Starting phenix.real_space_refine on Fri Jan 17 20:26:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qvi_14178/01_2025/7qvi_14178.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qvi_14178/01_2025/7qvi_14178.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qvi_14178/01_2025/7qvi_14178.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qvi_14178/01_2025/7qvi_14178.map" model { file = "/net/cci-nas-00/data/ceres_data/7qvi_14178/01_2025/7qvi_14178.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qvi_14178/01_2025/7qvi_14178.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 544 atoms to isotropic. 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 32 5.49 5 Mg 16 5.21 5 S 240 5.16 5 C 35760 2.51 5 N 10040 2.21 5 O 10512 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 335 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 56600 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 3503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3503 Classifications: {'peptide': 444} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 421} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 3528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3528 Classifications: {'peptide': 447} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 424} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 3503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3503 Classifications: {'peptide': 444} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 421} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 3528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3528 Classifications: {'peptide': 447} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 424} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 3503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3503 Classifications: {'peptide': 444} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 421} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 3528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3528 Classifications: {'peptide': 447} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 424} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 3503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3503 Classifications: {'peptide': 444} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 421} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 3528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3528 Classifications: {'peptide': 447} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 424} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 3528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3528 Classifications: {'peptide': 447} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 424} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 3503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3503 Classifications: {'peptide': 444} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 421} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 3528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3528 Classifications: {'peptide': 447} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 424} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 3503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3503 Classifications: {'peptide': 444} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 421} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 3528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3528 Classifications: {'peptide': 447} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 424} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 3503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3503 Classifications: {'peptide': 444} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 421} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 3528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3528 Classifications: {'peptide': 447} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 424} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 3503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3503 Classifications: {'peptide': 444} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 421} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 24.57, per 1000 atoms: 0.43 Number of scatterers: 56600 At special positions: 0 Unit cell: (134.757, 135.594, 209.25, 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 240 16.00 P 32 15.00 Mg 16 11.99 O 10512 8.00 N 10040 7.00 C 35760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 10.45 Conformation dependent library (CDL) restraints added in 5.4 seconds 14096 Ramachandran restraints generated. 7048 Oldfield, 0 Emsley, 7048 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12880 Finding SS restraints... Secondary structure from input PDB file: 358 helices and 60 sheets defined 52.8% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.30 Creating SS restraints... Processing helix chain 'A' and resid 12 through 16 removed outlier: 3.568A pdb=" N GLU A 15 " --> pdb=" O PRO A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 54 Processing helix chain 'A' and resid 62 through 66 Processing helix chain 'A' and resid 69 through 74 removed outlier: 4.090A pdb=" N TYR A 73 " --> pdb=" O ASP A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 94 removed outlier: 3.748A pdb=" N PHE A 94 " --> pdb=" O LEU A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 106 removed outlier: 3.732A pdb=" N ILE A 102 " --> pdb=" O SER A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 113 removed outlier: 3.727A pdb=" N GLY A 112 " --> pdb=" O ASN A 109 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE A 113 " --> pdb=" O VAL A 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 109 through 113' Processing helix chain 'A' and resid 127 through 132 Processing helix chain 'A' and resid 139 through 149 removed outlier: 4.036A pdb=" N VAL A 143 " --> pdb=" O THR A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 181 Processing helix chain 'A' and resid 199 through 217 removed outlier: 3.802A pdb=" N LEU A 205 " --> pdb=" O ARG A 201 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 246 Processing helix chain 'A' and resid 260 through 273 removed outlier: 3.511A pdb=" N GLU A 272 " --> pdb=" O ARG A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 289 removed outlier: 4.030A pdb=" N PHE A 287 " --> pdb=" O MET A 283 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG A 289 " --> pdb=" O ALA A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 308 Processing helix chain 'A' and resid 325 through 337 Processing helix chain 'A' and resid 343 through 347 Processing helix chain 'A' and resid 369 through 371 No H-bonds generated for 'chain 'A' and resid 369 through 371' Processing helix chain 'A' and resid 372 through 381 Processing helix chain 'A' and resid 389 through 394 removed outlier: 3.653A pdb=" N HIS A 393 " --> pdb=" O GLY A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 419 Processing helix chain 'A' and resid 422 through 436 removed outlier: 6.151A pdb=" N ARG A 428 " --> pdb=" O LEU A 424 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N GLU A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 448 Processing helix chain 'B' and resid 12 through 16 removed outlier: 3.584A pdb=" N GLU B 15 " --> pdb=" O PRO B 12 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR B 16 " --> pdb=" O TYR B 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 12 through 16' Processing helix chain 'B' and resid 42 through 54 removed outlier: 3.639A pdb=" N ALA B 48 " --> pdb=" O GLU B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 67 Processing helix chain 'B' and resid 90 through 94 Processing helix chain 'B' and resid 98 through 107 removed outlier: 3.649A pdb=" N ILE B 102 " --> pdb=" O SER B 98 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE B 106 " --> pdb=" O ILE B 102 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL B 107 " --> pdb=" O MET B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 132 Processing helix chain 'B' and resid 139 through 149 removed outlier: 3.876A pdb=" N VAL B 143 " --> pdb=" O THR B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 182 Processing helix chain 'B' and resid 199 through 219 removed outlier: 3.926A pdb=" N LEU B 205 " --> pdb=" O ARG B 201 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET B 208 " --> pdb=" O PHE B 204 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU B 209 " --> pdb=" O LEU B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 246 Processing helix chain 'B' and resid 259 through 273 Processing helix chain 'B' and resid 283 through 289 removed outlier: 4.129A pdb=" N PHE B 287 " --> pdb=" O MET B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 308 removed outlier: 3.699A pdb=" N LEU B 300 " --> pdb=" O HIS B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 337 Processing helix chain 'B' and resid 343 through 347 removed outlier: 3.574A pdb=" N GLY B 347 " --> pdb=" O PRO B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 371 No H-bonds generated for 'chain 'B' and resid 369 through 371' Processing helix chain 'B' and resid 372 through 381 Processing helix chain 'B' and resid 389 through 394 removed outlier: 3.709A pdb=" N HIS B 393 " --> pdb=" O GLY B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 419 removed outlier: 3.615A pdb=" N GLU B 419 " --> pdb=" O GLN B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 436 removed outlier: 6.811A pdb=" N ARG B 428 " --> pdb=" O LEU B 424 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N GLU B 429 " --> pdb=" O ALA B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 446 Processing helix chain 'C' and resid 13 through 18 removed outlier: 3.583A pdb=" N TYR C 18 " --> pdb=" O ARG C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 54 Processing helix chain 'C' and resid 62 through 68 removed outlier: 3.704A pdb=" N THR C 68 " --> pdb=" O ASN C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 74 removed outlier: 3.565A pdb=" N TYR C 73 " --> pdb=" O ASP C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 94 removed outlier: 3.578A pdb=" N PHE C 94 " --> pdb=" O LEU C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 105 Processing helix chain 'C' and resid 127 through 132 Processing helix chain 'C' and resid 139 through 149 removed outlier: 4.012A pdb=" N VAL C 143 " --> pdb=" O THR C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 182 Processing helix chain 'C' and resid 199 through 219 removed outlier: 3.819A pdb=" N LEU C 205 " --> pdb=" O ARG C 201 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET C 208 " --> pdb=" O PHE C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 246 Processing helix chain 'C' and resid 259 through 273 Processing helix chain 'C' and resid 283 through 288 removed outlier: 4.148A pdb=" N PHE C 287 " --> pdb=" O MET C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 308 removed outlier: 3.556A pdb=" N LEU C 300 " --> pdb=" O HIS C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 337 Processing helix chain 'C' and resid 343 through 347 Processing helix chain 'C' and resid 369 through 371 No H-bonds generated for 'chain 'C' and resid 369 through 371' Processing helix chain 'C' and resid 372 through 381 Processing helix chain 'C' and resid 389 through 394 removed outlier: 3.610A pdb=" N HIS C 393 " --> pdb=" O GLY C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 419 Processing helix chain 'C' and resid 422 through 436 removed outlier: 6.048A pdb=" N ARG C 428 " --> pdb=" O LEU C 424 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N GLU C 429 " --> pdb=" O ALA C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 448 Processing helix chain 'D' and resid 13 through 18 removed outlier: 3.639A pdb=" N TYR D 18 " --> pdb=" O ARG D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 54 removed outlier: 4.240A pdb=" N ALA D 48 " --> pdb=" O GLU D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 68 removed outlier: 3.547A pdb=" N THR D 68 " --> pdb=" O ASN D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 74 removed outlier: 3.943A pdb=" N TYR D 73 " --> pdb=" O ASP D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 94 removed outlier: 3.564A pdb=" N PHE D 94 " --> pdb=" O LEU D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 107 removed outlier: 3.536A pdb=" N ILE D 102 " --> pdb=" O SER D 98 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE D 106 " --> pdb=" O ILE D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 113 removed outlier: 4.148A pdb=" N PHE D 113 " --> pdb=" O VAL D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 132 Processing helix chain 'D' and resid 139 through 149 removed outlier: 4.153A pdb=" N VAL D 143 " --> pdb=" O THR D 139 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU D 144 " --> pdb=" O GLY