Starting phenix.real_space_refine (version: dev) on Tue Feb 21 15:18:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hds_34679/02_2023/8hds_34679.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hds_34679/02_2023/8hds_34679.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hds_34679/02_2023/8hds_34679.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hds_34679/02_2023/8hds_34679.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hds_34679/02_2023/8hds_34679.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hds_34679/02_2023/8hds_34679.pdb" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A ARG 85": "NH1" <-> "NH2" Residue "A PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 157": "NH1" <-> "NH2" Residue "A ARG 247": "NH1" <-> "NH2" Residue "A ARG 306": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ARG 402": "NH1" <-> "NH2" Residue "A ARG 437": "NH1" <-> "NH2" Residue "B ARG 85": "NH1" <-> "NH2" Residue "B PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 157": "NH1" <-> "NH2" Residue "B ARG 247": "NH1" <-> "NH2" Residue "B ARG 306": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B ARG 402": "NH1" <-> "NH2" Residue "B ARG 437": "NH1" <-> "NH2" Residue "C ARG 85": "NH1" <-> "NH2" Residue "C PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 157": "NH1" <-> "NH2" Residue "C ARG 247": "NH1" <-> "NH2" Residue "C ARG 306": "NH1" <-> "NH2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C ARG 402": "NH1" <-> "NH2" Residue "C ARG 437": "NH1" <-> "NH2" Residue "D ARG 85": "NH1" <-> "NH2" Residue "D PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 157": "NH1" <-> "NH2" Residue "D ARG 247": "NH1" <-> "NH2" Residue "D ARG 306": "NH1" <-> "NH2" Residue "D ARG 357": "NH1" <-> "NH2" Residue "D ARG 402": "NH1" <-> "NH2" Residue "D ARG 437": "NH1" <-> "NH2" Residue "E ARG 85": "NH1" <-> "NH2" Residue "E PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 157": "NH1" <-> "NH2" Residue "E ARG 247": "NH1" <-> "NH2" Residue "E ARG 306": "NH1" <-> "NH2" Residue "E ARG 357": "NH1" <-> "NH2" Residue "E ARG 402": "NH1" <-> "NH2" Residue "E ARG 437": "NH1" <-> "NH2" Residue "F ARG 85": "NH1" <-> "NH2" Residue "F PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 157": "NH1" <-> "NH2" Residue "F ARG 247": "NH1" <-> "NH2" Residue "F ARG 306": "NH1" <-> "NH2" Residue "F ARG 357": "NH1" <-> "NH2" Residue "F ARG 402": "NH1" <-> "NH2" Residue "F ARG 437": "NH1" <-> "NH2" Residue "G ARG 85": "NH1" <-> "NH2" Residue "G PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 157": "NH1" <-> "NH2" Residue "G ARG 247": "NH1" <-> "NH2" Residue "G ARG 306": "NH1" <-> "NH2" Residue "G ARG 357": "NH1" <-> "NH2" Residue "G ARG 402": "NH1" <-> "NH2" Residue "G ARG 437": "NH1" <-> "NH2" Residue "H ARG 85": "NH1" <-> "NH2" Residue "H PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 157": "NH1" <-> "NH2" Residue "H ARG 247": "NH1" <-> "NH2" Residue "H ARG 306": "NH1" <-> "NH2" Residue "H ARG 357": "NH1" <-> "NH2" Residue "H ARG 402": "NH1" <-> "NH2" Residue "H ARG 437": "NH1" <-> "NH2" Residue "I ARG 85": "NH1" <-> "NH2" Residue "I PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 157": "NH1" <-> "NH2" Residue "I ARG 247": "NH1" <-> "NH2" Residue "I ARG 306": "NH1" <-> "NH2" Residue "I ARG 357": "NH1" <-> "NH2" Residue "I ARG 402": "NH1" <-> "NH2" Residue "I ARG 437": "NH1" <-> "NH2" Residue "J ARG 85": "NH1" <-> "NH2" Residue "J PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 157": "NH1" <-> "NH2" Residue "J ARG 247": "NH1" <-> "NH2" Residue "J ARG 306": "NH1" <-> "NH2" Residue "J ARG 357": "NH1" <-> "NH2" Residue "J ARG 402": "NH1" <-> "NH2" Residue "J ARG 437": "NH1" <-> "NH2" Residue "K ARG 85": "NH1" <-> "NH2" Residue "K PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 157": "NH1" <-> "NH2" Residue "K ARG 247": "NH1" <-> "NH2" Residue "K ARG 306": "NH1" <-> "NH2" Residue "K ARG 357": "NH1" <-> "NH2" Residue "K ARG 402": "NH1" <-> "NH2" Residue "K ARG 437": "NH1" <-> "NH2" Residue "L ARG 85": "NH1" <-> "NH2" Residue "L PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 157": "NH1" <-> "NH2" Residue "L ARG 247": "NH1" <-> "NH2" Residue "L ARG 306": "NH1" <-> "NH2" Residue "L ARG 357": "NH1" <-> "NH2" Residue "L ARG 402": "NH1" <-> "NH2" Residue "L ARG 437": "NH1" <-> "NH2" Residue "a ARG 65": "NH1" <-> "NH2" Residue "a ARG 119": "NH1" <-> "NH2" Residue "a ARG 122": "NH1" <-> "NH2" Residue "b ARG 65": "NH1" <-> "NH2" Residue "b ARG 119": "NH1" <-> "NH2" Residue "b ARG 122": "NH1" <-> "NH2" Residue "c ARG 65": "NH1" <-> "NH2" Residue "c ARG 119": "NH1" <-> "NH2" Residue "c ARG 122": "NH1" <-> "NH2" Residue "d ARG 65": "NH1" <-> "NH2" Residue "d ARG 119": "NH1" <-> "NH2" Residue "d ARG 122": "NH1" <-> "NH2" Residue "e ARG 65": "NH1" <-> "NH2" Residue "e ARG 119": "NH1" <-> "NH2" Residue "e ARG 122": "NH1" <-> "NH2" Residue "f ARG 65": "NH1" <-> "NH2" Residue "f ARG 119": "NH1" <-> "NH2" Residue "f ARG 122": "NH1" <-> "NH2" Residue "g ARG 65": "NH1" <-> "NH2" Residue "g ARG 119": "NH1" <-> "NH2" Residue "g ARG 122": "NH1" <-> "NH2" Residue "h ARG 65": "NH1" <-> "NH2" Residue "h ARG 119": "NH1" <-> "NH2" Residue "h ARG 122": "NH1" <-> "NH2" Residue "i ARG 65": "NH1" <-> "NH2" Residue "i ARG 119": "NH1" <-> "NH2" Residue "i ARG 122": "NH1" <-> "NH2" Residue "j ARG 65": "NH1" <-> "NH2" Residue "j ARG 119": "NH1" <-> "NH2" Residue "j ARG 122": "NH1" <-> "NH2" Residue "k ARG 65": "NH1" <-> "NH2" Residue "k ARG 119": "NH1" <-> "NH2" Residue "k ARG 122": "NH1" <-> "NH2" Residue "l ARG 65": "NH1" <-> "NH2" Residue "l ARG 119": "NH1" <-> "NH2" Residue "l ARG 122": "NH1" <-> "NH2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 53532 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3494 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 18, 'TRANS': 423} Chain: "B" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3494 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 18, 'TRANS': 423} Chain: "C" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3494 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 18, 'TRANS': 423} Chain: "D" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3494 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 18, 'TRANS': 423} Chain: "E" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3494 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 18, 'TRANS': 423} Chain: "F" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3494 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 18, 'TRANS': 423} Chain: "G" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3494 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 18, 'TRANS': 423} Chain: "H" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3494 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 18, 'TRANS': 423} Chain: "I" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3494 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 18, 'TRANS': 423} Chain: "J" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3494 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 18, 'TRANS': 423} Chain: "K" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3494 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 18, 'TRANS': 423} Chain: "L" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3494 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 18, 'TRANS': 423} Chain: "a" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 967 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 9, 'TRANS': 120} Chain: "b" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 967 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 9, 'TRANS': 120} Chain: "c" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 967 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 9, 'TRANS': 120} Chain: "d" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 967 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 9, 'TRANS': 120} Chain: "e" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 967 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 9, 'TRANS': 120} Chain: "f" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 967 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 9, 'TRANS': 120} Chain: "g" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 967 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 9, 'TRANS': 120} Chain: "h" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 967 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 9, 'TRANS': 120} Chain: "i" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 967 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 9, 'TRANS': 120} Chain: "j" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 967 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 9, 'TRANS': 120} Chain: "k" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 967 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 9, 'TRANS': 120} Chain: "l" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 967 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 9, 'TRANS': 120} Time building chain proxies: 22.97, per 1000 atoms: 0.43 Number of scatterers: 53532 At special positions: 0 Unit cell: (161.067, 161.067, 190.444, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 216 16.00 O 10392 8.00 N 9384 7.00 C 33540 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.48 Conformation dependent library (CDL) restraints added in 6.0 seconds 13632 Ramachandran restraints generated. 6816 Oldfield, 0 Emsley, 6816 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12768 Finding SS restraints... Secondary structure from input PDB file: 228 helices and 49 sheets defined 36.4% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'A' and resid 39 through 48 removed outlier: 3.563A pdb=" N TYR A 43 " --> pdb=" O ARG A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 61 removed outlier: 3.505A pdb=" N VAL A 55 " --> pdb=" O ALA A 51 " (cutoff:3.500A) Proline residue: A 58 - end of helix Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.753A pdb=" N THR A 82 " --> pdb=" O ARG A 78 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU A 83 " --> pdb=" O ILE A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 102 removed outlier: 3.695A pdb=" N LEU A 98 " --> pdb=" O GLN A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 141 No H-bonds generated for 'chain 'A' and resid 139 through 141' Processing helix chain 'A' and resid 173 through 175 No H-bonds generated for 'chain 'A' and resid 173 through 175' Processing helix chain 'A' and resid 206 through 221 removed outlier: 3.684A pdb=" N SER A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA A 218 " --> pdb=" O ASP A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 242 removed outlier: 3.724A pdb=" N SER A 242 " --> pdb=" O GLU A 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 239 through 242' Processing helix chain 'A' and resid 243 through 259 removed outlier: 3.713A pdb=" N ARG A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS A 249 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG A 253 " --> pdb=" O LYS A 249 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 256 " --> pdb=" O ASP A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 300 removed outlier: 3.957A pdb=" N ILE A 293 " --> pdb=" O MET A 289 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 294 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE A 295 " --> pdb=" O GLN A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 