A pdb=" N ALA B 455 " --> pdb=" O VAL B 451 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA B 456 " --> pdb=" O LYS B 452 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N HIS B 457 " --> pdb=" O VAL B 453 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA B 458 " --> pdb=" O ARG B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 499 removed outlier: 3.557A pdb=" N ALA B 492 " --> pdb=" O VAL B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 504 No H-bonds generated for 'chain 'B' and resid 501 through 504' Processing helix chain 'C' and resid 13 through 26 removed outlier: 3.757A pdb=" N MET C 17 " --> pdb=" O ASP C 13 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN C 18 " --> pdb=" O ALA C 14 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE C 24 " --> pdb=" O LEU C 20 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 60 removed outlier: 3.577A pdb=" N ARG C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 56 through 60' Processing helix chain 'C' and resid 68 through 80 removed outlier: 4.576A pdb=" N LEU C 72 " --> pdb=" O ALA C 68 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ILE C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 107 removed outlier: 3.765A pdb=" N GLU C 103 " --> pdb=" O ARG C 99 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU C 104 " --> pdb=" O LYS C 100 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU C 105 " --> pdb=" O ALA C 101 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASP C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N GLN C 107 " --> pdb=" O GLU C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 131 removed outlier: 3.645A pdb=" N GLN C 123 " --> pdb=" O GLN C 119 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS C 124 " --> pdb=" O ALA C 120 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS C 130 " --> pdb=" O GLN C 126 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR C 131 " --> pdb=" O GLU C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 150 Processing helix chain 'C' and resid 169 through 172 No H-bonds generated for 'chain 'C' and resid 169 through 172' Processing helix chain 'C' and resid 249 through 273 removed outlier: 3.980A pdb=" N MET C 253 " --> pdb=" O PRO C 249 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU C 254 " --> pdb=" O ALA C 250 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU C 263 " --> pdb=" O GLU C 259 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LYS C 264 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASP C 265 " --> pdb=" O LYS C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 290 through 292 No H-bonds generated for 'chain 'C' and resid 290 through 292' Processing helix chain 'C' and resid 305 through 308 No H-bonds generated for 'chain 'C' and resid 305 through 308' Processing helix chain 'C' and resid 369 through 389 removed outlier: 3.788A pdb=" N ALA C 377 " --> pdb=" O GLU C 373 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ASP C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASP C 380 " --> pdb=" O ARG C 376 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY C 383 " --> pdb=" O ASP C 379 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL C 384 " --> pdb=" O ASP C 380 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N CYS C 387 " --> pdb=" O GLY C 383 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N THR C 388 " --> pdb=" O VAL C 384 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE C 389 " --> pdb=" O VAL C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 415 removed outlier: 3.555A pdb=" N LYS C 408 " --> pdb=" O GLU C 404 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU C 411 " --> pdb=" O MET C 407 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLU C 414 " --> pdb=" O ARG C 410 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLY C 415 " --> pdb=" O GLU C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 440 removed outlier: 4.243A pdb=" N GLU C 432 " --> pdb=" O ALA C 428 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N VAL C 433 " --> pdb=" O ASP C 429 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ILE C 434 " --> pdb=" O ALA C 430 " (cutoff:3.500A) Proline residue: C 435 - end of helix Processing helix chain 'C' and resid 448 through 458 removed outlier: 3.571A pdb=" N ALA C 455 " --> pdb=" O VAL C 451 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA C 456 " --> pdb=" O LYS C 452 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N HIS C 457 " --> pdb=" O VAL C 453 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA C 458 " --> pdb=" O ARG C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 499 removed outlier: 3.558A pdb=" N ALA C 492 " --> pdb=" O VAL C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 504 No H-bonds generated for 'chain 'C' and resid 501 through 504' Processing helix chain 'D' and resid 13 through 26 removed outlier: 3.749A pdb=" N MET D 17 " --> pdb=" O ASP D 13 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN D 18 " --> pdb=" O ALA D 14 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE D 24 " --> pdb=" O LEU D 20 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE D 25 " --> pdb=" O ALA D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 60 removed outlier: 3.568A pdb=" N ARG D 60 " --> pdb=" O VAL D 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 56 through 60' Processing helix chain 'D' and resid 67 through 80 removed outlier: 3.735A pdb=" N LYS D 70 " --> pdb=" O PRO D 67 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N MET D 71 " --> pdb=" O ALA D 68 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LEU D 72 " --> pdb=" O ALA D 69 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU D 80 " --> pdb=" O LYS D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 107 removed outlier: 3.766A pdb=" N GLU D 103 " --> pdb=" O ARG D 99 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU D 104 " --> pdb=" O LYS D 100 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU D 105 " --> pdb=" O ALA D 101 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASP D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N GLN D 107 " --> pdb=" O GLU D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 131 removed outlier: 3.643A pdb=" N GLN D 123 " --> pdb=" O GLN D 119 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS D 124 " --> pdb=" O ALA D 120 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS D 130 " --> pdb=" O GLN D 126 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR D 131 " --> pdb=" O GLU D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 150 Processing helix chain 'D' and resid 169 through 172 No H-bonds generated for 'chain 'D' and resid 169 through 172' Processing helix chain 'D' and resid 249 through 273 removed outlier: 3.975A pdb=" N MET D 253 " --> pdb=" O PRO D 249 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU D 254 " --> pdb=" O ALA D 250 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU D 263 " --> pdb=" O GLU D 259 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LYS D 264 " --> pdb=" O GLU D 260 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASP D 265 " --> pdb=" O LYS D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 290 through 292 No H-bonds generated for 'chain 'D' and resid 290 through 292' Processing helix chain 'D' and resid 305 through 308 No H-bonds generated for 'chain 'D' and resid 305 through 308' Processing helix chain 'D' and resid 369 through 389 removed outlier: 3.786A pdb=" N ALA D 377 " --> pdb=" O GLU D 373 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ASP D 379 " --> pdb=" O ALA D 375 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ASP D 380 " --> pdb=" O ARG D 376 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY D 383 " --> pdb=" O ASP D 379 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N VAL D 384 " --> pdb=" O ASP D 380 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL D 385 " --> pdb=" O ALA D 381 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N CYS D 387 " --> pdb=" O GLY D 383 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR D 388 " --> pdb=" O VAL D 384 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE D 389 " --> pdb=" O VAL D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 415 removed outlier: 3.555A pdb=" N LYS D 408 " --> pdb=" O GLU D 404 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLU D 411 " --> pdb=" O MET D 407 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU D 414 " --> pdb=" O ARG D 410 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLY D 415 " --> pdb=" O GLU D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 438 removed outlier: 3.500A pdb=" N LEU D 431 " --> pdb=" O PHE D 427 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU D 432 " --> pdb=" O ALA D 428 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N VAL D 433 " --> pdb=" O ASP D 429 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ILE D 434 " --> pdb=" O ALA D 430 " (cutoff:3.500A) Proline residue: D 435 - end of helix Processing helix chain 'D' and resid 448 through 458 removed outlier: 3.579A pdb=" N ALA D 455 " --> pdb=" O VAL D 451 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA D 456 " --> pdb=" O LYS D 452 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N HIS D 457 " --> pdb=" O VAL D 453 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ALA D 458 " --> pdb=" O ARG D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 499 removed outlier: 3.558A pdb=" N ALA D 492 " --> pdb=" O VAL D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 504 No H-bonds generated for 'chain 'D' and resid 501 through 504' Processing helix chain 'E' and resid 13 through 26 removed outlier: 3.744A pdb=" N MET E 17 " --> pdb=" O ASP E 13 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN E 18 " --> pdb=" O ALA E 14 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE E 24 " --> pdb=" O LEU E 20 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE E 25 " --> pdb=" O ALA E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 60 removed outlier: 3.578A pdb=" N ARG E 60 " --> pdb=" O VAL E 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 56 through 60' Processing helix chain 'E' and resid 67 through 80 removed outlier: 3.733A pdb=" N LYS E 70 " --> pdb=" O PRO E 67 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N MET E 71 " --> pdb=" O ALA E 68 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU E 72 " --> pdb=" O ALA E 69 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU E 80 " --> pdb=" O LYS E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 107 removed outlier: 3.767A pdb=" N GLU E 103 " --> pdb=" O ARG E 99 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU E 104 " --> pdb=" O LYS E 100 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU E 105 " --> pdb=" O ALA E 101 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ASP E 106 " --> pdb=" O GLU E 102 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N GLN E 107 " --> pdb=" O GLU E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 131 removed outlier: 3.643A pdb=" N GLN E 123 " --> pdb=" O GLN E 119 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS E 124 " --> pdb=" O ALA E 120 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS E 130 " --> pdb=" O GLN E 126 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR E 131 " --> pdb=" O GLU E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 150 Processing helix chain 'E' and resid 169 through 172 No H-bonds generated for 'chain 'E' and resid 169 through 172' Processing helix chain 'E' and resid 249 through 273 removed outlier: 3.976A pdb=" N MET E 253 " --> pdb=" O PRO E 249 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU E 254 " --> pdb=" O ALA E 250 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU E 263 " --> pdb=" O GLU E 259 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LYS E 264 " --> pdb=" O GLU E 260 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP E 265 " --> pdb=" O LYS E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 288 No H-bonds generated for 'chain 'E' and resid 286 through 288' Processing helix chain 'E' and resid 290 through 292 No H-bonds generated for 'chain 'E' and resid 290 through 292' Processing helix chain 'E' and resid 305 through 308 No H-bonds generated for 'chain 'E' and resid 305 through 308' Processing helix chain 'E' and resid 369 through 389 removed outlier: 3.788A pdb=" N ALA E 377 " --> pdb=" O GLU E 373 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASP E 379 " --> pdb=" O ALA E 375 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASP E 380 " --> pdb=" O ARG E 376 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY E 383 " --> pdb=" O ASP E 379 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL E 384 " --> pdb=" O ASP E 380 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL E 385 " --> pdb=" O ALA E 381 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N CYS E 387 " --> pdb=" O GLY E 383 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N THR E 388 " --> pdb=" O VAL E 384 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE E 389 " --> pdb=" O VAL E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 415 removed outlier: 3.555A pdb=" N LYS E 408 " --> pdb=" O GLU E 404 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU E 411 " --> pdb=" O MET E 407 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU E 414 " --> pdb=" O ARG E 410 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLY E 415 " --> pdb=" O GLU E 411 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 440 removed outlier: 4.240A pdb=" N GLU E 432 " --> pdb=" O ALA E 428 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N VAL E 433 " --> pdb=" O ASP E 429 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ILE E 434 " --> pdb=" O ALA E 430 " (cutoff:3.500A) Proline residue: E 435 - end of helix Processing helix chain 'E' and resid 448 through 458 removed outlier: 3.569A pdb=" N ALA E 455 " --> pdb=" O VAL E 451 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA E 456 " --> pdb=" O LYS E 452 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N HIS E 457 " --> pdb=" O VAL E 453 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ALA E 458 " --> pdb=" O ARG E 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 487 through 499 removed outlier: 3.559A pdb=" N ALA E 492 " --> pdb=" O VAL E 488 " (cutoff:3.500A) Processing helix chain 'E' and resid 501 through 504 No H-bonds generated for 'chain 'E' and resid 501 through 504' Processing helix chain 'F' and resid 13 through 26 removed outlier: 3.760A pdb=" N MET F 17 " --> pdb=" O ASP F 13 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN F 18 " --> pdb=" O ALA F 14 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE F 24 " --> pdb=" O LEU F 20 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE F 25 " --> pdb=" O ALA F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 60 removed outlier: 3.577A pdb=" N ARG F 60 " --> pdb=" O VAL F 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 56 through 60' Processing helix chain 'F' and resid 67 through 80 removed outlier: 3.734A pdb=" N LYS F 70 " --> pdb=" O PRO F 67 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N MET F 71 " --> pdb=" O ALA F 68 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU F 72 " --> pdb=" O ALA F 69 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU F 80 " --> pdb=" O LYS F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 107 removed outlier: 3.749A pdb=" N GLU F 103 " --> pdb=" O ARG F 99 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU F 104 " --> pdb=" O LYS F 100 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU F 105 " --> pdb=" O ALA F 101 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ASP F 106 " --> pdb=" O GLU F 102 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N GLN F 107 " --> pdb=" O GLU F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 131 removed outlier: 3.634A pdb=" N GLN F 123 " --> pdb=" O GLN F 119 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS F 124 " --> pdb=" O ALA F 120 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS F 130 " --> pdb=" O GLN F 126 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR F 131 " --> pdb=" O GLU F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 150 Processing helix chain 'F' and resid 169 through 172 No H-bonds generated for 'chain 'F' and resid 169 through 172' Processing helix chain 'F' and resid 249 through 273 removed outlier: 3.977A pdb=" N MET F 253 " --> pdb=" O PRO F 249 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU F 254 " --> pdb=" O ALA F 250 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU F 263 " --> pdb=" O GLU F 259 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS F 264 " --> pdb=" O GLU F 260 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP F 265 " --> pdb=" O LYS F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 288 No H-bonds generated for 'chain 'F' and resid 286 through 288' Processing helix chain 'F' and resid 290 through 292 No H-bonds generated for 'chain 'F' and resid 290 through 292' Processing helix chain 'F' and resid 305 through 308 No H-bonds generated for 'chain 'F' and resid 305 through 308' Processing helix chain 'F' and resid 369 through 389 removed outlier: 3.787A pdb=" N ALA F 377 " --> pdb=" O GLU F 373 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ASP F 379 " --> pdb=" O ALA F 375 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASP F 380 " --> pdb=" O ARG F 376 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY F 383 " --> pdb=" O ASP F 379 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL F 384 " --> pdb=" O ASP F 380 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL F 385 " --> pdb=" O ALA F 381 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N CYS F 387 " --> pdb=" O GLY F 383 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N THR F 388 " --> pdb=" O VAL F 384 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE F 389 " --> pdb=" O VAL F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 415 removed outlier: 3.553A pdb=" N LYS F 408 " --> pdb=" O GLU F 404 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU F 411 " --> pdb=" O MET F 407 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLU F 414 " --> pdb=" O ARG F 410 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLY F 415 " --> pdb=" O GLU F 411 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 440 removed outlier: 4.230A pdb=" N GLU F 432 " --> pdb=" O ALA F 428 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N VAL F 433 " --> pdb=" O ASP F 429 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ILE F 434 " --> pdb=" O ALA F 430 " (cutoff:3.500A) Proline residue: F 435 - end of helix Processing helix chain 'F' and resid 448 through 458 removed outlier: 3.569A pdb=" N ALA F 455 " --> pdb=" O VAL F 451 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA F 456 " --> pdb=" O LYS F 452 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N HIS F 457 " --> pdb=" O VAL F 453 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA F 458 " --> pdb=" O ARG F 454 " (cutoff:3.500A) Processing helix chain 'F' and resid 487 through 499 removed outlier: 3.556A pdb=" N ALA F 492 " --> pdb=" O VAL F 488 " (cutoff:3.500A) Processing helix chain 'F' and resid 501 through 504 No H-bonds generated for 'chain 'F' and resid 501 through 504' Processing helix chain 'G' and resid 13 through 26 removed outlier: 3.744A pdb=" N MET G 17 " --> pdb=" O ASP G 13 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN G 18 " --> pdb=" O ALA G 14 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE G 24 " --> pdb=" O LEU G 20 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE G 25 " --> pdb=" O ALA G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 60 removed outlier: 3.578A pdb=" N ARG G 60 " --> pdb=" O VAL G 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 56 through 60' Processing helix chain 'G' and resid 67 through 80 removed outlier: 3.732A pdb=" N LYS G 70 " --> pdb=" O PRO G 67 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N MET G 71 " --> pdb=" O ALA G 68 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU G 72 " --> pdb=" O ALA G 69 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU G 80 " --> pdb=" O LYS G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 107 removed outlier: 3.768A pdb=" N GLU G 103 " --> pdb=" O ARG G 99 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU G 104 " --> pdb=" O LYS G 100 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU G 105 " --> pdb=" O ALA G 101 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASP G 106 " --> pdb=" O GLU G 102 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N GLN G 107 " --> pdb=" O GLU G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 131 removed outlier: 3.643A pdb=" N GLN G 123 " --> pdb=" O GLN G 119 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS G 124 " --> pdb=" O ALA G 120 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS G 130 " --> pdb=" O GLN G 126 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR G 131 " --> pdb=" O GLU G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 150 Processing helix chain 'G' and resid 169 through 172 No H-bonds generated for 'chain 'G' and resid 169 through 172' Processing helix chain 'G' and resid 249 through 273 removed outlier: 3.974A pdb=" N MET G 253 " --> pdb=" O PRO G 249 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU G 254 " --> pdb=" O ALA G 250 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU G 263 " --> pdb=" O GLU G 259 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS G 264 " --> pdb=" O GLU G 260 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP G 265 " --> pdb=" O LYS G 261 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 288 No H-bonds generated for 'chain 'G' and resid 286 through 288' Processing helix chain 'G' and resid 290 through 292 No H-bonds generated for 'chain 'G' and resid 290 through 292' Processing helix chain 'G' and resid 305 through 308 No H-bonds generated for 'chain 'G' and resid 305 through 308' Processing helix chain 'G' and resid 369 through 389 removed outlier: 3.789A pdb=" N ALA G 377 " --> pdb=" O GLU G 373 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASP G 379 " --> pdb=" O ALA G 375 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ASP G 380 " --> pdb=" O ARG G 376 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY G 383 " --> pdb=" O ASP G 379 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N VAL G 384 " --> pdb=" O ASP G 380 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL G 385 " --> pdb=" O ALA G 381 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N CYS G 387 " --> pdb=" O GLY G 383 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N THR G 388 " --> pdb=" O VAL G 384 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE G 389 " --> pdb=" O VAL G 385 " (cutoff:3.500A) Processing helix chain 'G' and resid 401 through 415 removed outlier: 3.554A pdb=" N LYS G 408 " --> pdb=" O GLU G 404 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU G 411 " --> pdb=" O MET G 407 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU G 414 " --> pdb=" O ARG G 410 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLY G 415 " --> pdb=" O GLU G 411 " (cutoff:3.500A) Processing helix chain 'G' and resid 420 through 440 removed outlier: 4.240A pdb=" N GLU G 432 " --> pdb=" O ALA G 428 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N VAL G 433 " --> pdb=" O ASP G 429 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ILE G 434 " --> pdb=" O ALA G 430 " (cutoff:3.500A) Proline residue: G 435 - end of helix Processing helix chain 'G' and resid 448 through 458 removed outlier: 3.571A pdb=" N ALA G 455 " --> pdb=" O VAL G 451 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA G 456 " --> pdb=" O LYS G 452 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N HIS G 457 " --> pdb=" O VAL G 453 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ALA G 458 " --> pdb=" O ARG G 454 " (cutoff:3.500A) Processing helix chain 'G' and resid 487 through 499 removed outlier: 3.557A pdb=" N ALA G 492 " --> pdb=" O VAL G 488 " (cutoff:3.500A) Processing helix chain 'G' and resid 501 through 504 No H-bonds generated for 'chain 'G' and resid 501 through 504' Processing helix chain 'H' and resid 13 through 26 removed outlier: 3.757A pdb=" N MET H 17 " --> pdb=" O ASP H 13 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN H 18 " --> pdb=" O ALA H 14 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE H 24 " --> pdb=" O LEU H 20 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE H 25 " --> pdb=" O ALA H 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 60 removed outlier: 3.575A pdb=" N ARG H 60 " --> pdb=" O VAL H 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 56 through 60' Processing helix chain 'H' and resid 67 through 80 removed outlier: 3.735A pdb=" N LYS H 70 " --> pdb=" O PRO H 67 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N MET H 71 " --> pdb=" O ALA H 68 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU H 72 " --> pdb=" O ALA H 69 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU H 80 " --> pdb=" O LYS H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 107 removed outlier: 3.749A pdb=" N GLU H 103 " --> pdb=" O ARG H 99 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU H 104 " --> pdb=" O LYS H 100 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU H 105 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASP H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N GLN H 107 " --> pdb=" O GLU H 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 131 removed outlier: 3.629A pdb=" N GLN H 123 " --> pdb=" O GLN H 119 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS H 124 " --> pdb=" O ALA H 120 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS H 130 " --> pdb=" O GLN H 126 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR H 131 " --> pdb=" O GLU H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 146 through 150 Processing helix chain 'H' and resid 169 through 172 No H-bonds generated for 'chain 'H' and resid 169 through 172' Processing helix chain 'H' and resid 249 through 273 removed outlier: 3.975A pdb=" N MET H 253 " --> pdb=" O PRO H 249 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU H 254 " --> pdb=" O ALA H 250 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU H 263 " --> pdb=" O GLU H 259 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS H 264 " --> pdb=" O GLU H 260 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP H 265 " --> pdb=" O LYS H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 286 through 288 No H-bonds generated for 'chain 'H' and resid 286 through 288' Processing helix chain 'H' and resid 290 through 292 No H-bonds generated for 'chain 'H' and resid 290 through 292' Processing helix chain 'H' and resid 305 through 308 No H-bonds generated for 'chain 'H' and resid 305 through 308' Processing helix chain 'H' and resid 369 through 389 removed outlier: 3.788A pdb=" N ALA H 377 " --> pdb=" O GLU H 373 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASP H 379 " --> pdb=" O ALA H 375 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASP H 380 " --> pdb=" O ARG H 376 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY H 383 " --> pdb=" O ASP H 379 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N VAL H 384 " --> pdb=" O ASP H 380 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL H 385 " --> pdb=" O ALA H 381 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N CYS H 387 " --> pdb=" O GLY H 383 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N THR H 388 " --> pdb=" O VAL H 384 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE H 389 " --> pdb=" O VAL H 385 " (cutoff:3.500A) Processing helix chain 'H' and resid 401 through 415 removed outlier: 3.554A pdb=" N LYS H 408 " --> pdb=" O GLU H 404 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU H 411 " --> pdb=" O MET H 407 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU H 414 " --> pdb=" O ARG H 410 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLY H 415 " --> pdb=" O GLU H 411 " (cutoff:3.500A) Processing helix chain 'H' and resid 420 through 438 removed outlier: 3.503A pdb=" N LEU H 431 " --> pdb=" O PHE H 427 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLU H 432 " --> pdb=" O ALA H 428 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N VAL H 433 " --> pdb=" O ASP H 429 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ILE H 434 " --> pdb=" O ALA H 430 " (cutoff:3.500A) Proline residue: H 435 - end of helix Processing helix chain 'H' and resid 448 through 458 removed outlier: 3.576A pdb=" N ALA H 455 " --> pdb=" O VAL H 451 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA H 456 " --> pdb=" O LYS H 452 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N HIS H 457 " --> pdb=" O VAL H 453 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ALA H 458 " --> pdb=" O ARG H 454 " (cutoff:3.500A) Processing helix chain 'H' and resid 487 through 499 removed outlier: 3.557A pdb=" N ALA H 492 " --> pdb=" O VAL H 488 " (cutoff:3.500A) Processing helix chain 'H' and resid 501 through 504 No H-bonds generated for 'chain 'H' and resid 501 through 504' Processing helix chain 'I' and resid 13 through 26 removed outlier: 3.744A pdb=" N MET I 17 " --> pdb=" O ASP I 13 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN I 18 " --> pdb=" O ALA I 14 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE I 24 " --> pdb=" O LEU I 20 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE I 25 " --> pdb=" O ALA I 21 " (cutoff:3.500A) Processing helix chain 'I' and resid 56 through 60 removed outlier: 3.577A pdb=" N ARG I 60 " --> pdb=" O VAL I 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 56 through 60' Processing helix chain 'I' and resid 67 through 80 removed outlier: 3.733A pdb=" N LYS I 70 " --> pdb=" O PRO I 67 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N MET I 71 " --> pdb=" O ALA I 68 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LEU I 72 " --> pdb=" O ALA I 69 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU I 80 " --> pdb=" O LYS I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 107 removed outlier: 3.767A pdb=" N GLU I 103 " --> pdb=" O ARG I 99 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU I 104 " --> pdb=" O LYS I 100 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU I 105 " --> pdb=" O ALA I 101 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASP I 106 " --> pdb=" O GLU I 102 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N GLN I 107 " --> pdb=" O GLU I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 113 through 131 removed outlier: 3.642A pdb=" N GLN I 123 " --> pdb=" O GLN I 119 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS I 124 " --> pdb=" O ALA I 120 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS I 130 " --> pdb=" O GLN I 126 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR I 131 " --> pdb=" O GLU I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 146 through 150 Processing helix chain 'I' and resid 169 through 172 No H-bonds generated for 'chain 'I' and resid 169 through 172' Processing helix chain 'I' and resid 249 through 273 removed outlier: 3.975A pdb=" N MET I 253 " --> pdb=" O PRO I 249 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU I 254 " --> pdb=" O ALA I 250 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU I 263 " --> pdb=" O GLU I 259 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS I 264 " --> pdb=" O GLU I 260 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASP I 265 " --> pdb=" O LYS I 261 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 288 No H-bonds generated for 'chain 'I' and resid 286 through 288' Processing helix chain 'I' and resid 290 through 292 No H-bonds generated for 'chain 'I' and resid 290 through 292' Processing helix chain 'I' and resid 305 through 308 No H-bonds generated for 'chain 'I' and resid 305 through 308' Processing helix chain 'I' and resid 369 through 389 removed outlier: 3.788A pdb=" N ALA I 377 " --> pdb=" O GLU I 373 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASP I 379 " --> pdb=" O ALA I 375 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASP I 380 " --> pdb=" O ARG I 376 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY I 383 " --> pdb=" O ASP I 379 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VAL I 384 " --> pdb=" O ASP I 380 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL I 385 " --> pdb=" O ALA I 381 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N CYS I 387 " --> pdb=" O GLY I 383 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR I 388 " --> pdb=" O VAL I 384 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE I 389 " --> pdb=" O VAL I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 401 through 415 removed outlier: 3.554A pdb=" N LYS I 408 " --> pdb=" O GLU I 404 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLU I 411 " --> pdb=" O MET I 407 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU I 414 " --> pdb=" O ARG I 410 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLY I 415 " --> pdb=" O GLU I 411 " (cutoff:3.500A) Processing helix chain 'I' and resid 420 through 440 removed outlier: 4.245A pdb=" N GLU I 432 " --> pdb=" O ALA I 428 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N VAL I 433 " --> pdb=" O ASP I 429 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ILE I 434 " --> pdb=" O ALA I 430 " (cutoff:3.500A) Proline residue: I 435 - end of helix Processing helix chain 'I' and resid 448 through 458 removed outlier: 3.571A pdb=" N ALA I 455 " --> pdb=" O VAL I 451 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA I 456 " --> pdb=" O LYS I 452 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N HIS I 457 " --> pdb=" O VAL I 453 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ALA I 458 " --> pdb=" O ARG I 454 " (cutoff:3.500A) Processing helix chain 'I' and resid 487 through 499 removed outlier: 3.557A pdb=" N ALA I 492 " --> pdb=" O VAL I 488 " (cutoff:3.500A) Processing helix chain 'I' and resid 501 through 504 No H-bonds generated for 'chain 'I' and resid 501 through 504' Processing helix chain 'J' and resid 13 through 26 removed outlier: 3.760A pdb=" N MET J 17 " --> pdb=" O ASP J 13 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN J 18 " --> pdb=" O ALA J 14 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE J 24 " --> pdb=" O LEU J 20 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE J 25 " --> pdb=" O ALA J 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 60 removed outlier: 3.578A pdb=" N ARG J 60 " --> pdb=" O VAL J 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 56 through 60' Processing helix chain 'J' and resid 67 through 80 removed outlier: 3.734A pdb=" N LYS J 70 " --> pdb=" O PRO J 67 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N MET J 71 " --> pdb=" O ALA J 68 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU J 72 " --> pdb=" O ALA J 69 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU J 80 " --> pdb=" O LYS J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 107 removed outlier: 3.748A pdb=" N GLU J 103 " --> pdb=" O ARG J 99 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU J 104 " --> pdb=" O LYS J 100 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU J 105 " --> pdb=" O ALA J 101 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ASP J 106 " --> pdb=" O GLU J 102 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N GLN J 107 " --> pdb=" O GLU J 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 131 removed outlier: 3.633A pdb=" N GLN J 123 " --> pdb=" O GLN J 119 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS J 124 " --> pdb=" O ALA J 120 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS J 130 " --> pdb=" O GLN J 126 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR J 131 " --> pdb=" O GLU J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 146 through 150 Processing helix chain 'J' and resid 169 through 172 No H-bonds generated for 'chain 'J' and resid 169 through 172' Processing helix chain 'J' and resid 249 through 273 removed outlier: 3.976A pdb=" N MET J 253 " --> pdb=" O PRO J 249 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU J 254 " --> pdb=" O ALA J 250 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU J 263 " --> pdb=" O GLU J 259 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LYS J 264 " --> pdb=" O GLU J 260 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP J 265 " --> pdb=" O LYS J 261 " (cutoff:3.500A) Processing helix chain 'J' and resid 286 through 288 No H-bonds generated for 'chain 'J' and resid 286 through 288' Processing helix chain 'J' and resid 290 through 292 No H-bonds generated for 'chain 'J' and resid 290 through 292' Processing helix chain 'J' and resid 305 through 308 No H-bonds generated for 'chain 'J' and resid 305 through 308' Processing helix chain 'J' and resid 369 through 389 removed outlier: 3.787A pdb=" N ALA J 377 " --> pdb=" O GLU J 373 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASP J 379 " --> pdb=" O ALA J 375 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASP J 380 " --> pdb=" O ARG J 376 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY J 383 " --> pdb=" O ASP J 379 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL J 384 " --> pdb=" O ASP J 380 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL J 385 " --> pdb=" O ALA J 381 