D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 182 Processing helix chain 'D' and resid 199 through 219 removed outlier: 4.099A pdb=" N LEU D 205 " --> pdb=" O ARG D 201 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR D 206 " --> pdb=" O ASP D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 246 Processing helix chain 'D' and resid 259 through 273 removed outlier: 3.624A pdb=" N ARG D 269 " --> pdb=" O SER D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 287 removed outlier: 3.520A pdb=" N VAL D 286 " --> pdb=" O MET D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 308 removed outlier: 3.528A pdb=" N LEU D 300 " --> pdb=" O HIS D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 337 Processing helix chain 'D' and resid 343 through 347 Processing helix chain 'D' and resid 369 through 371 No H-bonds generated for 'chain 'D' and resid 369 through 371' Processing helix chain 'D' and resid 372 through 381 Processing helix chain 'D' and resid 389 through 394 removed outlier: 3.992A pdb=" N HIS D 393 " --> pdb=" O GLY D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 420 Processing helix chain 'D' and resid 422 through 436 removed outlier: 6.796A pdb=" N ARG D 428 " --> pdb=" O LEU D 424 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N GLU D 429 " --> pdb=" O ALA D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 448 removed outlier: 3.605A pdb=" N GLU D 443 " --> pdb=" O PRO D 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 18 Processing helix chain 'E' and resid 42 through 54 removed outlier: 4.539A pdb=" N ALA E 48 " --> pdb=" O GLU E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 68 removed outlier: 3.923A pdb=" N THR E 68 " --> pdb=" O ASN E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 74 removed outlier: 3.502A pdb=" N TYR E 73 " --> pdb=" O ASP E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 94 removed outlier: 3.785A pdb=" N PHE E 94 " --> pdb=" O LEU E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 106 removed outlier: 3.967A pdb=" N ILE E 102 " --> pdb=" O SER E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 113 removed outlier: 3.794A pdb=" N GLY E 112 " --> pdb=" O ASN E 109 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE E 113 " --> pdb=" O VAL E 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 109 through 113' Processing helix chain 'E' and resid 127 through 132 Processing helix chain 'E' and resid 139 through 149 removed outlier: 4.078A pdb=" N VAL E 143 " --> pdb=" O THR E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 182 Processing helix chain 'E' and resid 199 through 218 removed outlier: 3.847A pdb=" N LEU E 205 " --> pdb=" O ARG E 201 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU E 209 " --> pdb=" O LEU E 205 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA E 216 " --> pdb=" O ARG E 212 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU E 217 " --> pdb=" O LYS E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 246 Processing helix chain 'E' and resid 259 through 273 removed outlier: 3.616A pdb=" N ARG E 269 " --> pdb=" O SER E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 288 removed outlier: 4.057A pdb=" N PHE E 287 " --> pdb=" O MET E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 308 removed outlier: 3.539A pdb=" N LEU E 300 " --> pdb=" O HIS E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 337 removed outlier: 3.666A pdb=" N LEU E 329 " --> pdb=" O ARG E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 347 Processing helix chain 'E' and resid 369 through 371 No H-bonds generated for 'chain 'E' and resid 369 through 371' Processing helix chain 'E' and resid 372 through 381 removed outlier: 3.618A pdb=" N SER E 378 " --> pdb=" O PRO E 374 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ILE E 379 " --> pdb=" O ASP E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 394 removed outlier: 3.663A pdb=" N HIS E 393 " --> pdb=" O GLY E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 418 Processing helix chain 'E' and resid 422 through 436 removed outlier: 5.690A pdb=" N ARG E 428 " --> pdb=" O LEU E 424 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N GLU E 429 " --> pdb=" O ALA E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 448 Processing helix chain 'F' and resid 13 through 18 Processing helix chain 'F' and resid 42 through 54 Processing helix chain 'F' and resid 62 through 68 removed outlier: 3.658A pdb=" N LEU F 66 " --> pdb=" O TRP F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 73 Processing helix chain 'F' and resid 90 through 94 removed outlier: 3.939A pdb=" N PHE F 94 " --> pdb=" O LEU F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 107 removed outlier: 3.848A pdb=" N ILE F 102 " --> pdb=" O SER F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 113 removed outlier: 3.504A pdb=" N GLY F 112 " --> pdb=" O ASN F 109 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE F 113 " --> pdb=" O VAL F 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 109 through 113' Processing helix chain 'F' and resid 127 through 132 Processing helix chain 'F' and resid 140 through 149 Processing helix chain 'F' and resid 167 through 182 Processing helix chain 'F' and resid 199 through 219 removed outlier: 4.000A pdb=" N LEU F 205 " --> pdb=" O ARG F 201 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA F 216 " --> pdb=" O ARG F 212 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU F 217 " --> pdb=" O LYS F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 232 through 247 Processing helix chain 'F' and resid 255 through 259 Processing helix chain 'F' and resid 259 through 273 Processing helix chain 'F' and resid 283 through 289 removed outlier: 3.976A pdb=" N PHE F 287 " --> pdb=" O MET F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 308 removed outlier: 3.562A pdb=" N LEU F 300 " --> pdb=" O HIS F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 337 Processing helix chain 'F' and resid 343 through 347 Processing helix chain 'F' and resid 369 through 371 No H-bonds generated for 'chain 'F' and resid 369 through 371' Processing helix chain 'F' and resid 372 through 381 removed outlier: 3.530A pdb=" N SER F 378 " --> pdb=" O PRO F 374 " (cutoff:3.500A) Processing helix chain 'F' and resid 388 through 394 removed outlier: 3.596A pdb=" N THR F 392 " --> pdb=" O PHE F 388 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS F 393 " --> pdb=" O GLY F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 418 Processing helix chain 'F' and resid 422 through 438 removed outlier: 6.914A pdb=" N ARG F 428 " --> pdb=" O LEU F 424 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N GLU F 429 " --> pdb=" O ALA F 425 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TRP F 437 " --> pdb=" O GLU F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 438 through 448 Processing helix chain 'G' and resid 13 through 18 Processing helix chain 'G' and resid 42 through 54 Processing helix chain 'G' and resid 62 through 68 removed outlier: 3.556A pdb=" N ASN G 65 " --> pdb=" O VAL G 62 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU G 66 " --> pdb=" O TRP G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 73 Processing helix chain 'G' and resid 90 through 94 removed outlier: 3.707A pdb=" N LEU G 93 " --> pdb=" O PRO G 90 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE G 94 " --> pdb=" O LEU G 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 90 through 94' Processing helix chain 'G' and resid 98 through 106 removed outlier: 4.069A pdb=" N ILE G 102 " --> pdb=" O SER G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 113 removed outlier: 3.963A pdb=" N PHE G 111 " --> pdb=" O GLY G 108 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE G 113 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 132 Processing helix chain 'G' and resid 139 through 149 removed outlier: 3.960A pdb=" N VAL G 143 " --> pdb=" O THR G 139 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU G 144 " --> pdb=" O GLY G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 182 Processing helix chain 'G' and resid 199 through 219 removed outlier: 3.549A pdb=" N LEU G 205 " --> pdb=" O ARG G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 246 Processing helix chain 'G' and resid 259 through 274 Processing helix chain 'G' and resid 283 through 289 removed outlier: 4.016A pdb=" N PHE G 287 " --> pdb=" O MET G 283 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 308 removed outlier: 3.511A pdb=" N LEU G 300 " --> pdb=" O HIS G 296 " (cutoff:3.500A) Processing helix chain 'G' and resid 325 through 337 Processing helix chain 'G' and resid 343 through 347 Processing helix chain 'G' and resid 369 through 371 No H-bonds generated for 'chain 'G' and resid 369 through 371' Processing helix chain 'G' and resid 372 through 380 removed outlier: 3.512A pdb=" N SER G 378 " --> pdb=" O PRO G 374 " (cutoff:3.500A) Processing helix chain 'G' and resid 389 through 394 removed outlier: 3.811A pdb=" N HIS G 393 " --> pdb=" O GLY G 389 " (cutoff:3.500A) Processing helix chain 'G' and resid 398 through 418 Processing helix chain 'G' and resid 422 through 436 removed outlier: 6.418A pdb=" N ARG G 428 " --> pdb=" O LEU G 424 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N GLU G 429 " --> pdb=" O ALA G 425 " (cutoff:3.500A) Processing helix chain 'G' and resid 438 through 446 Processing helix chain 'H' and resid 12 through 16 Processing helix chain 'H' and resid 42 through 54 Processing helix chain 'H' and resid 62 through 68 removed outlier: 3.574A pdb=" N LEU H 66 " --> pdb=" O TRP H 63 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR H 68 " --> pdb=" O ASN H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 74 removed outlier: 3.659A pdb=" N TYR H 73 " --> pdb=" O ASP H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.529A pdb=" N LEU H 93 " --> pdb=" O PRO H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 98 through 106 Processing helix chain 'H' and resid 127 through 132 Processing helix chain 'H' and resid 140 through 149 removed outlier: 3.705A pdb=" N ASP H 146 " --> pdb=" O GLN H 142 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 182 removed outlier: 3.502A pdb=" N ARG H 173 " --> pdb=" O LYS H 169 " (cutoff:3.500A) Processing helix chain 'H' and resid 199 through 219 removed outlier: 4.007A pdb=" N LEU H 205 " --> pdb=" O ARG H 201 " (cutoff:3.500A) Processing helix chain 'H' and resid 232 through 246 Processing helix chain 'H' and resid 260 through 273 removed outlier: 3.510A pdb=" N ARG H 269 " --> pdb=" O SER H 265 " (cutoff:3.500A) Processing helix chain 'H' and resid 283 through 288 removed outlier: 4.332A pdb=" N PHE H 287 " --> pdb=" O MET H 283 " (cutoff:3.500A) Processing helix chain 'H' and resid 296 through 308 removed outlier: 3.625A pdb=" N LEU H 300 " --> pdb=" O HIS H 296 " (cutoff:3.500A) Processing helix chain 'H' and resid 324 through 337 Processing helix chain 'H' and resid 369 through 371 No H-bonds generated for 'chain 'H' and resid 369 through 371' Processing helix chain 'H' and resid 372 through 381 removed outlier: 3.529A pdb=" N SER H 378 " --> pdb=" O PRO H 374 " (cutoff:3.500A) Processing helix chain 'H' and resid 388 through 394 removed outlier: 3.957A pdb=" N HIS H 393 " --> pdb=" O GLY H 389 " (cutoff:3.500A) Processing helix chain 'H' and resid 397 through 418 removed outlier: 4.034A pdb=" N ALA H 401 " --> pdb=" O ARG H 397 " (cutoff:3.500A) Processing helix chain 'H' and resid 422 through 438 removed outlier: 6.627A pdb=" N ARG H 428 " --> pdb=" O LEU H 424 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N GLU H 429 " --> pdb=" O ALA H 425 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP H 437 " --> pdb=" O GLU H 433 " (cutoff:3.500A) Processing helix chain 'H' and resid 438 through 449 removed outlier: 3.746A pdb=" N ARG H 442 " --> pdb=" O CYS H 438 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU H 443 " --> pdb=" O PRO H 439 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA H 444 " --> pdb=" O GLU H 440 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU H 447 " --> pdb=" O GLU H 443 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TRP H 448 " --> pdb=" O ALA H 444 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 18 removed outlier: 4.347A pdb=" N THR I 16 " --> pdb=" O PRO I 12 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TYR I 18 " --> pdb=" O ARG I 14 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 54 Processing helix chain 'I' and resid 62 through 68 removed outlier: 3.521A pdb=" N LEU I 66 " --> pdb=" O TRP I 63 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR I 68 " --> pdb=" O ASN I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 74 removed outlier: 3.968A pdb=" N TYR I 73 " --> pdb=" O ASP I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 94 