Starting phenix.real_space_refine on Tue Jan 21 08:19:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jrt_36605/01_2025/8jrt_36605.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jrt_36605/01_2025/8jrt_36605.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jrt_36605/01_2025/8jrt_36605.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jrt_36605/01_2025/8jrt_36605.map" model { file = "/net/cci-nas-00/data/ceres_data/8jrt_36605/01_2025/8jrt_36605.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jrt_36605/01_2025/8jrt_36605.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 5 5.21 5 S 305 5.16 5 C 41912 2.51 5 N 11757 2.21 5 O 12770 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 66765 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 2998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2998 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 23, 'TRANS': 370} Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 55 Chain: "B" Number of atoms: 2851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2851 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 19, 'TRANS': 364} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 231 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 97 Chain: "C" Number of atoms: 2948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 2948 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 16, 'TRANS': 362} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "D" Number of atoms: 3039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3039 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 17, 'TRANS': 362} Chain: "G" Number of atoms: 1826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1826 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 8, 'TRANS': 231} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "H" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1708 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 10, 'TRANS': 221} Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 56 Chain: "I" Number of atoms: 1912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1912 Classifications: {'peptide': 250} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 244} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "J" Number of atoms: 1713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1713 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 6, 'TRANS': 232} Unresolved non-hydrogen bonds: 176 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 77 Chain: "K" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1759 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 225} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "L" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1850 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 227} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "M" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1856 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 234} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "V" Number of atoms: 3313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 479, 3313 Classifications: {'peptide': 479} Incomplete info: {'truncation_to_alanine': 159} Link IDs: {'PTRANS': 23, 'TRANS': 455} Chain breaks: 3 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 578 Unresolved non-hydrogen angles: 726 Unresolved non-hydrogen dihedrals: 478 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 10, 'TYR:plan': 5, 'ASN:plan1': 4, 'HIS:plan': 2, 'PHE:plan': 7, 'GLU:plan': 24, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 325 Chain: "W" Number of atoms: 3364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3364 Classifications: {'peptide': 456} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 104} Link IDs: {'PTRANS': 8, 'TRANS': 447} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 345 Unresolved non-hydrogen angles: 432 Unresolved non-hydrogen dihedrals: 275 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 7, 'GLU:plan': 12, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 173 Chain: "X" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 2958 Classifications: {'peptide': 380} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 10, 'TRANS': 369} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 20 Chain: "Y" Number of atoms: 3115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3115 Classifications: {'peptide': 378} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 370} Chain: "d" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1956 Classifications: {'peptide': 257} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 11, 'TRANS': 245} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 91 Chain: "e" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 331 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "f" Number of atoms: 4343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 881, 4343 Classifications: {'peptide': 881} Incomplete info: {'truncation_to_alanine': 740} Link IDs: {'PTRANS': 34, 'TRANS': 846} Chain breaks: 1 Unresolved chain link angles: 34 Unresolved non-hydrogen bonds: 2586 Unresolved non-hydrogen angles: 3290 Unresolved non-hydrogen dihedrals: 2116 Unresolved non-hydrogen chiralities: 246 Planarities with less than four sites: {'GLN:plan1': 29, 'HIS:plan': 21, 'TYR:plan': 25, 'ASN:plan1': 35, 'TRP:plan': 5, 'ASP:plan': 53, 'PHE:plan': 24, 'GLU:plan': 76, 'ARG:plan': 41} Unresolved non-hydrogen planarities: 1358 Chain: "E" Number of atoms: 2979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2979 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 18, 'TRANS': 356} Chain: "F" Number of atoms: 3093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3093 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 18, 'TRANS': 376} Chain: "U" Number of atoms: 6304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 808, 6304 Classifications: {'peptide': 808} Link IDs: {'PTRANS': 28, 'TRANS': 779} Chain breaks: 2 Chain: "Z" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2281 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 9, 'TRANS': 276} Chain: "a" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2557 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 131} Link IDs: {'PTRANS': 12, 'TRANS': 360} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 461 Unresolved non-hydrogen angles: 595 Unresolved non-hydrogen dihedrals: 374 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 7, 'TRP:plan': 2, 'HIS:plan': 4, 'PHE:plan': 6, 'GLU:plan': 13, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 242 Chain: "b" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1458 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 9, 'TRANS': 181} Chain: "c" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2260 Classifications: {'peptide': 287} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 276} Chain: "v" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 603 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "u" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 604 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "w" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 603 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N LEU v 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU v 73 " occ=0.45 residue: pdb=" N ARG v 74 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG v 74 " occ=0.45 residue: pdb=" N GLY v 75 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY v 75 " occ=0.25 residue: pdb=" N GLY v 76 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY v 76 " occ=0.25 residue: pdb=" N LEU u 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU u 73 " occ=0.45 residue: pdb=" N ARG u 74 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG u 74 " occ=0.45 residue: pdb=" N GLY u 75 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY u 75 " occ=0.25 residue: pdb=" N GLY u 76 " occ=0.25 ... (3 atoms not shown) pdb=" OXT GLY u 76 " occ=0.25 residue: pdb=" N LEU w 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU w 73 " occ=0.45 residue: pdb=" N ARG w 74 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG w 74 " occ=0.45 residue: pdb=" N GLY w 75 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY w 75 " occ=0.25 residue: pdb=" N GLY w 76 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY w 76 " occ=0.25 Time building chain proxies: 28.42, per 1000 atoms: 0.43 Number of scatterers: 66765 At special positions: 0 Unit cell: (254.8, 184.8, 233.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 305 16.00 P 16 15.00 Mg 5 11.99 O 12770 8.00 N 11757 7.00 C 41912 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 270 " distance=2.03 Simple disulfide: pdb=" SG CYS M 41 " - pdb=" SG CYS M 186 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 13.44 Conformation dependent library (CDL) restraints added in 6.9 seconds 17918 Ramachandran restraints generated. 8959 Oldfield, 0 Emsley, 8959 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16998 Finding SS restraints... Secondary structure from input PDB file: 431 helices and 38 sheets defined 57.4% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.63 Creating SS restraints... Processing helix chain 'A' and resid 41 through 64 removed outlier: 3.831A pdb=" N GLN A 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 89 Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 173 through 177 Processing helix chain 'A' and resid 180 through 192 removed outlier: 3.971A pdb=" N VAL A 190 " --> pdb=" O LYS A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 199 through 205 Processing helix chain 'A' and resid 221 through 233 Processing helix chain 'A' and resid 243 through 246 removed outlier: 3.767A pdb=" N VAL A 246 " --> pdb=" O SER A 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 243 through 246' Processing helix chain 'A' and resid 252 through 267 removed outlier: 3.867A pdb=" N LYS A 267 " --> pdb=" O MET A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 280 Processing helix chain 'A' and resid 293 through 307 removed outlier: 3.589A pdb=" N LEU A 306 " --> pdb=" O LEU A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 327 removed outlier: 3.780A pdb=" N THR A 326 " --> pdb=" O ARG A 323 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU A 327 " --> pdb=" O PRO A 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 323 through 327' Processing helix chain 'A' and resid 348 through 359 Processing helix chain 'A' and resid 369 through 377 removed outlier: 4.262A pdb=" N LEU A 373 " --> pdb=" O ARG A 369 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N CYS A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 399 removed outlier: 4.023A pdb=" N ALA A 399 " --> pdb=" O PHE A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 417 removed outlier: 3.525A pdb=" N PHE A 409 " --> pdb=" O THR A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 430 Processing helix chain 'B' and resid 58 through 86 removed outlier: 4.063A pdb=" N GLN B 82 " --> pdb=" O PHE B 78 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLU B 83 " --> pdb=" O ILE B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 103 Processing helix chain 'B' and resid 168 through 175 removed outlier: 4.100A pdb=" N THR B 172 " --> pdb=" O ASP B 168 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL B 173 " --> pdb=" O PRO B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 187 Processing helix chain 'B' and resid 192 through 201 removed outlier: 3.986A pdb=" N GLU B 196 " --> pdb=" O ASN B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 207 removed outlier: 4.032A pdb=" N LEU B 205 " --> pdb=" O VAL B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 215 removed outlier: 3.588A pdb=" N MET B 214 " --> pdb=" O TYR B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 243 removed outlier: 3.672A pdb=" N LEU B 235 " --> pdb=" O GLY B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 255 No H-bonds generated for 'chain 'B' and resid 253 through 255' Processing helix chain 'B' and resid 261 through 278 removed outlier: 3.860A pdb=" N LYS B 265 " --> pdb=" O GLY B 261 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N HIS B 277 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ALA B 278 " --> pdb=" O ALA B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 293 removed outlier: 3.844A pdb=" N LYS B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 318 removed outlier: 3.620A pdb=" N GLN B 306 " --> pdb=" O GLU B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 342 Processing helix chain 'B' and resid 357 through 369 Processing helix chain 'B' and resid 379 through 385 removed outlier: 4.056A pdb=" N LEU B 383 " --> pdb=" O THR B 379 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N MET B 385 " --> pdb=" O ASP B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 409 removed outlier: 3.963A pdb=" N ILE B 395 " --> pdb=" O SER B 391 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS B 396 " --> pdb=" O GLY B 392 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLU B 409 " --> pdb=" O MET B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 428 removed outlier: 3.658A pdb=" N PHE B 419 " --> pdb=" O THR B 415 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU B 424 " --> pdb=" O LYS B 