335 removed outlier: 3.727A pdb=" N SER A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 391 removed outlier: 3.619A pdb=" N LEU A 382 " --> pdb=" O GLU A 378 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 384 " --> pdb=" O GLY A 380 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU A 385 " --> pdb=" O LYS A 381 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL A 387 " --> pdb=" O HIS A 383 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A 389 " --> pdb=" O GLU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 412 removed outlier: 3.501A pdb=" N VAL A 404 " --> pdb=" O GLU A 400 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL A 410 " --> pdb=" O GLY A 406 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU A 411 " --> pdb=" O ASN A 407 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 412 " --> pdb=" O GLN A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 443 removed outlier: 3.619A pdb=" N SER A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 48 removed outlier: 3.562A pdb=" N TYR B 43 " --> pdb=" O ARG B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 61 removed outlier: 3.506A pdb=" N VAL B 55 " --> pdb=" O ALA B 51 " (cutoff:3.500A) Proline residue: B 58 - end of helix Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.753A pdb=" N THR B 82 " --> pdb=" O ARG B 78 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU B 83 " --> pdb=" O ILE B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 102 removed outlier: 3.695A pdb=" N LEU B 98 " --> pdb=" O GLN B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 141 No H-bonds generated for 'chain 'B' and resid 139 through 141' Processing helix chain 'B' and resid 173 through 175 No H-bonds generated for 'chain 'B' and resid 173 through 175' Processing helix chain 'B' and resid 206 through 221 removed outlier: 3.684A pdb=" N SER B 213 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA B 218 " --> pdb=" O ASP B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 242 removed outlier: 3.723A pdb=" N SER B 242 " --> pdb=" O GLU B 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 239 through 242' Processing helix chain 'B' and resid 243 through 259 removed outlier: 3.715A pdb=" N ARG B 247 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS B 249 " --> pdb=" O VAL B 245 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG B 253 " --> pdb=" O LYS B 249 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU B 256 " --> pdb=" O ASP B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 300 removed outlier: 3.957A pdb=" N ILE B 293 " --> pdb=" O MET B 289 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 294 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE B 295 " --> pdb=" O GLN B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 335 removed outlier: 3.728A pdb=" N SER B 332 " --> pdb=" O ASP B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 391 removed outlier: 3.620A pdb=" N LEU B 382 " --> pdb=" O GLU B 378 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA B 384 " --> pdb=" O GLY B 380 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU B 385 " --> pdb=" O LYS B 381 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL B 387 " --> pdb=" O HIS B 383 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN B 388 " --> pdb=" O ALA B 384 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL B 389 " --> pdb=" O GLU B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 412 removed outlier: 3.502A pdb=" N VAL B 404 " --> pdb=" O GLU B 400 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL B 410 " --> pdb=" O GLY B 406 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU B 411 " --> pdb=" O ASN B 407 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR B 412 " --> pdb=" O GLN B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 443 removed outlier: 3.620A pdb=" N SER B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 48 removed outlier: 3.562A pdb=" N TYR C 43 " --> pdb=" O ARG C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 61 removed outlier: 3.506A pdb=" N VAL C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) Proline residue: C 58 - end of helix Processing helix chain 'C' and resid 77 through 87 removed outlier: 3.752A pdb=" N THR C 82 " --> pdb=" O ARG C 78 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 102 removed outlier: 3.695A pdb=" N LEU C 98 " --> pdb=" O GLN C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 141 No H-bonds generated for 'chain 'C' and resid 139 through 141' Processing helix chain 'C' and resid 173 through 175 No H-bonds generated for 'chain 'C' and resid 173 through 175' Processing helix chain 'C' and resid 206 through 221 removed outlier: 3.684A pdb=" N SER C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA C 218 " --> pdb=" O ASP C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 242 removed outlier: 3.724A pdb=" N SER C 242 " --> pdb=" O GLU C 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 239 through 242' Processing helix chain 'C' and resid 243 through 259 removed outlier: 3.714A pdb=" N ARG C 247 " --> pdb=" O SER C 243 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS C 249 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG C 253 " --> pdb=" O LYS C 249 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU C 256 " --> pdb=" O ASP C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 300 removed outlier: 3.957A pdb=" N ILE C 293 " --> pdb=" O MET C 289 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE C 295 " --> pdb=" O GLN C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 335 removed outlier: 3.727A pdb=" N SER C 332 " --> pdb=" O ASP C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 391 removed outlier: 3.620A pdb=" N LEU C 382 " --> pdb=" O GLU C 378 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA C 384 " --> pdb=" O GLY C 380 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU C 385 " --> pdb=" O LYS C 381 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL C 387 " --> pdb=" O HIS C 383 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN C 388 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL C 389 " --> pdb=" O GLU C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 412 removed outlier: 3.501A pdb=" N VAL C 404 " --> pdb=" O GLU C 400 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL C 410 " --> pdb=" O GLY C 406 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU C 411 " --> pdb=" O ASN C 407 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR C 412 " --> pdb=" O GLN C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 443 removed outlier: 3.618A pdb=" N SER C 442 " --> pdb=" O SER C 438 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR C 443 " --> pdb=" O ALA C 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 48 removed outlier: 3.562A pdb=" N TYR D 43 " --> pdb=" O ARG D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 61 removed outlier: 3.506A pdb=" N VAL D 55 " --> pdb=" O ALA D 51 " (cutoff:3.500A) Proline residue: D 58 - end of helix Processing helix chain 'D' and resid 77 through 87 removed outlier: 3.752A pdb=" N THR D 82 " --> pdb=" O ARG D 78 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU D 83 " --> pdb=" O ILE D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 102 removed outlier: 3.695A pdb=" N LEU D 98 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 141 No H-bonds generated for 'chain 'D' and resid 139 through 141' Processing helix chain 'D' and resid 173 through 175 No H-bonds generated for 'chain 'D' and resid 173 through 175' Processing helix chain 'D' and resid 206 through 221 removed outlier: 3.684A pdb=" N SER D 213 " --> pdb=" O ALA D 209 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA D 218 " --> pdb=" O ASP D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 242 removed outlier: 3.723A pdb=" N SER D 242 " --> pdb=" O GLU D 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 239 through 242' Processing helix chain 'D' and resid 243 through 259 removed outlier: 3.714A pdb=" N ARG D 247 " --> pdb=" O SER D 243 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS D 249 " --> pdb=" O VAL D 245 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG D 253 " --> pdb=" O LYS D 249 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU D 256 " --> pdb=" O ASP D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 300 removed outlier: 3.957A pdb=" N ILE D 293 " --> pdb=" O MET D 289 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU D 294 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE D 295 " --> pdb=" O GLN D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 335 removed outlier: 3.727A pdb=" N SER D 332 " --> pdb=" O ASP D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 391 removed outlier: 3.620A pdb=" N LEU D 382 " --> pdb=" O GLU D 378 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA D 384 " --> pdb=" O GLY D 380 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU D 385 " --> pdb=" O LYS D 381 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL D 387 " --> pdb=" O HIS D 383 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN D 388 " --> pdb=" O ALA D 384 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL D 389 " --> pdb=" O GLU D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 412 removed outlier: 3.502A pdb=" N VAL D 404 " --> pdb=" O GLU D 400 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL D 410 " --> pdb=" O GLY D 406 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU D 411 " --> pdb=" O ASN D 407 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR D 412 " --> pdb=" O GLN D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 443 removed outlier: 3.619A pdb=" N SER D 442 " --> pdb=" O SER D 438 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR D 443 " --> pdb=" O ALA D 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 48 removed outlier: 3.562A pdb=" N TYR E 43 " --> pdb=" O ARG E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 61 removed outlier: 3.506A pdb=" N VAL E 55 " --> pdb=" O ALA E 51 " (cutoff:3.500A) Proline residue: E 58 - end of helix Processing helix chain 'E' and resid 77 through 87 removed outlier: 3.752A pdb=" N THR E 82 " --> pdb=" O ARG E 78 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU E 83 " --> pdb=" O ILE E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 102 removed outlier: 3.694A pdb=" N LEU E 98 " --> pdb=" O GLN E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 141 No H-bonds generated for 'chain 'E' and resid 139 through 141' Processing helix chain 'E' and resid 173 through 175 No H-bonds generated for 'chain 'E' and resid 173 through 175' Processing helix chain 'E' and resid 206 through 221 removed outlier: 3.685A pdb=" N SER E 213 " --> pdb=" O ALA E 209 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA E 218 " --> pdb=" O ASP E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 242 removed outlier: 3.724A pdb=" N SER E 242 " --> pdb=" O GLU E 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 239 through 242' Processing helix chain 'E' and resid 243 through 259 removed outlier: 3.713A pdb=" N ARG E 247 " --> pdb=" O SER E 243 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS E 249 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG E 253 " --> pdb=" O LYS E 249 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU E 256 " --> pdb=" O ASP E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 300 removed outlier: 3.957A pdb=" N ILE E 293 " --> pdb=" O MET E 289 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU E 294 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE E 295 " --> pdb=" O GLN E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 335 removed outlier: 3.728A pdb=" N SER E 332 " --> pdb=" O ASP E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 391 removed outlier: 3.620A pdb=" N LEU E 382 " --> pdb=" O GLU E 378 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA E 384 " --> pdb=" O GLY E 380 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU E 385 " --> pdb=" O LYS E 381 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL E 387 " --> pdb=" O HIS E 383 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN E 388 " --> pdb=" O ALA E 384 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL E 389 " --> pdb=" O GLU E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 412 removed outlier: 3.501A pdb=" N VAL E 404 " --> pdb=" O GLU E 400 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL E 410 " --> pdb=" O GLY E 406 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU E 411 " --> pdb=" O ASN E 407 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR E 412 " --> pdb=" O GLN E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 436 through 443 removed outlier: 3.619A pdb=" N SER E 442 " --> pdb=" O SER E 438 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR E 443 " --> pdb=" O ALA E 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 48 removed outlier: 3.563A pdb=" N TYR F 43 " --> pdb=" O ARG F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 61 removed outlier: 3.506A pdb=" N VAL F 55 " --> pdb=" O ALA F 51 " (cutoff:3.500A) Proline residue: F 58 - end of helix Processing helix chain 'F' and resid 77 through 87 removed outlier: 3.752A pdb=" N THR F 82 " --> pdb=" O ARG F 78 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU F 83 " --> pdb=" O ILE F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 102 removed outlier: 3.695A pdb=" N LEU F 98 " --> pdb=" O GLN F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 141 No H-bonds generated for 'chain 'F' and resid 139 through 141' Processing helix chain 'F' and resid 173 through 175 No H-bonds generated for 'chain 'F' and resid 173 through 175' Processing helix chain 'F' and resid 206 through 221 removed outlier: 3.684A pdb=" N SER F 213 " --> pdb=" O ALA F 209 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA F 218 " --> pdb=" O ASP F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 242 removed outlier: 3.724A pdb=" N SER F 242 " --> pdb=" O GLU F 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 239 through 242' Processing helix chain 'F' and resid 243 through 259 removed outlier: 3.714A pdb=" N ARG F 247 " --> pdb=" O SER F 243 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS F 249 " --> pdb=" O VAL F 245 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG F 253 " --> pdb=" O LYS F 249 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU F 256 " --> pdb=" O ASP F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 300 removed outlier: 3.957A pdb=" N ILE F 293 " --> pdb=" O MET F 289 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU F 294 " --> pdb=" O GLU F 290 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE F 295 " --> pdb=" O GLN F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 335 removed outlier: 3.727A pdb=" N SER F 332 " --> pdb=" O ASP F 328 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 391 removed outlier: 3.621A pdb=" N LEU F 382 " --> pdb=" O GLU F 378 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA F 384 " --> pdb=" O GLY F 380 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU F 385 " --> pdb=" O LYS F 381 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL F 387 " --> pdb=" O HIS F 383 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN F 388 " --> pdb=" O ALA F 384 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL F 389 " --> pdb=" O GLU F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 412 removed outlier: 3.501A pdb=" N VAL F 404 " --> pdb=" O GLU F 400 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL F 410 " --> pdb=" O GLY F 406 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU F 411 " --> pdb=" O ASN F 407 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR F 412 " --> pdb=" O GLN F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 436 through 443 removed outlier: 3.619A pdb=" N SER F 442 " --> pdb=" O SER F 438 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR F 443 " --> pdb=" O ALA F 439 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 48 removed outlier: 3.562A pdb=" N TYR G 43 " --> pdb=" O ARG G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 61 removed outlier: 3.505A pdb=" N VAL G 55 " --> pdb=" O ALA G 51 " (cutoff:3.500A) Proline residue: G 58 - end of helix Processing helix chain 'G' and resid 77 through 87 removed outlier: 3.752A pdb=" N THR G 82 " --> pdb=" O ARG G 78 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 102 removed outlier: 3.695A pdb=" N LEU G 98 " --> pdb=" O GLN G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 141 No H-bonds generated for 'chain 'G' and resid 139 through 141' Processing helix chain 'G' and resid 173 through 175 No H-bonds generated for 'chain 'G' and resid 173 through 175' Processing helix chain 'G' and resid 206 through 221 removed outlier: 3.684A pdb=" N SER G 213 " --> pdb=" O ALA G 209 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA G 218 " --> pdb=" O ASP G 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 239 through 242 removed outlier: 3.724A pdb=" N SER G 242 " --> pdb=" O GLU G 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 239 through 242' Processing helix chain 'G' and resid 243 through 259 removed outlier: 3.714A pdb=" N ARG G 247 " --> pdb=" O SER G 243 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS G 249 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ARG G 253 " --> pdb=" O LYS G 249 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU G 256 " --> pdb=" O ASP G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 287 through 300 removed outlier: 3.957A pdb=" N ILE G 293 " --> pdb=" O MET G 289 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU G 294 " --> pdb=" O GLU G 290 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE G 295 " --> pdb=" O GLN G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 325 through 335 removed outlier: 3.727A pdb=" N SER G 332 " --> pdb=" O ASP G 328 " (cutoff:3.500A) Processing helix chain 'G' and resid 372 through 391 removed outlier: 3.620A pdb=" N LEU G 382 " --> pdb=" O GLU G 378 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA G 384 " --> pdb=" O GLY G 380 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU G 385 " --> pdb=" O LYS G 381 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL G 387 " --> pdb=" O HIS G 383 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN G 388 " --> pdb=" O ALA G 384 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL G 389 " --> pdb=" O GLU G 385 " (cutoff:3.500A) Processing helix chain 'G' and resid 400 through 412 removed outlier: 3.502A pdb=" N VAL G 404 " --> pdb=" O GLU G 400 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL G 410 " --> pdb=" O GLY G 406 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU G 411 " --> pdb=" O ASN G 407 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR G 412 " --> pdb=" O GLN G 408 " (cutoff:3.500A) Processing helix chain 'G' and resid 436 through 443 removed outlier: 3.619A pdb=" N SER G 442 " --> pdb=" O SER G 438 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR G 443 " --> pdb=" O ALA G 439 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 48 removed outlier: 3.562A pdb=" N TYR H 43 " --> pdb=" O ARG H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 61 removed outlier: 3.506A pdb=" N VAL H 55 " --> pdb=" O ALA H 51 " (cutoff:3.500A) Proline residue: H 58 - end of helix Processing helix chain 'H' and resid 77 through 87 removed outlier: 3.752A pdb=" N THR H 82 " --> pdb=" O ARG H 78 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU H 83 " --> pdb=" O ILE H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 102 removed outlier: 3.695A pdb=" N LEU H 98 " --> pdb=" O GLN H 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 141 No H-bonds generated for 'chain 'H' and resid 139 through 141' Processing helix chain 'H' and resid 173 through 175 No H-bonds generated for 'chain 'H' and resid 173 through 175' Processing helix chain 'H' and resid 206 through 221 removed outlier: 3.684A pdb=" N SER H 213 " --> pdb=" O ALA H 209 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA H 218 " --> pdb=" O ASP H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 239 through 242 removed outlier: 3.724A pdb=" N SER H 242 " --> pdb=" O GLU H 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 239 through 242' Processing helix chain 'H' and resid 243 through 259 removed outlier: 3.713A pdb=" N ARG H 247 " --> pdb=" O SER H 243 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS H 249 " --> pdb=" O VAL H 245 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG H 253 " --> pdb=" O LYS H 249 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU H 256 " --> pdb=" O ASP H 252 " (cutoff:3.500A) Processing helix chain 'H' and resid 287 through 300 removed outlier: 3.957A pdb=" N ILE H 293 " --> pdb=" O MET H 289 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU H 294 " --> pdb=" O GLU H 290 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE H 295 " --> pdb=" O GLN H 291 " (cutoff:3.500A) Processing helix chain 'H' and resid 325 through 335 removed outlier: 3.727A pdb=" N SER H 332 " --> pdb=" O ASP H 328 " (cutoff:3.500A) Processing helix chain 'H' and resid 372 through 391 removed outlier: 3.620A pdb=" N LEU H 382 " --> pdb=" O GLU H 378 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA H 384 " --> pdb=" O GLY H 380 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU H 385 " --> pdb=" O LYS H 381 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL H 387 " --> pdb=" O HIS H 383 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN H 388 " --> pdb=" O ALA H 384 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL H 389 " --> pdb=" O GLU H 385 " (cutoff:3.500A) Processing helix chain 'H' and resid 400 through 412 removed outlier: 3.501A pdb=" N VAL H 404 " --> pdb=" O GLU H 400 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL H 410 " --> pdb=" O GLY H 406 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU H 411 " --> pdb=" O ASN H 407 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR H 412 " --> pdb=" O GLN H 408 " (cutoff:3.500A) Processing helix chain 'H' and resid 436 through 443 removed outlier: 3.619A pdb=" N SER H 442 " --> pdb=" O SER H 438 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR H 443 " --> pdb=" O ALA H 439 " (cutoff:3.500A) Processing helix chain 'I' and resid 39 through 48 removed outlier: 3.562A pdb=" N TYR I 43 " --> pdb=" O ARG I 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 61 removed outlier: 3.505A pdb=" N VAL I 55 " --> pdb=" O ALA I 51 " (cutoff:3.500A) Proline residue: I 58 - end of helix Processing helix chain 'I' and resid 77 through 87 removed outlier: 