removed outlier: 3.558A pdb=" N PHE I 94 " --> pdb=" O LEU I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 106 removed outlier: 3.954A pdb=" N ILE I 102 " --> pdb=" O SER I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 113 removed outlier: 3.858A pdb=" N GLY I 112 " --> pdb=" O ASN I 109 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE I 113 " --> pdb=" O VAL I 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 109 through 113' Processing helix chain 'I' and resid 127 through 132 Processing helix chain 'I' and resid 139 through 149 removed outlier: 4.136A pdb=" N VAL I 143 " --> pdb=" O THR I 139 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU I 144 " --> pdb=" O GLY I 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 181 Processing helix chain 'I' and resid 199 through 219 removed outlier: 3.730A pdb=" N LEU I 205 " --> pdb=" O ARG I 201 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU I 217 " --> pdb=" O LYS I 213 " (cutoff:3.500A) Processing helix chain 'I' and resid 232 through 246 removed outlier: 3.512A pdb=" N PHE I 242 " --> pdb=" O LYS I 238 " (cutoff:3.500A) Processing helix chain 'I' and resid 255 through 259 Processing helix chain 'I' and resid 259 through 273 Processing helix chain 'I' and resid 296 through 308 removed outlier: 3.730A pdb=" N LEU I 300 " --> pdb=" O HIS I 296 " (cutoff:3.500A) Processing helix chain 'I' and resid 324 through 337 Processing helix chain 'I' and resid 369 through 371 No H-bonds generated for 'chain 'I' and resid 369 through 371' Processing helix chain 'I' and resid 372 through 381 Processing helix chain 'I' and resid 389 through 394 removed outlier: 3.635A pdb=" N HIS I 393 " --> pdb=" O GLY I 389 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 418 removed outlier: 3.525A pdb=" N GLY I 402 " --> pdb=" O GLY I 398 " (cutoff:3.500A) Processing helix chain 'I' and resid 426 through 436 Processing helix chain 'I' and resid 438 through 448 removed outlier: 3.567A pdb=" N ARG I 442 " --> pdb=" O CYS I 438 " (cutoff:3.500A) Processing helix chain 'J' and resid 12 through 16 removed outlier: 3.691A pdb=" N GLU J 15 " --> pdb=" O PRO J 12 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 55 removed outlier: 3.555A pdb=" N SER J 55 " --> pdb=" O ALA J 51 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 68 removed outlier: 3.718A pdb=" N LEU J 66 " --> pdb=" O TRP J 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 74 removed outlier: 3.846A pdb=" N TYR J 73 " --> pdb=" O ASP J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 94 No H-bonds generated for 'chain 'J' and resid 92 through 94' Processing helix chain 'J' and resid 98 through 106 removed outlier: 3.834A pdb=" N ILE J 102 " --> pdb=" O SER J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 113 removed outlier: 3.730A pdb=" N GLY J 112 " --> pdb=" O ASN J 109 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE J 113 " --> pdb=" O VAL J 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 109 through 113' Processing helix chain 'J' and resid 127 through 132 Processing helix chain 'J' and resid 140 through 149 removed outlier: 3.511A pdb=" N ASP J 146 " --> pdb=" O GLN J 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 167 through 182 Processing helix chain 'J' and resid 199 through 219 Processing helix chain 'J' and resid 232 through 246 removed outlier: 3.734A pdb=" N LYS J 238 " --> pdb=" O GLU J 234 " (cutoff:3.500A) Processing helix chain 'J' and resid 259 through 273 Processing helix chain 'J' and resid 283 through 288 removed outlier: 3.891A pdb=" N PHE J 287 " --> pdb=" O MET J 283 " (cutoff:3.500A) Processing helix chain 'J' and resid 296 through 308 removed outlier: 3.612A pdb=" N LEU J 300 " --> pdb=" O HIS J 296 " (cutoff:3.500A) Processing helix chain 'J' and resid 324 through 337 Processing helix chain 'J' and resid 369 through 371 No H-bonds generated for 'chain 'J' and resid 369 through 371' Processing helix chain 'J' and resid 372 through 381 Processing helix chain 'J' and resid 389 through 394 removed outlier: 3.777A pdb=" N HIS J 393 " --> pdb=" O GLY J 389 " (cutoff:3.500A) Processing helix chain 'J' and resid 398 through 419 Processing helix chain 'J' and resid 426 through 438 removed outlier: 3.880A pdb=" N TRP J 437 " --> pdb=" O GLU J 433 " (cutoff:3.500A) Processing helix chain 'J' and resid 438 through 448 Processing helix chain 'K' and resid 12 through 16 Processing helix chain 'K' and resid 42 through 54 Processing helix chain 'K' and resid 62 through 68 removed outlier: 3.629A pdb=" N LEU K 66 " --> pdb=" O TRP K 63 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR K 68 " --> pdb=" O ASN K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 73 Processing helix chain 'K' and resid 90 through 94 removed outlier: 3.537A pdb=" N LEU K 93 " --> pdb=" O PRO K 90 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE K 94 " --> pdb=" O LEU K 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 90 through 94' Processing helix chain 'K' and resid 98 through 106 removed outlier: 3.867A pdb=" N ILE K 102 " --> pdb=" O SER K 98 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 113 removed outlier: 3.967A pdb=" N PHE K 111 " --> pdb=" O GLY K 108 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY K 112 " --> pdb=" O ASN K 109 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N PHE K 113 " --> pdb=" O VAL K 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 108 through 113' Processing helix chain 'K' and resid 127 through 132 Processing helix chain 'K' and resid 141 through 149 Processing helix chain 'K' and resid 167 through 182 Processing helix chain 'K' and resid 199 through 219 Processing helix chain 'K' and resid 232 through 246 Processing helix chain 'K' and resid 259 through 273 Processing helix chain 'K' and resid 283 through 289 removed outlier: 4.169A pdb=" N PHE K 287 " --> pdb=" O MET K 283 " (cutoff:3.500A) Processing helix chain 'K' and resid 296 through 308 removed outlier: 3.526A pdb=" N LEU K 300 " --> pdb=" O HIS K 296 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS K 302 " --> pdb=" O ARG K 298 " (cutoff:3.500A) Processing helix chain 'K' and resid 324 through 337 Processing helix chain 'K' and resid 343 through 347 removed outlier: 3.872A pdb=" N GLY K 347 " --> pdb=" O PRO K 344 " (cutoff:3.500A) Processing helix chain 'K' and resid 369 through 371 No H-bonds generated for 'chain 'K' and resid 369 through 371' Processing helix chain 'K' and resid 372 through 381 removed outlier: 3.574A pdb=" N SER K 378 " --> pdb=" O PRO K 374 " (cutoff:3.500A) Processing helix chain 'K' and resid 389 through 394 removed outlier: 3.983A pdb=" N HIS K 393 " --> pdb=" O GLY K 389 " (cutoff:3.500A) Processing helix chain 'K' and resid 397 through 420 removed outlier: 4.167A pdb=" N ALA K 401 " --> pdb=" O ARG K 397 " (cutoff:3.500A) Processing helix chain 'K' and resid 422 through 436 removed outlier: 5.766A pdb=" N ARG K 428 " --> pdb=" O LEU K 424 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N GLU K 429 " --> pdb=" O ALA K 425 " (cutoff:3.500A) Processing helix chain 'K' and resid 438 through 448 Processing helix chain 'L' and resid 12 through 16 removed outlier: 3.570A pdb=" N GLU L 15 " --> pdb=" O PRO L 12 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 53 Processing helix chain 'L' and resid 62 through 68 removed outlier: 3.690A pdb=" N LEU L 66 " --> pdb=" O TRP L 63 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N THR L 68 " --> pdb=" O ASN L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 73 removed outlier: 3.563A pdb=" N ARG L 72 " --> pdb=" O ASP L 69 " (cutoff:3.500A) Processing helix chain 'L' and resid 90 through 94 removed outlier: 3.606A pdb=" N LEU L 93 " --> pdb=" O PRO L 90 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE L 94 " --> pdb=" O LEU L 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 90 through 94' Processing helix chain 'L' and resid 98 through 105 Processing helix chain 'L' and resid 109 through 113 removed outlier: 3.610A pdb=" N GLY L 112 " --> pdb=" O ASN L 109 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE L 113 " --> pdb=" O VAL L 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 109 through 113' Processing helix chain 'L' and resid 127 through 132 Processing helix chain 'L' and resid 139 through 149 removed outlier: 4.192A pdb=" N VAL L 143 " --> pdb=" O THR L 139 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 182 Processing helix chain 'L' and resid 199 through 219 removed outlier: 3.732A pdb=" N LEU L 205 " --> pdb=" O ARG L 201 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET L 208 " --> pdb=" O PHE L 204 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU L 209 " --> pdb=" O LEU L 205 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA L 210 " --> pdb=" O TYR L 206 " (cutoff:3.500A) Processing helix chain 'L' and resid 232 through 247 Processing helix chain 'L' and resid 260 through 274 Processing helix chain 'L' and resid 283 through 287 Processing helix chain 'L' and resid 296 through 308 removed outlier: 3.502A pdb=" N LEU L 300 " --> pdb=" O HIS L 296 " (cutoff:3.500A) Processing helix chain 'L' and resid 324 through 337 removed outlier: 3.640A pdb=" N ARG L 336 " --> pdb=" O ALA L 332 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU L 337 " --> pdb=" O ASP L 333 " (cutoff:3.500A) Processing helix chain 'L' and resid 343 through 347 Processing helix chain 'L' and resid 369 through 371 No H-bonds generated for 'chain 'L' and resid 369 through 371' Processing helix chain 'L' and resid 372 through 381 Processing helix chain 'L' and resid 389 through 394 removed outlier: 3.754A pdb=" N HIS L 393 " --> pdb=" O GLY L 389 " (cutoff:3.500A) Processing helix chain 'L' and resid 398 through 418 Processing helix chain 'L' and resid 422 through 438 removed outlier: 6.902A pdb=" N ARG L 428 " --> pdb=" O LEU L 424 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N GLU L 429 " --> pdb=" O ALA L 425 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N TRP L 437 " --> pdb=" O GLU L 433 " (cutoff:3.500A) Processing helix chain 'L' and resid 438 through 448 Processing helix chain 'M' and resid 13 through 18 removed outlier: 3.525A pdb=" N TYR M 18 " --> pdb=" O ARG M 14 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 54 Processing helix chain 'M' and resid 62 through 68 removed outlier: 3.625A pdb=" N LEU M 66 " --> pdb=" O TRP M 63 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR M 68 " --> pdb=" O ASN M 65 " (cutoff:3.500A) Processing helix chain 'M' and resid 69 through 74 removed outlier: 4.098A pdb=" N TYR M 73 " --> pdb=" O ASP M 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 90 through 94 removed outlier: 3.667A pdb=" N LEU M 93 " --> pdb=" O PRO M 90 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE M 94 " --> pdb=" O LEU M 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 90 through 94' Processing helix chain 'M' and resid 98 through 106 removed outlier: 3.629A pdb=" N ILE M 106 " --> pdb=" O ILE M 102 " (cutoff:3.500A) Processing helix chain 'M' and resid 127 through 132 Processing helix chain 'M' and resid 139 through 149 removed outlier: 4.244A pdb=" N VAL M 143 " --> pdb=" O THR M 139 " (cutoff:3.500A) Processing helix chain 'M' and resid 167 through 182 Processing helix chain 'M' and resid 199 through 219 removed outlier: 4.044A pdb=" N LEU M 205 " --> pdb=" O ARG M 201 " (cutoff:3.500A) Processing helix chain 'M' and resid 232 through 246 Processing helix chain 'M' and resid 259 through 274 Processing helix chain 'M' and resid 284 through 289 Processing helix chain 'M' and resid 296 through 308 removed outlier: 3.564A pdb=" N LEU M 300 " --> pdb=" O HIS M 296 " (cutoff:3.500A) Processing helix chain 'M' and resid 324 through 337 Processing helix chain 'M' and resid 343 through 347 removed outlier: 3.579A pdb=" N GLY M 347 " --> pdb=" O PRO M 344 " (cutoff:3.500A) Processing helix chain 'M' and resid 369 through 371 No H-bonds generated for 'chain 'M' and resid 369 through 371' Processing helix chain 'M' and resid 372 through 381 Processing helix chain 'M' and resid 389 through 394 removed outlier: 3.832A pdb=" N HIS M 393 " --> pdb=" O GLY M 389 " (cutoff:3.500A) Processing helix chain 'M' and resid 398 through 419 Processing helix chain 'M' and resid 422 through 435 removed outlier: 5.856A pdb=" N ARG M 428 " --> pdb=" O LEU M 424 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N GLU M 429 " --> pdb=" O ALA M 425 " (cutoff:3.500A) Processing helix chain 'M' and resid 438 through 448 removed outlier: 4.002A pdb=" N GLU M 446 " --> pdb=" O ARG M 442 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU M 447 " --> pdb=" O GLU M 443 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N TRP M 448 " --> pdb=" O ALA M 444 " (cutoff:3.500A) Processing helix chain 'N' and resid 12 through 16 removed outlier: 3.618A