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N CYS J 387 " --> pdb=" O GLY J 383 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR J 388 " --> pdb=" O VAL J 384 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE J 389 " --> pdb=" O VAL J 385 " (cutoff:3.500A) Processing helix chain 'J' and resid 401 through 415 removed outlier: 3.554A pdb=" N LYS J 408 " --> pdb=" O GLU J 404 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU J 411 " --> pdb=" O MET J 407 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU J 414 " --> pdb=" O ARG J 410 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLY J 415 " --> pdb=" O GLU J 411 " (cutoff:3.500A) Processing helix chain 'J' and resid 420 through 440 removed outlier: 4.230A pdb=" N GLU J 432 " --> pdb=" O ALA J 428 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N VAL J 433 " --> pdb=" O ASP J 429 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ILE J 434 " --> pdb=" O ALA J 430 " (cutoff:3.500A) Proline residue: J 435 - end of helix Processing helix chain 'J' and resid 448 through 458 removed outlier: 3.571A pdb=" N ALA J 455 " --> pdb=" O VAL J 451 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA J 456 " --> pdb=" O LYS J 452 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N HIS J 457 " --> pdb=" O VAL J 453 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA J 458 " --> pdb=" O ARG J 454 " (cutoff:3.500A) Processing helix chain 'J' and resid 487 through 499 removed outlier: 3.556A pdb=" N ALA J 492 " --> pdb=" O VAL J 488 " (cutoff:3.500A) Processing helix chain 'J' and resid 501 through 504 No H-bonds generated for 'chain 'J' and resid 501 through 504' Processing helix chain 'K' and resid 13 through 26 removed outlier: 3.745A pdb=" N MET K 17 " --> pdb=" O ASP K 13 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN K 18 " --> pdb=" O ALA K 14 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE K 24 " --> pdb=" O LEU K 20 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE K 25 " --> pdb=" O ALA K 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 56 through 60 removed outlier: 3.579A pdb=" N ARG K 60 " --> pdb=" O VAL K 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 56 through 60' Processing helix chain 'K' and resid 67 through 80 removed outlier: 3.733A pdb=" N LYS K 70 " --> pdb=" O PRO K 67 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N MET K 71 " --> pdb=" O ALA K 68 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU K 72 " --> pdb=" O ALA K 69 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU K 80 " --> pdb=" O LYS K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 107 removed outlier: 3.745A pdb=" N GLU K 103 " --> pdb=" O ARG K 99 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU K 104 " --> pdb=" O LYS K 100 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU K 105 " --> pdb=" O ALA K 101 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ASP K 106 " --> pdb=" O GLU K 102 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N GLN K 107 " --> pdb=" O GLU K 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 113 through 131 removed outlier: 3.636A pdb=" N GLN K 123 " --> pdb=" O GLN K 119 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS K 124 " --> pdb=" O ALA K 120 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS K 130 " --> pdb=" O GLN K 126 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR K 131 " --> pdb=" O GLU K 127 " (cutoff:3.500A) Processing helix chain 'K' and resid 146 through 150 Processing helix chain 'K' and resid 169 through 172 No H-bonds generated for 'chain 'K' and resid 169 through 172' Processing helix chain 'K' and resid 249 through 273 removed outlier: 3.976A pdb=" N MET K 253 " --> pdb=" O PRO K 249 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU K 254 " --> pdb=" O ALA K 250 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU K 263 " --> pdb=" O GLU K 259 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LYS K 264 " --> pdb=" O GLU K 260 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASP K 265 " --> pdb=" O LYS K 261 " (cutoff:3.500A) Processing helix chain 'K' and resid 286 through 288 No H-bonds generated for 'chain 'K' and resid 286 through 288' Processing helix chain 'K' and resid 290 through 292 No H-bonds generated for 'chain 'K' and resid 290 through 292' Processing helix chain 'K' and resid 305 through 308 No H-bonds generated for 'chain 'K' and resid 305 through 308' Processing helix chain 'K' and resid 369 through 389 removed outlier: 3.786A pdb=" N ALA K 377 " --> pdb=" O GLU K 373 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ASP K 379 " --> pdb=" O ALA K 375 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ASP K 380 " --> pdb=" O ARG K 376 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY K 383 " --> pdb=" O ASP K 379 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL K 384 " --> pdb=" O ASP K 380 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL K 385 " --> pdb=" O ALA K 381 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N CYS K 387 " --> pdb=" O GLY K 383 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N THR K 388 " --> pdb=" O VAL K 384 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE K 389 " --> pdb=" O VAL K 385 " (cutoff:3.500A) Processing helix chain 'K' and resid 401 through 415 removed outlier: 3.544A pdb=" N LYS K 408 " --> pdb=" O GLU K 404 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU K 411 " --> pdb=" O MET K 407 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU K 414 " --> pdb=" O ARG K 410 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N GLY K 415 " --> pdb=" O GLU K 411 " (cutoff:3.500A) Processing helix chain 'K' and resid 420 through 440 removed outlier: 4.238A pdb=" N GLU K 432 " --> pdb=" O ALA K 428 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N VAL K 433 " --> pdb=" O ASP K 429 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N ILE K 434 " --> pdb=" O ALA K 430 " (cutoff:3.500A) Proline residue: K 435 - end of helix Processing helix chain 'K' and resid 448 through 458 removed outlier: 3.570A pdb=" N ALA K 455 " --> pdb=" O VAL K 451 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA K 456 " --> pdb=" O LYS K 452 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N HIS K 457 " --> pdb=" O VAL K 453 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ALA K 458 " --> pdb=" O ARG K 454 " (cutoff:3.500A) Processing helix chain 'K' and resid 487 through 499 removed outlier: 3.556A pdb=" N ALA K 492 " --> pdb=" O VAL K 488 " (cutoff:3.500A) Processing helix chain 'K' and resid 501 through 504 No H-bonds generated for 'chain 'K' and resid 501 through 504' Processing helix chain 'L' and resid 13 through 26 removed outlier: 3.745A pdb=" N MET L 17 " --> pdb=" O ASP L 13 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN L 18 " --> pdb=" O ALA L 14 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE L 24 " --> pdb=" O LEU L 20 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE L 25 " --> pdb=" O ALA L 21 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 60 removed outlier: 3.577A pdb=" N ARG L 60 " --> pdb=" O VAL L 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 56 through 60' Processing helix chain 'L' and resid 67 through 80 removed outlier: 3.734A pdb=" N LYS L 70 " --> pdb=" O PRO L 67 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N MET L 71 " --> pdb=" O ALA L 68 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU L 72 " --> pdb=" O ALA L 69 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU L 80 " --> pdb=" O LYS L 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 107 removed outlier: 3.766A pdb=" N GLU L 103 " --> pdb=" O ARG L 99 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU L 104 " --> pdb=" O LYS L 100 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU L 105 " --> pdb=" O ALA L 101 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASP L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N GLN L 107 " --> pdb=" O GLU L 103 " (cutoff:3.500A) Processing helix chain 'L' and resid 113 through 131 removed outlier: 3.644A pdb=" N GLN L 123 " --> pdb=" O GLN L 119 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS L 124 " --> pdb=" O ALA L 120 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS L 130 " --> pdb=" O GLN L 126 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR L 131 " --> pdb=" O GLU L 127 " (cutoff:3.500A) Processing helix chain 'L' and resid 146 through 150 Processing helix chain 'L' and resid 169 through 172 No H-bonds generated for 'chain 'L' and resid 169 through 172' Processing helix chain 'L' and resid 249 through 273 removed outlier: 3.975A pdb=" N MET L 253 " --> pdb=" O PRO L 249 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU L 254 " --> pdb=" O ALA L 250 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU L 263 " --> pdb=" O GLU L 259 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS L 264 " --> pdb=" O GLU L 260 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP L 265 " --> pdb=" O LYS L 261 " (cutoff:3.500A) Processing helix chain 'L' and resid 286 through 288 No H-bonds generated for 'chain 'L' and resid 286 through 288' Processing helix chain 'L' and resid 290 through 292 No H-bonds generated for 'chain 'L' and resid 290 through 292' Processing helix chain 'L' and resid 305 through 308 No H-bonds generated for 'chain 'L' and resid 305 through 308' Processing helix chain 'L' and resid 369 through 389 removed outlier: 3.788A pdb=" N ALA L 377 " --> pdb=" O GLU L 373 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ASP L 379 " --> pdb=" O ALA L 375 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ASP L 380 " --> pdb=" O ARG L 376 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY L 383 " --> pdb=" O ASP L 379 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL L 384 " --> pdb=" O ASP L 380 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL L 385 " --> pdb=" O ALA L 381 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N CYS L 387 " --> pdb=" O GLY L 383 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N THR L 388 " --> pdb=" O VAL L 384 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE L 389 " --> pdb=" O VAL L 385 " (cutoff:3.500A) Processing helix chain 'L' and resid 401 through 415 removed outlier: 3.554A pdb=" N LYS L 408 " --> pdb=" O GLU L 404 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU L 411 " --> pdb=" O MET L 407 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU L 414 " --> pdb=" O ARG L 410 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLY L 415 " --> pdb=" O GLU L 411 " (cutoff:3.500A) Processing helix chain 'L' and resid 420 through 440 removed outlier: 4.249A pdb=" N GLU L 432 " --> pdb=" O ALA L 428 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N VAL L 433 " --> pdb=" O ASP L 429 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ILE L 434 " --> pdb=" O ALA L 430 " (cutoff:3.500A) Proline residue: L 435 - end of helix Processing helix chain 'L' and resid 448 through 458 removed outlier: 3.568A pdb=" N ALA L 455 " --> pdb=" O VAL L 451 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA L 456 " --> pdb=" O LYS L 452 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N HIS L 457 " --> pdb=" O VAL L 453 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ALA L 458 " --> pdb=" O ARG L 454 " (cutoff:3.500A) Processing helix chain 'L' and resid 487 through 499 removed outlier: 3.557A pdb=" N ALA L 492 " --> pdb=" O VAL L 488 " (cutoff:3.500A) Processing helix chain 'L' and resid 501 through 504 No H-bonds generated for 'chain 'L' and resid 501 through 504' Processing helix chain 'M' and resid 13 through 26 removed outlier: 3.756A pdb=" N MET M 17 " --> pdb=" O ASP M 13 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN M 18 " --> pdb=" O ALA M 14 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE M 24 " --> pdb=" O LEU M 20 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE M 25 " --> pdb=" O ALA M 21 " (cutoff:3.500A) Processing helix chain 'M' and resid 56 through 60 removed outlier: 3.575A pdb=" N ARG M 60 " --> pdb=" O VAL M 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 56 through 60' Processing helix chain 'M' and resid 68 through 80 removed outlier: 4.576A pdb=" N LEU M 72 " --> pdb=" O ALA M 68 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ILE M 73 " --> pdb=" O ALA M 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 88 through 107 removed outlier: 3.765A pdb=" N GLU M 103 " --> pdb=" O ARG M 99 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU M 104 " --> pdb=" O