3.753A pdb=" N THR I 82 " --> pdb=" O ARG I 78 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU I 83 " --> pdb=" O ILE I 79 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 102 removed outlier: 3.695A pdb=" N LEU I 98 " --> pdb=" O GLN I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 139 through 141 No H-bonds generated for 'chain 'I' and resid 139 through 141' Processing helix chain 'I' and resid 173 through 175 No H-bonds generated for 'chain 'I' and resid 173 through 175' Processing helix chain 'I' and resid 206 through 221 removed outlier: 3.683A pdb=" N SER I 213 " --> pdb=" O ALA I 209 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA I 218 " --> pdb=" O ASP I 214 " (cutoff:3.500A) Processing helix chain 'I' and resid 239 through 242 removed outlier: 3.724A pdb=" N SER I 242 " --> pdb=" O GLU I 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 239 through 242' Processing helix chain 'I' and resid 243 through 259 removed outlier: 3.714A pdb=" N ARG I 247 " --> pdb=" O SER I 243 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS I 249 " --> pdb=" O VAL I 245 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ARG I 253 " --> pdb=" O LYS I 249 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU I 256 " --> pdb=" O ASP I 252 " (cutoff:3.500A) Processing helix chain 'I' and resid 287 through 300 removed outlier: 3.958A pdb=" N ILE I 293 " --> pdb=" O MET I 289 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU I 294 " --> pdb=" O GLU I 290 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE I 295 " --> pdb=" O GLN I 291 " (cutoff:3.500A) Processing helix chain 'I' and resid 325 through 335 removed outlier: 3.728A pdb=" N SER I 332 " --> pdb=" O ASP I 328 " (cutoff:3.500A) Processing helix chain 'I' and resid 372 through 391 removed outlier: 3.620A pdb=" N LEU I 382 " --> pdb=" O GLU I 378 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA I 384 " --> pdb=" O GLY I 380 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU I 385 " --> pdb=" O LYS I 381 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL I 387 " --> pdb=" O HIS I 383 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN I 388 " --> pdb=" O ALA I 384 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL I 389 " --> pdb=" O GLU I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 400 through 412 removed outlier: 3.501A pdb=" N VAL I 404 " --> pdb=" O GLU I 400 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL I 410 " --> pdb=" O GLY I 406 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU I 411 " --> pdb=" O ASN I 407 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR I 412 " --> pdb=" O GLN I 408 " (cutoff:3.500A) Processing helix chain 'I' and resid 436 through 443 removed outlier: 3.619A pdb=" N SER I 442 " --> pdb=" O SER I 438 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR I 443 " --> pdb=" O ALA I 439 " (cutoff:3.500A) Processing helix chain 'J' and resid 39 through 48 removed outlier: 3.562A pdb=" N TYR J 43 " --> pdb=" O ARG J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 61 removed outlier: 3.506A pdb=" N VAL J 55 " --> pdb=" O ALA J 51 " (cutoff:3.500A) Proline residue: J 58 - end of helix Processing helix chain 'J' and resid 77 through 87 removed outlier: 3.752A pdb=" N THR J 82 " --> pdb=" O ARG J 78 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU J 83 " --> pdb=" O ILE J 79 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 102 removed outlier: 3.695A pdb=" N LEU J 98 " --> pdb=" O GLN J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 139 through 141 No H-bonds generated for 'chain 'J' and resid 139 through 141' Processing helix chain 'J' and resid 173 through 175 No H-bonds generated for 'chain 'J' and resid 173 through 175' Processing helix chain 'J' and resid 206 through 221 removed outlier: 3.684A pdb=" N SER J 213 " --> pdb=" O ALA J 209 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA J 218 " --> pdb=" O ASP J 214 " (cutoff:3.500A) Processing helix chain 'J' and resid 239 through 242 removed outlier: 3.723A pdb=" N SER J 242 " --> pdb=" O GLU J 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 239 through 242' Processing helix chain 'J' and resid 243 through 259 removed outlier: 3.714A pdb=" N ARG J 247 " --> pdb=" O SER J 243 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS J 249 " --> pdb=" O VAL J 245 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG J 253 " --> pdb=" O LYS J 249 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU J 256 " --> pdb=" O ASP J 252 " (cutoff:3.500A) Processing helix chain 'J' and resid 287 through 300 removed outlier: 3.958A pdb=" N ILE J 293 " --> pdb=" O MET J 289 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU J 294 " --> pdb=" O GLU J 290 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE J 295 " --> pdb=" O GLN J 291 " (cutoff:3.500A) Processing helix chain 'J' and resid 325 through 335 removed outlier: 3.728A pdb=" N SER J 332 " --> pdb=" O ASP J 328 " (cutoff:3.500A) Processing helix chain 'J' and resid 372 through 391 removed outlier: 3.620A pdb=" N LEU J 382 " --> pdb=" O GLU J 378 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA J 384 " --> pdb=" O GLY J 380 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU J 385 " --> pdb=" O LYS J 381 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL J 387 " --> pdb=" O HIS J 383 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN J 388 " --> pdb=" O ALA J 384 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL J 389 " --> pdb=" O GLU J 385 " (cutoff:3.500A) Processing helix chain 'J' and resid 400 through 412 removed outlier: 3.502A pdb=" N VAL J 404 " --> pdb=" O GLU J 400 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL J 410 " --> pdb=" O GLY J 406 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU J 411 " --> pdb=" O ASN J 407 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR J 412 " --> pdb=" O GLN J 408 " (cutoff:3.500A) Processing helix chain 'J' and resid 436 through 443 removed outlier: 3.618A pdb=" N SER J 442 " --> pdb=" O SER J 438 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR J 443 " --> pdb=" O ALA J 439 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 48 removed outlier: 3.562A pdb=" N TYR K 43 " --> pdb=" O ARG K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 61 removed outlier: 3.505A pdb=" N VAL K 55 " --> pdb=" O ALA K 51 " (cutoff:3.500A) Proline residue: K 58 - end of helix Processing helix chain 'K' and resid 77 through 87 removed outlier: 3.752A pdb=" N THR K 82 " --> pdb=" O ARG K 78 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU K 83 " --> pdb=" O ILE K 79 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 102 removed outlier: 3.695A pdb=" N LEU K 98 " --> pdb=" O GLN K 94 " (cutoff:3.500A) Processing helix chain 'K' and resid 139 through 141 No H-bonds generated for 'chain 'K' and resid 139 through 141' Processing helix chain 'K' and resid 173 through 175 No H-bonds generated for 'chain 'K' and resid 173 through 175' Processing helix chain 'K' and resid 206 through 221 removed outlier: 3.684A pdb=" N SER K 213 " --> pdb=" O ALA K 209 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA K 218 " --> pdb=" O ASP K 214 " (cutoff:3.500A) Processing helix chain 'K' and resid 239 through 242 removed outlier: 3.724A pdb=" N SER K 242 " --> pdb=" O GLU K 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 239 through 242' Processing helix chain 'K' and resid 243 through 259 removed outlier: 3.714A pdb=" N ARG K 247 " --> pdb=" O SER K 243 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS K 249 " --> pdb=" O VAL K 245 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG K 253 " --> pdb=" O LYS K 249 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU K 256 " --> pdb=" O ASP K 252 " (cutoff:3.500A) Processing helix chain 'K' and resid 287 through 300 removed outlier: 3.957A pdb=" N ILE K 293 " --> pdb=" O MET K 289 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU K 294 " --> pdb=" O GLU K 290 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE K 295 " --> pdb=" O GLN K 291 " (cutoff:3.500A) Processing helix chain 'K' and resid 325 through 335 removed outlier: 3.727A pdb=" N SER K 332 " --> pdb=" O ASP K 328 " (cutoff:3.500A) Processing helix chain 'K' and resid 372 through 391 removed outlier: 3.619A pdb=" N LEU K 382 " --> pdb=" O GLU K 378 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA K 384 " --> pdb=" O GLY K 380 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU K 385 " --> pdb=" O LYS K 381 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL K 387 " --> pdb=" O HIS K 383 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN K 388 " --> pdb=" O ALA K 384 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL K 389 " --> pdb=" O GLU K 385 " (cutoff:3.500A) Processing helix chain 'K' and resid 400 through 412 removed outlier: 3.502A pdb=" N VAL K 404 " --> pdb=" O GLU K 400 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL K 410 " --> pdb=" O GLY K 406 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU K 411 " --> pdb=" O ASN K 407 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR K 412 " --> pdb=" O GLN K 408 " (cutoff:3.500A) Processing helix chain 'K' and resid 436 through 443 removed outlier: 3.618A pdb=" N SER K 442 " --> pdb=" O SER K 438 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR K 443 " --> pdb=" O ALA K 439 " (cutoff:3.500A) Processing helix chain 'L' and resid 39 through 48 removed outlier: 3.562A pdb=" N TYR L 43 " --> pdb=" O ARG L 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 61 removed outlier: 3.506A pdb=" N VAL L 55 " --> pdb=" O ALA L 51 " (cutoff:3.500A) Proline residue: L 58 - end of helix Processing helix chain 'L' and resid 77 through 87 removed outlier: 3.752A pdb=" N THR L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU L 83 " --> pdb=" O ILE L 79 " (cutoff:3.500A) Processing helix chain 'L' and resid 87 through 102 removed outlier: 3.694A pdb=" N LEU L 98 " --> pdb=" O GLN L 94 " (cutoff:3.500A) Processing helix chain 'L' and resid 139 through 141 No H-bonds generated for 'chain 'L' and resid 139 through 141' Processing helix chain 'L' and resid 173 through 175 No H-bonds generated for 'chain 'L' and resid 173 through 175' Processing helix chain 'L' and resid 206 through 221 removed outlier: 3.683A pdb=" N SER L 213 " --> pdb=" O ALA L 209 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA L 218 " --> pdb=" O ASP L 214 " (cutoff:3.500A) Processing helix chain 'L' and resid 239 through 242 removed outlier: 3.724A pdb=" N SER L 242 " --> pdb=" O GLU L 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 239 through 242' Processing helix chain 'L' and resid 243 through 259 removed outlier: 3.713A pdb=" N ARG L 247 " --> pdb=" O SER L 243 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS L 249 " --> pdb=" O VAL L 245 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG L 253 " --> pdb=" O LYS L 249 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU L 256 " --> pdb=" O ASP L 252 " (cutoff:3.500A) Processing helix chain 'L' and resid 287 through 300 removed outlier: 3.957A pdb=" N ILE L 293 " --> pdb=" O MET L 289 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU L 294 " --> pdb=" O GLU L 290 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE L 295 " --> pdb=" O GLN L 291 " (cutoff:3.500A) Processing helix chain 'L' and resid 325 