pdb=" N GLU N 15 " --> pdb=" O PRO N 12 " (cutoff:3.500A) Processing helix chain 'N' and resid 42 through 54 removed outlier: 3.535A pdb=" N SER N 54 " --> pdb=" O VAL N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 68 removed outlier: 3.561A pdb=" N LEU N 66 " --> pdb=" O TRP N 63 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR N 68 " --> pdb=" O ASN N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 69 through 73 removed outlier: 3.614A pdb=" N ARG N 72 " --> pdb=" O ASP N 69 " (cutoff:3.500A) Processing helix chain 'N' and resid 90 through 94 Processing helix chain 'N' and resid 98 through 106 removed outlier: 3.660A pdb=" N ILE N 102 " --> pdb=" O SER N 98 " (cutoff:3.500A) Processing helix chain 'N' and resid 127 through 132 Processing helix chain 'N' and resid 139 through 149 removed outlier: 4.109A pdb=" N VAL N 143 " --> pdb=" O THR N 139 " (cutoff:3.500A) Processing helix chain 'N' and resid 167 through 182 removed outlier: 3.528A pdb=" N GLY N 182 " --> pdb=" O CYS N 178 " (cutoff:3.500A) Processing helix chain 'N' and resid 199 through 219 removed outlier: 3.873A pdb=" N LEU N 205 " --> pdb=" O ARG N 201 " (cutoff:3.500A) Processing helix chain 'N' and resid 232 through 247 Processing helix chain 'N' and resid 255 through 259 Processing helix chain 'N' and resid 259 through 274 removed outlier: 3.594A pdb=" N ARG N 269 " --> pdb=" O SER N 265 " (cutoff:3.500A) Processing helix chain 'N' and resid 283 through 288 removed outlier: 3.818A pdb=" N PHE N 287 " --> pdb=" O MET N 283 " (cutoff:3.500A) Processing helix chain 'N' and resid 296 through 308 Processing helix chain 'N' and resid 324 through 337 Processing helix chain 'N' and resid 369 through 372 Processing helix chain 'N' and resid 373 through 381 removed outlier: 4.548A pdb=" N ILE N 379 " --> pdb=" O ASP N 375 " (cutoff:3.500A) Processing helix chain 'N' and resid 389 through 394 removed outlier: 3.731A pdb=" N HIS N 393 " --> pdb=" O GLY N 389 " (cutoff:3.500A) Processing helix chain 'N' and resid 398 through 419 Processing helix chain 'N' and resid 422 through 436 removed outlier: 6.244A pdb=" N ARG N 428 " --> pdb=" O LEU N 424 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N GLU N 429 " --> pdb=" O ALA N 425 " (cutoff:3.500A) Processing helix chain 'N' and resid 438 through 448 Processing helix chain 'O' and resid 13 through 18 Processing helix chain 'O' and resid 42 through 54 Processing helix chain 'O' and resid 62 through 67 Processing helix chain 'O' and resid 69 through 74 removed outlier: 3.601A pdb=" N TYR O 73 " --> pdb=" O ASP O 69 " (cutoff:3.500A) Processing helix chain 'O' and resid 90 through 94 removed outlier: 3.788A pdb=" N PHE O 94 " --> pdb=" O LEU O 91 " (cutoff:3.500A) Processing helix chain 'O' and resid 98 through 106 removed outlier: 3.710A pdb=" N ILE O 102 " --> pdb=" O SER O 98 " (cutoff:3.500A) Processing helix chain 'O' and resid 109 through 113 removed outlier: 3.788A pdb=" N PHE O 113 " --> pdb=" O VAL O 110 " (cutoff:3.500A) Processing helix chain 'O' and resid 127 through 132 Processing helix chain 'O' and resid 139 through 149 removed outlier: 4.159A pdb=" N VAL O 143 " --> pdb=" O THR O 139 " (cutoff:3.500A) Processing helix chain 'O' and resid 167 through 182 Processing helix chain 'O' and resid 199 through 219 removed outlier: 3.677A pdb=" N LEU O 205 " --> pdb=" O ARG O 201 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET O 208 " --> pdb=" O PHE O 204 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU O 217 " --> pdb=" O LYS O 213 " (cutoff:3.500A) Processing helix chain 'O' and resid 232 through 246 Processing helix chain 'O' and resid 260 through 273 Processing helix chain 'O' and resid 296 through 308 Processing helix chain 'O' and resid 324 through 337 removed outlier: 3.511A pdb=" N LEU O 329 " --> pdb=" O ARG O 325 " (cutoff:3.500A) Processing helix chain 'O' and resid 369 through 371 No H-bonds generated for 'chain 'O' and resid 369 through 371' Processing helix chain 'O' and resid 372 through 381 removed outlier: 3.572A pdb=" N SER O 378 " --> pdb=" O PRO O 374 " (cutoff:3.500A) Processing helix chain 'O' and resid 389 through 394 removed outlier: 3.786A pdb=" N HIS O 393 " --> pdb=" O GLY O 389 " (cutoff:3.500A) Processing helix chain 'O' and resid 398 through 418 Processing helix chain 'O' and resid 422 through 436 removed outlier: 6.187A pdb=" N ARG O 428 " --> pdb=" O LEU O 424 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLU O 429 " --> pdb=" O ALA O 425 " (cutoff:3.500A) Processing helix chain 'O' and resid 438 through 448 removed outlier: 3.641A pdb=" N GLU O 443 " --> pdb=" O PRO O 439 " (cutoff:3.500A) Processing helix chain 'P' and resid 13 through 18 Processing helix chain 'P' and resid 42 through 54 Processing helix chain 'P' and resid 62 through 68 removed outlier: 3.649A pdb=" N LEU P 66 " --> pdb=" O TRP P 63 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR P 68 " --> pdb=" O ASN P 65 " (cutoff:3.500A) Processing helix chain 'P' and resid 69 through 74 removed outlier: 3.669A pdb=" N TYR P 73 " --> pdb=" O ASP P 69 " (cutoff:3.500A) Processing helix chain 'P' and resid 90 through 94 removed outlier: 3.783A pdb=" N PHE P 94 " --> pdb=" O LEU P 91 " (cutoff:3.500A) Processing helix chain 'P' and resid 98 through 106 removed outlier: 3.878A pdb=" N ILE P 102 " --> pdb=" O SER P 98 " (cutoff:3.500A) Processing helix chain 'P' and resid 109 through 113 removed outlier: 3.587A pdb=" N GLY P 112 " --> pdb=" O ASN P 109 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N PHE P 113 " --> pdb=" O VAL P 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 109 through 113' Processing helix chain 'P' and resid 127 through 132 Processing helix chain 'P' and resid 139 through 149 removed outlier: 4.089A pdb=" N VAL P 143 " --> pdb=" O THR P 139 " (cutoff:3.500A) Processing helix chain 'P' and resid 167 through 182 removed outlier: 3.577A pdb=" N GLY P 182 " --> pdb=" O CYS P 178 " (cutoff:3.500A) Processing helix chain 'P' and resid 199 through 219 Processing helix chain 'P' and resid 232 through 247 removed outlier: 3.543A pdb=" N PHE P 242 " --> pdb=" O LYS P 238 " (cutoff:3.500A) Processing helix chain 'P' and resid 259 through 273 Processing helix chain 'P' and resid 283 through 289 removed outlier: 3.962A pdb=" N PHE P 287 " --> pdb=" O MET P 283 " (cutoff:3.500A) Processing helix chain 'P' and resid 296 through 308 removed outlier: 3.556A pdb=" N LEU P 300 " --> pdb=" O HIS P 296 " (cutoff:3.500A) Processing helix chain 'P' and resid 324 through 337 removed outlier: 3.632A pdb=" N LEU P 329 " --> pdb=" O ARG P 325 " (cutoff:3.500A) Processing helix chain 'P' and resid 343 through 347 removed outlier: 3.791A pdb=" N GLY P 347 " --> pdb=" O PRO P 344 " (cutoff:3.500A) Processing helix chain 'P' and resid 369 through 371 No H-bonds generated for 'chain 'P' and resid 369 through 371' Processing helix chain 'P' and resid 372 through 381 removed outlier: 3.512A pdb=" N SER P 378 " --> pdb=" O PRO P 374 " (cutoff:3.500A) Processing helix chain 'P' and resid 389 through 394 removed outlier: 3.534A pdb=" N HIS P 393 " --> pdb=" O GLY P 389 " (cutoff:3.500A) Processing helix chain 'P' and resid 398 through 418 Processing helix chain 'P' and resid 422 through 438 removed outlier: 5.791A pdb=" N ARG P 428 " --> pdb=" O LEU P 424 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLU P 429 " --> pdb=" O ALA P 425 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TRP P 437 " --> pdb=" O GLU P 433 " (cutoff:3.500A) Processing helix chain 'P' and resid 438 through 448 Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 81 removed outlier: 5.799A pdb=" N CYS A 77 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ALA A 88 " --> pdb=" O CYS A 77 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG A 79 " --> pdb=" O TYR A 86 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL A 84 " --> pdb=" O GLU A 81 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU A 30 " --> pdb=" O MET A 124 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N MET A 124 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ALA A 32 " --> pdb=" O GLU A 122 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY A 294 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 155 through 157 removed outlier: 6.379A pdb=" N VAL A 312 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N SER A 365 " --> pdb=" O VAL A 312 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N HIS A 311 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N HIS A 313 " --> pdb=" O CYS A 279 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE A 251 " --> pdb=" O HIS A 278 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N HIS A 280 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL A 253 " --> pdb=" O HIS A 280 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N HIS A 224 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N MET A 252 " --> pdb=" O HIS A 224 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU A 226 " --> pdb=" O MET A 252 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N ASP A 254 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N THR A 186 " --> pdb=" O TRP A 225 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N ASN A 227 " --> pdb=" O THR A 186 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 339 through 340 Processing sheet with id=AA4, first strand: chain 'B' and resid 76 through 80 removed outlier: 5.848A pdb=" N CYS B 77 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ALA B 88 " --> pdb=" O CYS B 77 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG B 79 " --> pdb=" O TYR B 86 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP B 123 " --> pdb=" O ALA B 32 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ARG B 34 " --> pdb=" O LEU B 121 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N LEU B 121 " --> pdb=" O ARG B 34 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N THR B 36 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N LEU B 119 " --> pdb=" O THR B 36 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N GLY B 294 " --> pdb=" O GLN B 117 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU B 119 " --> pdb=" O GLY B 294 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 186 through 187 removed outlier: 7.630A pdb=" N THR B 186 " --> pdb=" O TRP B 225 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 250 through 254 removed outlier: 6.241A pdb=" N ILE B 251 " --> pdb=" O HIS B 278 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N HIS B 280 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL B 253 " --> pdb=" O HIS B 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 311 through 313 removed outlier: 6.490A pdb=" N VAL B 312 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N SER B 365 " --> pdb=" O VAL B 312 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 339 through 340 Processing sheet with id=AA9, first strand: chain 'C' and resid 76 through 80 removed outlier: 5.819A pdb=" N CYS C 77 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ALA C 88 " --> pdb=" O CYS C 77 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG C 79 " --> pdb=" O TYR C 86 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU C 30 " --> pdb=" O ARG C 125 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP C 123 " --> pdb=" O ALA C 32 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ARG C 34 " --> pdb=" O LEU C 121 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N LEU C 121 " --> pdb=" O ARG C 34 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N THR C 36 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LEU C 119 " --> pdb=" O THR C 36 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N GLY C 294 " --> pdb=" O GLN C 117 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU C 119 " --> pdb=" O GLY C 294 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 155 through 157 removed outlier: 6.472A pdb=" N VAL C 312 " --> pdb=" O VAL C 363 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N SER C 365 " --> pdb=" O VAL C 312 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 186 through 187 removed outlier: 7.567A pdb=" N THR C 186 " --> pdb=" O TRP C 225 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ASN C 227 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N HIS C 224 " --> pdb=" O TYR C 250 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N MET C 252 " --> pdb=" O HIS C 224 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LEU C 226 " --> pdb=" O MET C 252 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ASP C 254 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE C 251 " --> pdb=" O HIS C 278 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N HIS C 280 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL C 253 " --> pdb=" O HIS C 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 339 