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 67 removed outlier: 3.613A pdb=" N TYR C 24 " --> pdb=" O LEU C 20 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN C 36 " --> pdb=" O GLN C 32 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ASP C 37 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS C 38 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG C 44 " --> pdb=" O GLN C 40 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LEU C 45 " --> pdb=" O ASN C 41 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA C 47 " --> pdb=" O ARG C 43 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN C 48 " --> pdb=" O ARG C 44 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG C 49 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU C 63 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLN C 64 " --> pdb=" O ARG C 60 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 132 through 142 Processing helix chain 'C' and resid 147 through 151 removed outlier: 3.606A pdb=" N MET C 150 " --> pdb=" O THR C 147 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE C 151 " --> pdb=" O TYR C 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 147 through 151' Processing helix chain 'C' and resid 154 through 166 removed outlier: 3.809A pdb=" N VAL C 164 " --> pdb=" O GLU C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 171 removed outlier: 3.629A pdb=" N LYS C 170 " --> pdb=" O GLU C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 179 removed outlier: 3.781A pdb=" N PHE C 175 " --> pdb=" O HIS C 171 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU C 178 " --> pdb=" O LEU C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 207 Processing helix chain 'C' and resid 220 through 225 removed outlier: 3.700A pdb=" N ILE C 224 " --> pdb=" O VAL C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 233 No H-bonds generated for 'chain 'C' and resid 231 through 233' Processing helix chain 'C' and resid 234 through 239 Processing helix chain 'C' and resid 240 through 242 No H-bonds generated for 'chain 'C' and resid 240 through 242' Processing helix chain 'C' and resid 258 through 263 Processing helix chain 'C' and resid 268 through 280 Processing helix chain 'C' and resid 297 through 301 Processing helix chain 'C' and resid 302 through 306 Processing helix chain 'C' and resid 321 through 333 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 343 through 350 removed outlier: 4.065A pdb=" N ILE C 347 " --> pdb=" O ASN C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 373 removed outlier: 4.342A pdb=" N LYS C 360 " --> pdb=" O GLY C 356 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY C 361 " --> pdb=" O ALA C 357 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY C 367 " --> pdb=" O CYS C 363 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N MET C 368 " --> pdb=" O THR C 364 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR C 369 " --> pdb=" O GLU C 365 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA C 370 " --> pdb=" O ALA C 366 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU C 373 " --> pdb=" O TYR C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 394 removed outlier: 3.579A pdb=" N PHE C 383 " --> pdb=" O THR C 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 54 removed outlier: 4.208A pdb=" N LEU D 47 " --> pdb=" O ARG D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 78 removed outlier: 3.728A pdb=" N GLU D 59 " --> pdb=" O GLU D 55 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR D 60 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE D 61 " --> pdb=" O GLN D 57 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS D 66 " --> pdb=" O LYS D 62 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS D 69 " --> pdb=" O GLN D 65 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS D 70 " --> pdb=" O LYS D 66 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N HIS D 74 " --> pdb=" O LYS D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 82 removed outlier: 3.795A pdb=" N ILE D 82 " --> pdb=" O VAL D 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 79 through 82' Processing helix chain 'D' and resid 170 through 181 Processing helix chain 'D' and resid 181 through 187 Processing helix chain 'D' and resid 187 through 195 removed outlier: 3.801A pdb=" N TYR D 191 " --> pdb=" O HIS D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 223 removed outlier: 3.967A pdb=" N ALA D 216 " --> pdb=" O LYS D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 235 No H-bonds generated for 'chain 'D' and resid 233 through 235' Processing helix chain 'D' and resid 241 through 258 removed outlier: 4.018A pdb=" N ARG D 245 " --> pdb=" O GLY D 241 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL D 250 " --> pdb=" O MET D 246 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA D 258 " --> pdb=" O ALA D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 270 Processing helix chain 'D' and resid 280 through 298 Processing helix chain 'D' and resid 318 through 323 removed outlier: 3.563A pdb=" N ARG D 323 " --> pdb=" O ALA D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 350 removed outlier: 3.707A pdb=" N ARG D 342 " --> pdb=" O ARG D 338 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU D 343 " --> pdb=" O ARG D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 365 removed outlier: 3.690A pdb=" N ALA D 365 " --> pdb=" O GLU D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 389 removed outlier: 3.692A pdb=" N GLU D 389 " --> pdb=" O LEU D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 408 removed outlier: 3.664A pdb=" N PHE D 399 " --> pdb=" O LEU D 395 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE D 407 " --> pdb=" O TYR D 403 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS D 408 " --> pdb=" O LYS D 404 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 33 removed outlier: 4.174A pdb=" N GLU G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ALA G 28 " --> pdb=" O GLN G 24 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE G 29 " --> pdb=" O VAL G 25 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS G 30 " --> pdb=" O GLU G 26 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASN G 33 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 66 removed outlier: 3.541A pdb=" N THR G 65 " --> pdb=" O ASP G 62 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL G 66 " --> pdb=" O SER G 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 62 through 66' Processing helix chain 'G' and resid 83 through 106 Processing helix chain 'G' and resid 110 through 124 removed outlier: 4.026A pdb=" N VAL G 124 " --> pdb=" O ASP G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 127 No H-bonds generated for 'chain 'G' and resid 125 through 127' Processing helix chain 'G' and resid 171 through 184 Processing helix chain 'G' and resid 190 through 207 removed outlier: 3.618A pdb=" N LEU G 202 " --> pdb=" O ALA G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 231 through 243 Processing helix chain 'H' and resid 19 through 30 removed outlier: 3.668A pdb=" N GLU H 23 " --> pdb=" O LEU H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 102 removed outlier: 4.337A pdb=" N ARG H 84 " --> pdb=" O GLY H 80 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL H 85 " --> pdb=" O PRO H 81 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU H 86 " --> pdb=" O ASP H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 121 Processing helix chain 'H' and resid 166 through 178 Processing helix chain 'H' and resid 183 through 196 Processing helix chain 'H' and resid 222 through 231 Processing helix chain 'I' and resid 18 through 28 removed outlier: 3.881A pdb=" N GLU I 22 " --> pdb=" O LEU I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 102 removed outlier: 3.787A pdb=" N LEU I 92 " --> pdb=" O ASN I 88 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE I 93 " --> pdb=" O GLU I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 121 removed outlier: 3.571A pdb=" N LEU I 110 " --> pdb=" O PRO I 106 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N TYR I 121 " --> pdb=" O ILE I 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 178 Processing helix chain 'I' and resid 187 through 201 removed outlier: 4.110A pdb=" N ALA I 191 " --> pdb=" O LYS I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 207 through 209 No H-bonds generated for 'chain 'I' and resid 207 through 209' Processing helix chain 'I' and resid 232 through 251 removed outlier: 3.804A pdb=" N LEU I 236 " --> pdb=" O GLU I 232 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS I 251 " --> pdb=" O ALA I 247 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 27 Processing helix chain 'J' and resid 55 through 59 removed outlier: 3.516A pdb=" N VAL J 59 " --> pdb=" O GLU J 56 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 97 removed outlier: 3.820A pdb=" N VAL J 83 " --> pdb=" O ASP J 79 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG J 95 " --> pdb=" O CYS J 91 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU J 96 " --> pdb=" O GLN J 92 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR J 97 " --> pdb=" O SER J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 118 removed outlier: 3.639A pdb=" N ILE J 107 " --> pdb=" O THR J 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 164 through 174 removed outlier: 3.917A pdb=" N VAL J 168 " --> pdb=" O GLY J 164 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS J 174 " --> pdb=" O GLU J 170 " (cutoff:3.500A) Processing helix chain 'J' and resid 178 through 182 Processing helix chain 'J' and resid 183 through 197 Processing helix chain 'J' and resid 223 through 240 Processing helix chain 'K' and resid 21 through 30 Processing helix chain 'K' and resid 84 through 104 removed outlier: 4.348A pdb=" N LEU K 88 " --> pdb=" O ASP K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 118 removed outlier: 3.627A pdb=" N ASN K 118 " --> pdb=" O GLN K 114 " (cutoff:3.500A) Processing helix chain 'K' and resid 173 through 182 Processing helix chain 'K' and resid 190 through 206 Processing helix chain 'K' and resid 235 through 240 removed outlier: 3.757A pdb=" N ASP K 240 " --> pdb=" O GLU K 236 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 8 removed outlier: 3.824A pdb=" N ASP L 7 " --> pdb=" O ASN L 4 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASN L 8 " --> pdb=" O GLN L 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 4 through 8' Processing helix chain 'L' and resid 19 through 29 removed outlier: 3.993A pdb=" N GLU L 23 " --> pdb=" O ILE L 19 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 77 through 99 removed outlier: 3.582A pdb=" N ALA L 81 " --> pdb=" O LEU L 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 104 through 117 Processing helix chain 'L' and resid 118 through 121 Processing helix chain 'L' and resid 165 through 175 Processing helix chain 'L' and resid 176 through 181 removed outlier: 3.952A pdb=" N GLU L 181 " --> pdb=" O GLU L 178 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 196 removed outlier: 3.832A pdb=" N LYS L 189 " --> pdb=" O ASN L 185 " (cutoff:3.500A) Processing helix chain 'L' and resid 197 through 199 No H-bonds generated for 'chain 'L' and resid 197 through 199' Processing helix chain 'L' and resid 229 through 234 Processing helix chain 'M' and resid 21 through 31 Processing helix chain 'M' and resid 80 through 102 Processing helix chain 'M' and resid 107 through 121 removed outlier: 4.147A pdb=" N ASP M 113 " --> pdb=" O LYS M 109 " (cutoff:3.500A) Processing helix chain 'M' and resid 168 through 179 removed outlier: 3.692A pdb=" N GLU M 175 " --> pdb=" O ALA M 171 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS M 178 " --> pdb=" O THR M 174 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU M 179 " --> pdb=" O GLU M 175 " (cutoff:3.500A) Processing helix chain 'M' and resid 188 through 199 removed outlier: 3.800A pdb=" N GLU M 192 " --> pdb=" O ASP M 188 " (cutoff:3.500A) Processing helix chain 'M' and resid 219 through 221 No H-bonds generated for 'chain 'M' and resid 219 through 221' Processing helix chain 'M' and resid 228 through 240 Processing helix chain 'M' and resid 241 through 244 removed outlier: 3.557A pdb=" N LYS M 244 " --> pdb=" O GLU M 241 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 241 through 244' Processing helix chain 'V' and resid 19 through 23 removed outlier: 3.600A pdb=" N GLY V 22 " --> pdb=" O PRO V 19 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLU V 23 " --> pdb=" O GLY V 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 19 through 23' Processing helix chain 'V' and resid 29 through 38 removed outlier: 3.572A pdb=" N GLN V 33 " --> pdb=" O PRO V 29 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS V 38 " --> pdb=" O ASP V 34 " (cutoff:3.500A) Processing helix chain 'V' and resid 40 through 51 removed outlier: 3.514A pdb=" N GLY V 49 " --> pdb=" O GLY V 45 " (cutoff:3.500A) Processing helix chain 'V' and resid 57 through 62 removed outlier: 3.649A pdb=" N HIS V 62 " --> pdb=" O ALA V 58 " (cutoff:3.500A) Processing helix chain 'V' and resid 62 through 75 removed outlier: 3.666A pdb=" N GLU V 73 " --> pdb=" O THR V 69 