through 335 removed outlier: 3.728A pdb=" N SER L 332 " --> pdb=" O ASP L 328 " (cutoff:3.500A) Processing helix chain 'L' and resid 372 through 391 removed outlier: 3.620A pdb=" N LEU L 382 " --> pdb=" O GLU L 378 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA L 384 " --> pdb=" O GLY L 380 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU L 385 " --> pdb=" O LYS L 381 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL L 387 " --> pdb=" O HIS L 383 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN L 388 " --> pdb=" O ALA L 384 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL L 389 " --> pdb=" O GLU L 385 " (cutoff:3.500A) Processing helix chain 'L' and resid 400 through 412 removed outlier: 3.501A pdb=" N VAL L 404 " --> pdb=" O GLU L 400 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL L 410 " --> pdb=" O GLY L 406 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU L 411 " --> pdb=" O ASN L 407 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR L 412 " --> pdb=" O GLN L 408 " (cutoff:3.500A) Processing helix chain 'L' and resid 436 through 443 removed outlier: 3.618A pdb=" N SER L 442 " --> pdb=" O SER L 438 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR L 443 " --> pdb=" O ALA L 439 " (cutoff:3.500A) Processing helix chain 'a' and resid 9 through 14 Processing helix chain 'a' and resid 21 through 26 removed outlier: 3.901A pdb=" N VAL a 25 " --> pdb=" O SER a 21 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN a 26 " --> pdb=" O ASP a 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 21 through 26' Processing helix chain 'a' and resid 28 through 33 Processing helix chain 'a' and resid 46 through 60 removed outlier: 3.979A pdb=" N ALA a 54 " --> pdb=" O LEU a 50 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU a 60 " --> pdb=" O MET a 56 " (cutoff:3.500A) Processing helix chain 'a' and resid 111 through 125 removed outlier: 3.889A pdb=" N PHE a 117 " --> pdb=" O TYR a 113 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU a 120 " --> pdb=" O THR a 116 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU a 123 " --> pdb=" O ARG a 119 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN a 124 " --> pdb=" O LEU a 120 " (cutoff:3.500A) Processing helix chain 'b' and resid 9 through 14 Processing helix chain 'b' and resid 21 through 26 removed outlier: 3.901A pdb=" N VAL b 25 " --> pdb=" O SER b 21 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN b 26 " --> pdb=" O ASP b 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 21 through 26' Processing helix chain 'b' and resid 28 through 33 Processing helix chain 'b' and resid 46 through 60 removed outlier: 3.981A pdb=" N ALA b 54 " --> pdb=" O LEU b 50 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU b 60 " --> pdb=" O MET b 56 " (cutoff:3.500A) Processing helix chain 'b' and resid 111 through 125 removed outlier: 3.889A pdb=" N PHE b 117 " --> pdb=" O TYR b 113 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU b 120 " --> pdb=" O THR b 116 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU b 123 " --> pdb=" O ARG b 119 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN b 124 " --> pdb=" O LEU b 120 " (cutoff:3.500A) Processing helix chain 'c' and resid 9 through 14 Processing helix chain 'c' and resid 21 through 26 removed outlier: 3.902A pdb=" N VAL c 25 " --> pdb=" O SER c 21 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN c 26 " --> pdb=" O ASP c 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 21 through 26' Processing helix chain 'c' and resid 28 through 33 Processing helix chain 'c' and resid 46 through 60 removed outlier: 3.980A pdb=" N ALA c 54 " --> pdb=" O LEU c 50 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU c 60 " --> pdb=" O MET c 56 " (cutoff:3.500A) Processing helix chain 'c' and resid 111 through 125 removed outlier: 3.888A pdb=" N PHE c 117 " --> pdb=" O TYR c 113 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU c 120 " --> pdb=" O THR c 116 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU c 123 " --> pdb=" O ARG c 119 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN c 124 " --> pdb=" O LEU c 120 " (cutoff:3.500A) Processing helix chain 'd' and resid 9 through 14 Processing helix chain 'd' and resid 21 through 26 removed outlier: 3.901A pdb=" N VAL d 25 " --> pdb=" O SER d 21 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN d 26 " --> pdb=" O ASP d 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 21 through 26' Processing helix chain 'd' and resid 28 through 33 Processing helix chain 'd' and resid 46 through 60 removed outlier: 3.980A pdb=" N ALA d 54 " --> pdb=" O LEU d 50 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU d 60 " --> pdb=" O MET d 56 " (cutoff:3.500A) Processing helix chain 'd' and resid 111 through 125 removed outlier: 3.889A pdb=" N PHE d 117 " --> pdb=" O TYR d 113 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU d 120 " --> pdb=" O THR d 116 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU d 123 " --> pdb=" O ARG d 119 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN d 124 " --> pdb=" O LEU d 120 " (cutoff:3.500A) Processing helix chain 'e' and resid 9 through 14 Processing helix chain 'e' and resid 21 through 26 removed outlier: 3.902A pdb=" N VAL e 25 " --> pdb=" O SER e 21 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN e 26 " --> pdb=" O ASP e 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 21 through 26' Processing helix chain 'e' and resid 28 through 33 Processing helix chain 'e' and resid 46 through 60 removed outlier: 3.980A pdb=" N ALA e 54 " --> pdb=" O LEU e 50 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU e 60 " --> pdb=" O MET e 56 " (cutoff:3.500A) Processing helix chain 'e' and resid 111 through 125 removed outlier: 3.889A pdb=" N PHE e 117 " --> pdb=" O TYR e 113 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU e 120 " --> pdb=" O THR e 116 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU e 123 " --> pdb=" O ARG e 119 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN e 124 " --> pdb=" O LEU e 120 " (cutoff:3.500A) Processing helix chain 'f' and resid 9 through 14 Processing helix chain 'f' and resid 21 through 26 removed outlier: 3.901A pdb=" N VAL f 25 " --> pdb=" O SER f 21 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN f 26 " --> pdb=" O ASP f 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 21 through 26' Processing helix chain 'f' and resid 28 through 33 Processing helix chain 'f' and resid 46 through 60 removed outlier: 3.980A pdb=" N ALA f 54 " --> pdb=" O LEU f 50 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU f 60 " --> pdb=" O MET f 56 " (cutoff:3.500A) Processing helix chain 'f' and resid 111 through 125 removed outlier: 3.889A pdb=" N PHE f 117 " --> pdb=" O TYR f 113 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU f 120 " --> pdb=" O THR f 116 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU f 123 " --> pdb=" O ARG f 119 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN f 124 " --> pdb=" O LEU f 120 " (cutoff:3.500A) Processing helix chain 'g' and resid 9 through 14 Processing helix chain 'g' and resid 21 through 26 removed outlier: 3.901A pdb=" N VAL g 25 " --> pdb=" O SER g 21 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN g 26 " --> pdb=" O ASP g 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 21 through 26' Processing helix chain 'g' and resid 28 through 33 Processing helix chain 'g' and resid 46 through 60 removed outlier: 3.980A pdb=" N ALA g 54 " --> pdb=" O LEU g 50 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU g 60 " --> pdb=" O MET g 56 " (cutoff:3.500A) Processing helix chain 'g' and resid 111 through 125 removed outlier: 3.888A pdb=" N PHE g 117 " --> pdb=" O TYR g 113 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU g 120 " --> pdb=" O THR g 116 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU g 123 " --> pdb=" O ARG g 119 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN g 124 " --> pdb=" O LEU g 120 " (cutoff:3.500A) Processing helix chain 'h' and resid 9 through 14 Processing helix chain 'h' and resid 21 through 26 removed outlier: 3.901A pdb=" N VAL h 25 " --> pdb=" O SER h 21 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN h 26 " --> pdb=" O ASP h 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 21 through 26' Processing helix chain 'h' and resid 28 through 33 Processing helix chain 'h' and resid 46 through 60 removed outlier: 3.980A pdb=" N ALA h 54 " --> pdb=" O LEU h 50 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU h 60 " --> pdb=" O MET h 56 " (cutoff:3.500A) Processing helix chain 'h' and resid 111 through 125 removed outlier: 3.889A pdb=" N PHE h 117 " --> pdb=" O TYR h 113 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU h 120 " --> pdb=" O THR h 116 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU h 123 " --> pdb=" O ARG h 119 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN h 124 " --> pdb=" O LEU h 120 " (cutoff:3.500A) Processing helix chain 'i' and resid 9 through 14 Processing helix chain 'i' and resid 21 through 26 removed outlier: 3.902A pdb=" N VAL i 25 " --> pdb=" O SER i 21 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN i 26 " --> pdb=" O ASP i 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 21 through 26' Processing helix chain 'i' and resid 28 through 33 Processing helix chain 'i' and resid 46 through 60 removed outlier: 3.980A pdb=" N ALA i 54 " --> pdb=" O LEU i 50 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU i 60 " --> pdb=" O MET i 56 " (cutoff:3.500A) Processing helix chain 'i' and resid 111 through 125 removed outlier: 3.888A pdb=" N PHE i 117 " --> pdb=" O TYR i 113 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU i 120 " --> pdb=" O THR i 116 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU i 123 " --> pdb=" O ARG i 119 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN i 124 " --> pdb=" O LEU i 120 " (cutoff:3.500A) Processing helix chain 'j' and resid 9 through 14 Processing helix chain 'j' and resid 21 through 26 removed outlier: 3.901A pdb=" N VAL j 25 " --> pdb=" O SER j 21 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN j 26 " --> pdb=" O ASP j 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 21 through 26' Processing helix chain 'j' and resid 28 through 33 Processing helix chain 'j' and resid 46 through 60 removed outlier: 3.980A pdb=" N ALA j 54 " --> pdb=" O LEU j 50 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU j 60 " --> pdb=" O MET j 56 " (cutoff:3.500A) Processing helix chain 'j' and resid 111 through 125 removed outlier: 3.889A pdb=" N PHE j 117 " --> pdb=" O TYR j 113 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU j 120 " --> pdb=" O THR j 116 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU j 123 " --> pdb=" O ARG j 119 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN j 124 " --> pdb=" O LEU j 120 " (cutoff:3.500A) Processing helix chain 'k' and resid 9 through 14 Processing helix chain 'k' and resid 21 through 26 removed outlier: 3.901A pdb=" N VAL k 25 " --> pdb=" O SER k 21 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN k 26 " --> pdb=" O ASP k 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 21 through 26' Processing helix chain 'k' and resid 28 through 33 Processing helix chain 'k' and resid 46 through 60 removed outlier: 3.980A