through 340 Processing sheet with id=AB4, first strand: chain 'D' and resid 76 through 80 removed outlier: 5.824A pdb=" N CYS D 77 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ALA D 88 " --> pdb=" O CYS D 77 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG D 79 " --> pdb=" O TYR D 86 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU D 30 " --> pdb=" O MET D 124 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N MET D 124 " --> pdb=" O LEU D 30 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA D 32 " --> pdb=" O GLU D 122 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 276 through 280 removed outlier: 6.295A pdb=" N ILE D 251 " --> pdb=" O HIS D 278 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N HIS D 280 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL D 253 " --> pdb=" O HIS D 280 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N HIS D 224 " --> pdb=" O TYR D 250 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N MET D 252 " --> pdb=" O HIS D 224 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU D 226 " --> pdb=" O MET D 252 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ASP D 254 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N THR D 186 " --> pdb=" O TRP D 225 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N ASN D 227 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N KCX D 187 " --> pdb=" O LEU D 156 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLY D 158 " --> pdb=" O KCX D 187 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU D 155 " --> pdb=" O PHE D 386 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N PHE D 388 " --> pdb=" O LEU D 155 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLY D 157 " --> pdb=" O PHE D 388 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY D 366 " --> pdb=" O LEU D 387 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL D 312 " --> pdb=" O VAL D 363 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N SER D 365 " --> pdb=" O VAL D 312 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 339 through 340 Processing sheet with id=AB7, first strand: chain 'E' and resid 76 through 81 removed outlier: 5.733A pdb=" N CYS E 77 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ALA E 88 " --> pdb=" O CYS E 77 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ARG E 79 " --> pdb=" O TYR E 86 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU E 30 " --> pdb=" O MET E 124 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N MET E 124 " --> pdb=" O LEU E 30 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ALA E 32 " --> pdb=" O GLU E 122 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY E 294 " --> pdb=" O LEU E 119 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 155 through 157 removed outlier: 6.519A pdb=" N VAL E 312 " --> pdb=" O VAL E 363 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 226 through 227 removed outlier: 6.246A pdb=" N LEU E 226 " --> pdb=" O MET E 252 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N ASP E 254 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE E 251 " --> pdb=" O HIS E 278 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N HIS E 280 " --> pdb=" O ILE E 251 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL E 253 " --> pdb=" O HIS E 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'E' and resid 339 through 340 Processing sheet with id=AC2, first strand: chain 'F' and resid 76 through 80 removed outlier: 5.965A pdb=" N CYS F 77 " --> pdb=" O ALA F 88 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ALA F 88 " --> pdb=" O CYS F 77 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG F 79 " --> pdb=" O TYR F 86 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP F 123 " --> pdb=" O ALA F 32 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ARG F 34 " --> pdb=" O LEU F 121 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N LEU F 121 " --> pdb=" O ARG F 34 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N THR F 36 " --> pdb=" O LEU F 119 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N LEU F 119 " --> pdb=" O THR F 36 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY F 294 " --> pdb=" O LEU F 119 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 155 through 157 removed outlier: 6.791A pdb=" N LEU F 155 " --> pdb=" O PHE F 386 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL F 312 " --> pdb=" O VAL F 363 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 186 through 187 removed outlier: 7.123A pdb=" N THR F 186 " --> pdb=" O TRP F 225 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'F' and resid 250 through 254 removed outlier: 6.271A pdb=" N ILE F 251 " --> pdb=" O HIS F 278 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N HIS F 280 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL F 253 " --> pdb=" O HIS F 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'F' and resid 339 through 340 Processing sheet with id=AC7, first strand: chain 'G' and resid 76 through 80 removed outlier: 5.846A pdb=" N CYS G 77 " --> pdb=" O ALA G 88 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ALA G 88 " --> pdb=" O CYS G 77 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG G 79 " --> pdb=" O TYR G 86 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU G 30 " --> pdb=" O MET G 124 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N MET G 124 " --> pdb=" O LEU G 30 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ALA G 32 " --> pdb=" O GLU G 122 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 155 through 157 removed outlier: 6.234A pdb=" N VAL G 312 " --> pdb=" O VAL G 363 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N SER G 365 " --> pdb=" O VAL G 312 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N HIS G 311 " --> pdb=" O LEU G 277 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N HIS G 313 " --> pdb=" O CYS G 279 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE G 251 " --> pdb=" O HIS G 278 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N HIS G 280 " --> pdb=" O ILE G 251 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL G 253 " --> pdb=" O HIS G 280 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N HIS G 224 " --> pdb=" O TYR G 250 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N MET G 252 " --> pdb=" O HIS G 224 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU G 226 " --> pdb=" O MET G 252 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ASP G 254 " --> pdb=" O LEU G 226 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N THR G 186 " --> pdb=" O TRP G 225 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N ASN G 227 " --> pdb=" O THR G 186 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 339 through 340 Processing sheet with id=AD1, first strand: chain 'H' and resid 76 through 80 removed outlier: 3.558A pdb=" N ARG H 76 " --> pdb=" O ALA H 88 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N TYR H 86 " --> pdb=" O TYR H 78 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ILE H 80 " --> pdb=" O VAL H 84 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL H 84 " --> pdb=" O ILE H 80 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP H 123 " --> pdb=" O ALA H 32 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ARG H 34 " --> pdb=" O LEU H 121 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LEU H 121 " --> pdb=" O ARG H 34 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR H 36 " --> pdb=" O LEU H 119 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N LEU H 119 " --> pdb=" O THR H 36 " (cutoff:3.500A) removed outlier: 8.778A pdb=" N GLY H 294 " --> pdb=" O GLN H 117 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU H 119 " --> pdb=" O GLY H 294 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 276 through 280 removed outlier: 6.426A pdb=" N ILE H 251 " --> pdb=" O HIS H 278 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N HIS H 280 " --> pdb=" O ILE H 251 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL H 253 " --> pdb=" O HIS H 280 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N HIS H 224 " --> pdb=" O TYR H 250 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N MET H 252 " --> pdb=" O HIS H 224 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N LEU H 226 " --> pdb=" O MET H 252 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ASP H 254 " --> pdb=" O LEU H 226 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N THR H 186 " --> pdb=" O TRP H 225 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N ASN H 227 " --> pdb=" O THR H 186 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N KCX H 187 " --> pdb=" O LEU H 156 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLY H 158 " --> pdb=" O KCX H 187 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LEU H 155 " --> pdb=" O PHE H 386 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL H 312 " --> pdb=" O VAL H 363 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N SER H 365 " --> pdb=" O VAL H 312 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 339 through 340 Processing sheet with id=AD4, first strand: chain 'I' and resid 76 through 81 removed outlier: 5.964A pdb=" N CYS I 77 " --> pdb=" O ALA I 88 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ALA I 88 " --> pdb=" O CYS I 77 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG I 79 " --> pdb=" O TYR I 86 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU I 30 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N MET I 124 " --> pdb=" O LEU I 30 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ALA I 32 " --> pdb=" O GLU I 122 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 155 through 157 removed outlier: 6.259A pdb=" N VAL I 312 " --> pdb=" O VAL I 363 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N SER I 365 " --> pdb=" O VAL I 312 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 185 through 187 removed outlier: 7.418A pdb=" N THR I 186 " --> pdb=" O TRP I 225 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N ASN I 227 " --> pdb=" O THR I 186 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N HIS I 224 " --> pdb=" O TYR I 250 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N MET I 252 " --> pdb=" O HIS I 224 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU I 226 " --> pdb=" O MET I 252 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N ASP I 254 " --> pdb=" O LEU I 226 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE I 251 " --> pdb=" O HIS I 278 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N HIS I 280 " --> pdb=" O ILE I 251 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL I 253 " --> pdb=" O HIS I 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'I' and resid 339 through 340 Processing sheet with id=AD8, first strand: chain 'J' and resid 76 through 80 removed outlier: 5.780A pdb=" N CYS J 77 " --> pdb=" O ALA J 88 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ALA J 88 " --> pdb=" O CYS J 77 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG J 79 " --> pdb=" O TYR J 86 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU J 30 " --> pdb=" O MET J 124 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N MET J 124 " --> pdb=" O LEU J 30 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA J 32 " --> pdb=" O GLU J 122 " (cutoff:3.500A) removed outlier: 8.728A pdb=" N GLY J 294 " --> pdb=" O GLN J 117 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU J 119 " --> pdb=" O GLY J 294 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 155 through 157 removed outlier: 6.251A pdb=" N VAL J 312 " --> pdb=" O VAL J 363 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N HIS J 313 " --> pdb=" O CYS J 279 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE J 251 " --> pdb=" O HIS J 278 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N HIS J 280 " --> pdb=" O ILE J 251 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL J 253 " --> pdb=" O HIS J 280 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 185 through 187 removed outlier: 7.323A pdb=" N THR J 186 " --> pdb=" O TRP J 225 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'J' and resid 339 through 340 Processing sheet with id=AE3, first strand: chain 'K' and resid 76 through 80 removed outlier: 5.953A pdb=" N CYS K 77 " --> pdb=" O ALA K 88 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ALA K 88 " --> pdb=" O CYS K 77 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU K 30 " --> pdb=" O MET K 124 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N MET K 124 " --> pdb=" O LEU K 30 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA K 32 " --> pdb=" O GLU K 122 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 155 through 157 removed outlier: 6.923A pdb=" N LEU K 155 " --> pdb=" O PHE K 386 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N