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE V 75 " --> pdb=" O THR V 71 " (cutoff:3.500A) Processing helix chain 'V' and resid 91 through 95 removed outlier: 3.592A pdb=" N LEU V 95 " --> pdb=" O PRO V 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 91 through 95' Processing helix chain 'V' and resid 100 through 121 removed outlier: 4.391A pdb=" N LEU V 108 " --> pdb=" O THR V 104 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN V 109 " --> pdb=" O SER V 105 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL V 112 " --> pdb=" O LEU V 108 " (cutoff:3.500A) Processing helix chain 'V' and resid 136 through 140 Processing helix chain 'V' and resid 147 through 164 removed outlier: 3.838A pdb=" N LYS V 153 " --> pdb=" O PRO V 149 " (cutoff:3.500A) Proline residue: V 158 - end of helix Proline residue: V 161 - end of helix Processing helix chain 'V' and resid 172 through 187 removed outlier: 3.680A pdb=" N MET V 176 " --> pdb=" O VAL V 172 " (cutoff:3.500A) Processing helix chain 'V' and resid 202 through 220 removed outlier: 4.789A pdb=" N LYS V 209 " --> pdb=" O LEU V 205 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N CYS V 210 " --> pdb=" O VAL V 206 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ALA V 215 " --> pdb=" O TYR V 211 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG V 216 " --> pdb=" O TYR V 212 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR V 218 " --> pdb=" O HIS V 214 " (cutoff:3.500A) Processing helix chain 'V' and resid 224 through 238 removed outlier: 3.619A pdb=" N ARG V 236 " --> pdb=" O HIS V 232 " (cutoff:3.500A) Processing helix chain 'V' and resid 248 through 259 removed outlier: 4.367A pdb=" N ASN V 257 " --> pdb=" O LEU V 253 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU V 259 " --> pdb=" O LEU V 255 " (cutoff:3.500A) Processing helix chain 'V' and resid 266 through 272 removed outlier: 3.503A pdb=" N VAL V 271 " --> pdb=" O ALA V 267 " (cutoff:3.500A) Processing helix chain 'V' and resid 273 through 276 removed outlier: 4.358A pdb=" N PHE V 276 " --> pdb=" O LYS V 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 273 through 276' Processing helix chain 'V' and resid 283 through 298 removed outlier: 4.003A pdb=" N ARG V 287 " --> pdb=" O ASN V 283 " (cutoff:3.500A) Processing helix chain 'V' and resid 302 through 315 removed outlier: 3.535A pdb=" N ARG V 306 " --> pdb=" O TYR V 302 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARG V 307 " --> pdb=" O SER V 303 " (cutoff:3.500A) Processing helix chain 'V' and resid 322 through 339 removed outlier: 4.048A pdb=" N THR V 327 " --> pdb=" O GLY V 323 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU V 336 " --> pdb=" O LEU V 332 " (cutoff:3.500A) Processing helix chain 'V' and resid 350 through 355 removed outlier: 4.640A pdb=" N ARG V 355 " --> pdb=" O PRO V 351 " (cutoff:3.500A) Processing helix chain 'V' and resid 357 through 369 removed outlier: 3.784A pdb=" N THR V 369 " --> pdb=" O GLN V 365 " (cutoff:3.500A) Processing helix chain 'V' and resid 372 through 389 removed outlier: 3.880A pdb=" N GLN V 381 " --> pdb=" O GLN V 377 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLU V 384 " --> pdb=" O ASP V 380 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N LYS V 385 " --> pdb=" O GLN V 381 " (cutoff:3.500A) Processing helix chain 'V' and resid 391 through 396 Processing helix chain 'V' and resid 398 through 413 Processing helix chain 'V' and resid 419 through 427 removed outlier: 3.761A pdb=" N ALA V 423 " --> pdb=" O LEU V 419 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N GLN V 424 " --> pdb=" O ALA V 420 " (cutoff:3.500A) Processing helix chain 'V' and resid 431 through 444 removed outlier: 3.733A pdb=" N GLU V 435 " --> pdb=" O PRO V 431 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE V 436 " --> pdb=" O GLU V 432 " (cutoff:3.500A) Processing helix chain 'V' and resid 465 through 469 removed outlier: 3.727A pdb=" N SER V 468 " --> pdb=" O ASP V 465 " (cutoff:3.500A) Processing helix chain 'V' and resid 470 through 493 removed outlier: 3.514A pdb=" N LEU V 474 " --> pdb=" O ARG V 470 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG V 479 " --> pdb=" O ALA V 475 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE V 482 " --> pdb=" O GLN V 478 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N HIS V 487 " --> pdb=" O CYS V 483 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN V 488 " --> pdb=" O LEU V 484 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA V 493 " --> pdb=" O MET V 489 " (cutoff:3.500A) Processing helix chain 'V' and resid 510 through 525 removed outlier: 3.761A pdb=" N ARG V 514 " --> pdb=" O GLU V 510 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET V 525 " --> pdb=" O PHE V 521 " (cutoff:3.500A) Processing helix chain 'W' and resid 2 through 19 removed outlier: 5.086A pdb=" N VAL W 14 " --> pdb=" O ASP W 10 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS W 15 " --> pdb=" O GLY W 11 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU W 17 " --> pdb=" O ILE W 13 " (cutoff:3.500A) Processing helix chain 'W' and resid 21 through 38 removed outlier: 3.739A pdb=" N ASP W 25 " --> pdb=" O SER W 21 " (cutoff:3.500A) Proline residue: W 29 - end of helix removed outlier: 3.681A pdb=" N LEU W 34 " --> pdb=" O GLU W 30 " (cutoff:3.500A) Processing helix chain 'W' and resid 42 through 65 Processing helix chain 'W' and resid 71 through 86 Processing helix chain 'W' and resid 97 through 111 Processing helix chain 'W' and resid 116 through 128 removed outlier: 3.679A pdb=" N LEU W 122 " --> pdb=" O LEU W 118 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ARG W 123 " --> pdb=" O PRO W 119 " (cutoff:3.500A) Processing helix chain 'W' and resid 129 through 131 No H-bonds generated for 'chain 'W' and resid 129 through 131' Processing helix chain 'W' and resid 136 through 156 Processing helix chain 'W' and resid 159 through 167 Processing helix chain 'W' and resid 168 through 172 removed outlier: 3.838A pdb=" N GLU W 172 " --> pdb=" O LEU W 169 " (cutoff:3.500A) Processing helix chain 'W' and resid 178 through 197 removed outlier: 4.038A pdb=" N GLN W 189 " --> pdb=" O PHE W 185 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N MET W 190 " --> pdb=" O ILE W 186 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ARG W 191 " --> pdb=" O LEU W 187 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU W 192 " --> pdb=" O GLU W 188 " (cutoff:3.500A) Processing helix chain 'W' and resid 198 through 207 removed outlier: 3.953A pdb=" N LYS W 207 " --> pdb=" O GLN W 203 " (cutoff:3.500A) Processing helix chain 'W' and resid 219 through 235 removed outlier: 3.681A pdb=" N LYS W 223 " --> pdb=" O THR W 219 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU W 229 " --> pdb=" O LYS W 225 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N MET W 230 " --> pdb=" O TYR W 226 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE W 231 " --> pdb=" O TYR W 227 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLN W 232 " --> pdb=" O ASN W 228 " (cutoff:3.500A) Processing helix chain 'W' and resid 241 through 250 Processing helix chain 'W' and resid 259 through 277 removed outlier: 5.335A pdb=" N GLN W 265 " --> pdb=" O GLU W 261 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL W 270 " --> pdb=" O ALA W 266 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N VAL W 271 " --> pdb=" O LEU W 267 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE W 275 " --> pdb=" O VAL W 271 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU W 276 " --> pdb=" O LEU W 272 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA W 277 " --> pdb=" O TYR W 273 " (cutoff:3.500A) Processing helix chain 'W' and resid 280 through 291 removed outlier: 3.991A pdb=" N HIS W 288 " --> pdb=" O SER W 284 " (cutoff:3.500A) Processing helix chain 'W' and resid 293 through 298 Processing helix chain 'W' and resid 299 through 311 removed outlier: 3.522A pdb=" N LYS W 303 " --> pdb=" O ILE W 299 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR W 311 " --> pdb=" O LYS W 307 " (cutoff:3.500A) Processing helix chain 'W' and resid 317 through 325 removed outlier: 3.655A pdb=" N VAL W 321 " --> pdb=" O TRP W 317 " (cutoff:3.500A) Processing helix chain 'W' and resid 326 through 330 removed outlier: 3.898A pdb=" N ARG W 329 " --> pdb=" O MET W 326 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS W 330 " --> pdb=" O GLU W 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 326 through 330' Processing helix chain 'W' and resid 334 through 342 Processing helix chain 'W' and resid 343 through 370 Processing helix chain 'W' and resid 375 through 382 Processing helix chain 'W' and resid 385 through 399 removed outlier: 4.110A pdb=" N ASN W 395 " --> pdb=" O ALA W 391 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU W 396 " --> pdb=" O PHE W 392 " (cutoff:3.500A) Processing helix chain 'W' and resid 420 through 452 removed outlier: 3.588A pdb=" N LEU W 424 " --> pdb=" O ASP W 420 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU W 425 " --> pdb=" O PRO W 421 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N THR W 443 " --> pdb=" O VAL W 439 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N HIS W 444 " --> pdb=" O ASN W 440 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU W 445 " --> pdb=" O LYS W 441 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE W 452 " --> pdb=" O LYS W 448 " (cutoff:3.500A) Processing helix chain 'X' and resid 44 through 61 Processing helix chain 'X' and resid 63 through 73 removed outlier: 3.546A pdb=" N VAL X 73 " --> pdb=" O LEU X 69 " (cutoff:3.500A) Processing helix chain 'X' and resid 73 through 78 removed outlier: 4.282A pdb=" N ASN X 78 " --> pdb=" O ARG X 74 " (cutoff:3.500A) Processing helix chain 'X' and resid 81 through 98 removed outlier: 3.937A pdb=" N LEU X 95 " --> pdb=" O SER X 91 " (cutoff:3.500A) Processing helix chain 'X' and resid 107 through 121 Processing helix chain 'X' and resid 122 through 139 removed outlier: 3.915A pdb=" N PHE X 138 " --> pdb=" O VAL X 134 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASP X 139 " --> pdb=" O SER X 135 " (cutoff:3.500A) Processing helix chain 'X' and resid 147 through 160 removed outlier: 3.853A pdb=" N ARG X 155 " --> pdb=" O SER X 151 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU X 156 " --> pdb=" O GLN X 152 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS X 159 " --> pdb=" O ARG X 155 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N MET X 160 " --> pdb=" O GLU X 156 " (cutoff:3.500A) Processing helix chain 'X' and resid 163 through 180 Processing helix chain 'X' and resid 182 through 197 Processing helix chain 'X' and resid 205 through 221 removed outlier: 3.628A pdb=" N THR X 209 " --> pdb=" O LYS X 205 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU X 221 " --> pdb=" O ILE X 217 " (cutoff:3.500A) Processing helix chain 'X' and resid 224 through 239 removed outlier: 3.758A pdb=" N ALA X 228 " --> pdb=" O ASP X 224 " (cutoff:3.500A) Processing helix chain 'X' and resid 243 through 261 removed outlier: 3.932A pdb=" N THR X 249 " --> pdb=" O PRO X 245 " (cutoff:3.500A) Processing helix chain 'X' and resid 263 through 272 removed outlier: 3.721A pdb=" N VAL X 267 " --> pdb=" O THR X 263 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER X 272 " --> pdb=" O GLN X 268 " (cutoff:3.500A) Processing helix chain 'X' and resid 273 through 279 removed outlier: 3.524A pdb=" N TYR X 279 " --> pdb=" O LEU X 275 " (cutoff:3.500A) Processing helix chain 'X' and resid 281 through 297 removed outlier: 3.830A pdb=" N GLU X 285 " --> pdb=" O GLY X 281 " (cutoff:3.500A) Processing helix chain 'X' and resid 298 through 309 removed outlier: 3.682A pdb=" N PHE X 302 " --> pdb=" O SER X 298 " (cutoff:3.500A) Processing helix chain 'X' and resid 309 through 314 Processing helix chain 'X' and resid 318 through 340 removed outlier: 3.863A pdb=" N HIS X 322 " --> pdb=" O ILE X 318 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ALA X 324 " --> pdb=" O SER X 320 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N LYS X 325 " --> pdb=" O THR X 321 " (cutoff:3.500A) Processing helix chain 'X' and resid 346 through 355 removed outlier: 3.834A pdb=" N ILE X 350 " --> pdb=" O GLN X 346 " (cutoff:3.500A) Processing helix chain 'X' and resid 358 through 371 Processing helix chain 'X' and resid 395 through 414 removed outlier: 4.353A pdb=" N ALA X 399 " --> pdb=" O LYS X 395 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA X 400 " --> pdb=" O THR X 396 " (cutoff:3.500A) Processing helix chain 'X' and resid 414 through 419 Processing helix chain 'Y' and resid 16 through 28 removed outlier: 3.651A pdb=" N ALA Y 20 " --> pdb=" O ASP Y 16 " (cutoff:3.500A) Processing helix chain 'Y' and resid 35 through 46 removed outlier: 3.542A pdb=" N LEU Y 41 " --> pdb=" O VAL Y 37 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG Y 46 " --> pdb=" O MET Y 42 " (cutoff:3.500A) Processing helix chain 'Y' and resid 47 through 49 No H-bonds generated for 'chain 'Y' and resid 47 through 49' Processing helix chain 'Y' and resid 50 through 52 No H-bonds generated for 'chain 'Y' and resid 50 through 52' Processing helix chain 'Y' and resid 53 through 60 removed outlier: 4.115A