pdb=" N ALA k 54 " --> pdb=" O LEU k 50 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU k 60 " --> pdb=" O MET k 56 " (cutoff:3.500A) Processing helix chain 'k' and resid 111 through 125 removed outlier: 3.888A pdb=" N PHE k 117 " --> pdb=" O TYR k 113 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU k 120 " --> pdb=" O THR k 116 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU k 123 " --> pdb=" O ARG k 119 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN k 124 " --> pdb=" O LEU k 120 " (cutoff:3.500A) Processing helix chain 'l' and resid 9 through 14 Processing helix chain 'l' and resid 21 through 26 removed outlier: 3.902A pdb=" N VAL l 25 " --> pdb=" O SER l 21 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN l 26 " --> pdb=" O ASP l 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 21 through 26' Processing helix chain 'l' and resid 28 through 33 Processing helix chain 'l' and resid 46 through 60 removed outlier: 3.980A pdb=" N ALA l 54 " --> pdb=" O LEU l 50 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU l 60 " --> pdb=" O MET l 56 " (cutoff:3.500A) Processing helix chain 'l' and resid 111 through 125 removed outlier: 3.888A pdb=" N PHE l 117 " --> pdb=" O TYR l 113 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU l 120 " --> pdb=" O THR l 116 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU l 123 " --> pdb=" O ARG l 119 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN l 124 " --> pdb=" O LEU l 120 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 69 removed outlier: 3.576A pdb=" N ILE A 364 " --> pdb=" O ASP A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 132 through 137 removed outlier: 3.752A pdb=" N THR A 134 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE A 107 " --> pdb=" O VAL A 178 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 161 through 162 Processing sheet with id=AA4, first strand: chain 'A' and resid 276 through 279 removed outlier: 3.533A pdb=" N THR A 276 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N LEU L 267 " --> pdb=" O ASN A 228 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ASP A 230 " --> pdb=" O LEU L 267 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N LEU L 269 " --> pdb=" O ASP A 230 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ILE A 232 " --> pdb=" O LEU L 269 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 267 through 270 removed outlier: 3.533A pdb=" N THR B 276 " --> pdb=" O VAL B 231 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 68 through 69 removed outlier: 3.576A pdb=" N ILE B 364 " --> pdb=" O ASP B 68 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 132 through 137 removed outlier: 3.752A pdb=" N THR B 134 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B 107 " --> pdb=" O VAL B 178 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 161 through 162 Processing sheet with id=AA9, first strand: chain 'B' and resid 267 through 270 removed outlier: 3.532A pdb=" N THR C 276 " --> pdb=" O VAL C 231 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 68 through 69 removed outlier: 3.576A pdb=" N ILE C 364 " --> pdb=" O ASP C 68 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 132 through 137 removed outlier: 3.751A pdb=" N THR C 134 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE C 107 " --> pdb=" O VAL C 178 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 161 through 162 Processing sheet with id=AB4, first strand: chain 'C' and resid 267 through 270 removed outlier: 3.532A pdb=" N THR D 276 " --> pdb=" O VAL D 231 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 68 through 69 removed outlier: 3.575A pdb=" N ILE D 364 " --> pdb=" O ASP D 68 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 132 through 137 removed outlier: 3.751A pdb=" N THR D 134 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE D 107 " --> pdb=" O VAL D 178 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 161 through 162 Processing sheet with id=AB8, first strand: chain 'D' and resid 267 through 270 removed outlier: 3.533A pdb=" N THR E 276 " --> pdb=" O VAL E 231 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 68 through 69 removed outlier: 3.576A pdb=" N ILE E 364 " --> pdb=" O ASP E 68 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 132 through 137 removed outlier: 3.751A pdb=" N THR E 134 " --> pdb=" O VAL E 108 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE E 107 " --> pdb=" O VAL E 178 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 161 through 162 Processing sheet with id=AC3, first strand: chain 'E' and resid 267 through 270 removed outlier: 3.533A pdb=" N THR F 276 " --> pdb=" O VAL F 231 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 68 through 69 removed outlier: 3.576A pdb=" N ILE F 364 " --> pdb=" O ASP F 68 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 132 through 137 removed outlier: 3.751A pdb=" N THR F 134 " --> pdb=" O VAL F 108 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE F 107 " --> pdb=" O VAL F 178 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 161 through 162 Processing sheet with id=AC7, first strand: chain 'F' and resid 267 through 270 removed outlier: 3.532A pdb=" N THR G 276 " --> pdb=" O VAL G 231 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 68 through 69 removed outlier: 3.576A pdb=" N ILE G 364 " --> pdb=" O ASP G 68 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 132 through 137 removed outlier: 3.751A pdb=" N THR G 134 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE G 107 " --> pdb=" O VAL G 178 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 161 through 162 Processing sheet with id=AD2, first strand: chain 'G' and resid 267 through 270 removed outlier: 3.533A pdb=" N THR H 276 " --> pdb=" O VAL H 231 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 68 through 69 removed outlier: 3.577A pdb=" N ILE H 364 " --> pdb=" O ASP H 68 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 132 through 137 removed outlier: 3.752A pdb=" N THR H 134 " --> pdb=" O VAL H 108 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE H 107 " --> pdb=" O VAL H 178 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 161 through 162 Processing sheet with id=AD6, first strand: chain 'H' and resid 267 through 270 removed outlier: 3.533A pdb=" N THR I 276 " --> pdb=" O VAL I 231 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 68 through 69 removed outlier: 3.576A pdb=" N ILE I 364 " --> pdb=" O ASP I 68 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 132 through 137 removed outlier: 3.751A pdb=" N THR I 134 " --> pdb=" O VAL I 108 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE I 107 " --> pdb=" O VAL I 178 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 161 through 162 Processing sheet with id=AE1, first strand: chain 'I' and resid 267 through 270 removed outlier: 3.534A pdb=" N THR J 276 " --> pdb=" O VAL J 231 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 68 through 69 removed outlier: 3.576A pdb=" N ILE J 364 " --> pdb=" O ASP J 68 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 132 through 137 removed outlier: 3.751A pdb=" N THR J 134 " --> pdb=" O VAL J 108 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE J 107 " --> pdb=" O VAL J 178 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 161 through 162 Processing sheet with id=AE5, first strand: chain 'J' and resid 267 through 270 removed outlier: 3.533A pdb=" N THR K 276 " --> pdb=" O VAL K 231 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 68 through 69 removed outlier: 3.576A pdb=" N ILE K 364 " --> pdb=" O ASP K 68 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 132 through 137 removed outlier: 3.752A pdb=" N THR K 134 " --> pdb=" O VAL K 108 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE K 107 " --> pdb=" O VAL K 178 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 161 through 162 Processing sheet with id=AE9, first strand: chain 'K' and resid 267 through 270 removed outlier: 3.533A pdb=" N THR L 276 " --> pdb=" O VAL L 231 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 68 through 69 removed outlier: 3.576A pdb=" N ILE L 364 " --> pdb=" O ASP L 68 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 132 through 137 removed outlier: 3.752A pdb=" N THR L 134 " --> pdb=" O VAL L 108 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE L 107 " --> pdb=" O VAL L 178 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 161 through 162 Processing sheet with id=AF4, first strand: chain 'a' and resid 79 through 83 removed outlier: 6.680A pdb=" N THR a 90 " --> pdb=" O LEU a 80 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ARG a 82 " --> pdb=" O SER a 88 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N SER a 88 " --> pdb=" O ARG a 82 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LEU l 80 " --> pdb=" O PHE a 91 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR l 90 " --> pdb=" O LEU l 80 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ARG l 82 " --> pdb=" O SER l 88 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N SER l 88 " --> pdb=" O ARG l 82 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU k 80 " --> pdb=" O PHE l 91 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR k 90 " --> pdb=" O LEU k 80 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ARG k 82 " --> pdb=" O SER k 88 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N SER k 88 " --> pdb=" O ARG k 82 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU j 80 " --> pdb=" O PHE k 91 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR j 90 " --> pdb=" O LEU j 80 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ARG j 82 " --> pdb=" O SER j 88 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N SER j 88 " --> pdb=" O ARG j 82 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU i 80 " --> pdb=" O PHE j 91 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR i 90 " --> pdb=" O LEU i 80 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ARG i 82 " --> pdb=" O SER i 88 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N SER i 88 " --> pdb=" O ARG i 82 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LEU h 80 " --> pdb=" O PHE i 91 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR h 90 " --> pdb=" O LEU h 80 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ARG h 82 " --> pdb=" O SER h 88 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N SER h 88 " --> pdb=" O ARG h 82 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU g 80 " --> pdb=" O PHE h 91 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR g 90 " --> pdb=" O LEU g 80 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ARG g 82 " --> pdb=" O SER g 88 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N SER g 88 " --> pdb=" O ARG g 82 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR g 89 " --> pdb=" O ARG f 82 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG f 82 " --> pdb=" O THR g 89 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU f 80 " --> pdb=" O PHE g 91 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR f 90 " --> pdb=" O LEU f 80 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ARG f 82 " --> pdb=" O SER f 88 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N SER f 88 " --> pdb=" O ARG f 82 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LEU e 80 " --> pdb=" O PHE f 91 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR e 90 " --> pdb=" O LEU e 80 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ARG e 82 " --> pdb=" O SER e 88 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N SER e 88 " --> pdb=" O ARG e 82 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU d 80 " --> pdb=" O PHE e 91 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR d 90 " --> pdb=" O LEU d 80 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ARG d 82 " --> pdb=" O SER d 88 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N SER d 88 " --> pdb=" O ARG d 82 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU c 80 " --> pdb=" O PHE d 91 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR c 90 " --> pdb=" O LEU c 80 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ARG c 82 " --> pdb=" O SER c 88 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N SER c 88 " --> pdb=" O ARG c 82 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU b 80 " --> pdb=" O PHE c 91 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR b 90 " --> pdb=" O LEU b 80 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ARG b 82 " --> pdb=" O SER b 88 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N SER b 88 " --> pdb=" O ARG b 82 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU a 80 " --> pdb=" O PHE b 91 " (cutoff:3.500A) 1410 hydrogen bonds defined for protein. 