LYS M 100 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU M 105 " --> pdb=" O ALA M 101 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ASP M 106 " --> pdb=" O GLU M 102 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N GLN M 107 " --> pdb=" O GLU M 103 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 131 removed outlier: 3.643A pdb=" N GLN M 123 " --> pdb=" O GLN M 119 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS M 124 " --> pdb=" O ALA M 120 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS M 130 " --> pdb=" O GLN M 126 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR M 131 " --> pdb=" O GLU M 127 " (cutoff:3.500A) Processing helix chain 'M' and resid 146 through 150 Processing helix chain 'M' and resid 169 through 172 No H-bonds generated for 'chain 'M' and resid 169 through 172' Processing helix chain 'M' and resid 249 through 273 removed outlier: 3.976A pdb=" N MET M 253 " --> pdb=" O PRO M 249 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU M 254 " --> pdb=" O ALA M 250 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU M 263 " --> pdb=" O GLU M 259 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS M 264 " --> pdb=" O GLU M 260 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP M 265 " --> pdb=" O LYS M 261 " (cutoff:3.500A) Processing helix chain 'M' and resid 286 through 288 No H-bonds generated for 'chain 'M' and resid 286 through 288' Processing helix chain 'M' and resid 290 through 292 No H-bonds generated for 'chain 'M' and resid 290 through 292' Processing helix chain 'M' and resid 305 through 308 No H-bonds generated for 'chain 'M' and resid 305 through 308' Processing helix chain 'M' and resid 369 through 389 removed outlier: 3.787A pdb=" N ALA M 377 " --> pdb=" O GLU M 373 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASP M 379 " --> pdb=" O ALA M 375 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ASP M 380 " --> pdb=" O ARG M 376 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY M 383 " --> pdb=" O ASP M 379 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL M 384 " --> pdb=" O ASP M 380 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL M 385 " --> pdb=" O ALA M 381 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N CYS M 387 " --> pdb=" O GLY M 383 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N THR M 388 " --> pdb=" O VAL M 384 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE M 389 " --> pdb=" O VAL M 385 " (cutoff:3.500A) Processing helix chain 'M' and resid 401 through 415 removed outlier: 3.554A pdb=" N LYS M 408 " --> pdb=" O GLU M 404 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU M 411 " --> pdb=" O MET M 407 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLU M 414 " --> pdb=" O ARG M 410 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLY M 415 " --> pdb=" O GLU M 411 " (cutoff:3.500A) Processing helix chain 'M' and resid 420 through 440 removed outlier: 4.246A pdb=" N GLU M 432 " --> pdb=" O ALA M 428 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N VAL M 433 " --> pdb=" O ASP M 429 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ILE M 434 " --> pdb=" O ALA M 430 " (cutoff:3.500A) Proline residue: M 435 - end of helix Processing helix chain 'M' and resid 448 through 458 removed outlier: 3.569A pdb=" N ALA M 455 " --> pdb=" O VAL M 451 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA M 456 " --> pdb=" O LYS M 452 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N HIS M 457 " --> pdb=" O VAL M 453 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ALA M 458 " --> pdb=" O ARG M 454 " (cutoff:3.500A) Processing helix chain 'M' and resid 487 through 499 removed outlier: 3.558A pdb=" N ALA M 492 " --> pdb=" O VAL M 488 " (cutoff:3.500A) Processing helix chain 'M' and resid 501 through 504 No H-bonds generated for 'chain 'M' and resid 501 through 504' Processing helix chain 'N' and resid 13 through 26 removed outlier: 3.750A pdb=" N MET N 17 " --> pdb=" O ASP N 13 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN N 18 " --> pdb=" O ALA N 14 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE N 24 " --> pdb=" O LEU N 20 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE N 25 " --> pdb=" O ALA N 21 " (cutoff:3.500A) Processing helix chain 'N' and resid 56 through 60 removed outlier: 3.567A pdb=" N ARG N 60 " --> pdb=" O VAL N 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 56 through 60' Processing helix chain 'N' and resid 67 through 80 removed outlier: 3.735A pdb=" N LYS N 70 " --> pdb=" O PRO N 67 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N MET N 71 " --> pdb=" O ALA N 68 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LEU N 72 " --> pdb=" O ALA N 69 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU N 80 " --> pdb=" O LYS N 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 88 through 107 removed outlier: 3.764A pdb=" N GLU N 103 " --> pdb=" O ARG N 99 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU N 104 " --> pdb=" O LYS N 100 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU N 105 " --> pdb=" O ALA N 101 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASP N 106 " --> pdb=" O GLU N 102 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N GLN N 107 " --> pdb=" O GLU N 103 " (cutoff:3.500A) Processing helix chain 'N' and resid 113 through 131 removed outlier: 3.643A pdb=" N GLN N 123 " --> pdb=" O GLN N 119 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS N 124 " --> pdb=" O ALA N 120 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS N 130 " --> pdb=" O GLN N 126 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR N 131 " --> pdb=" O GLU N 127 " (cutoff:3.500A) Processing helix chain 'N' and resid 146 through 150 Processing helix chain 'N' and resid 169 through 172 No H-bonds generated for 'chain 'N' and resid 169 through 172' Processing helix chain 'N' and resid 249 through 273 removed outlier: 3.975A pdb=" N MET N 253 " --> pdb=" O PRO N 249 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU N 254 " --> pdb=" O ALA N 250 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU N 263 " --> pdb=" O GLU N 259 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS N 264 " --> pdb=" O GLU N 260 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP N 265 " --> pdb=" O LYS N 261 " (cutoff:3.500A) Processing helix chain 'N' and resid 286 through 288 No H-bonds generated for 'chain 'N' and resid 286 through 288' Processing helix chain 'N' and resid 290 through 292 No H-bonds generated for 'chain 'N' and resid 290 through 292' Processing helix chain 'N' and resid 305 through 308 No H-bonds generated for 'chain 'N' and resid 305 through 308' Processing helix chain 'N' and resid 369 through 389 removed outlier: 3.787A pdb=" N ALA N 377 " --> pdb=" O GLU N 373 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ASP N 379 " --> pdb=" O ALA N 375 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASP N 380 " --> pdb=" O ARG N 376 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY N 383 " --> pdb=" O ASP N 379 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VAL N 384 " --> pdb=" O ASP N 380 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL N 385 " --> pdb=" O ALA N 381 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N CYS N 387 " --> pdb=" O GLY N 383 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N THR N 388 " --> pdb=" O VAL N 384 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE N 389 " --> pdb=" O VAL N 385 " (cutoff:3.500A) Processing helix chain 'N' and resid 401 through 415 removed outlier: 3.555A pdb=" N LYS N 408 " --> pdb=" O GLU N 404 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU N 411 " --> pdb=" O MET N 407 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU N 414 " --> pdb=" O ARG N 410 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLY N 415 " --> pdb=" O GLU N 411 " (cutoff:3.500A) Processing helix chain 'N' and resid 420 through 438 removed outlier: 3.502A pdb=" N LEU N 431 " --> pdb=" O PHE N 427 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU N 432 " --> pdb=" O ALA N 428 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N VAL N 433 " --> pdb=" O ASP N 429 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ILE N 434 " --> pdb=" O ALA N 430 " (cutoff:3.500A) Proline residue: N 435 - end of helix Processing helix chain 'N' and resid 448 through 458 removed outlier: 3.579A pdb=" N ALA N 455 " --> pdb=" O VAL N 451 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA N 456 " --> pdb=" O LYS N 452 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N HIS N 457 " --> pdb=" O VAL N 453 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ALA N 458 " --> pdb=" O ARG N 454 " (cutoff:3.500A) Processing helix chain 'N' and resid 487 through 499 removed outlier: 3.558A pdb=" N ALA N 492 " --> pdb=" O VAL N 488 " (cutoff:3.500A) Processing helix chain 'N' and resid 501 through 504 No H-bonds generated for 'chain 'N' and resid 501 through 504' Processing helix chain 'O' and resid 13 through 26 removed outlier: 3.745A pdb=" N MET O 17 " --> pdb=" O ASP O 13 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN O 18 " --> pdb=" O ALA O 14 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE O 24 " --> pdb=" O LEU O 20 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE O 25 " --> pdb=" O ALA O 21 " (cutoff:3.500A) Processing helix chain 'O' and resid 56 through 60 removed outlier: 3.578A pdb=" N ARG O 60 " --> pdb=" O VAL O 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 56 through 60' Processing helix chain 'O' and resid 67 through 80 removed outlier: 3.736A pdb=" N LYS O 70 " --> pdb=" O PRO O 67 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N MET O 71 " --> pdb=" O ALA O 68 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU O 72 " --> pdb=" O ALA O 69 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU O 80 " --> pdb=" O LYS O 77 " (cutoff:3.500A) Processing helix chain 'O' and resid 88 through 107 removed outlier: 3.752A pdb=" N GLU O 103 " --> pdb=" O ARG O 99 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU O 104 " --> pdb=" O LYS O 100 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU O 105 " --> pdb=" O ALA O 101 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASP O 106 " --> pdb=" O GLU O 102 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLN O 107 " --> pdb=" O GLU O 103 " (cutoff:3.500A) Processing helix chain 'O' and resid 113 through 131 removed outlier: 3.634A pdb=" N GLN O 123 " --> pdb=" O GLN O 119 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS O 124 " --> pdb=" O ALA O 120 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS O 130 " --> pdb=" O GLN O 126 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR O 131 " --> pdb=" O GLU O 127 " (cutoff:3.500A) Processing helix chain 'O' and resid 146 through 150 Processing helix chain 'O' and resid 169 through 172 No H-bonds generated for 'chain 'O' and resid 169 through 172' Processing helix chain 'O' and resid 249 through 273 removed outlier: 3.975A pdb=" N MET O 253 " --> pdb=" O PRO O 249 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU O 254 " --> pdb=" O ALA O 250 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU O 263 " --> pdb=" O GLU O 259 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS O 264 " --> pdb=" O GLU O 260 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP O 265 " --> pdb=" O LYS O 261 " (cutoff:3.500A) Processing helix chain 'O' and resid 286 through 288 No H-bonds generated for 'chain 'O' and resid 286 through 288' Processing helix chain 'O' and resid 290 through 292 No H-bonds generated for 'chain 'O' and resid 290 through 292' Processing helix chain 'O' and resid 305 through 308 No H-bonds generated for 'chain 'O' and resid 305 through 308' Processing helix chain 'O' and resid 369 through 389 removed outlier: 3.787A pdb=" N ALA O 377 " --> pdb=" O GLU O 373 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASP O 379 " --> pdb=" O ALA O 375 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASP O 380 " --> pdb=" O ARG O 376 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY O 383 " --> pdb=" O ASP O 379 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL O 384 " --> pdb=" O ASP O 380 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL O 385 " --> pdb=" O ALA O 381 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N CYS O 387 " --> pdb=" O GLY O 383 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N THR O 388 " --> pdb=" O VAL O 384 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE O 389 " --> pdb=" O VAL O 385 " (cutoff:3.500A) Processing helix chain 'O' and resid 401 through 415 removed outlier: 3.554A pdb=" N LYS O 408 " --> pdb=" O GLU O 404 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU O 411 " --> pdb=" O MET O 407 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU O 414 " --> pdb=" O ARG O 410 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLY O 415 " --> pdb=" O GLU O 411 " (cutoff:3.500A) Processing helix chain 'O' and resid 420 through 440 removed outlier: 4.247A pdb=" N GLU O 432 " --> pdb=" O ALA O 428 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N VAL O 433 " --> pdb=" O ASP O 429 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ILE O 434 " --> pdb=" O ALA O 430 " (cutoff:3.500A) Proline residue: O 435 - end of helix Processing helix chain 'O' and resid 448 through 458 removed outlier: 3.571A pdb=" N ALA O 455 " --> pdb=" O VAL O 451 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA O 456 " --> pdb=" O LYS O 452 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N HIS O 457 " --> pdb=" O VAL O 453 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ALA O 458 " --> pdb=" O ARG O 454 " (cutoff:3.500A) Processing helix chain 'O' and resid 487 through 499 removed outlier: 3.558A pdb=" N ALA O 492 " --> pdb=" O VAL O 488 " (cutoff:3.500A) Processing helix chain 'O' and resid 501 through 504 No H-bonds generated for 'chain 'O' and resid 501 through 504' Processing sheet with id= A, first strand: chain 'U' and resid 40 through 42 Processing sheet with id= B, first strand: chain 'U' and resid 188 through 191 removed outlier: 4.254A pdb=" N MET U 361 " --> pdb=" O LYS U 188 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLU U 190 " --> pdb=" O MET U 361 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ILE U 363 " --> pdb=" O GLU U 190 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'U' and resid 205 through 208 Processing sheet with id= D, first strand: chain 'U' and resid 226 through 229 removed outlier: 6.296A pdb=" N VAL U 277 " --> pdb=" O ALA U 227 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU U 229 " --> pdb=" O VAL U 277 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N PHE U 279 " --> pdb=" O LEU U 229 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 40 through 42 Processing sheet with id= F, first strand: chain 'A' and resid 188 through 191 removed outlier: 4.254A pdb=" N MET A 361 " --> pdb=" O LYS A 188 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLU A 190 " --> pdb=" O MET A 361 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ILE A 363 " --> pdb=" O GLU A 190 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 205 through 208 Processing sheet with id= H, first strand: chain 'A' and resid 226 through 229 removed outlier: 6.297A pdb=" N VAL A 277 " --> pdb=" O ALA A 227 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU A 229 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N PHE A 279 " --> pdb=" O LEU A 229 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 40 through 42 Processing sheet with id= J, first strand: chain 'B' and resid 188 through 191 removed outlier: 4.254A pdb=" N MET B 361 " --> pdb=" O LYS B 188 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLU B 190 " --> pdb=" O MET B 361 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ILE B 363 " --> pdb=" O GLU B 190 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 205 through 208 Processing sheet with id= L, first strand: chain 'B' and resid 226 through 229 removed outlier: 6.297A pdb=" N VAL B 277 " --> pdb=" O ALA B 227 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU B 229 " --> pdb=" O VAL B 277 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N PHE B 279 " --> pdb=" O LEU B 229 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'C' and resid 40 through 42 Processing sheet with id= N, first strand: chain 'C' and resid 188 through 191 removed outlier: 4.254A pdb=" N MET C 361 " --> pdb=" O LYS C 188 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU C 190 " --> pdb=" O MET C 361 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ILE C 363 " --> pdb=" O GLU C 190 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 205 through 208 Processing sheet with id= P, first strand: chain 'C' and resid 226 through 229 removed outlier: 6.295A pdb=" N VAL C 277 " --> pdb=" O ALA C 227 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LEU C 229 " --> pdb=" O VAL C 277 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N PHE C 279 " --> pdb=" O LEU C 229 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'D' and resid 40 through 42 Processing sheet with id= R, first strand: chain 'D' and resid 188 through 191 removed outlier: 4.254A pdb=" N MET D 361 " --> pdb=" O LYS D 188 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLU D 190 " --> pdb=" O MET D 361 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ILE D 363 " --> pdb=" O GLU D 190 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 205 through 208 Processing sheet with id= T, first strand: chain 'D' and resid 226 through 229 removed outlier: 6.296A pdb=" N VAL D 277 " --> pdb=" O ALA D 227 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU D 229 " --> pdb=" O VAL D 277 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N PHE D 279 " --> pdb=" O LEU D 229 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'E' and resid 40 through 42 Processing sheet with id= V, first strand: chain 'E' and resid 188 through 191 removed outlier: 4.254A pdb=" N MET E 361 " --> pdb=" O LYS E 188 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLU E 190 " --> pdb=" O MET E 361 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ILE E 363 " --> pdb=" O GLU E 190 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 205 through 208 Processing sheet with id= X, first strand: chain 'E' and resid 226 through 229 removed outlier: 6.297A pdb=" N VAL E 277 " --> pdb=" O ALA E 227 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU E 229 " --> pdb=" O VAL E 277 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N PHE E 279 " --> pdb=" O LEU E 229 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'F' and resid 40 through 42 Processing sheet with id= Z, first strand: chain 'F' and resid 188 through 191 removed outlier: 4.255A pdb=" N MET F 361 " --> pdb=" O LYS F 188 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLU F 190 " --> pdb=" O MET F 361 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ILE F 363 " --> pdb=" O GLU F 190 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 205 through 208 Processing sheet with id= AB, first strand: chain 'F' and resid 226 through 229 removed outlier: 6.296A pdb=" N VAL F 277 " --> pdb=" O ALA F 227 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU F 229 " --> pdb=" O VAL F 277 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N PHE F 279 " --> pdb=" O LEU F 229 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'G' and resid 40 through 42 Processing sheet with id= AD, first strand: chain 'G' and resid 188 through 191 removed outlier: 4.254A pdb=" N MET G 361 " --> pdb=" O LYS G 188 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLU G 190 " --> pdb=" O MET G 361 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ILE G 363 " --> pdb=" O GLU G 190 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'G' and resid 205 through 208 Processing sheet with id= AF, first strand: chain 'G' and resid 226 through 229 removed outlier: 6.297A pdb=" N VAL G 277 " --> pdb=" O ALA G 227 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU G 229 " --> pdb=" O VAL G 277 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N PHE G 279 " --> pdb=" O LEU G 229 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'H' and resid 40 through 42 Processing sheet with id= AH, first strand: chain 'H' and resid 188 through 191 removed outlier: 4.254A pdb=" N MET H 361 " --> pdb=" O LYS H 188 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLU H 190 " --> pdb=" O MET H 361 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ILE H 363 " --> pdb=" O GLU H 190 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'H' and resid 205 through 208 Processing sheet with id= AJ, first strand: chain 'H' and resid 226 through 229 removed outlier: 6.296A pdb=" N VAL H 277 " --> pdb=" O ALA H 227 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU H 229 " --> pdb=" O VAL H 277 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N PHE H 279 " --> pdb=" O LEU H 229 " (cutoff:3.500A) No H-bonds generated for sheet with id= AJ Processing sheet with id= AK, first strand: chain 'I' and resid 40 through 42 Processing sheet with id= AL, first strand: chain 'I' and resid 188 through 191 removed outlier: 4.254A pdb=" N MET I 361 " --> pdb=" O LYS I 188 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLU I 190 " --> pdb=" O MET I 361 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ILE I 363 " --> pdb=" O GLU I 190 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'I' and resid 205 through 208 Processing sheet with id= AN, first strand: chain 'I' and resid 226 through 229 removed outlier: 6.297A pdb=" N VAL I 277 " --> pdb=" O ALA I 227 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU I 229 " --> pdb=" O VAL I 277 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N PHE I 279 " --> pdb=" O LEU I 229 " (cutoff:3.500A) No H-bonds generated for sheet with id= AN Processing sheet with id= AO, first strand: chain 'J' and resid 40 through 42 Processing sheet with id= AP, first strand: chain 'J' and resid 188 through 191 removed outlier: 4.255A pdb=" N MET J 361 " --> pdb=" O LYS J 188 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLU J 190 " --> pdb=" O MET J 361 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ILE J 363 " --> pdb=" O GLU J 190 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'J' and resid 205 through 208 Processing sheet with id= AR, first strand: chain 'J' and resid 226 through 229 removed outlier: 6.297A pdb=" N VAL J 277 " --> pdb=" O ALA J 227 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU J 229 " --> pdb=" O VAL J 277 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N PHE J 279 " --> pdb=" O LEU J 229 " (cutoff:3.500A) No H-bonds generated for sheet with id= AR Processing sheet with id= AS, first strand: chain 'K' and resid 40 through 42 Processing sheet with id= AT, first strand: chain 'K' and resid 188 through 191 removed outlier: 4.256A pdb=" N MET K 361 " --> pdb=" O LYS K 188 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLU K 190 " --> pdb=" O MET K 361 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ILE K 363 " --> pdb=" O GLU K 190 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'K' and resid 205 through 208 Processing sheet with id= AV, first strand: chain 'K' and resid 226 through 229 removed outlier: 6.297A pdb=" N VAL K 277 " --> pdb=" O ALA K 227 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU K 229 " --> pdb=" O VAL K 277 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N PHE K 279 " --> pdb=" O LEU K 229 " (cutoff:3.500A) No H-bonds generated for sheet with id= AV Processing sheet with id= AW, first strand: chain 'L' and resid 40 through 42 Processing sheet with id= AX, first strand: chain 'L' and resid 188 through 191 removed outlier: 4.254A pdb=" N MET L 361 " --> pdb=" O LYS L 188 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLU L 190 " --> pdb=" O MET L 361 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ILE L 363 " --> pdb=" O GLU L 190 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'L' and resid 205 through 208 Processing sheet with id= AZ, first strand: chain 'L' and resid 226 through 229 removed outlier: 6.296A pdb=" N VAL L 277 " --> pdb=" O ALA L 227 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU L 229 " --> pdb=" O VAL L 277 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N PHE L 279 " --> pdb=" O LEU L 229 " (cutoff:3.500A) No H-bonds generated for sheet with id= AZ Processing sheet with id= BA, first strand: chain 'M' and resid 40 through 42 Processing sheet with id= BB, first strand: chain 'M' and resid 188 through 191 removed outlier: 4.255A pdb=" N MET M 361 " --> pdb=" O LYS M 188 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLU M 190 " --> pdb=" O MET M 361 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ILE M 363 " --> pdb=" O GLU M 190 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'M' and resid 205 through 208 Processing sheet with id= BD, first strand: chain 'M' and resid 226 through 229 removed outlier: 6.297A pdb=" N