pdb=" N CYS Y 58 " --> pdb=" O TYR Y 54 " (cutoff:3.500A) Processing helix chain 'Y' and resid 66 through 94 removed outlier: 3.796A pdb=" N LYS Y 93 " --> pdb=" O GLU Y 89 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASN Y 94 " --> pdb=" O ASP Y 90 " (cutoff:3.500A) Processing helix chain 'Y' and resid 98 through 115 removed outlier: 4.191A pdb=" N GLU Y 109 " --> pdb=" O MET Y 105 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TYR Y 110 " --> pdb=" O ALA Y 106 " (cutoff:3.500A) Processing helix chain 'Y' and resid 116 through 128 removed outlier: 3.698A pdb=" N ALA Y 120 " --> pdb=" O ASP Y 116 " (cutoff:3.500A) Processing helix chain 'Y' and resid 133 through 152 removed outlier: 3.523A pdb=" N ARG Y 137 " --> pdb=" O ALA Y 133 " (cutoff:3.500A) Processing helix chain 'Y' and resid 153 through 169 removed outlier: 3.962A pdb=" N GLU Y 169 " --> pdb=" O LYS Y 165 " (cutoff:3.500A) Processing helix chain 'Y' and resid 173 through 191 removed outlier: 3.509A pdb=" N ALA Y 190 " --> pdb=" O LEU Y 186 " (cutoff:3.500A) Processing helix chain 'Y' and resid 194 through 201 Processing helix chain 'Y' and resid 215 through 231 removed outlier: 3.912A pdb=" N ILE Y 229 " --> pdb=" O TYR Y 225 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU Y 231 " --> pdb=" O SER Y 227 " (cutoff:3.500A) Processing helix chain 'Y' and resid 232 through 240 Processing helix chain 'Y' and resid 243 through 251 removed outlier: 4.093A pdb=" N VAL Y 249 " --> pdb=" O GLU Y 245 " (cutoff:3.500A) Processing helix chain 'Y' and resid 253 through 266 removed outlier: 3.550A pdb=" N LEU Y 263 " --> pdb=" O TYR Y 259 " (cutoff:3.500A) Processing helix chain 'Y' and resid 267 through 284 removed outlier: 3.850A pdb=" N PHE Y 272 " --> pdb=" O TYR Y 268 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLN Y 273 " --> pdb=" O SER Y 269 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER Y 274 " --> pdb=" O VAL Y 270 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS Y 284 " --> pdb=" O GLN Y 280 " (cutoff:3.500A) Processing helix chain 'Y' and resid 288 through 290 No H-bonds generated for 'chain 'Y' and resid 288 through 290' Processing helix chain 'Y' and resid 291 through 306 removed outlier: 3.506A pdb=" N TYR Y 295 " --> pdb=" O HIS Y 291 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL Y 296 " --> pdb=" O TYR Y 292 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE Y 301 " --> pdb=" O ARG Y 297 " (cutoff:3.500A) Processing helix chain 'Y' and resid 316 through 323 removed outlier: 3.919A pdb=" N ALA Y 320 " --> pdb=" O LEU Y 316 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU Y 321 " --> pdb=" O GLY Y 317 " (cutoff:3.500A) Processing helix chain 'Y' and resid 326 through 340 Processing helix chain 'Y' and resid 363 through 387 removed outlier: 3.881A pdb=" N GLU Y 368 " --> pdb=" O TRP Y 364 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N THR Y 369 " --> pdb=" O GLN Y 365 " (cutoff:3.500A) Processing helix chain 'd' and resid 3 through 7 Processing helix chain 'd' and resid 18 through 32 removed outlier: 4.317A pdb=" N GLY d 24 " --> pdb=" O GLY d 20 " (cutoff:3.500A) Processing helix chain 'd' and resid 45 through 66 removed outlier: 3.807A pdb=" N ALA d 51 " --> pdb=" O GLN d 47 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP d 53 " --> pdb=" O ILE d 49 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLY d 58 " --> pdb=" O ILE d 54 " (cutoff:3.500A) Processing helix chain 'd' and resid 67 through 85 removed outlier: 3.770A pdb=" N PHE d 83 " --> pdb=" O LYS d 79 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TYR d 85 " --> pdb=" O TYR d 81 " (cutoff:3.500A) Processing helix chain 'd' and resid 94 through 109 Processing helix chain 'd' and resid 111 through 120 removed outlier: 4.005A pdb=" N PHE d 115 " --> pdb=" O ARG d 111 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N HIS d 116 " --> pdb=" O VAL d 112 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU d 120 " --> pdb=" O HIS d 116 " (cutoff:3.500A) Processing helix chain 'd' and resid 124 through 129 removed outlier: 3.566A pdb=" N THR d 129 " --> pdb=" O LYS d 125 " (cutoff:3.500A) Processing helix chain 'd' and resid 130 through 145 Proline residue: d 136 - end of helix removed outlier: 4.117A pdb=" N GLU d 145 " --> pdb=" O GLN d 141 " (cutoff:3.500A) Processing helix chain 'd' and resid 148 through 156 removed outlier: 3.861A pdb=" N GLY d 156 " --> pdb=" O PHE d 152 " (cutoff:3.500A) Processing helix chain 'd' and resid 163 through 186 removed outlier: 4.218A pdb=" N ILE d 169 " --> pdb=" O PHE d 165 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU d 177 " --> pdb=" O THR d 173 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU d 183 " --> pdb=" O ALA d 179 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LYS d 184 " --> pdb=" O GLY d 180 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA d 185 " --> pdb=" O CYS d 181 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N TYR d 186 " --> pdb=" O ILE d 182 " (cutoff:3.500A) Processing helix chain 'd' and resid 190 through 198 Processing helix chain 'd' and resid 203 through 213 removed outlier: 4.355A pdb=" N THR d 207 " --> pdb=" O PRO d 203 " (cutoff:3.500A) Processing helix chain 'd' and resid 235 through 255 removed outlier: 4.067A pdb=" N ALA d 243 " --> pdb=" O SER d 239 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLN d 252 " --> pdb=" O GLU d 248 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU d 253 " --> pdb=" O TYR d 249 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLU d 254 " --> pdb=" O ALA d 250 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N MET d 255 " --> pdb=" O ARG d 251 " (cutoff:3.500A) Processing helix chain 'e' and resid 47 through 52 removed outlier: 3.631A pdb=" N ASP e 51 " --> pdb=" O ASN e 47 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE e 52 " --> pdb=" O VAL e 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 47 through 52' Processing helix chain 'e' and resid 53 through 55 No H-bonds generated for 'chain 'e' and resid 53 through 55' Processing helix chain 'e' and resid 58 through 68 removed outlier: 4.126A pdb=" N GLU e 68 " --> pdb=" O GLY e 64 " (cutoff:3.500A) Processing helix chain 'f' and resid 11 through 24 Proline residue: f 17 - end of helix Proline residue: f 21 - end of helix Processing helix chain 'f' and resid 27 through 46 removed outlier: 3.640A pdb=" N GLU f 32 " --> pdb=" O PRO f 28 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP f 35 " --> pdb=" O LYS f 31 " (cutoff:3.500A) Processing helix chain 'f' and resid 63 through 70 removed outlier: 3.782A pdb=" N ASP f 67 " --> pdb=" O LEU f 63 " (cutoff:3.500A) Processing helix chain 'f' and resid 81 through 91 removed outlier: 3.888A pdb=" N SER f 85 " --> pdb=" O GLN f 81 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER f 88 " --> pdb=" O SER f 84 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N MET f 89 " --> pdb=" O SER f 85 " (cutoff:3.500A) Processing helix chain 'f' and resid 93 through 98 removed outlier: 3.897A pdb=" N PHE f 98 " --> pdb=" O LYS f 94 " (cutoff:3.500A) Processing helix chain 'f' and resid 102 through 106 removed outlier: 4.053A pdb=" N LEU f 106 " --> pdb=" O TYR f 103 " (cutoff:3.500A) Processing helix chain 'f' and resid 117 through 121 Processing helix chain 'f' and resid 130 through 140 removed outlier: 3.672A pdb=" N LEU f 140 " --> pdb=" O GLU f 136 " (cutoff:3.500A) Processing helix chain 'f' and resid 140 through 149 removed outlier: 4.512A pdb=" N GLN f 148 " --> pdb=" O LEU f 144 " (cutoff:3.500A) Processing helix chain 'f' and resid 153 through 158 removed outlier: 3.807A pdb=" N GLU f 157 " --> pdb=" O SER f 153 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR f 158 " --> pdb=" O TRP f 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 153 through 158' Processing helix chain 'f' and resid 158 through 171 removed outlier: 3.840A pdb=" N GLN f 171 " --> pdb=" O ALA f 167 " (cutoff:3.500A) Processing helix chain 'f' and resid 177 through 189 removed outlier: 3.530A pdb=" N ARG f 181 " --> pdb=" O GLU f 177 " (cutoff:3.500A) Proline residue: f 183 - end of helix Processing helix chain 'f' and resid 193 through 207 removed outlier: 3.948A pdb=" N ALA f 197 " --> pdb=" O PRO f 193 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU f 203 " --> pdb=" O ASN f 199 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA f 204 " --> pdb=" O ALA f 200 " (cutoff:3.500A) Processing helix chain 'f' and resid 210 through 225 removed outlier: 4.279A pdb=" N VAL f 214 " --> pdb=" O GLU f 210 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ASP f 215 " --> pdb=" O ILE f 211 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N MET f 216 " --> pdb=" O GLU f 212 " (cutoff:3.500A) Processing helix chain 'f' and resid 228 through 239 removed outlier: 3.759A pdb=" N VAL f 237 " --> pdb=" O LEU f 233 " (cutoff:3.500A) Processing helix chain 'f' and resid 241 through 246 Processing helix chain 'f' and resid 252 through 257 Processing helix chain 'f' and resid 265 through 279 Processing helix chain 'f' and resid 284 through 292 removed outlier: 4.103A pdb=" N LYS f 292 " --> pdb=" O VAL f 288 " (cutoff:3.500A) Processing helix chain 'f' and resid 315 through 322 removed outlier: 3.728A pdb=" N GLU f 319 " --> pdb=" O GLU f 315 " (cutoff:3.500A) Processing helix chain 'f' and resid 322 through 336 Processing helix chain 'f' and resid 353 through 357 removed outlier: 3.510A pdb=" N ASN f 356 " --> pdb=" O LEU f 353 " (cutoff:3.500A) Processing helix chain 'f' and resid 368 through 382 removed outlier: 3.542A pdb=" N LEU f 372 " --> pdb=" O ALA f 368 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA f 373 " --> pdb=" O ARG f 369 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL f 381 " --> pdb=" O VAL f 377 " (cutoff:3.500A) Processing helix chain 'f' and resid 392 through 399 Processing helix chain 'f' and resid 403 through 418 removed outlier: 3.750A pdb=" N LEU f 414 " --> pdb=" O ALA f 410 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLY f 415 " --> pdb=" O ALA f 411 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET f 416 " --> pdb=" O ALA f 412 " (cutoff:3.500A) Processing helix chain 'f' and resid 424 through 434 removed outlier: 3.933A pdb=" N LYS f 431 " --> pdb=" O THR f 427 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N TYR f 432 " --> pdb=" O GLN f 428 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N TYR f 434 " --> pdb=" O ASP f 430 " (cutoff:3.500A) Processing helix chain 'f' and resid 439 through 452 Processing helix chain 'f' and resid 464 through 470 Processing helix chain 'f' and resid 482 through 489 Processing helix chain 'f' and resid 494 through 506 removed outlier: 3.877A pdb=" N LEU f 498 " --> pdb=" O ARG f 494 " (cutoff:3.500A) Proline residue: f 503 - end of helix Processing helix chain 'f' and resid 511 through 524 Processing helix chain 'f' and resid 530 through 546 removed outlier: 4.129A pdb=" N VAL f 534 " --> pdb=" O CYS f 530 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER f 546 " --> pdb=" O ILE f 542 " (cutoff:3.500A) Processing helix chain 'f' and resid 557 through 566 removed outlier: 3.742A pdb=" N GLY f 561 " --> pdb=" O TRP f 557 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU f 562 " --> pdb=" O LEU f 558 " (cutoff:3.500A) Processing helix chain 'f' and resid 572 through 582 Processing helix chain 'f' and resid 591 through 599 removed outlier: 3.578A pdb=" N VAL f 595 " --> pdb=" O ALA f 591 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASP f 596 " --> pdb=" O ASN f 592 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL f 597 " --> pdb=" O THR f 593 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA f 599 " --> pdb=" O VAL f 595 " (cutoff:3.500A) Processing helix chain 'f' and resid 605 through 616 removed outlier: 3.786A pdb=" N LEU f 613 " --> pdb=" O VAL f 609 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE f 615 " --> pdb=" O GLN f 611 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N CYS f 616 " --> pdb=" O LEU f 612 " (cutoff:3.500A) Processing helix chain 'f' and resid 618 through 622 removed outlier: 4.458A pdb=" N SER f 622 " --> pdb=" O HIS f 619 " (cutoff:3.500A) Processing helix chain 'f' and resid 625 through 637 Processing helix chain 'f' and resid 646 through 659 removed outlier: 4.082A pdb=" N GLN f 650 " --> pdb=" O MET f 646 " (cutoff:3.500A) Processing helix chain 'f' and resid 665 through 670 Processing helix chain 'f' and resid 672 through 679 removed outlier: 4.199A pdb=" N GLY f 676 " --> pdb=" O LEU f 672 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N HIS f 677 " --> pdb=" O ARG f 673 " (cutoff:3.500A) Processing helix chain 'f' and resid 683 through 695 Proline residue: f 691 - end of helix Processing helix chain 'f' and resid 702 through 712 removed outlier: 3.920A pdb=" N ILE f 706 " --> pdb=" O PRO f 702 " (cutoff:3.500A) Processing helix chain 'f' and resid 722 through 736 removed outlier: 4.069A pdb=" N ILE f 726 " --> pdb=" O SER f 722 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLY f 735 " --> pdb=" O MET f 731 " (cutoff:3.500A) Processing helix chain 'f' and resid 738 through 754 removed outlier: 6.741A pdb=" N MET f 744 " --> pdb=" O ARG f 740 