4089 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: 13.26 Time building geometry restraints manager: 17.05 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: 14978 1.33 - 1.45: 8920 1.45 - 1.57: 30258 1.57 - 1.69: 0 1.69 - 1.80: 420 Bond restraints: 54576 Sorted by residual: bond pdb=" CB PHE E 30 " pdb=" CG PHE E 30 " ideal model delta sigma weight residual 1.502 1.455 0.047 2.30e-02 1.89e+03 4.22e+00 bond pdb=" CB PHE G 30 " pdb=" CG PHE G 30 " ideal model delta sigma weight residual 1.502 1.455 0.047 2.30e-02 1.89e+03 4.21e+00 bond pdb=" CB PHE F 30 " pdb=" CG PHE F 30 " ideal model delta sigma weight residual 1.502 1.455 0.047 2.30e-02 1.89e+03 4.16e+00 bond pdb=" CB PHE A 30 " pdb=" CG PHE A 30 " ideal model delta sigma weight residual 1.502 1.455 0.047 2.30e-02 1.89e+03 4.12e+00 bond pdb=" CB PHE C 30 " pdb=" CG PHE C 30 " ideal model delta sigma weight residual 1.502 1.455 0.047 2.30e-02 1.89e+03 4.11e+00 ... (remaining 54571 not shown) Histogram of bond angle deviations from ideal: 99.84 - 106.72: 1809 106.72 - 113.60: 29386 113.60 - 120.48: 22253 120.48 - 127.36: 19968 127.36 - 134.24: 612 Bond angle restraints: 74028 Sorted by residual: angle pdb=" CA LEU G 409 " pdb=" CB LEU G 409 " pdb=" CG LEU G 409 " ideal model delta sigma weight residual 116.30 132.67 -16.37 3.50e+00 8.16e-02 2.19e+01 angle pdb=" CA LEU C 409 " pdb=" CB LEU C 409 " pdb=" CG LEU C 409 " ideal model delta sigma weight residual 116.30 132.67 -16.37 3.50e+00 8.16e-02 2.19e+01 angle pdb=" CA LEU K 409 " pdb=" CB LEU K 409 " pdb=" CG LEU K 409 " ideal model delta sigma weight residual 116.30 132.66 -16.36 3.50e+00 8.16e-02 2.19e+01 angle pdb=" CA LEU F 409 " pdb=" CB LEU F 409 " pdb=" CG LEU F 409 " ideal model delta sigma weight residual 116.30 132.66 -16.36 3.50e+00 8.16e-02 2.19e+01 angle pdb=" CA LEU E 409 " pdb=" CB LEU E 409 " pdb=" CG LEU E 409 " ideal model delta sigma weight residual 116.30 132.65 -16.35 3.50e+00 8.16e-02 2.18e+01 ... (remaining 74023 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.28: 30894 15.28 - 30.56: 1722 30.56 - 45.83: 372 45.83 - 61.11: 12 61.11 - 76.39: 48 Dihedral angle restraints: 33048 sinusoidal: 13248 harmonic: 19800 Sorted by residual: dihedral pdb=" CA TYR j 62 " pdb=" C TYR j 62 " pdb=" N PRO j 63 " pdb=" CA PRO j 63 " ideal model delta harmonic sigma weight residual -180.00 -135.44 -44.56 0 5.00e+00 4.00e-02 7.94e+01 dihedral pdb=" CA TYR f 62 " pdb=" C TYR f 62 " pdb=" N PRO f 63 " pdb=" CA PRO f 63 " ideal model delta harmonic sigma weight residual -180.00 -135.45 -44.55 0 5.00e+00 4.00e-02 7.94e+01 dihedral pdb=" CA TYR k 62 " pdb=" C TYR k 62 " pdb=" N PRO k 63 " pdb=" CA PRO k 63 " ideal model delta harmonic sigma weight residual -180.00 -135.45 -44.55 0 5.00e+00 4.00e-02 7.94e+01 ... (remaining 33045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 4693 0.043 - 0.085: 2500 0.085 - 0.128: 786 0.128 - 0.170: 145 0.170 - 0.213: 72 Chirality restraints: 8196 Sorted by residual: chirality pdb=" CA PHE L 154 " pdb=" N PHE L 154 " pdb=" C PHE L 154 " pdb=" CB PHE L 154 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA PHE G 154 " pdb=" N PHE G 154 " pdb=" C PHE G 154 " pdb=" CB PHE G 154 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CB VAL l 128 " pdb=" CA VAL l 128 " pdb=" CG1 VAL l 128 " pdb=" CG2 VAL l 128 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 8193 not shown) Planarity restraints: 9804 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS D 159 " 0.015 2.00e-02 2.50e+03 2.91e-02 8.47e+00 pdb=" C LYS D 159 " -0.050 2.00e-02 2.50e+03 pdb=" O LYS D 159 " 0.018 2.00e-02 2.50e+03 pdb=" N ARG D 160 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 159 " 0.015 2.00e-02 2.50e+03 2.91e-02 8.46e+00 pdb=" C LYS F 159 " -0.050 2.00e-02 2.50e+03 pdb=" O LYS F 159 " 0.018 2.00e-02 2.50e+03 pdb=" N ARG F 160 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS G 159 " 0.015 2.00e-02 2.50e+03 2.91e-02 8.45e+00 pdb=" C LYS G 159 " -0.050 2.00e-02 2.50e+03 pdb=" O LYS G 159 " 0.018 2.00e-02 2.50e+03 pdb=" N ARG G 160 " 0.017 2.00e-02 2.50e+03 ... (remaining 9801 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 16845 2.83 - 3.35: 46849 3.35 - 3.86: 84411 3.86 - 4.38: 98012 4.38 - 4.90: 167433 Nonbonded interactions: 413550 Sorted by model distance: nonbonded pdb=" OG SER A 316 " pdb=" O SER L 311 " model vdw 2.312 2.440 nonbonded pdb=" O SER B 311 " pdb=" OG SER C 316 " model vdw 2.317 2.440 nonbonded pdb=" O SER I 311 " pdb=" OG SER J 316 " model vdw 2.324 2.440 nonbonded pdb=" O SER D 311 " pdb=" OG SER E 316 " model vdw 2.326 2.440 nonbonded pdb=" O SER H 311 " pdb=" OG SER I 316 " model vdw 2.330 2.440 ... (remaining 413545 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 216 5.16 5 C 33540 2.51 5 N 9384 2.21 5 O 10392 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 9.560 Check model and map are aligned: 0.600 Process input model: 97.270 Find NCS groups from input model: 2.960 Set up NCS constraints: 0.400 Set refine NCS operators: 0.000 Set scattering table: 0.370 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 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 : 0.007 0.068 54576 Z= 0.462 Angle : 1.108 16.375 74028 Z= 0.598 Chirality : 0.057 0.213 8196 Planarity : 0.008 0.070 9804 Dihedral : 10.701 76.391 20280 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.87 % Favored : 89.13 % Rotamer Outliers : 0.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 7.41 % Twisted General : 0.18 % 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: -6.20 (0.07), residues: 6816 helix: -4.89 (0.03), residues: 2472 sheet: -3.18 (0.20), residues: 540 loop : -3.83 (0.07), residues: 3804 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13632 Ramachandran restraints generated. 6816 Oldfield, 0 Emsley, 6816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13632 Ramachandran restraints generated. 6816 Oldfield, 0 Emsley, 6816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2038 residues out of total 5712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 2002 time to evaluate : 4.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 1 residues processed: 2026 average time/residue: 0.5882 time to fit residues: 1882.6228 Evaluate side-chains 1293 residues out of total 5712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1292 time to evaluate : 4.796 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3768 time to fit residues: 7.2415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 577 optimal weight: 0.2980 chunk 518 optimal weight: 0.0770 chunk 287 optimal weight: 10.0000 chunk 177 optimal weight: 9.9990 chunk 349 optimal weight: 8.9990 chunk 276 optimal weight: 7.9990 chunk 536 optimal weight: 0.2980 chunk 207 optimal weight: 10.0000 chunk 325 optimal weight: 8.9990 chunk 399 optimal weight: 0.8980 chunk 621 optimal weight: 0.0870 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 47 ASN A 70 GLN ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 291 GLN A 321 HIS A 325 ASN B 40 GLN B 70 GLN B 321 HIS C 40 GLN C 47 ASN C 70 GLN ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS C 325 ASN D 40 GLN D 47 ASN D 70 GLN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 ASN D 291 GLN D 321 HIS E 40 GLN E 70 GLN E 321 HIS E 325 ASN F 40 GLN F 47 ASN F 70 GLN F 185 HIS F 291 GLN G 40 GLN G 47 ASN G 70 GLN G 215 ASN G 291 GLN G 321 HIS H 40 GLN H 70 GLN H 321 HIS H 325 ASN I 40 GLN I 47 ASN I 70 GLN I 185 HIS J 40 GLN J 47 ASN J 70 GLN ** J 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 291 GLN J 321 HIS J 325 ASN K 40 GLN K 70 GLN K 321 HIS L 40 GLN L 47 ASN L 70 GLN ** L 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 185 HIS f 104 ASN Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 54576 Z= 0.158 Angle : 0.652 9.042 74028 Z= 0.335 Chirality : 0.042 0.163 8196 Planarity : 0.006 0.062 9804 Dihedral : 6.102 32.589 7464 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer Outliers : 3.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.47 % 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: -4.60 (0.08), residues: 6816 helix: -3.20 (0.07), residues: 2364 sheet: -2.22 (0.22), residues: 420 loop : -3.19 (0.08), residues: 4032 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13632 Ramachandran restraints generated. 6816 Oldfield, 0 Emsley, 6816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13632 Ramachandran restraints generated. 6816 Oldfield, 0 Emsley, 6816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1650 residues out of total 5712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 1477 time to evaluate : 4.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 173 outliers final: 97 residues processed: 1570 average time/residue: 0.5730 time to fit residues: 1476.5023 Evaluate side-chains 1301 residues out of total 5712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 1204 time to evaluate : 4.806 Switching outliers to nearest non-outliers outliers start: 97 outliers final: 0 residues processed: 97 average time/residue: 0.3820 time to fit residues: 77.4985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 345 optimal weight: 9.9990 chunk 192 optimal weight: 6.9990 chunk 516 optimal weight: 5.9990 chunk 422 optimal weight: 10.0000 chunk 171 optimal weight: 5.9990 chunk 622 optimal weight: 6.9990 chunk 672 optimal weight: 2.9990 chunk 554 optimal weight: 9.9990 chunk 617 optimal weight: 1.9990 chunk 212 optimal weight: 5.9990 chunk 499 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 GLN B 26 ASN B 70 GLN B 408 GLN C 70 GLN C 325 ASN C 408 GLN D 70 GLN D 408 GLN E 26 ASN E 70 GLN E 408 GLN F 70 GLN F 408 GLN G 70 GLN G 408 GLN H 70 GLN H 408 GLN I 70 GLN I 408 GLN J 70 GLN ** J 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 408 GLN K 26 ASN K 70 GLN K 408 GLN L 70 GLN L 408 GLN ** c 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.060 54576 Z= 0.354 Angle : 0.739 9.399 74028 Z= 0.384 Chirality : 0.047 0.152 8196 Planarity : 0.006 0.050 9804 Dihedral : 6.106 27.609 7464 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer Outliers : 3.