PHE K 388 " --> pdb=" O LEU K 155 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLY K 157 " --> pdb=" O PHE K 388 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY K 366 " --> pdb=" O LEU K 387 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N VAL K 312 " --> pdb=" O VAL K 363 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N SER K 365 " --> pdb=" O VAL K 312 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 186 through 187 removed outlier: 7.672A pdb=" N THR K 186 " --> pdb=" O TRP K 225 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'K' and resid 250 through 254 removed outlier: 6.257A pdb=" N ILE K 251 " --> pdb=" O HIS K 278 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N HIS K 280 " --> pdb=" O ILE K 251 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL K 253 " --> pdb=" O HIS K 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'K' and resid 339 through 340 Processing sheet with id=AE8, first strand: chain 'L' and resid 76 through 80 removed outlier: 5.979A pdb=" N CYS L 77 " --> pdb=" O ALA L 88 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ALA L 88 " --> pdb=" O CYS L 77 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG L 79 " --> pdb=" O TYR L 86 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU L 30 " --> pdb=" O MET L 124 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N MET L 124 " --> pdb=" O LEU L 30 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ALA L 32 " --> pdb=" O GLU L 122 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 185 through 187 removed outlier: 7.407A pdb=" N THR L 186 " --> pdb=" O TRP L 225 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N ASN L 227 " --> pdb=" O THR L 186 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N HIS L 224 " --> pdb=" O TYR L 250 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N MET L 252 " --> pdb=" O HIS L 224 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N LEU L 226 " --> pdb=" O MET L 252 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ASP L 254 " --> pdb=" O LEU L 226 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N HIS L 313 " --> pdb=" O CYS L 279 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL L 312 " --> pdb=" O VAL L 363 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N SER L 365 " --> pdb=" O VAL L 312 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 339 through 340 Processing sheet with id=AF2, first strand: chain 'M' and resid 76 through 80 removed outlier: 6.079A pdb=" N CYS M 77 " --> pdb=" O ALA M 88 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ALA M 88 " --> pdb=" O CYS M 77 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG M 79 " --> pdb=" O TYR M 86 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU M 30 " --> pdb=" O MET M 124 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N MET M 124 " --> pdb=" O LEU M 30 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ALA M 32 " --> pdb=" O GLU M 122 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA M 118 " --> pdb=" O THR M 36 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N GLY M 294 " --> pdb=" O GLN M 117 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU M 119 " --> pdb=" O GLY M 294 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 223 through 225 removed outlier: 7.448A pdb=" N THR M 186 " --> pdb=" O TRP M 225 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU M 156 " --> pdb=" O THR M 185 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N KCX M 187 " --> pdb=" O LEU M 156 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N GLY M 158 " --> pdb=" O KCX M 187 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU M 155 " --> pdb=" O PHE M 386 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL M 312 " --> pdb=" O VAL M 363 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N HIS M 313 " --> pdb=" O CYS M 279 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE M 251 " --> pdb=" O HIS M 278 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N HIS M 280 " --> pdb=" O ILE M 251 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL M 253 " --> pdb=" O HIS M 280 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 339 through 340 Processing sheet with id=AF5, first strand: chain 'N' and resid 76 through 80 removed outlier: 5.766A pdb=" N CYS N 77 " --> pdb=" O ALA N 88 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ALA N 88 " --> pdb=" O CYS N 77 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG N 79 " --> pdb=" O TYR N 86 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ARG N 34 " --> pdb=" O LEU N 121 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N LEU N 121 " --> pdb=" O ARG N 34 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N THR N 36 " --> pdb=" O LEU N 119 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N LEU N 119 " --> pdb=" O THR N 36 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'N' and resid 155 through 157 removed outlier: 7.893A pdb=" N LEU N 387 " --> pdb=" O PRO N 362 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ALA N 364 " --> pdb=" O LEU N 387 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N LEU N 277 " --> pdb=" O HIS N 311 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE N 251 " --> pdb=" O HIS N 278 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N HIS N 280 " --> pdb=" O ILE N 251 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL N 253 " --> pdb=" O HIS N 280 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'N' and resid 185 through 187 removed outlier: 7.376A pdb=" N THR N 186 " --> pdb=" O TRP N 225 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'N' and resid 339 through 340 Processing sheet with id=AF9, first strand: chain 'O' and resid 76 through 81 removed outlier: 5.739A pdb=" N CYS O 77 " --> pdb=" O ALA O 88 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ALA O 88 " --> pdb=" O CYS O 77 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG O 79 " --> pdb=" O TYR O 86 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU O 30 " --> pdb=" O MET O 124 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N MET O 124 " --> pdb=" O LEU O 30 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA O 32 " --> pdb=" O GLU O 122 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY O 294 " --> pdb=" O LEU O 119 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'O' and resid 223 through 225 removed outlier: 7.607A pdb=" N THR O 186 " --> pdb=" O TRP O 225 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL O 312 " --> pdb=" O VAL O 363 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N SER O 365 " --> pdb=" O VAL O 312 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N HIS O 311 " --> pdb=" O LEU O 277 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N HIS O 313 " --> pdb=" O CYS O 279 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE O 251 " --> pdb=" O HIS O 278 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N HIS O 280 " --> pdb=" O ILE O 251 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL O 253 " --> pdb=" O HIS O 280 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'O' and resid 339 through 340 Processing sheet with id=AG3, first strand: chain 'P' and resid 76 through 80 removed outlier: 6.015A pdb=" N CYS P 77 " --> pdb=" O ALA P 88 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA P 88 " --> pdb=" O CYS P 77 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG P 79 " --> pdb=" O TYR P 86 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU P 30 " --> pdb=" O MET P 124 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N MET P 124 " --> pdb=" O LEU P 30 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ALA P 32 " --> pdb=" O GLU P 122 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'P' and resid 155 through 157 removed outlier: 6.534A pdb=" N LEU P 155 " --> pdb=" O PHE P 386 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL P 312 " --> pdb=" O VAL P 363 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N HIS P 313 " --> pdb=" O CYS P 279 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE P 251 " --> pdb=" O HIS P 278 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N HIS P 280 " --> pdb=" O ILE P 251 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL P 253 " --> pdb=" O HIS P 280 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'P' and resid 186 through 187 removed outlier: 7.613A pdb=" N THR P 186 " --> pdb=" O TRP P 225 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'P' and resid 339 through 340 2467 hydrogen bonds defined for protein. 6939 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: 25.65 Time building geometry restraints manager: 12.43 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: 17629 1.33 - 1.45: 9284 1.45 - 1.57: 30614 1.57 - 1.69: 1 1.69 - 1.81: 432 Bond restraints: 57960 Sorted by residual: bond pdb=" O5 CAP F 501 " pdb=" P2 CAP F 501 " ideal model delta sigma weight residual 1.610 1.758 -0.148 2.00e-02 2.50e+03 5.46e+01 bond pdb=" O5 CAP L 501 " pdb=" P2 CAP L 501 " ideal model delta sigma weight residual 1.610 1.757 -0.147 2.00e-02 2.50e+03 5.37e+01 bond pdb=" O5 CAP D 501 " pdb=" P2 CAP D 501 " ideal model delta sigma weight residual 1.610 1.756 -0.146 2.00e-02 2.50e+03 5.33e+01 bond pdb=" O5 CAP H 501 " pdb=" P2 CAP H 501 " ideal model delta sigma weight residual 1.610 1.756 -0.146 2.00e-02 2.50e+03 5.30e+01 bond pdb=" O5 CAP B 501 " pdb=" P2 CAP B 501 " ideal model delta sigma weight residual 1.610 1.755 -0.145 2.00e-02 2.50e+03 5.27e+01 ... (remaining 57955 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 77607 2.57 - 5.14: 776 5.14 - 7.72: 152 7.72 - 10.29: 40 10.29 - 12.86: 25 Bond angle restraints: 78600 Sorted by residual: angle pdb=" CA PRO H 439 " pdb=" N PRO H 439 " pdb=" CD PRO H 439 " ideal model delta sigma weight residual 112.00 104.66 7.34 1.40e+00 5.10e-01 2.75e+01 angle pdb=" O5 CAP E 501 " pdb=" P2 CAP E 501 " pdb=" O6P CAP E 501 " ideal model delta sigma weight residual 109.50 96.64 12.86 3.00e+00 1.11e-01 1.84e+01 angle pdb=" CA THR M 56 " pdb=" C THR M 56 " pdb=" N GLY M 57 " ideal model delta sigma weight residual 116.84 123.55 -6.71 1.71e+00 3.42e-01 1.54e+01 angle pdb=" O5 CAP I 501 " pdb=" P2 CAP I 501 " pdb=" O6P CAP I 501 " ideal model delta sigma weight residual 109.50 97.98 11.52 3.00e+00 1.11e-01 1.47e+01 angle pdb=" O1 CAP I 501 " pdb=" P1 CAP I 501 " pdb=" O3P CAP I 501 " ideal model delta sigma weight residual 109.50 98.09 11.41 3.00e+00 1.11e-01 1.45e+01 ... (remaining 78595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.43: 33461 34.43 - 68.86: 630 68.86 - 103.30: 48 103.30 - 137.73: 13 137.73 - 172.16: 16 Dihedral angle restraints: 34168 sinusoidal: 13920 harmonic: 20248 Sorted by residual: dihedral pdb=" C3 CAP P 501 " pdb=" C CAP P 501 " pdb=" C2 CAP P 501 " pdb=" O6 CAP P 501 " ideal model delta sinusoidal sigma weight residual 81.86 -105.98 -172.16 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C3 CAP J 501 " pdb=" C CAP J 501 " pdb=" C2 CAP J 501 " pdb=" O6 CAP J 501 " ideal model delta sinusoidal sigma weight residual 81.86 -106.99 -171.15 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" C3 CAP D 501 " pdb=" C CAP D 501 " pdb=" C2 CAP D 501 " pdb=" O6 CAP D 501 " ideal model delta sinusoidal sigma weight residual 81.86 -107.51 -170.62 1 2.00e+01 2.50e-03 4.77e+01 ... (remaining 34165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 5781 0.039 - 0.078: 1903 0.078 - 0.116: 499 0.116 - 0.155: 61 0.155 - 0.194: 4 Chirality restraints: 8248 Sorted by residual: chirality pdb=" CG LEU B 304 " pdb=" CB LEU B 304 " pdb=" CD1 LEU B 304 " pdb=" CD2 LEU B 304 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.39e-01 chirality pdb=" CA PRO H 439 " pdb=" N PRO H 439 " pdb=" C PRO H 439 " pdb=" CB PRO H 439 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.91e-01 chirality pdb=" CB ILE M 379 " pdb=" CA ILE M 379 " pdb=" CG1 ILE M 379 " pdb=" CG2 ILE M 379 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.33e-01 ... (remaining 8245 not shown) Planarity restraints: 10328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS H 438 " 0.074 5.00e-02 4.00e+02 1.07e-01 1.84e+01 pdb=" N PRO H 439 " -0.185 5.00e-02 4.00e+02 pdb=" CA PRO H 439 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO H 439 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS I 438 " 0.032 5.00e-02 4.00e+02 4.88e-02 3.82e+00 pdb=" N PRO I 439 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO I 439 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO I 439 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS O 358 " -0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO O 359 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO O 359 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO O 359 " -0.026 5.00e-02 4.00e+02 ... (remaining 10325 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 612 2.55 - 3.14: 43311 3.14 - 3.72: 91760 3.72 - 4.31: 137456 4.31 - 4.90: 230294 Nonbonded interactions: 503433 Sorted by model distance: nonbonded pdb=" OD1 ASP O 189 " pdb="MG MG O 502 " model vdw 1.960 2.170 nonbonded pdb=" OD1 ASP M 189 " pdb="MG MG M 502 " model vdw 1.963 2.170 nonbonded pdb=" O3 CAP O 501 " pdb="MG MG O 502 " model vdw 1.981 2.170 nonbonded pdb=" OD1 ASP P 189 " pdb="MG MG P 502 " model vdw 1.991 2.170 nonbonded pdb=" OE1 GLU C 190 " pdb="MG MG C 502 " model vdw 1.993 2.170 ... (remaining 503428 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 6 through 449 or resid 501 through 502)) selection = chain 'C' selection = (chain 'D' and (resid 6 through 449 or resid 501 through 502)) selection = chain 'E' selection = (chain 'F' and (resid 6 through 449 or resid 501 through 502)) selection = chain 'G' selection = (chain 'H' and (resid 6 through 449 or resid 501 through 502)) selection = (chain 'I' and (resid 6 through 449 or resid 501 through 502)) selection = chain 'J' selection = (chain 'K' and (resid 6 through 449 or resid 501 through 502)) selection = chain 'L' selection = (chain 'M' and (resid 6 through 449 or resid 501 through 502)) selection = chain 'N' selection = (chain 'O' and (resid 6 through 449 or resid 501 through 502)) selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.270 Construct map_model_manager: 0.080 Extract box with map and model: 1.770 Check model and map are aligned: 0.310 Set scattering table: 0.410 Process input model: 102.300 Find NCS groups from input model: 2.670 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:11.