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N LEU f 745 " --> pdb=" O LEU f 741 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA f 753 " --> pdb=" O ALA f 749 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LYS f 754 " --> pdb=" O GLN f 750 " (cutoff:3.500A) Processing helix chain 'f' and resid 774 through 785 Proline residue: f 780 - end of helix Processing helix chain 'f' and resid 787 through 789 No H-bonds generated for 'chain 'f' and resid 787 through 789' Processing helix chain 'f' and resid 790 through 800 removed outlier: 4.253A pdb=" N ALA f 794 " --> pdb=" O GLN f 790 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU f 796 " --> pdb=" O ALA f 792 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU f 797 " --> pdb=" O VAL f 793 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 48 removed outlier: 4.588A pdb=" N ILE E 22 " --> pdb=" O GLU E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 52 Processing helix chain 'E' and resid 116 through 124 removed outlier: 3.689A pdb=" N HIS E 124 " --> pdb=" O TYR E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 135 removed outlier: 3.867A pdb=" N ILE E 135 " --> pdb=" O TYR E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 150 removed outlier: 3.972A pdb=" N ARG E 143 " --> pdb=" O SER E 139 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N VAL E 148 " --> pdb=" O GLU E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 156 through 163 removed outlier: 3.725A pdb=" N GLN E 160 " --> pdb=" O PRO E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 190 removed outlier: 3.791A pdb=" N ALA E 184 " --> pdb=" O LYS E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 203 No H-bonds generated for 'chain 'E' and resid 201 through 203' Processing helix chain 'E' and resid 209 through 225 removed outlier: 4.001A pdb=" N ILE E 215 " --> pdb=" O SER E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 238 Processing helix chain 'E' and resid 251 through 264 removed outlier: 3.610A pdb=" N MET E 258 " --> pdb=" O GLN E 254 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET E 264 " --> pdb=" O LEU E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 318 removed outlier: 3.893A pdb=" N GLY E 318 " --> pdb=" O LYS E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 335 removed outlier: 4.109A pdb=" N ILE E 331 " --> pdb=" O ASP E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 356 removed outlier: 3.760A pdb=" N LEU E 343 " --> pdb=" O ASN E 339 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG E 344 " --> pdb=" O GLY E 340 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASN E 345 " --> pdb=" O ALA E 341 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY E 351 " --> pdb=" O CYS E 347 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA E 354 " --> pdb=" O ALA E 350 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG E 356 " --> pdb=" O MET E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 359 No H-bonds generated for 'chain 'E' and resid 357 through 359' Processing helix chain 'E' and resid 363 through 376 removed outlier: 3.774A pdb=" N PHE E 367 " --> pdb=" O VAL E 363 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG E 372 " --> pdb=" O MET E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 381 removed outlier: 3.780A pdb=" N LEU E 380 " --> pdb=" O SER E 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 85 removed outlier: 4.160A pdb=" N LYS F 53 " --> pdb=" O ASP F 49 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN F 83 " --> pdb=" O LYS F 79 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS F 84 " --> pdb=" O ILE F 80 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THR F 85 " --> pdb=" O LYS F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 145 Processing helix chain 'F' and resid 169 through 174 Processing helix chain 'F' and resid 184 through 188 Processing helix chain 'F' and resid 191 through 203 removed outlier: 3.626A pdb=" N GLN F 196 " --> pdb=" O ASP F 192 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA F 201 " --> pdb=" O GLU F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 208 removed outlier: 3.641A pdb=" N ASN F 207 " --> pdb=" O VAL F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 214 removed outlier: 3.722A pdb=" N PHE F 212 " --> pdb=" O HIS F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 232 through 244 Processing helix chain 'F' and resid 254 through 257 Processing helix chain 'F' and resid 262 through 278 removed outlier: 3.629A pdb=" N LYS F 266 " --> pdb=" O GLY F 262 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU F 267 " --> pdb=" O ASP F 263 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU F 277 " --> pdb=" O ALA F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 291 Processing helix chain 'F' and resid 304 through 317 removed outlier: 3.627A pdb=" N GLU F 312 " --> pdb=" O ARG F 308 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASN F 315 " --> pdb=" O LEU F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 343 Processing helix chain 'F' and resid 358 through 370 removed outlier: 3.819A pdb=" N ALA F 363 " --> pdb=" O GLU F 359 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG F 364 " --> pdb=" O GLU F 360 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 385 Processing helix chain 'F' and resid 392 through 410 removed outlier: 4.278A pdb=" N CYS F 400 " --> pdb=" O CYS F 396 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL F 401 " --> pdb=" O LYS F 397 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA F 407 " --> pdb=" O ALA F 403 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ARG F 410 " --> pdb=" O ILE F 406 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 429 removed outlier: 3.513A pdb=" N TYR F 420 " --> pdb=" O THR F 416 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU F 425 " --> pdb=" O MET F 421 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA F 429 " --> pdb=" O LEU F 425 " (cutoff:3.500A) Processing helix chain 'U' and resid 7 through 14 Processing helix chain 'U' and resid 16 through 31 removed outlier: 3.886A pdb=" N HIS U 25 " --> pdb=" O GLU U 21 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ALA U 29 " --> pdb=" O HIS U 25 " (cutoff:3.500A) Processing helix chain 'U' and resid 34 through 40 Processing helix chain 'U' and resid 41 through 51 removed outlier: 4.062A pdb=" N ILE U 45 " --> pdb=" O SER U 41 " (cutoff:3.500A) Processing helix chain 'U' and resid 56 through 72 removed outlier: 4.225A pdb=" N ALA U 60 " --> pdb=" O SER U 56 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA U 61 " --> pdb=" O ARG U 57 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU U 62 " --> pdb=" O GLN U 58 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL U 63 " --> pdb=" O PHE U 59 " (cutoff:3.500A) Processing helix chain 'U' and resid 73 through 85 Processing helix chain 'U' and resid 86 through 90 removed outlier: 4.039A pdb=" N VAL U 90 " --> pdb=" O LEU U 87 " (cutoff:3.500A) Processing helix chain 'U' and resid 94 through 116 Processing helix chain 'U' and resid 127 through 144 Processing helix chain 'U' and resid 146 through 157 removed outlier: 3.801A pdb=" N ALA U 150 " --> pdb=" O LYS U 146 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY U 152 " --> pdb=" O LYS U 148 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LEU U 155 " --> pdb=" O ILE U 151 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU U 156 " --> pdb=" O GLY U 152 " (cutoff:3.500A) Processing helix chain 'U' and resid 159 through 167 removed outlier: 4.007A pdb=" N PHE U 163 " --> pdb=" O ARG U 159 " (cutoff:3.500A) Processing helix chain 'U' and resid 172 through 188 removed outlier: 3.757A pdb=" N MET U 176 " --> pdb=" O ASP U 172 " (cutoff:3.500A) Processing helix chain 'U' and resid 190 through 203 removed outlier: 4.277A pdb=" N LYS U 196 " --> pdb=" O GLN U 192 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS U 203 " --> pdb=" O ARG U 199 " (cutoff:3.500A) Processing helix chain 'U' and resid 203 through 208 Processing helix chain 'U' and resid 212 through 223 removed outlier: 3.686A pdb=" N VAL U 216 " --> pdb=" O ASP U 212 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLN U 218 " --> pdb=" O ILE U 214 " (cutoff:3.500A) Processing helix chain 'U' and resid 225 through 239 Processing helix chain 'U' and resid 242 through 254 removed outlier: 3.875A pdb=" N CYS U 249 " --> pdb=" O ALA U 245 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU U 254 " --> pdb=" O PHE U 250 " (cutoff:3.500A) Processing helix chain 'U' and resid 257 through 270 removed outlier: 4.702A pdb=" N GLN U 266 " --> pdb=" O SER U 262 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN U 267 " --> pdb=" O SER U 263 " (cutoff:3.500A) Processing helix chain 'U' and resid 321 through 329 removed outlier: 4.212A pdb=" N MET U 325 " --> pdb=" O GLN U 321 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ILE U 326 " --> pdb=" O THR U 322 " (cutoff:3.500A) Processing helix chain 'U' and resid 331 through 345 Processing helix chain 'U' and resid 350 through 358 removed outlier: 4.084A pdb=" N ASP U 358 " --> pdb=" O LYS U 354 " (cutoff:3.500A) Processing helix chain 'U' and resid 362 through 377 removed outlier: 4.140A pdb=" N SER U 374 " --> pdb=" O VAL U 370 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE U 375 " --> pdb=" O ILE U 371 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET U 376 " --> pdb=" O ALA U 372 " (cutoff:3.500A) Processing helix chain 'U' and resid 383 through 388 Processing helix chain 'U' and resid 389 through 394 Processing helix chain 'U' and resid 395 through 397 No H-bonds generated for 'chain 'U' and resid 395 through 397' Processing helix chain 'U' and resid 398 through 412 removed outlier: 3.729A pdb=" N PHE U 402 " --> pdb=" O ASN U 398 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY U 409 " --> pdb=" O THR U 405 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL U 410 " --> pdb=" O ALA U 406 " (cutoff:3.500A) Processing helix chain 'U' and resid 415 through 427 removed outlier: 3.671A pdb=" N ALA U 419 " --> pdb=" O HIS U 415 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LEU U 420 " --> pdb=" O GLU U 416 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N GLN U 421 " --> pdb=" O LYS U 417 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR U 426 " --> pdb=" O LEU U 422 " (cutoff:3.500A) Processing helix chain 'U' and resid 436 through 450 removed outlier: 4.593A pdb=" N GLY U 442 " --> pdb=" O GLN U 438 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU U 443 " --> pdb=" O GLU U 439 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TYR U 444 " --> pdb=" O GLY U 440 " (cutoff:3.500A) Processing helix chain 'U' and resid 455 through 466 removed outlier: 3.802A pdb=" N ASP U 459 " --> pdb=" O GLY U 455 " (cutoff:3.500A) Processing helix chain 'U' and resid 470 through 485 Processing helix chain 'U' and resid 490 through 502 Processing helix chain 'U' and resid 508 through 520 Processing helix chain 'U' and resid 525 through 538 removed outlier: 3.693A pdb=" N GLY U 534 " --> pdb=" O GLU U 530 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR U 535 " --> pdb=" O ASP U 531 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA U 536 " --> pdb=" O MET U 532 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU U 538 " --> pdb=" O GLY U 534 " (cutoff:3.500A) Processing helix chain 'U' and resid 541 through 555 removed outlier: 4.086A pdb=" N LEU U 545 " --> pdb=" O HIS U 541 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N VAL U 550 " --> pdb=" O ARG U 546 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY U 551 " --> pdb=" O GLY U 547 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA U 553 " --> pdb=" O ALA U 549 " (cutoff:3.500A) Processing helix chain 'U' and resid 559 through 562 Processing helix chain 'U' and resid 563 through 571 Processing helix chain 'U' and resid 575 through 590 removed outlier: 3.552A pdb=" N MET U 583 " --> pdb=" O ARG U 579 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR U 584 " --> pdb=" O ARG U 580 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR U 590 " --> pdb=" O VAL U 586 " (cutoff:3.500A) Processing helix chain 'U' and resid 595 through 609 removed outlier: 3.639A pdb=" N ALA U 606 " --> pdb=" O LEU U 602 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL U 607 " --> pdb=" O LEU U 603 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER U 608 " --> pdb=" O HIS U 604 " (cutoff:3.500A) Processing helix chain 'U' and resid 611 through 621 removed outlier: 3.705A pdb=" N VAL U 619 " --> pdb=" O ARG U 615 " (cutoff:3.500A) Processing helix chain 'U' and resid 621 through 627 removed outlier: 3.716A pdb=" N ILE U 625 " --> pdb=" O SER U 621 " (cutoff:3.500A) Processing helix chain 'U' and resid 633 through 641 removed outlier: 3.674A pdb=" N SER U 638 " --> pdb=" O PRO U 634 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N LEU U 639 " --> pdb=" O SER U 635 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU U 640 " --> pdb=" O VAL U 636 " (cutoff:3.500A) Processing helix chain 'U' and resid 645 through 660 removed outlier: 3.669A pdb=" N ARG U 649 " --> pdb=" O ASN U 645 " (cutoff:3.500A) Processing helix chain 'U' and resid 665 through 