VAL M 277 " --> pdb=" O ALA M 227 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU M 229 " --> pdb=" O VAL M 277 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N PHE M 279 " --> pdb=" O LEU M 229 " (cutoff:3.500A) No H-bonds generated for sheet with id= BD Processing sheet with id= BE, first strand: chain 'N' and resid 40 through 42 Processing sheet with id= BF, first strand: chain 'N' and resid 188 through 191 removed outlier: 4.254A pdb=" N MET N 361 " --> pdb=" O LYS N 188 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLU N 190 " --> pdb=" O MET N 361 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ILE N 363 " --> pdb=" O GLU N 190 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'N' and resid 205 through 208 Processing sheet with id= BH, first strand: chain 'N' and resid 226 through 229 removed outlier: 6.297A pdb=" N VAL N 277 " --> pdb=" O ALA N 227 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU N 229 " --> pdb=" O VAL N 277 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N PHE N 279 " --> pdb=" O LEU N 229 " (cutoff:3.500A) No H-bonds generated for sheet with id= BH Processing sheet with id= BI, first strand: chain 'O' and resid 40 through 42 Processing sheet with id= BJ, first strand: chain 'O' and resid 188 through 191 removed outlier: 4.254A pdb=" N MET O 361 " --> pdb=" O LYS O 188 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLU O 190 " --> pdb=" O MET O 361 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ILE O 363 " --> pdb=" O GLU O 190 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'O' and resid 205 through 208 Processing sheet with id= BL, first strand: chain 'O' and resid 226 through 229 removed outlier: 6.297A pdb=" N VAL O 277 " --> pdb=" O ALA O 227 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU O 229 " --> pdb=" O VAL O 277 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N PHE O 279 " --> pdb=" O LEU O 229 " (cutoff:3.500A) No H-bonds generated for sheet with id= BL 1735 hydrogen bonds defined for protein. 4671 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: 16.48 Time building geometry restraints manager: 19.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 21152 1.34 - 1.46: 9431 1.46 - 1.58: 30345 1.58 - 1.69: 80 1.69 - 1.81: 656 Bond restraints: 61664 Sorted by residual: bond pdb=" C4 ATP I 601 " pdb=" C5 ATP I 601 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 7.01e+01 bond pdb=" C4 ATP A 601 " pdb=" C5 ATP A 601 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 7.00e+01 bond pdb=" C4 ATP N 601 " pdb=" C5 ATP N 601 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.96e+01 bond pdb=" C4 ATP M 601 " pdb=" C5 ATP M 601 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.95e+01 bond pdb=" C4 ATP K 601 " pdb=" C5 ATP K 601 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.92e+01 ... (remaining 61659 not shown) Histogram of bond angle deviations from ideal: 100.79 - 107.86: 1363 107.86 - 114.93: 40096 114.93 - 122.01: 28658 122.01 - 129.08: 12827 129.08 - 136.15: 144 Bond angle restraints: 83088 Sorted by residual: angle pdb=" PB ATP N 601 " pdb=" O3B ATP N 601 " pdb=" PG ATP N 601 " ideal model delta sigma weight residual 139.87 120.89 18.98 1.00e+00 1.00e+00 3.60e+02 angle pdb=" PB ATP I 601 " pdb=" O3B ATP I 601 " pdb=" PG ATP I 601 " ideal model delta sigma weight residual 139.87 120.90 18.97 1.00e+00 1.00e+00 3.60e+02 angle pdb=" PB ATP L 601 " pdb=" O3B ATP L 601 " pdb=" PG ATP L 601 " ideal model delta sigma weight residual 139.87 120.90 18.97 1.00e+00 1.00e+00 3.60e+02 angle pdb=" PB ATP D 601 " pdb=" O3B ATP D 601 " pdb=" PG ATP D 601 " ideal model delta sigma weight residual 139.87 120.90 18.97 1.00e+00 1.00e+00 3.60e+02 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 120.90 18.97 1.00e+00 1.00e+00 3.60e+02 ... (remaining 83083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 37759 17.94 - 35.88: 740 35.88 - 53.83: 45 53.83 - 71.77: 16 71.77 - 89.71: 16 Dihedral angle restraints: 38576 sinusoidal: 15392 harmonic: 23184 Sorted by residual: dihedral pdb=" CB MET H 502 " pdb=" CG MET H 502 " pdb=" SD MET H 502 " pdb=" CE MET H 502 " ideal model delta sinusoidal sigma weight residual 60.00 101.48 -41.48 3 1.50e+01 4.44e-03 7.42e+00 dihedral pdb=" CB MET M 502 " pdb=" CG MET M 502 " pdb=" SD MET M 502 " pdb=" CE MET M 502 " ideal model delta sinusoidal sigma weight residual 60.00 101.46 -41.46 3 1.50e+01 4.44e-03 7.42e+00 dihedral pdb=" CB MET C 502 " pdb=" CG MET C 502 " pdb=" SD MET C 502 " pdb=" CE MET C 502 " ideal model delta sinusoidal sigma weight residual 60.00 101.44 -41.44 3 1.50e+01 4.44e-03 7.41e+00 ... (remaining 38573 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 5371 0.023 - 0.046: 2952 0.046 - 0.070: 988 0.070 - 0.093: 428 0.093 - 0.116: 421 Chirality restraints: 10160 Sorted by residual: chirality pdb=" CA ILE E 363 " pdb=" N ILE E 363 " pdb=" C ILE E 363 " pdb=" CB ILE E 363 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.38e-01 chirality pdb=" CA ILE K 363 " pdb=" N ILE K 363 " pdb=" C ILE K 363 " pdb=" CB ILE K 363 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.35e-01 chirality pdb=" CA ILE C 363 " pdb=" N ILE C 363 " pdb=" C ILE C 363 " pdb=" CB ILE C 363 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.32e-01 ... (remaining 10157 not shown) Planarity restraints: 10656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 66 " -0.014 5.00e-02 4.00e+02 2.05e-02 6.71e-01 pdb=" N PRO B 67 " 0.035 5.00e-02 4.00e+02 pdb=" CA PRO B 67 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO B 67 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS K 66 " 0.013 5.00e-02 4.00e+02 2.04e-02 6.65e-01 pdb=" N PRO K 67 " -0.035 5.00e-02 4.00e+02 pdb=" CA PRO K 67 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO K 67 " 0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS I 66 " 0.013 5.00e-02 4.00e+02 2.03e-02 6.62e-01 pdb=" N PRO I 67 " -0.035 5.00e-02 4.00e+02 pdb=" CA PRO I 67 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO I 67 " 0.011 5.00e-02 4.00e+02 ... (remaining 10653 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 16062 2.81 - 3.33: 54875 3.33 - 3.85: 89384 3.85 - 4.38: 101911 4.38 - 4.90: 176246 Nonbonded interactions: 438478 Sorted by model distance: nonbonded pdb=" O VAL L 109 " pdb=" ND1 HIS L 110 " model vdw 2.283 2.520 nonbonded pdb=" O VAL M 109 " pdb=" ND1 HIS M 110 " model vdw 2.285 2.520 nonbonded pdb=" O VAL C 109 " pdb=" ND1 HIS C 110 " model vdw 2.286 2.520 nonbonded pdb=" O VAL U 109 " pdb=" ND1 HIS U 110 " model vdw 2.289 2.520 nonbonded pdb=" O VAL E 109 " pdb=" ND1 HIS E 110 " model vdw 2.290 2.520 ... (remaining 438473 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 48 5.49 5 S 384 5.16 5 C 37888 2.51 5 N 10592 2.21 5 O 12384 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 9.060 Check model and map are aligned: 0.710 Process input model: 115.360 Find NCS groups from input model: 3.600 Set up NCS constraints: 0.500 Set refine NCS operators: 0.000 Set scattering table: 0.420 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 133.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6136 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 : 0.003 0.084 61664 Z= 0.193 Angle : 0.606 18.976 83088 Z= 0.476 Chirality : 0.038 0.116 10160 Planarity : 0.002 0.020 10656 Dihedral : 6.785 89.711 23536 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.99 % Allowed : 13.96 % Favored : 85.05 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (0.08), residues: 8080 helix: -2.12 (0.08), residues: 3216 sheet: -0.11 (0.19), residues: 832 loop : -3.60 (0.07), residues: 4032 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16160 Ramachandran restraints generated. 8080 Oldfield, 0 Emsley, 8080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16160 Ramachandran restraints generated. 8080 Oldfield, 0 Emsley, 8080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 772 time to evaluate : 5.352 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 772 average time/residue: 0.5646 time to fit residues: 742.6644 Evaluate side-chains 477 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 477 time to evaluate : 5.335 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.6711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 675 optimal weight: 2.9990 chunk 606 optimal weight: 0.7980 chunk 336 optimal weight: 30.0000 chunk 207 optimal weight: 6.9990 chunk 409 optimal weight: 6.9990 chunk 323 optimal weight: 20.0000 chunk 627 optimal weight: 0.3980 chunk 242 optimal weight: 0.6980 chunk 381 optimal weight: 5.9990 chunk 466 optimal weight: 20.0000 chunk 726 optimal weight: 8.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 457 HIS A 457 HIS B 457 HIS C 457 HIS D 457 HIS E 457 HIS F 15 GLN F 457 HIS G 457 HIS H 457 HIS I 457 HIS J 457 HIS K 457 HIS L 457 HIS M 457 HIS N 421 GLN N 457 HIS O 457 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 61664 Z= 0.222 Angle : 0.562 7.834 83088 Z= 0.291 Chirality : 0.043 0.202 10160 Planarity : 0.003 0.027 10656 Dihedral : 4.603 67.674 8544 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.84 % Favored : 92.76 % Rotamer Outliers : 1.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.08), residues: 8080 helix: -1.32 (0.09), residues: 3264 sheet: -0.06 (0.18), residues: 896 loop : -3.27 (0.08), residues: 3920 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16160 Ramachandran restraints generated. 8080 Oldfield, 0 Emsley, 8080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16160 Ramachandran restraints generated. 8080 Oldfield, 0 Emsley, 8080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 544 time to evaluate : 5.370 Fit side-chains outliers start: 107 outliers final: 33 residues processed: 625 average time/residue: 0.5461 time to fit residues: 591.2997 Evaluate side-chains 456 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 423 time to evaluate : 5.351 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.4146 time to fit residues: 34.0007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 403 optimal weight: 7.9990 chunk 225 optimal weight: 20.0000 chunk 604 optimal weight: 2.9990 chunk 494 optimal weight: 4.9990 chunk 200 optimal weight: 10.0000 chunk 727 optimal weight: 50.0000 chunk 786 optimal weight: 10.0000 chunk 648 optimal weight: 10.0000 chunk 721 optimal weight: 0.0980 chunk 248 optimal weight: 7.9990 chunk 583 optimal weight: 7.9990 overall best weight: 4.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 369 HIS B 369 HIS C 369 HIS D 369 HIS F 15 GLN F 369 HIS H 369 HIS J 369 HIS K 369 HIS L 369 HIS N 369 HIS O 369 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.053 61664 Z= 0.397 Angle : 0.694 7.888 83088 Z= 0.356 Chirality : 0.048 0.166 10160 Planarity : 0.004 0.050 10656 Dihedral : 4.932 58.984 8544 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.40 % Allowed : 10.28 % Favored : 89.32 % Rotamer Outliers : 1.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.08), residues: 8080 helix: -1.45 (0.09), residues: 3328 sheet: 0.16 (0.19), residues: 896 loop : -3.29 (0.08), residues: 3856 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16160 Ramachandran restraints generated. 8080 Oldfield, 0 Emsley, 8080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16160 Ramachandran restraints generated. 8080 Oldfield, 0 Emsley, 8080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 499 time to evaluate : 5.535 Fit side-chains outliers start: 100 outliers final: 68 residues processed: 589 average time/residue: 0.5564 time to fit residues: 580.7457 Evaluate side-chains 492 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 424 time to evaluate : 5.390 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 0 residues processed: 68 average time/residue: 0.4516 time to fit residues: 66.3222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 719 optimal weight: 50.0000 chunk 547 optimal weight: 0.0370 chunk 377 optimal weight: 10.0000 chunk 80 optimal weight: 0.8980 chunk 347 optimal weight: 5.9990 chunk 488 optimal weight: 9.9990 chunk 730 optimal weight: 0.0030 chunk 773 optimal weight: 30.0000 chunk 381 optimal weight: 0.0770 chunk 692 optimal weight: 0.6980 chunk 208 optimal weight: 0.9990 overall best weight: 0.3426 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.4221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 61664 Z= 0.107 Angle : 0.444 7.888 83088 Z= 0.228 Chirality : 0.039 0.121 10160 Planarity : 0.002 0.026 10656 Dihedral : 3.690 43.789 8544 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.40 % Allowed : 4.52 % Favored : 95.09 % Rotamer Outliers : 0.