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 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 : 0.005 0.148 57960 Z= 0.328 Angle : 0.730 12.860 78600 Z= 0.373 Chirality : 0.040 0.194 8248 Planarity : 0.004 0.107 10328 Dihedral : 14.799 172.159 21288 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.28 (0.10), residues: 7048 helix: -0.90 (0.09), residues: 3032 sheet: -0.60 (0.16), residues: 920 loop : -0.66 (0.11), residues: 3096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 437 HIS 0.006 0.001 HIS F 284 PHE 0.019 0.002 PHE E 287 TYR 0.018 0.001 TYR A 250 ARG 0.024 0.000 ARG N 268 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14096 Ramachandran restraints generated. 7048 Oldfield, 0 Emsley, 7048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14096 Ramachandran restraints generated. 7048 Oldfield, 0 Emsley, 7048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 5664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 700 time to evaluate : 4.727 Fit side-chains revert: symmetry clash REVERT: A 149 ASN cc_start: 0.8815 (t0) cc_final: 0.8614 (t0) REVERT: B 190 GLU cc_start: 0.8226 (pm20) cc_final: 0.7512 (pm20) REVERT: B 220 GLU cc_start: 0.8098 (mp0) cc_final: 0.7866 (mp0) REVERT: B 437 TRP cc_start: 0.7052 (p-90) cc_final: 0.6411 (m100) REVERT: C 61 GLU cc_start: 0.7409 (mm-30) cc_final: 0.7001 (tp30) REVERT: C 124 MET cc_start: 0.7569 (ttp) cc_final: 0.7335 (ttp) REVERT: C 433 GLU cc_start: 0.7526 (mp0) cc_final: 0.7292 (mp0) REVERT: E 149 ASN cc_start: 0.8915 (t0) cc_final: 0.8596 (t0) REVERT: E 159 THR cc_start: 0.8963 (m) cc_final: 0.8725 (m) REVERT: E 415 GLN cc_start: 0.8121 (tm-30) cc_final: 0.7526 (tp-100) REVERT: F 144 GLU cc_start: 0.7317 (tt0) cc_final: 0.7073 (tt0) REVERT: F 159 THR cc_start: 0.8162 (m) cc_final: 0.7943 (m) REVERT: F 290 GLN cc_start: 0.8406 (mm110) cc_final: 0.8140 (mp10) REVERT: G 415 GLN cc_start: 0.8340 (tm-30) cc_final: 0.8005 (tm-30) REVERT: G 419 GLU cc_start: 0.7730 (pt0) cc_final: 0.7486 (pt0) REVERT: H 306 MET cc_start: 0.8618 (mtp) cc_final: 0.8305 (mtp) REVERT: I 11 ARG cc_start: 0.7984 (mtt180) cc_final: 0.7675 (mmp80) REVERT: I 415 GLN cc_start: 0.8176 (tm-30) cc_final: 0.7892 (tm-30) REVERT: J 149 ASN cc_start: 0.8927 (t0) cc_final: 0.8683 (t0) REVERT: L 316 THR cc_start: 0.8308 (p) cc_final: 0.8100 (p) REVERT: L 337 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7789 (tt0) REVERT: L 436 ARG cc_start: 0.7801 (mtm110) cc_final: 0.7588 (ttp80) REVERT: M 428 ARG cc_start: 0.7657 (mmm160) cc_final: 0.7205 (mmt-90) REVERT: N 337 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7706 (mm-30) REVERT: P 375 ASP cc_start: 0.7908 (m-30) cc_final: 0.7645 (m-30) outliers start: 0 outliers final: 0 residues processed: 700 average time/residue: 1.6031 time to fit residues: 1385.4127 Evaluate side-chains 473 residues out of total 5664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 473 time to evaluate : 4.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 704 random chunks: chunk 594 optimal weight: 0.9990 chunk 533 optimal weight: 0.9980 chunk 296 optimal weight: 0.9990 chunk 182 optimal weight: 0.9980 chunk 359 optimal weight: 8.9990 chunk 285 optimal weight: 10.0000 chunk 551 optimal weight: 2.9990 chunk 213 optimal weight: 7.9990 chunk 335 optimal weight: 0.9990 chunk 410 optimal weight: 5.9990 chunk 639 optimal weight: 2.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 117 GLN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN ** B 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 ASN ** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 GLN E 293 HIS ** E 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 393 HIS ** F 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 149 ASN ** G 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 191 ASN I 311 HIS J 109 ASN J 117 GLN J 142 GLN ** J 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 142 GLN ** K 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 ASN L 393 HIS M 109 ASN ** M 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 117 GLN ** O 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 415 GLN P 193 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.111003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.094986 restraints weight = 79461.680| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.96 r_work: 0.2981 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 57960 Z= 0.197 Angle : 0.566 9.116 78600 Z= 0.293 Chirality : 0.041 0.164 8248 Planarity : 0.005 0.050 10328 Dihedral : 9.417 179.767 8208 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.20 % Allowed : 8.09 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.10), residues: 7048 helix: 0.38 (0.09), residues: 2968 sheet: -0.36 (0.18), residues: 832 loop : -0.51 (0.11), residues: 3248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 437 HIS 0.005 0.001 HIS A 311 PHE 0.019 0.001 PHE B 297 TYR 0.016 0.001 TYR H 17 ARG 0.009 0.000 ARG I 428 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14096 Ramachandran restraints generated. 7048 Oldfield, 0 Emsley, 7048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14096 Ramachandran restraints generated. 7048 Oldfield, 0 Emsley, 7048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 5664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 562 time to evaluate : 4.699 Fit side-chains revert: symmetry clash REVERT: A 7 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7640 (tt0) REVERT: A 13 TYR cc_start: 0.8122 (OUTLIER) cc_final: 0.7219 (m-80) REVERT: A 149 ASN cc_start: 0.8966 (t0) cc_final: 0.8724 (t0) REVERT: B 190 GLU cc_start: 0.8586 (pm20) cc_final: 0.7978 (pm20) REVERT: B 220 GLU cc_start: 0.8506 (mp0) cc_final: 0.8114 (mp0) REVERT: B 437 TRP cc_start: 0.7097 (p-90) cc_final: 0.6370 (m100) REVERT: C 61 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7348 (tp30) REVERT: C 424 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7932 (mm) REVERT: C 433 GLU cc_start: 0.8141 (mp0) cc_final: 0.7854 (mp0) REVERT: C 436 ARG cc_start: 0.8615 (mtm110) cc_final: 0.8341 (mtp85) REVERT: D 146 ASP cc_start: 0.7959 (m-30) cc_final: 0.7688 (m-30) REVERT: D 205 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8406 (mp) REVERT: E 252 MET cc_start: 0.8841 (ttt) cc_final: 0.8623 (ttt) REVERT: E 346 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8317 (mtm180) REVERT: E 415 GLN cc_start: 0.8306 (tm-30) cc_final: 0.7613 (tp-100) REVERT: F 159 THR cc_start: 0.8238 (m) cc_final: 0.8027 (m) REVERT: F 361 PHE cc_start: 0.9135 (OUTLIER) cc_final: 0.8750 (m-80) REVERT: G 415 GLN cc_start: 0.8657 (tm-30) cc_final: 0.8157 (tm-30) REVERT: G 419 GLU cc_start: 0.8054 (pt0) cc_final: 0.7800 (pt0) REVERT: H 245 GLU cc_start: 0.8702 (pp20) cc_final: 0.8489 (tm-30) REVERT: H 306 MET cc_start: 0.8871 (mtp) cc_final: 0.8614 (mtp) REVERT: H 375 ASP cc_start: 0.8052 (OUTLIER) cc_final: 0.7665 (t0) REVERT: I 11 ARG cc_start: 0.8380 (mtt180) cc_final: 0.7659 (mmp80) REVERT: I 117 GLN cc_start: 0.8296 (mm110) cc_final: 0.8056 (mm110) REVERT: I 415 GLN cc_start: 0.8466 (tm-30) cc_final: 0.7923 (tm-30) REVERT: I 419 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8319 (mt-10) REVERT: J 149 ASN cc_start: 0.9137 (t0) cc_final: 0.8835 (t0) REVERT: K 142 GLN cc_start: 0.7815 (mm-40) cc_final: 0.7563 (mp-120) REVERT: K 198 ASN cc_start: 0.8420 (t0) cc_final: 0.8191 (t0) REVERT: K 241 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7884 (mt-10) REVERT: K 269 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.7466 (tpt-90) REVERT: L 337 GLU cc_start: 0.8582 (mm-30) cc_final: 0.7851 (tt0) REVERT: L 446 GLU cc_start: 0.8273 (tm-30) cc_final: 0.7870 (tm-30) REVERT: N 163 LYS cc_start: 0.8277 (tttm) cc_final: 0.8040 (tttt) REVERT: O 102 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8529 (tt) REVERT: O 208 MET cc_start: 0.8634 (mmt) cc_final: 0.8371 (mmp) REVERT: P 205 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8599 (mt) REVERT: P 375 ASP cc_start: 0.8522 (m-30) cc_final: 0.8254 (m-30) outliers start: 68 outliers final: 13 residues processed: 602 average time/residue: 1.4475 time to fit residues: 1097.1732 Evaluate side-chains 500 residues out of total 5664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 478 time to evaluate : 4.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 TYR Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain E residue 346 ARG Chi-restraints excluded: chain F residue 15 GLU Chi-restraints excluded: chain F residue 361 PHE Chi-restraints excluded: chain G residue 424 LEU Chi-restraints excluded: chain H residue 186 THR Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain H residue 375 ASP Chi-restraints excluded: chain I residue 358 LYS Chi-restraints excluded: chain K residue 269 ARG Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain N residue 72 ARG Chi-restraints excluded: chain N residue 338 ASP Chi-restraints excluded: chain O residue 102 ILE Chi-restraints excluded: chain P residue 205 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 704 random chunks: chunk 88 optimal weight: 20.0000 chunk 165 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 256 optimal weight: 6.9990 chunk 421 optimal weight: 4.9990 chunk 181 optimal weight: 4.9990 chunk 305 optimal weight: 5.9990 chunk 205 optimal weight: 3.9990 chunk 586 optimal weight: 5.9990 chunk 342 optimal weight: 9.9990 chunk 353 optimal weight: 0.3980 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN A 406 ASN B 101 ASN B 195 GLN ** B 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 GLN ** E 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 393 HIS ** G 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 GLN ** H 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 101 ASN I 193 ASN ** I 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 109 ASN J 117 GLN J 142 GLN ** J 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 406 ASN ** K 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 393 HIS O 117 GLN ** O 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 415 GLN P 117 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.106336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.090283 restraints weight = 81176.373| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 1.94 r_work: 0.2915 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 57960 Z= 0.439 Angle : 0.629 8.622 78600 Z= 0.321 Chirality : 0.045 0.199 8248 Planarity : 0.005 0.050 10328 Dihedral : 9.144 179.137 8208 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.87 % Allowed : 10.79 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.10), residues: 7048 helix: 0.56 (0.09), residues: 2976 sheet: -0.37 (0.17), residues: 832 loop : -0.54 (0.11), residues: 3240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K 200 HIS 0.006 0.001 HIS I 311 PHE 0.021 0.002 PHE J 113 TYR 0.017 0.002 TYR D 250 ARG 0.008 0.000 ARG G 436 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14096 Ramachandran restraints generated. 7048 Oldfield, 0 Emsley, 7048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14096 Ramachandran restraints generated. 