676 removed outlier: 3.504A pdb=" N ILE U 669 " --> pdb=" O ASN U 665 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASN U 670 " --> pdb=" O LYS U 666 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU U 671 " --> pdb=" O GLU U 667 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU U 672 " --> pdb=" O ALA U 668 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU U 673 " --> pdb=" O ILE U 669 " (cutoff:3.500A) Proline residue: U 674 - end of helix No H-bonds generated for 'chain 'U' and resid 665 through 676' Processing helix chain 'U' and resid 680 through 695 removed outlier: 3.596A pdb=" N MET U 695 " --> pdb=" O SER U 691 " (cutoff:3.500A) Processing helix chain 'U' and resid 705 through 719 removed outlier: 3.584A pdb=" N ASN U 718 " --> pdb=" O SER U 714 " (cutoff:3.500A) Processing helix chain 'U' and resid 726 through 738 removed outlier: 3.672A pdb=" N ASP U 738 " --> pdb=" O GLN U 734 " (cutoff:3.500A) Processing helix chain 'U' and resid 739 through 742 Processing helix chain 'U' and resid 756 through 768 removed outlier: 3.539A pdb=" N VAL U 760 " --> pdb=" O HIS U 756 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN U 768 " --> pdb=" O LEU U 764 " (cutoff:3.500A) Processing helix chain 'U' and resid 769 through 771 No H-bonds generated for 'chain 'U' and resid 769 through 771' Processing helix chain 'U' and resid 772 through 781 removed outlier: 4.014A pdb=" N HIS U 777 " --> pdb=" O PRO U 774 " (cutoff:3.500A) Processing helix chain 'U' and resid 807 through 812 Processing helix chain 'U' and resid 885 through 890 removed outlier: 3.745A pdb=" N LEU U 889 " --> pdb=" O PRO U 886 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N LYS U 890 " --> pdb=" O ALA U 887 " (cutoff:3.500A) Processing helix chain 'Z' and resid 12 through 30 removed outlier: 4.077A pdb=" N LEU Z 16 " --> pdb=" O HIS Z 12 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN Z 24 " --> pdb=" O VAL Z 20 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL Z 29 " --> pdb=" O ARG Z 25 " (cutoff:3.500A) Processing helix chain 'Z' and resid 71 through 84 removed outlier: 4.252A pdb=" N LEU Z 75 " --> pdb=" O ASP Z 71 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY Z 80 " --> pdb=" O GLU Z 76 " (cutoff:3.500A) Processing helix chain 'Z' and resid 104 through 113 removed outlier: 3.719A pdb=" N LEU Z 111 " --> pdb=" O ALA Z 107 " (cutoff:3.500A) Processing helix chain 'Z' and resid 165 through 176 removed outlier: 3.758A pdb=" N VAL Z 170 " --> pdb=" O GLU Z 166 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU Z 175 " --> pdb=" O GLY Z 171 " (cutoff:3.500A) Processing helix chain 'Z' and resid 185 through 192 Processing helix chain 'Z' and resid 193 through 217 removed outlier: 3.535A pdb=" N LYS Z 214 " --> pdb=" O SER Z 210 " (cutoff:3.500A) Processing helix chain 'Z' and resid 223 through 237 removed outlier: 3.836A pdb=" N ILE Z 227 " --> pdb=" O ASN Z 223 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU Z 237 " --> pdb=" O VAL Z 233 " (cutoff:3.500A) Processing helix chain 'Z' and resid 242 through 287 removed outlier: 3.680A pdb=" N ALA Z 248 " --> pdb=" O GLU Z 244 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASP Z 255 " --> pdb=" O LEU Z 251 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N VAL Z 258 " --> pdb=" O ASN Z 254 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL Z 259 " --> pdb=" O ASP Z 255 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL Z 260 " --> pdb=" O GLN Z 256 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALA Z 285 " --> pdb=" O ALA Z 281 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LYS Z 287 " --> pdb=" O ARG Z 283 " (cutoff:3.500A) Processing helix chain 'Z' and resid 288 through 290 No H-bonds generated for 'chain 'Z' and resid 288 through 290' Processing helix chain 'a' and resid 5 through 13 Processing helix chain 'a' and resid 17 through 31 removed outlier: 4.213A pdb=" N VAL a 21 " --> pdb=" O GLY a 17 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU a 27 " --> pdb=" O HIS a 23 " (cutoff:3.500A) Processing helix chain 'a' and resid 33 through 47 removed outlier: 3.873A pdb=" N GLN a 46 " --> pdb=" O LEU a 42 " (cutoff:3.500A) Processing helix chain 'a' and resid 53 through 69 removed outlier: 5.808A pdb=" N LEU a 59 " --> pdb=" O GLY a 55 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N TYR a 60 " --> pdb=" O LEU a 56 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU a 61 " --> pdb=" O ILE a 57 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLU a 66 " --> pdb=" O ASN a 62 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N PHE a 67 " --> pdb=" O PHE a 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 72 through 87 removed outlier: 4.011A pdb=" N LEU a 76 " --> pdb=" O ASN a 72 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL a 77 " --> pdb=" O PRO a 73 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N HIS a 82 " --> pdb=" O GLU a 78 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG a 85 " --> pdb=" O LEU a 81 " (cutoff:3.500A) Processing helix chain 'a' and resid 89 through 103 removed outlier: 3.995A pdb=" N LYS a 103 " --> pdb=" O LYS a 99 " (cutoff:3.500A) Processing helix chain 'a' and resid 107 through 125 removed outlier: 3.606A pdb=" N VAL a 111 " --> pdb=" O SER a 107 " (cutoff:3.500A) Processing helix chain 'a' and resid 127 through 145 Processing helix chain 'a' and resid 149 through 167 removed outlier: 3.687A pdb=" N SER a 153 " --> pdb=" O THR a 149 " (cutoff:3.500A) Processing helix chain 'a' and resid 168 through 183 Processing helix chain 'a' and resid 189 through 207 removed outlier: 3.538A pdb=" N GLN a 193 " --> pdb=" O PRO a 189 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLU a 195 " --> pdb=" O SER a 191 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ARG a 196 " --> pdb=" O GLU a 192 " (cutoff:3.500A) Processing helix chain 'a' and resid 212 through 217 Processing helix chain 'a' and resid 219 through 224 Processing helix chain 'a' and resid 225 through 230 removed outlier: 5.546A pdb=" N ASP a 229 " --> pdb=" O ARG a 226 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ARG a 230 " --> pdb=" O ASN a 227 " (cutoff:3.500A) Processing helix chain 'a' and resid 231 through 243 Processing helix chain 'a' and resid 245 through 250 Processing helix chain 'a' and resid 260 through 284 removed outlier: 4.522A pdb=" N ASN a 264 " --> pdb=" O ASP a 260 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ALA a 266 " --> pdb=" O ALA a 262 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N GLN a 267 " --> pdb=" O ALA a 263 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG a 270 " --> pdb=" O ALA a 266 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET a 278 " --> pdb=" O LEU a 274 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG a 284 " --> pdb=" O MET a 280 " (cutoff:3.500A) Processing helix chain 'a' and resid 293 through 301 Processing helix chain 'a' and resid 303 through 305 No H-bonds generated for 'chain 'a' and resid 303 through 305' Processing helix chain 'a' and resid 306 through 317 Processing helix chain 'a' and resid 345 through 371 removed outlier: 3.722A pdb=" N MET a 349 " --> pdb=" O GLN a 345 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ASP a 359 " --> pdb=" O PHE a 355 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL a 360 " --> pdb=" O TRP a 356 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N HIS a 369 " --> pdb=" O MET a 365 " (cutoff:3.500A) Processing helix chain 'b' and resid 13 through 18 Processing helix chain 'b' and resid 24 through 44 removed outlier: 3.524A pdb=" N ALA b 28 " --> pdb=" O THR b 24 " (cutoff:3.500A) Processing helix chain 'b' and resid 68 through 78 Processing helix chain 'b' and resid 85 through 98 removed outlier: 3.612A pdb=" N LYS b 98 " --> pdb=" O HIS b 94 " (cutoff:3.500A) Processing helix chain 'b' and resid 120 through 135 Processing helix chain 'b' and resid 147 through 149 No H-bonds generated for 'chain 'b' and resid 147 through 149' Processing helix chain 'b' and resid 150 through 160 removed outlier: 3.931A pdb=" N ALA b 155 " --> pdb=" O GLU b 151 " (cutoff:3.500A) Processing helix chain 'b' and resid 179 through 184 Processing helix chain 'c' and resid 34 through 48 removed outlier: 3.536A pdb=" N LEU c 38 " --> pdb=" O SER c 34 " (cutoff:3.500A) Processing helix chain 'c' and resid 89 through 99 removed outlier: 4.213A pdb=" N ASP c 97 " --> pdb=" O ALA c 93 " (cutoff:3.500A) Processing helix chain 'c' and resid 100 through 103 Processing helix chain 'c' and resid 125 through 137 removed outlier: 3.790A pdb=" N SER c 132 " --> pdb=" O ASN c 128 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE c 133 " --> pdb=" O THR c 129 " (cutoff:3.500A) Processing helix chain 'c' and resid 165 through 170 Processing helix chain 'c' and resid 179 through 183 removed outlier: 4.342A pdb=" N GLY c 182 " --> pdb=" O SER c 179 " (cutoff:3.500A) Processing helix chain 'c' and resid 188 through 194 removed outlier: 3.855A pdb=" N HIS c 194 " --> pdb=" O GLN c 190 " (cutoff:3.500A) Processing helix chain 'c' and resid 195 through 198 Processing helix chain 'c' and resid 210 through 218 removed outlier: 3.684A pdb=" N GLN c 214 " --> pdb=" O ASN c 210 " (cutoff:3.500A) Processing helix chain 'c' and resid 224 through 229 Processing helix chain 'c' and resid 233 through 261 removed outlier: 3.616A pdb=" N HIS c 237 " --> pdb=" O ASP c 233 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N CYS c 238 " --> pdb=" O TYR c 234 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LYS c 239 " --> pdb=" O SER c 235 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N LYS c 246 " --> pdb=" O GLU c 242 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU c 247 " --> pdb=" O SER c 243 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN c 254 " --> pdb=" O GLU c 250 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ASN c 256 " --> pdb=" O ALA c 252 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N LYS c 257 " --> pdb=" O LYS c 253 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA c 258 " --> pdb=" O ASN c 254 " (cutoff:3.500A) Processing helix chain 'c' and resid 266 through 268 No H-bonds generated for 'chain 'c' and resid 266 through 268' Processing helix chain 'c' and resid 269 through 276 removed outlier: 4.013A pdb=" N GLY c 276 " --> pdb=" O ILE c 272 " (cutoff:3.500A) Processing helix chain 'c' and resid 279 through 309 removed outlier: 3.667A pdb=" N GLU c 285 " --> pdb=" O LYS c 281 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLU c 286 " --> pdb=" O ARG c 282 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N HIS c 287 " --> pdb=" O HIS c 283 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL c 288 " --> pdb=" O LEU c 284 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL c 297 " --> pdb=" O THR c 293 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYS c 299 " --> pdb=" O ASN c 295 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA c 302 " --> pdb=" O GLN c 298 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET c 303 " --> pdb=" O CYS c 299 " (cutoff:3.500A) Processing helix chain 'v' and resid 22 through 35 Processing helix chain 'v' and resid 37 through 39 No H-bonds generated for 'chain 'v' and resid 37 through 39' Processing helix chain 'v' and resid 56 through 60 removed outlier: 3.646A pdb=" N TYR v 59 " --> pdb=" O LEU v 56 " (cutoff:3.500A) Processing helix chain 'u' and resid 22 through 35 Processing helix chain 'w' and resid 22 through 35 Processing helix chain 'w' and resid 56 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 105 removed outlier: 6.984A pdb=" N ILE A 112 " --> pdb=" O ILE A 102 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ALA A 104 " --> pdb=" O LYS A 110 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LYS A 110 " --> pdb=" O ALA A 104 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 121 through 123 current: chain 'A' and resid 149 through 152 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 149 through 152 current: chain 'B' and resid 120 through 124 removed outlier: 3.622A pdb=" N VAL B 123 " --> pdb=" O HIS B 131 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 130 through 131 current: chain 'B' and resid 159 through 162 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 159 through 162 current: chain 'C' and resid 84 through 88 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 94 through 99 current: chain 'C' and resid 122 through 123 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 122 through 123 current: chain 'D' and resid 100 through 105 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 110 through 114 current: chain 'D' and resid 139 through 142 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 139 through 142 current: chain 'E' and resid 69 through 73 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 78 through 81 current: chain 'E' and resid 107 through 111 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 107 through 111 current: chain 'F' and resid 122 through 126 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 131 through 134 current: chain 'F' and resid 160 through 163 Processing sheet with id=AA2, first strand: chain 'A' and resid 237 through 241 removed