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.09), residues: 8080 helix: -0.62 (0.09), residues: 3200 sheet: 0.43 (0.19), residues: 896 loop : -3.12 (0.08), residues: 3984 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16160 Ramachandran restraints generated. 8080 Oldfield, 0 Emsley, 8080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16160 Ramachandran restraints generated. 8080 Oldfield, 0 Emsley, 8080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 512 time to evaluate : 5.433 Fit side-chains outliers start: 57 outliers final: 23 residues processed: 561 average time/residue: 0.5447 time to fit residues: 540.5810 Evaluate side-chains 454 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 431 time to evaluate : 5.356 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.4372 time to fit residues: 26.9083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 644 optimal weight: 4.9990 chunk 438 optimal weight: 20.0000 chunk 11 optimal weight: 7.9990 chunk 575 optimal weight: 7.9990 chunk 319 optimal weight: 9.9990 chunk 659 optimal weight: 4.9990 chunk 534 optimal weight: 50.0000 chunk 0 optimal weight: 10.0000 chunk 394 optimal weight: 0.5980 chunk 694 optimal weight: 5.9990 chunk 195 optimal weight: 2.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 HIS ** E 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 369 HIS G 369 HIS ** I 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 369 HIS M 369 HIS N 355 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.4834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 61664 Z= 0.318 Angle : 0.596 9.737 83088 Z= 0.298 Chirality : 0.044 0.146 10160 Planarity : 0.003 0.029 10656 Dihedral : 4.201 28.080 8544 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.60 % Favored : 91.03 % Rotamer Outliers : 1.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.09), residues: 8080 helix: -0.92 (0.09), residues: 3232 sheet: 0.49 (0.19), residues: 896 loop : -3.14 (0.08), residues: 3952 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16160 Ramachandran restraints generated. 8080 Oldfield, 0 Emsley, 8080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16160 Ramachandran restraints generated. 8080 Oldfield, 0 Emsley, 8080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 442 time to evaluate : 5.478 Fit side-chains outliers start: 100 outliers final: 60 residues processed: 519 average time/residue: 0.5259 time to fit residues: 490.1241 Evaluate side-chains 475 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 415 time to evaluate : 5.537 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 0 residues processed: 60 average time/residue: 0.4381 time to fit residues: 57.8900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 260 optimal weight: 1.9990 chunk 696 optimal weight: 0.0020 chunk 152 optimal weight: 0.0670 chunk 454 optimal weight: 0.7980 chunk 190 optimal weight: 0.3980 chunk 774 optimal weight: 5.9990 chunk 642 optimal weight: 0.6980 chunk 358 optimal weight: 0.9990 chunk 64 optimal weight: 7.9990 chunk 256 optimal weight: 0.7980 chunk 406 optimal weight: 6.9990 overall best weight: 0.3926 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 355 HIS A 355 HIS B 355 HIS C 355 HIS D 355 HIS ** E 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 355 HIS ** G 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 355 HIS I 355 HIS J 355 HIS ** K 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 355 HIS O 355 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.4766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 61664 Z= 0.103 Angle : 0.448 8.919 83088 Z= 0.225 Chirality : 0.039 0.116 10160 Planarity : 0.002 0.032 10656 Dihedral : 3.511 28.657 8544 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.28 % Favored : 95.35 % Rotamer Outliers : 0.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.09), residues: 8080 helix: -0.40 (0.10), residues: 3216 sheet: 0.70 (0.19), residues: 896 loop : -2.96 (0.08), residues: 3968 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16160 Ramachandran restraints generated. 8080 Oldfield, 0 Emsley, 8080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16160 Ramachandran restraints generated. 8080 Oldfield, 0 Emsley, 8080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 459 time to evaluate : 5.445 Fit side-chains outliers start: 29 outliers final: 13 residues processed: 474 average time/residue: 0.5281 time to fit residues: 451.1262 Evaluate side-chains 434 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 421 time to evaluate : 5.498 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.4853 time to fit residues: 19.6473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 746 optimal weight: 0.0470 chunk 87 optimal weight: 20.0000 chunk 441 optimal weight: 3.9990 chunk 565 optimal weight: 0.6980 chunk 437 optimal weight: 10.0000 chunk 651 optimal weight: 0.9980 chunk 432 optimal weight: 50.0000 chunk 771 optimal weight: 0.0070 chunk 482 optimal weight: 9.9990 chunk 470 optimal weight: 0.3980 chunk 355 optimal weight: 6.9990 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 355 HIS G 355 HIS K 355 HIS M 355 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.4782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 61664 Z= 0.101 Angle : 0.429 9.699 83088 Z= 0.214 Chirality : 0.039 0.116 10160 Planarity : 0.002 0.034 10656 Dihedral : 3.295 30.950 8544 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.46 % Favored : 95.30 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.09), residues: 8080 helix: -0.11 (0.10), residues: 3216 sheet: 0.91 (0.20), residues: 896 loop : -2.80 (0.08), residues: 3968 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16160 Ramachandran restraints generated. 8080 Oldfield, 0 Emsley, 8080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16160 Ramachandran restraints generated. 8080 Oldfield, 0 Emsley, 8080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 442 time to evaluate : 5.370 Fit side-chains outliers start: 25 outliers final: 18 residues processed: 453 average time/residue: 0.5255 time to fit residues: 428.2055 Evaluate side-chains 437 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 419 time to evaluate : 5.448 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.4732 time to fit residues: 23.4432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 477 optimal weight: 50.0000 chunk 307 optimal weight: 8.9990 chunk 460 optimal weight: 2.9990 chunk 232 optimal weight: 0.4980 chunk 151 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 chunk 490 optimal weight: 0.9990 chunk 525 optimal weight: 10.0000 chunk 381 optimal weight: 10.0000 chunk 71 optimal weight: 0.8980 chunk 606 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.4873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 61664 Z= 0.113 Angle : 0.440 10.174 83088 Z= 0.217 Chirality : 0.039 0.116 10160 Planarity : 0.002 0.031 10656 Dihedral : 3.295 31.743 8544 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.86 % Favored : 94.94 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.09), residues: 8080 helix: 0.02 (0.10), residues: 3216 sheet: 1.03 (0.20), residues: 896 loop : -2.68 (0.08), residues: 3968 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16160 Ramachandran restraints generated. 8080 Oldfield, 0 Emsley, 8080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16160 Ramachandran restraints generated. 8080 Oldfield, 0 Emsley, 8080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 423 time to evaluate : 5.513 Fit side-chains outliers start: 24 outliers final: 17 residues processed: 443 average time/residue: 0.5395 time to fit residues: 429.4686 Evaluate side-chains 427 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 410 time to evaluate : 5.422 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.4724 time to fit residues: 23.1728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 701 optimal weight: 0.3980 chunk 738 optimal weight: 20.0000 chunk 673 optimal weight: 0.7980 chunk 718 optimal weight: 0.9980 chunk 432 optimal weight: 30.0000 chunk 313 optimal weight: 0.0020 chunk 564 optimal weight: 6.9990 chunk 220 optimal weight: 50.0000 chunk 649 optimal weight: 0.5980 chunk 679 optimal weight: 10.0000 chunk 716 optimal weight: 40.0000 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.4914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 61664 Z= 0.103 Angle : 0.445 11.031 83088 Z= 0.217 Chirality : 0.039 0.144 10160 Planarity : 0.002 0.033 10656 Dihedral : 3.218 32.632 8544 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.74 % Favored : 95.10 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.09), residues: 8080 helix: 0.20 (0.10), residues: 3216 sheet: 1.08 (0.20), residues: 896 loop : -2.59 (0.08), residues: 3968 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16160 Ramachandran restraints generated. 8080 Oldfield, 0 Emsley, 8080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16160 Ramachandran restraints generated. 8080 Oldfield, 0 Emsley, 8080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 429 time to evaluate : 5.489 Fit side-chains outliers start: 20 outliers final: 17 residues processed: 432 average time/residue: 0.5338 time to fit residues: 413.6587 Evaluate side-chains 425 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 408 time to evaluate : 5.353 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.4824 time to fit residues: 22.7597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 471 optimal weight: 4.9990 chunk 759 optimal weight: 7.9990 chunk 463 optimal weight: 9.9990 chunk 360 optimal weight: 0.0170 chunk 528 optimal weight: 1.9990 chunk 797 optimal weight: 0.0060 chunk 733 optimal weight: 8.9990 chunk 634 optimal weight: 10.0000 chunk 65 optimal weight: 0.0980 chunk 490 optimal weight: 0.9980 chunk 389 optimal weight: 5.9990 overall best weight: 0.6236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 61664 Z= 0.104 Angle : 0.442 11.684 83088 Z= 0.216 Chirality : 0.039 0.138 10160 Planarity : 0.002 0.031 10656 Dihedral : 3.184 33.062 8544 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.96 % Favored : 94.90 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.09), residues: 8080 helix: 0.34 (0.10), residues: 3216 sheet: 1.13 (0.20), residues: 896 loop : -2.51 (0.08), residues: 3968 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16160 Ramachandran restraints generated. 8080 Oldfield, 0 Emsley, 8080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16160 Ramachandran restraints generated. 8080 Oldfield, 0 Emsley, 8080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 411 time to evaluate : 5.408 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 415 average time/residue: 0.5309 time to fit residues: 397.6870 Evaluate side-chains 412 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 409 time to evaluate : 5.449 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4654 time to fit residues: 10.3967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 800 random chunks: chunk 504 optimal weight: 0.9990 chunk 676 optimal weight: 0.0270 chunk 194 optimal weight: 4.9990 chunk 585 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 chunk 176 optimal weight: 2.9990 chunk 635 optimal weight: 50.0000 chunk 266 optimal weight: 8.9990 chunk 652 optimal weight: 0.2980 chunk 80 optimal weight: 0.0270 chunk 117 optimal weight: 3.9990 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5218 r_free = 0.5218 target = 0.294667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.249662 restraints weight = 73149.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.241585 restraints weight = 115402.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.242369 restraints weight = 133534.721| |-----------------------------------------------------------------------------| r_work (final): 0.4434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.5047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 61664 Z= 0.111 Angle : 0.444 11.865 83088 Z= 0.216 Chirality : 0.039 0.129 10160 Planarity : 0.002 0.032 10656 Dihedral : 3.204 32.901 8544 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.05 % Favored : 94.79 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.09), residues: 8080 helix: 0.41 (0.10), residues: 3216 sheet: 1.15 (0.20), residues: 896 loop : -2.49 (0.08), residues: 3968 =============================================================================== Job complete usr+sys time: 9302.96 seconds wall clock time: 167 minutes 4.27 seconds (10024.27 seconds total)