7048 Oldfield, 0 Emsley, 7048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 5664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 501 time to evaluate : 4.820 Fit side-chains REVERT: A 7 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7718 (tt0) REVERT: A 13 TYR cc_start: 0.8151 (OUTLIER) cc_final: 0.7273 (m-80) REVERT: A 149 ASN cc_start: 0.9002 (t0) cc_final: 0.8756 (t0) REVERT: A 209 GLU cc_start: 0.8656 (tp30) cc_final: 0.8338 (tp30) REVERT: A 250 TYR cc_start: 0.9044 (m-80) cc_final: 0.8768 (m-80) REVERT: A 276 MET cc_start: 0.8739 (mtp) cc_final: 0.8350 (mtp) REVERT: B 220 GLU cc_start: 0.8578 (mp0) cc_final: 0.8199 (mp0) REVERT: B 437 TRP cc_start: 0.7168 (p-90) cc_final: 0.6432 (m100) REVERT: C 433 GLU cc_start: 0.8286 (mp0) cc_final: 0.7878 (mp0) REVERT: C 436 ARG cc_start: 0.8599 (mtm110) cc_final: 0.8311 (mtp85) REVERT: D 146 ASP cc_start: 0.8034 (m-30) cc_final: 0.7755 (m-30) REVERT: E 23 GLU cc_start: 0.8215 (tt0) cc_final: 0.7764 (pm20) REVERT: E 252 MET cc_start: 0.9101 (ttt) cc_final: 0.8895 (ttt) REVERT: E 346 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8228 (mtm180) REVERT: E 415 GLN cc_start: 0.8372 (tm-30) cc_final: 0.7572 (tp-100) REVERT: F 159 THR cc_start: 0.8340 (m) cc_final: 0.8132 (m) REVERT: F 276 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.8445 (ttm) REVERT: F 361 PHE cc_start: 0.9191 (OUTLIER) cc_final: 0.8873 (m-80) REVERT: G 415 GLN cc_start: 0.8748 (tm-30) cc_final: 0.8018 (tm-30) REVERT: H 440 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8071 (tp30) REVERT: I 11 ARG cc_start: 0.8429 (mtt180) cc_final: 0.7711 (mmp80) REVERT: I 250 TYR cc_start: 0.8422 (m-80) cc_final: 0.8146 (m-80) REVERT: I 283 MET cc_start: 0.9164 (ttt) cc_final: 0.8961 (ttt) REVERT: I 415 GLN cc_start: 0.8433 (tm-30) cc_final: 0.7775 (tm-30) REVERT: I 419 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8217 (mt-10) REVERT: I 436 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.8093 (mtp180) REVERT: J 212 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.7982 (mtp180) REVERT: K 142 GLN cc_start: 0.7926 (mm-40) cc_final: 0.7712 (mp-120) REVERT: K 269 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7494 (tpt-90) REVERT: K 333 ASP cc_start: 0.8385 (m-30) cc_final: 0.8182 (m-30) REVERT: L 337 GLU cc_start: 0.8672 (mm-30) cc_final: 0.7908 (tt0) REVERT: O 102 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8570 (tt) REVERT: P 109 ASN cc_start: 0.8466 (OUTLIER) cc_final: 0.8243 (t0) REVERT: P 205 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8619 (mt) REVERT: P 245 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8140 (mt-10) REVERT: P 375 ASP cc_start: 0.8534 (m-30) cc_final: 0.8233 (m-30) outliers start: 106 outliers final: 31 residues processed: 561 average time/residue: 1.5568 time to fit residues: 1090.2058 Evaluate side-chains 495 residues out of total 5664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 452 time to evaluate : 4.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 TYR Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 358 LYS Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 346 ARG Chi-restraints excluded: chain F residue 276 MET Chi-restraints excluded: chain F residue 361 PHE Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 424 LEU Chi-restraints excluded: chain H residue 126 ILE Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 440 GLU Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 146 ASP Chi-restraints excluded: chain I residue 423 ILE Chi-restraints excluded: chain I residue 424 LEU Chi-restraints excluded: chain I residue 436 ARG Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 212 ARG Chi-restraints excluded: chain J residue 265 SER Chi-restraints excluded: chain K residue 269 ARG Chi-restraints excluded: chain K residue 375 ASP Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 307 VAL Chi-restraints excluded: chain L residue 317 VAL Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 245 GLU Chi-restraints excluded: chain M residue 288 ASP Chi-restraints excluded: chain N residue 72 ARG Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 338 ASP Chi-restraints excluded: chain O residue 102 ILE Chi-restraints excluded: chain P residue 60 THR Chi-restraints excluded: chain P residue 109 ASN Chi-restraints excluded: chain P residue 205 LEU Chi-restraints excluded: chain P residue 245 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 704 random chunks: chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 125 optimal weight: 0.7980 chunk 242 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 432 optimal weight: 0.8980 chunk 327 optimal weight: 0.8980 chunk 269 optimal weight: 10.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN B 195 GLN ** B 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 GLN ** G 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 ASN H 406 ASN I 191 ASN J 117 GLN J 142 GLN ** J 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 290 GLN ** K 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 117 GLN O 311 HIS O 415 GLN P 117 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.110743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.094799 restraints weight = 79878.081| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.95 r_work: 0.2985 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 57960 Z= 0.166 Angle : 0.513 7.574 78600 Z= 0.264 Chirality : 0.040 0.198 8248 Planarity : 0.004 0.039 10328 Dihedral : 8.717 178.769 8208 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.57 % Allowed : 12.68 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.10), residues: 7048 helix: 1.02 (0.10), residues: 2984 sheet: -0.28 (0.17), residues: 872 loop : -0.43 (0.11), residues: 3192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 437 HIS 0.007 0.001 HIS A 311 PHE 0.016 0.001 PHE A 297 TYR 0.016 0.001 TYR K 250 ARG 0.008 0.000 ARG I 442 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14096 Ramachandran restraints generated. 7048 Oldfield, 0 Emsley, 7048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14096 Ramachandran restraints generated. 7048 Oldfield, 0 Emsley, 7048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 5664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 531 time to evaluate : 4.799 Fit side-chains revert: symmetry clash REVERT: A 7 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7724 (tt0) REVERT: A 13 TYR cc_start: 0.7905 (OUTLIER) cc_final: 0.7161 (m-80) REVERT: A 250 TYR cc_start: 0.8958 (m-80) cc_final: 0.8704 (m-80) REVERT: B 61 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7695 (mt-10) REVERT: B 190 GLU cc_start: 0.8540 (pm20) cc_final: 0.8002 (pm20) REVERT: B 220 GLU cc_start: 0.8566 (mp0) cc_final: 0.8148 (mp0) REVERT: B 437 TRP cc_start: 0.7161 (p-90) cc_final: 0.6396 (m100) REVERT: C 61 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7280 (tp30) REVERT: C 433 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7947 (mt-10) REVERT: C 436 ARG cc_start: 0.8616 (mtm110) cc_final: 0.8289 (mtp85) REVERT: D 146 ASP cc_start: 0.7916 (m-30) cc_final: 0.7645 (m-30) REVERT: D 419 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7474 (mt-10) REVERT: E 23 GLU cc_start: 0.8298 (tt0) cc_final: 0.7842 (pm20) REVERT: E 107 VAL cc_start: 0.9199 (m) cc_final: 0.8931 (p) REVERT: E 234 GLU cc_start: 0.8311 (mp0) cc_final: 0.7817 (mp0) REVERT: E 252 MET cc_start: 0.8921 (ttt) cc_final: 0.8692 (ttt) REVERT: E 415 GLN cc_start: 0.8252 (tm-30) cc_final: 0.7379 (tp-100) REVERT: F 159 THR cc_start: 0.8206 (m) cc_final: 0.7971 (m) REVERT: G 415 GLN cc_start: 0.8665 (tm-30) cc_final: 0.8057 (tm-30) REVERT: G 419 GLU cc_start: 0.8035 (pt0) cc_final: 0.7632 (pt0) REVERT: G 445 MET cc_start: 0.9090 (mtp) cc_final: 0.8818 (mtm) REVERT: H 109 ASN cc_start: 0.8235 (OUTLIER) cc_final: 0.7944 (t160) REVERT: H 283 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.8518 (ttm) REVERT: H 375 ASP cc_start: 0.8170 (OUTLIER) cc_final: 0.7840 (t0) REVERT: H 440 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7990 (tp30) REVERT: I 11 ARG cc_start: 0.8442 (mtt180) cc_final: 0.7699 (mmp80) REVERT: I 415 GLN cc_start: 0.8390 (tm-30) cc_final: 0.7704 (tm-30) REVERT: I 419 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8195 (mt-10) REVERT: I 436 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.8194 (mtp180) REVERT: J 10 VAL cc_start: 0.9163 (t) cc_final: 0.8880 (p) REVERT: K 198 ASN cc_start: 0.8426 (t0) cc_final: 0.8212 (t0) REVERT: K 241 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7837 (mt-10) REVERT: K 269 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7454 (tpt-90) REVERT: K 424 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8128 (mt) REVERT: K 436 ARG cc_start: 0.8543 (mmm160) cc_final: 0.8333 (mmm-85) REVERT: K 445 MET cc_start: 0.8399 (ttp) cc_final: 0.8074 (mtm) REVERT: L 72 ARG cc_start: 0.8789 (mtp180) cc_final: 0.8445 (mtp-110) REVERT: L 142 GLN cc_start: 0.8397 (mp10) cc_final: 0.8093 (mp10) REVERT: L 144 GLU cc_start: 0.8693 (tt0) cc_final: 0.8469 (tt0) REVERT: L 337 GLU cc_start: 0.8566 (mm-30) cc_final: 0.7836 (tt0) REVERT: L 411 GLU cc_start: 0.8424 (tp30) cc_final: 0.8061 (mt-10) REVERT: L 436 ARG cc_start: 0.8364 (ttp80) cc_final: 0.7458 (tmm160) REVERT: N 163 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8045 (tttt) REVERT: P 205 LEU cc_start: 0.8946 (tp) cc_final: 0.8613 (mt) REVERT: P 375 ASP cc_start: 0.8523 (m-30) cc_final: 0.8214 (m-30) REVERT: P 432 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8005 (mt-10) outliers start: 89 outliers final: 23 residues processed: 590 average time/residue: 1.5198 time to fit residues: 1122.0359 Evaluate side-chains 511 residues out of total 5664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 477 time to evaluate : 4.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 TYR Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 358 LYS Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 358 LYS Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 436 ARG Chi-restraints excluded: chain G residue 424 LEU Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 283 MET Chi-restraints excluded: chain H residue 375 ASP Chi-restraints excluded: chain H residue 440 GLU Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain I residue 436 ARG Chi-restraints excluded: chain J residue 186 THR Chi-restraints excluded: chain J residue 232 SER Chi-restraints excluded: chain J residue 245 GLU Chi-restraints excluded: chain K residue 269 ARG Chi-restraints excluded: chain K residue 424 LEU Chi-restraints excluded: chain L residue 307 VAL Chi-restraints excluded: chain M residue 7 GLU Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain N residue 72 ARG Chi-restraints excluded: chain N residue 163 LYS Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain P residue 173 ARG Chi-restraints excluded: chain P residue 185 THR Chi-restraints excluded: chain P residue 432 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- 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: 70.4266 > 50: distance: 20 - 44: 37.514 distance: 39 - 44: 34.258 distance: 44 - 45: 29.197 distance: 45 - 46: 17.306 distance: 45 - 48: 22.010 distance: 46 - 47: 26.601 distance: 46 - 53: 8.715 distance: 48 - 49: 44.598 distance: 49 - 50: 20.402 distance: 50 - 51: 11.732 distance: 51 - 52: 5.073 distance: 53 - 54: 15.340 distance: 54 - 55: 48.695 distance: 54 - 57: 27.278 distance: 55 - 56: 47.982 distance: 57 - 58: 23.899 distance: 57 - 59: 22.027 distance: 60 - 61: 21.051 distance: 61 - 62: 29.645 distance: 61 - 64: 58.291 distance: 62 - 63: 19.364 distance: 62 - 71: 42.613 distance: 64 - 65: 13.829 distance: 65 - 66: 26.376 distance: 65 - 67: 18.411 distance: 66 - 68: 15.964 distance: 67 - 69: 18.375 distance: 68 - 70: 6.667 distance: 71 - 72: 41.364 distance: 71 - 77: 3.795 distance: 72 - 73: 30.615 distance: 72 - 75: 38.236 distance: 73 - 74: 33.002 distance: 73 - 78: 34.897 distance: 75 - 76: 23.151 distance: 76 - 77: 50.904 distance: 78 - 79: 42.676 distance: 79 - 80: 10.648 distance: 80 - 81: 51.417 distance: 80 - 82: 28.327 distance: 82 - 83: 28.461 distance: 82 - 88: 26.392 distance: 83 - 84: 22.069 distance: 83 - 86: 13.655 distance: 84 - 85: 45.647 distance: 84 - 89: 39.432 distance: 86 - 87: 19.363 distance: 87 - 88: 53.268 distance: 89 - 90: 17.610 distance: 89 - 95: 30.351 distance: 90 - 91: 11.290 distance: 90 - 93: 20.558 distance: 91 - 92: 52.989 distance: 91 - 96: 14.789 distance: 93 - 94: 13.110 distance: 94 - 95: 38.627 distance: 96 - 97: 23.296 distance: 97 - 100: 44.326 distance: 98 - 99: 51.374 distance: 98 - 103: 32.517 distance: 100 - 101: 26.595 distance: 103 - 104: 31.549 distance: 104 - 105: 26.688 distance: 105 - 106: 34.599 distance: 105 - 107: 13.193 distance: 106 - 131: 33.197 distance: 107 - 108: 9.923 distance: 108 - 109: 8.767 distance: 108 - 111: 5.736 distance: 109 - 110: 12.623 distance: 109 - 115: 7.930 distance: 110 - 138: 18.643 distance: 111 - 112: 7.707 distance: 111 - 113: 5.509 distance: 112 - 114: 9.366