outlier: 6.625A pdb=" N ILE A 238 " --> pdb=" O PHE A 273 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N ASP A 275 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL A 240 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS A 316 " --> pdb=" O CYS A 270 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU A 214 " --> pdb=" O THR A 321 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 246 through 251 removed outlier: 6.545A pdb=" N THR B 246 " --> pdb=" O ILE B 281 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N PHE B 283 " --> pdb=" O THR B 246 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU B 248 " --> pdb=" O PHE B 283 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ASP B 285 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL B 250 " --> pdb=" O ASP B 285 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL B 222 " --> pdb=" O MET B 329 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N THR B 331 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N LEU B 224 " --> pdb=" O THR B 331 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 210 through 213 removed outlier: 3.537A pdb=" N LYS C 290 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N VAL C 186 " --> pdb=" O MET C 293 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N THR C 295 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N LEU C 188 " --> pdb=" O THR C 295 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 228 through 231 removed outlier: 3.563A pdb=" N ASP D 265 " --> pdb=" O VAL D 230 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N ILE D 331 " --> pdb=" O GLY D 201 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU D 203 " --> pdb=" O ILE D 331 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 165 through 169 removed outlier: 6.120A pdb=" N THR G 38 " --> pdb=" O GLN G 53 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN G 53 " --> pdb=" O THR G 38 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG G 228 " --> pdb=" O VAL G 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 69 through 73 removed outlier: 5.875A pdb=" N LYS G 71 " --> pdb=" O CYS G 78 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N CYS G 78 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL G 151 " --> pdb=" O PHE G 163 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 160 through 163 removed outlier: 3.589A pdb=" N ILE H 212 " --> pdb=" O ARG H 219 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG H 219 " --> pdb=" O ILE H 212 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASN H 214 " --> pdb=" O GLY H 217 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 66 through 69 removed outlier: 3.567A pdb=" N LEU H 74 " --> pdb=" O GLU H 66 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE H 72 " --> pdb=" O ILE H 68 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 161 through 163 Processing sheet with id=AB2, first strand: chain 'I' and resid 66 through 69 removed outlier: 6.252A pdb=" N MET I 72 " --> pdb=" O LEU I 68 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 77 through 78 removed outlier: 3.509A pdb=" N SER I 133 " --> pdb=" O ALA I 77 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 158 through 161 removed outlier: 3.849A pdb=" N VAL J 210 " --> pdb=" O LYS J 218 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS J 218 " --> pdb=" O VAL J 210 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 62 through 66 removed outlier: 6.847A pdb=" N VAL J 69 " --> pdb=" O LEU J 65 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 167 through 170 removed outlier: 3.603A pdb=" N HIS K 227 " --> pdb=" O THR K 219 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 68 through 71 removed outlier: 6.420A pdb=" N ILE K 74 " --> pdb=" O ILE K 70 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 158 through 161 Processing sheet with id=AB9, first strand: chain 'L' and resid 63 through 67 removed outlier: 5.484A pdb=" N HIS L 65 " --> pdb=" O ILE L 72 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE L 72 " --> pdb=" O HIS L 65 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 162 through 166 removed outlier: 4.733A pdb=" N THR M 35 " --> pdb=" O GLU M 50 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU M 50 " --> pdb=" O THR M 35 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL M 216 " --> pdb=" O VAL M 45 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N PHE M 47 " --> pdb=" O SER M 214 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER M 214 " --> pdb=" O PHE M 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 66 through 70 removed outlier: 6.435A pdb=" N VAL M 73 " --> pdb=" O VAL M 69 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL M 156 " --> pdb=" O ASP M 152 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'V' and resid 450 through 451 Processing sheet with id=AC4, first strand: chain 'W' and resid 372 through 374 Processing sheet with id=AC5, first strand: chain 'X' and resid 376 through 378 Processing sheet with id=AC6, first strand: chain 'f' and resid 825 through 829 Processing sheet with id=AC7, first strand: chain 'E' and resid 195 through 199 removed outlier: 3.835A pdb=" N ALA E 278 " --> pdb=" O MET E 232 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLY E 169 " --> pdb=" O ARG E 297 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N ILE E 299 " --> pdb=" O GLY E 169 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU E 171 " --> pdb=" O ILE E 299 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 248 through 252 removed outlier: 6.619A pdb=" N LEU F 249 " --> pdb=" O PHE F 284 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ASP F 286 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU F 251 " --> pdb=" O ASP F 286 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'U' and resid 744 through 746 Processing sheet with id=AD1, first strand: chain 'U' and resid 788 through 791 removed outlier: 6.182A pdb=" N ILE U 789 " --> pdb=" O ILE U 912 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU U 914 " --> pdb=" O ILE U 789 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N LEU U 791 " --> pdb=" O LEU U 914 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ASP U 916 " --> pdb=" O LEU U 791 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'U' and resid 877 through 878 removed outlier: 3.634A pdb=" N LYS U 803 " --> pdb=" O THR U 893 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Z' and resid 8 through 11 removed outlier: 6.606A pdb=" N LYS Z 8 " --> pdb=" O LEU Z 48 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N VAL Z 50 " --> pdb=" O LYS Z 8 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL Z 10 " --> pdb=" O VAL Z 50 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N ASN Z 52 " --> pdb=" O VAL Z 10 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N LEU Z 48 " --> pdb=" O GLN Z 44 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N GLN Z 44 " --> pdb=" O LEU Z 48 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N VAL Z 50 " --> pdb=" O SER Z 42 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N SER Z 42 " --> pdb=" O VAL Z 50 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLY Z 37 " --> pdb=" O TRP Z 94 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TRP Z 94 " --> pdb=" O GLY Z 37 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU Z 39 " --> pdb=" O VAL Z 92 " (cutoff:3.500A) removed outlier: 10.186A pdb=" N VAL Z 120 " --> pdb=" O ARG Z 90 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N VAL Z 92 " --> pdb=" O VAL Z 120 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N VAL Z 122 " --> pdb=" O VAL Z 92 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TRP Z 94 " --> pdb=" O VAL Z 122 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ILE Z 124 " --> pdb=" O TRP Z 94 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N HIS Z 96 " --> pdb=" O ILE Z 124 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N THR Z 135 " --> pdb=" O SER Z 160 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N SER Z 160 " --> pdb=" O THR Z 135 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA Z 137 " --> pdb=" O VAL Z 158 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Z' and resid 58 through 60 Processing sheet with id=AD5, first strand: chain 'a' and resid 290 through 292 removed outlier: 6.734A pdb=" N LYS a 321 " --> pdb=" O THR a 334 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'b' and resid 59 through 65 removed outlier: 7.388A pdb=" N LEU b 61 " --> pdb=" O THR b 53 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N THR b 53 " --> pdb=" O LEU b 61 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N THR b 63 " --> pdb=" O LEU b 51 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LEU b 51 " --> pdb=" O THR b 63 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASP b 11 " --> pdb=" O PHE b 112 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N MET b 107 " --> pdb=" O ASN b 137 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ASP b 139 " --> pdb=" O MET b 107 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ILE b 109 " --> pdb=" O ASP b 139 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ILE b 141 " --> pdb=" O ILE b 109 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ALA b 111 " --> pdb=" O ILE b 141 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS b 169 " --> pdb=" O VAL b 138 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE b 140 " --> pdb=" O HIS b 169 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL b 171 " --> pdb=" O ILE b 140 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'c' and resid 200 through 202 removed outlier: 4.569A pdb=" N VAL c 156 " --> pdb=" O ASP c 146 " (cutoff:3.500A) removed outlier: 10.890A pdb=" N VAL c 141 " --> pdb=" O MET c 107 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL c 109 " --> pdb=" O VAL c 141 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N VAL c 143 " --> pdb=" O VAL c 109 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N TRP c 111 " --> pdb=" O VAL c 143 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N VAL c 145 " --> pdb=" O TRP c 111 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N HIS c 113 " --> pdb=" O VAL c 145 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N VAL c 108 " --> pdb=" O GLY c 59 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N GLY c 59 " --> pdb=" O VAL c 108 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N MET c 54 " --> pdb=" O ALA c 74 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ALA c 74 " --> pdb=" O MET c 54 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU c 56 " --> pdb=" O VAL c 72 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N VAL c 72 " --> pdb=" O LEU c 56 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N LEU c 58 " --> pdb=" O ILE c 70 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL c 62 " --> pdb=" O THR c 66 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR c 66 " --> pdb=" O VAL c 62 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL c 31 " --> pdb=" O ASN c 206 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'c' and resid 77 through 79 removed outlier: 3.744A pdb=" N SER c 78 " --> pdb=" O GLU c 85 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU c 85 " --> pdb=" O SER c 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'v' and resid 12 through 16 removed outlier: 8.917A pdb=" N LEU v 67 " --> pdb=" O GLN v 2 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N PHE v 4 " --> pdb=" O LEU v 67 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N LEU v 69 " --> pdb=" O PHE v 4 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LYS v 6 " --> pdb=" O LEU v 69 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N LEU v 71 " --> pdb=" O LYS v 6 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'u' and resid 12 through 16 Processing sheet with id=AE2, first strand: chain 'w' and resid 12 through 16 removed outlier: 3.807A pdb=" N SER w 65 " --> pdb=" O GLN w 2 " (cutoff:3.500A) 3392 hydrogen bonds defined for protein. 9807 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: 27.64 Time building geometry restraints manager: 16.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 21312 1.33 - 1.46: 9457 1.46 - 1.58: 36464 1.58 - 1.70: 12 1.70 - 1.82: 510 Bond restraints: 67755 Sorted by residual: bond pdb=" CA GLN V 247 " pdb=" C GLN V 247 " ideal model delta sigma weight residual 1.522 1.485 0.036 1.72e-02 3.38e+03 4.46e+00 bond pdb=" O3B ATP D 501 " pdb=" PB ATP D 501 " ideal model delta sigma weight residual 1.592 1.538 0.054 3.00e-02 1.11e+03 3.20e+00 bond pdb=" O3B ATP A 501 " pdb=" PB ATP A 501 " ideal model delta sigma weight residual 1.592 1.539 0.053 3.00e-02 1.11e+03 3.17e+00 bond pdb=" CG LEU C 198 " pdb=" CD1 LEU C 198 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 2.95e+00 bond pdb=" CB THR A 223 " pdb=" CG2 THR A 223 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 2.94e+00 ... (remaining 67750 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 89034 1.84 - 3.67: 2411 3.67 - 5.51: 337 5.51 - 7.35: 91 7.35 - 9.19: 14 Bond angle restraints: 91887 Sorted by residual: angle pdb=" N GLU e 59 " pdb=" CA GLU e 59 " pdb=" C GLU e 59 " ideal model delta sigma weight residual 111.28 105.90 5.38 1.09e+00 8.42e-01 2.43e+01 angle pdb=" N SER e 53 " pdb=" CA SER e 53 " pdb=" C SER e 53 " ideal model delta sigma weight residual 113.20 107.30 5.90 1.21e+00 6.83e-01 2.38e+01 angle pdb=" CA GLN V 247 " pdb=" C GLN V 247 " pdb=" N ALA V 248 " ideal model delta sigma weight residual 118.59 111.35 7.24 1.63e+00 3.76e-01 1.97e+01 angle pdb=" N VAL e 8 " pdb=" CA VAL e 8 " pdb=" C VAL e 8 " ideal model delta sigma weight residual 108.86 115.73 -6.87 1.63e+00 3.76e-01 1.78e+01 angle pdb=" CA GLU c 242 " pdb=" CB GLU c 242 " pdb=" CG GLU c 242 " ideal model delta sigma weight residual 114.10 106.07 8.03 2.00e+00 2.50e-01 1.61e+01 ... (remaining 91882 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.20: 40056 30.20 - 60.40: 1212 60.40 - 90.61: 113 90.61 - 120.81: 2 120.81 - 151.01: 4 Dihedral angle restraints: 41387 sinusoidal: 15137 harmonic: 26250 Sorted by residual: dihedral pdb=" CB CYS M 41 " pdb=" SG CYS M 41 " pdb=" SG CYS M 186 " pdb=" CB CYS M 186 " ideal model delta sinusoidal sigma weight residual -86.00 -25.16 -60.84 1 1.00e+01 1.00e-02 4.92e+01 dihedral pdb=" O1B ADP F 501 " pdb=" O3A ADP F 501 " pdb=" PB ADP F 501 " pdb=" PA ADP F 501 " ideal model delta sinusoidal sigma weight residual -60.00 91.01 -151.01 1 2.00e+01 2.50e-03 4.50e+01 dihedral pdb=" O2A ADP F 501 " pdb=" O3A ADP F 501 " pdb=" PA ADP F 501 " pdb=" PB ADP F 501 " ideal model delta sinusoidal sigma weight residual -60.00 85.82 -145.82 1 2.00e+01 2.50e-03 4.39e+01 ... (remaining 41384 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 7729 0.049 - 0.097: 2471 0.097 - 0.146: 477 0.146 - 0.194: 37 0.194 - 0.243: 4 Chirality restraints: 10718 Sorted by residual: chirality pdb=" CA GLN E 226 " pdb=" N GLN E 226 " pdb=" C GLN E 226 " pdb=" CB GLN E 226 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA PRO e 7 " pdb=" N PRO e 7 " pdb=" C PRO e 7 " pdb=" CB PRO e 7 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA TYR d 186 " pdb=" N TYR d 186 " pdb=" C TYR d 186 " pdb=" CB TYR d 186 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.21 2.00e-01 2.50e+01 1.05e+00 ... (remaining 10715 not shown) Planarity restraints: 12016 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET C 351 " -0.061 5.00e-02 4.00e+02 9.23e-02 1.36e+01 pdb=" N PRO C 352 " 0.160 5.00e-02 4.00e+02 pdb=" CA PRO C 352 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO C 352 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN U 880 " -0.054 5.00e-02 4.00e+02 8.21e-02 1.08e+01 pdb=" N PRO U 881 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO U 881 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO U 881 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 125 " 0.054 5.00e-02 4.00e+02 8.11e-02 1.05e+01 pdb=" N PRO D 126 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO D 126 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO D 126 " 0.045 5.00e-02 4.00e+02 ... (remaining 12013 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 236 2.48 - 3.08: 49672 3.08 - 3.69: 97489 3.69 - 4.29: 132819 4.29 - 4.90: 217947 Nonbonded interactions: 498163 Sorted by model distance: nonbonded pdb=" O1B ADP F 501 " pdb="MG MG F 502 " model vdw 1.872 2.170 nonbonded pdb=" O1G ATP B 501 " pdb="MG MG B 502 " model vdw 1.884 2.170 nonbonded pdb=" OG1 THR A 223 " pdb="MG MG A 502 " model vdw 1.987 2.170 nonbonded pdb=" O2G ATP E 401 " pdb="MG MG E 402 " model vdw 1.991 2.170 nonbonded pdb=" OG1 THR B 233 " pdb="MG MG B 502 " model vdw 2.003 2.170 ... (remaining 498158 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'u' and (resid 1 through 75 or (resid 76 and (name N or name CA or name C \ or name O )))) selection = chain 'v' selection = chain 'w' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.25 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: 5.540 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: 0.110 Extract box with map and model: 2.020 Check model and map are aligned: 0.400 Set scattering table: 0.480 Process input model: 117.300 Find NCS groups from input model: 1.840 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 130.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 67755 Z= 0.382 Angle : 0.737 9.186 91887 Z= 0.399 Chirality : 0.047 0.243 10718 Planarity : 0.006 0.092 12016 Dihedral : 14.332 151.009 24383 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.66 % Favored : 92.08 % Rotamer: Outliers : 1.50 % Allowed : 5.43 % Favored : 93.07 % 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: -1.49 (0.08), residues: 8959 helix: -0.16 (0.08), residues: 4380 sheet: -0.20 (0.17), residues: 862 loop : -2.19 (0.09), residues: 3717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP U 770 HIS 0.010 0.001 HIS b 105 PHE 0.034 0.002 PHE B 319 TYR 0.044 0.002 TYR D 417 ARG 0.016 0.001 ARG v 54 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17918 Ramachandran restraints generated. 8959 Oldfield, 0 Emsley, 8959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17918 Ramachandran restraints generated. 8959 Oldfield, 0 Emsley, 8959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1077 residues out of total 7822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 981 time to evaluate : 6.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 MET cc_start: 0.7912 (mtm) cc_final: 0.7451 (mtm) REVERT: A 319 MET cc_start: 0.7815 (mtm) cc_final: 0.7601 (mtm) REVERT: B 145 GLU cc_start: 0.7948 (pt0) cc_final: 0.7637 (pt0) REVERT: B 412 MET cc_start: 0.7772 (tpp) cc_final: 0.7521 (tpp) REVERT: C 151 ILE cc_start: 0.7758 (mm) cc_final: 0.7461 (mm) REVERT: C 273 MET cc_start: 0.8542 (mtp) cc_final: 0.8147 (mtp) REVERT: C 293 MET cc_start: 0.8100 (mtp) cc_final: 0.7854 (mtp) REVERT: H 58 ASP cc_start: 0.8290 (t70) cc_final: 0.8005 (t70) REVERT: K 20 ARG cc_start: 0.7698 (mtm180) cc_final: 0.7099 (mtm180) REVERT: L 185 ASN cc_start: 0.7904 (t0) cc_final: 0.7612 (t0) REVERT: M 27 MET cc_start: 0.8235 (mmp) cc_final: 0.7473 (mmt) REVERT: V 240 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8913 (mt) REVERT: W 120 ILE cc_start: 0.7413 (OUTLIER) cc_final: 0.7099 (tp) REVERT: W 121 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8704 (mptt) REVERT: W 138 VAL cc_start: 0.8149 (OUTLIER) cc_final: 0.7798 (p) REVERT: W 139 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8493 (mp0) REVERT: W 141 GLU cc_start: 0.8393 (tt0) cc_final: 0.8089 (tt0) REVERT: W 230 MET cc_start: 0.7898 (mpp) cc_final: 0.7414 (mpp) REVERT: X 211 ASP cc_start: 0.7762 (t0) cc_final: 0.7539 (t70) REVERT: X 329 ASN cc_start: 0.8326 (t0) cc_final: 0.8067 (t0) REVERT: Y 42 MET cc_start: 0.8228 (pmm) cc_final: 0.7989 (pmm) REVERT: Y 54 TYR cc_start: 0.6894 (m-80) cc_final: 0.6336 (m-80) REVERT: Y 240 VAL cc_start: 0.9205 (m) cc_final: 0.8985 (t) REVERT: d 126 ASP cc_start: 0.9122 (OUTLIER) cc_final: 0.8518 (p0) REVERT: d 168 ASP cc_start: 0.8283 (t0) cc_final: 0.8001 (t0) REVERT: e 43 TRP cc_start: 0.8928 (p90) cc_final: 0.8633 (p90) REVERT: e 49 GLU cc_start: 0.8841 (tp30) cc_final: 0.8615 (tp30) REVERT: e 56 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7488 (tt) REVERT: E 108 MET cc_start: 0.8698 (mmm) cc_final: 0.8323 (mmm) REVERT: F 390 ASP cc_start: 0.8622 (t0) cc_final: 0.8183 (t0) REVERT: F 421 MET cc_start: 0.8559 (mmm) cc_final: 0.8341 (mmm) REVERT: U 176 MET cc_start: 0.5354 (mmt) cc_final: 0.4993 (mmm) REVERT: U 333 MET cc_start: 0.8647 (mpt) cc_final: 0.8267 (mpp) REVERT: U 585 THR cc_start: 0.8813 (m) cc_final: 0.8545 (p) REVERT: U 675 MET cc_start: 0.9508 (mmm) cc_final: 0.9133 (mmt) REVERT: Z 151 THR cc_start: 0.6757 (p) cc_final: 0.6486 (t) REVERT: a 163 TYR cc_start: 0.8737 (m-80) cc_final: 0.8135 (m-80) REVERT: a 185 ILE cc_start: 0.7648 (mm) cc_final: 0.7406 (mm) REVERT: a 212 ASN cc_start: 0.8116 (t0) cc_final: 0.7825 (t0) REVERT: b 20 ASP cc_start: 0.8761 (p0) cc_final: 0.8384 (p0) REVERT: b 57 ASP cc_start: 0.8495 (m-30) cc_final: 0.8196 (m-30) REVERT: b 79 GLN cc_start: 0.8345 (tt0) cc_final: 0.7789 (tm-30) REVERT: b 121 GLU cc_start: 0.9024 (tp30) cc_final: 0.8497 (pm20) REVERT: b 161 ASN cc_start: 0.8143 (m-40) cc_final: 0.7805 (t0) REVERT: c 107 MET cc_start: 0.7417 (mmt) cc_final: 0.7084 (mmt) REVERT: c 134 GLU cc_start: 0.8707 (tt0) cc_final: 0.8375 (tp30) REVERT: c 158 ASP cc_start: 0.8132 (t0) cc_final: 0.7884 (t0) REVERT: c 215 LYS cc_start: 0.9368 (tptt) cc_final: 0.8971 (tttt) REVERT: c 232 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.7777 (tm-30) REVERT: c 265 MET cc_start: 0.5095 (mpp) cc_final: 0.3814 (mpp) REVERT: c 274 ASN cc_start: 0.8085 (m-40) cc_final: 0.7822 (t0) REVERT: v 4 PHE cc_start: 0.7584 (m-80) cc_final: 0.7288 (m-80) REVERT: v 24 GLU cc_start: 0.7613 (pp20) cc_final: 0.7072 (pm20) REVERT: u 9 THR cc_start: 0.8904 (p) cc_final: 0.8689 (p) REVERT: u 15 LEU cc_start: 0.8939 (mm) cc_final: 0.8728 (mm) REVERT: u 21 ASP cc_start: 0.8254 (m-30) cc_final: 0.7932 (m-30) REVERT: u 31 GLN cc_start: 0.9035 (tt0) cc_final: 0.8827 (tt0) REVERT: u 51 GLU cc_start: 0.7231 (pm20) cc_final: 0.6952 (pm20) REVERT: u 71 LEU cc_start: 0.8509 (mt) cc_final: 0.8245 (mt) REVERT: w 1 MET cc_start: 0.6828 (ppp) cc_final: 0.6495 (ppp) REVERT: w 4 PHE cc_start: 0.7150 (m-80) cc_final: 0.6792 (m-80) REVERT: w 6 LYS cc_start: 0.8519 (tmtt) cc_final: 0.8130 (mtmm) REVERT: w 34 GLU cc_start: 0.7529 (mm-30) cc_final: 0.6818 (mp0) outliers start: 96 outliers final: 29 residues processed: 1055 average time/residue: 0.6602 time to fit residues: 1195.7592 Evaluate side-chains 709 residues out of total 7822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 673 time to evaluate : 5.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain K residue 13 ASN Chi-restraints excluded: chain K residue 17 PRO Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 129 ASP Chi-restraints excluded: chain L residue 9 ASP Chi-restraints excluded: chain V residue 240 LEU Chi-restraints excluded: chain V residue 242 HIS Chi-restraints excluded: chain V residue 451 ILE Chi-restraints excluded: chain W residue 120 ILE Chi-restraints excluded: chain W residue 121 LYS Chi-restraints excluded: chain W residue 137 TYR Chi-restraints excluded: chain W residue 138 VAL Chi-restraints excluded: chain W residue 184 GLU Chi-restraints excluded: chain Y residue 200 LEU Chi-restraints excluded: chain d residue 36 LEU Chi-restraints excluded: chain d residue 42 LYS Chi-restraints excluded: chain d residue 61 TRP Chi-restraints excluded: chain d residue 104 LEU Chi-restraints excluded: chain d residue 107 LEU Chi-restraints excluded: chain d residue 126 ASP Chi-restraints excluded: chain e residue 56 LEU Chi-restraints excluded: chain F residue 76 ASN Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain U residue 880 ASN Chi-restraints excluded: chain U residue 883 ARG Chi-restraints excluded: chain a residue 281 THR Chi-restraints excluded: chain c residue 230 THR Chi-restraints excluded: chain c residue 232 GLN Chi-restraints excluded: chain v residue 72 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.2967 > 50: distance: 27 - 32: 11.515 distance: 32 - 33: 13.436 distance: 33 - 34: 13.218 distance: 33 - 36: 12.787 distance: 34 - 35: 31.569 distance: 34 - 40: 13.487 distance: 36 - 37: 27.694 distance: 37 - 38: 22.035 distance: 37 - 39: 15.463 distance: 40 - 41: 12.459 distance: 41 - 42: 14.900 distance: 41 - 44: 14.514 distance: 42 - 43: 21.441 distance: 42 - 49: 21.102 distance: 44 - 45: 5.795 distance: 45 - 46: 7.276 distance: 46 - 47: 10.593 distance: 47 - 48: 18.007 distance: 49 - 50: 14.955 distance: 50 - 51: 18.952 distance: 50 - 53: 36.745 distance: 51 - 52: 7.773 distance: 51 - 57: 18.281 distance: 53 - 54: 12.093 distance: 54 - 55: 9.955 distance: 55 - 56: 12.063 distance: 57 - 58: 18.726 distance: 57 - 63: 16.892 distance: 58 - 59: 23.691 distance: 58 - 61: 3.244 distance: 59 - 60: 27.087 distance: 59 - 64: 3.241 distance: 61 - 62: 8.939 distance: 62 - 63: 11.177 distance: 64 - 65: 7.636 distance: 65 - 66: 12.028 distance: 65 - 68: 4.651 distance: 66 - 67: 33.770 distance: 66 - 73: 12.842 distance: 68 - 69: 17.254 distance: 69 - 70: 18.890 distance: 70 - 71: 17.486 distance: 71 - 72: 23.016 distance: 73 - 74: 14.454 distance: 74 - 75: 4.912 distance: 74 - 77: 17.795 distance: 75 - 76: 11.645 distance: 75 - 80: 4.047 distance: 77 - 78: 14.266 distance: 77 - 79: 13.013 distance: 80 - 81: 9.441 distance: 81 - 82: 11.058 distance: 81 - 84: 6.085 distance: 82 - 83: 7.643 distance: 82 - 89: 7.899 distance: 84 - 85: 8.092 distance: 85 - 86: 8.601 distance: 86 - 88: 5.573 distance: 89 - 90: 10.932 distance: 89 - 155: 10.288 distance: 90 - 91: 11.186 distance: 90 - 93: 7.624 distance: 91 - 92: 8.522 distance: 91 - 101: 14.066 distance: 92 - 152: 5.442 distance: 93 - 94: 9.097 distance: 94 - 95: 14.169 distance: 94 - 96: 12.211 distance: 95 - 97: 7.446 distance: 96 - 98: 8.372 distance: 97 - 99: 16.533 distance: 98 - 99: 9.831 distance: 99 - 100: 9.053 distance: 101 - 102: 5.773 distance: 102 - 103: 4.937 distance: 102 - 105: 9.625 distance: 103 - 104: 12.951 distance: 103 - 110: 3.406 distance: 104 - 180: 12.956 distance: 105 - 106: 6.960 distance: 106 - 107: 5.717 distance: 107 - 108: 12.990 distance: 108 - 109: 7.043 distance: 110 - 111: 8.275 distance: 111 - 112: 12.589 distance: 111 - 114: 14.739 distance: 112 - 113: 26.965 distance: 114 - 115: 12.663