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.33 (0.08), residues: 6816 helix: -2.55 (0.08), residues: 2520 sheet: -2.78 (0.19), residues: 564 loop : -3.22 (0.08), residues: 3732 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13632 Ramachandran restraints generated. 6816 Oldfield, 0 Emsley, 6816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13632 Ramachandran restraints generated. 6816 Oldfield, 0 Emsley, 6816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1441 residues out of total 5712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 1261 time to evaluate : 4.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 180 outliers final: 109 residues processed: 1359 average time/residue: 0.5896 time to fit residues: 1286.7146 Evaluate side-chains 1277 residues out of total 5712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 1168 time to evaluate : 4.797 Switching outliers to nearest non-outliers outliers start: 109 outliers final: 0 residues processed: 109 average time/residue: 0.4478 time to fit residues: 93.4438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 614 optimal weight: 6.9990 chunk 467 optimal weight: 7.9990 chunk 322 optimal weight: 40.0000 chunk 68 optimal weight: 7.9990 chunk 296 optimal weight: 2.9990 chunk 417 optimal weight: 0.9980 chunk 624 optimal weight: 7.9990 chunk 661 optimal weight: 2.9990 chunk 326 optimal weight: 7.9990 chunk 591 optimal weight: 0.5980 chunk 178 optimal weight: 3.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 ASN ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN ** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 215 ASN ** G 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN ** I 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN ** L 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 107 ASN ** c 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 54576 Z= 0.213 Angle : 0.626 6.733 74028 Z= 0.324 Chirality : 0.042 0.144 8196 Planarity : 0.005 0.050 9804 Dihedral : 5.584 27.128 7464 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer Outliers : 3.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.71 (0.09), residues: 6816 helix: -1.75 (0.09), residues: 2436 sheet: -2.79 (0.19), residues: 588 loop : -2.99 (0.09), residues: 3792 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13632 Ramachandran restraints generated. 6816 Oldfield, 0 Emsley, 6816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13632 Ramachandran restraints generated. 6816 Oldfield, 0 Emsley, 6816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1430 residues out of total 5712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 1258 time to evaluate : 4.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 172 outliers final: 102 residues processed: 1329 average time/residue: 0.5759 time to fit residues: 1229.1281 Evaluate side-chains 1277 residues out of total 5712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 1175 time to evaluate : 4.829 Switching outliers to nearest non-outliers outliers start: 102 outliers final: 0 residues processed: 102 average time/residue: 0.3849 time to fit residues: 80.8613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 550 optimal weight: 20.0000 chunk 375 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 492 optimal weight: 3.9990 chunk 272 optimal weight: 2.9990 chunk 564 optimal weight: 9.9990 chunk 457 optimal weight: 0.0000 chunk 0 optimal weight: 10.0000 chunk 337 optimal weight: 8.9990 chunk 593 optimal weight: 0.0670 chunk 166 optimal weight: 4.9990 overall best weight: 2.2128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 ASN ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 ASN D 215 ASN ** D 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 ASN ** F 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 26 ASN ** I 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 325 ASN ** J 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 107 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 54576 Z= 0.205 Angle : 0.609 6.591 74028 Z= 0.313 Chirality : 0.042 0.140 8196 Planarity : 0.004 0.045 9804 Dihedral : 5.359 26.424 7464 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.71 % Favored : 90.29 % Rotamer Outliers : 2.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.09), residues: 6816 helix: -1.28 (0.10), residues: 2448 sheet: -2.62 (0.19), residues: 588 loop : -2.91 (0.09), residues: 3780 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13632 Ramachandran restraints generated. 6816 Oldfield, 0 Emsley, 6816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13632 Ramachandran restraints generated. 6816 Oldfield, 0 Emsley, 6816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1345 residues out of total 5712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 1222 time to evaluate : 4.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 123 outliers final: 71 residues processed: 1270 average time/residue: 0.5748 time to fit residues: 1184.8265 Evaluate side-chains 1242 residues out of total 5712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 1171 time to evaluate : 4.820 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 0 residues processed: 71 average time/residue: 0.4131 time to fit residues: 60.9728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 222 optimal weight: 0.0010 chunk 595 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 388 optimal weight: 0.9980 chunk 163 optimal weight: 9.9990 chunk 661 optimal weight: 6.9990 chunk 549 optimal weight: 4.9990 chunk 306 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 218 optimal weight: 3.9990 chunk 347 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 ASN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 ASN ** F 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 54576 Z= 0.190 Angle : 0.596 6.514 74028 Z= 0.305 Chirality : 0.042 0.131 8196 Planarity : 0.004 0.047 9804 Dihedral : 5.158 26.034 7464 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.48 % Favored : 90.52 % Rotamer Outliers : 2.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.09), residues: 6816 helix: -0.92 (0.10), residues: 2448 sheet: -2.50 (0.20), residues: 588 loop : -2.82 (0.09), residues: 3780 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13632 Ramachandran restraints generated. 6816 Oldfield, 0 Emsley, 6816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13632 Ramachandran restraints generated. 6816 Oldfield, 0 Emsley, 6816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1353 residues out of total 5712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 1237 time to evaluate : 4.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 116 outliers final: 67 residues processed: 1264 average time/residue: 0.5774 time to fit residues: 1178.9414 Evaluate side-chains 1240 residues out of total 5712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 1173 time to evaluate : 4.827 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 0 residues processed: 67 average time/residue: 0.3954 time to fit residues: 56.5244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 638 optimal weight: 4.9990 chunk 74 optimal weight: 0.0170 chunk 377 optimal weight: 8.9990 chunk 483 optimal weight: 5.9990 chunk 374 optimal weight: 9.9990 chunk 557 optimal weight: 0.1980 chunk 369 optimal weight: 20.0000 chunk 659 optimal weight: 0.0050 chunk 412 optimal weight: 4.9990 chunk 401 optimal weight: 10.0000 chunk 304 optimal weight: 0.6980 overall best weight: 1.1834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 185 HIS G 228 ASN ** H 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 185 HIS ** I 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 26 ASN ** L 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.049 54576 Z= 0.158 Angle : 0.579 7.364 74028 Z= 0.295 Chirality : 0.041 0.150 8196 Planarity : 0.004 0.042 9804 Dihedral : 4.957 25.151 7464 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.10), residues: 6816 helix: -0.59 (0.11), residues: 2460 sheet: -2.38 (0.20), residues: 588 loop : -2.73 (0.09), residues: 3768 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13632 Ramachandran restraints generated. 6816 Oldfield, 0 Emsley, 6816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13632 Ramachandran restraints generated. 6816 Oldfield, 0 Emsley, 6816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1327 residues out of total 5712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 1244 time to evaluate : 4.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 83 outliers final: 36 residues processed: 1265 average time/residue: 0.5767 time to fit residues: 1182.6029 Evaluate side-chains 1208 residues out of total 5712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 1172 time to evaluate : 4.816 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.3969 time to fit residues: 33.4226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 407 optimal weight: 0.0370 chunk 263 optimal weight: 20.0000 chunk 393 optimal weight: 10.0000 chunk 198 optimal weight: 1.9990 chunk 129 optimal weight: 10.0000 chunk 127 optimal weight: 1.9990 chunk 419 optimal weight: 5.9990 chunk 449 optimal weight: 7.9990 chunk 325 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 518 optimal weight: 9.9990 overall best weight: 3.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN C 26 ASN C 185 HIS ** D 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 325 ASN ** E 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 ASN ** H 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 185 HIS ** L 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 124 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.069 54576 Z= 0.275 Angle : 0.650 8.269 74028 Z= 0.333 Chirality : 0.044 0.176 8196 Planarity : 0.005 0.042 9804 Dihedral : 5.242 27.107 7464 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.81 % Favored : 89.19 % Rotamer Outliers : 1.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.09), residues: 6816 helix: -0.65 (0.11), residues: 2460 sheet: -2.44 (0.20), residues: 588 loop : -2.74 (0.09), residues: 3768 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13632 Ramachandran restraints generated. 6816 Oldfield, 0 Emsley, 6816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13632 Ramachandran restraints generated. 6816 Oldfield, 0 Emsley, 6816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1288 residues out of total 5712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 1180 time to evaluate : 4.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 108 outliers final: 64 residues processed: 1213 average time/residue: 0.5790 time to fit residues: 1134.8036 Evaluate side-chains 1212 residues out of total 5712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 1148 time to evaluate : 4.820 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 0 residues processed: 64 average time/residue: 0.4077 time to fit residues: 55.9198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 599 optimal weight: 8.9990 chunk 631 optimal weight: 10.0000 chunk 576 optimal weight: 30.0000 chunk 614 optimal weight: 1.9990 chunk 369 optimal weight: 9.9990 chunk 267 optimal weight: 0.7980 chunk 482 optimal weight: 0.9980 chunk 188 optimal weight: 7.9990 chunk 555 optimal weight: 10.0000 chunk 581 optimal weight: 6.9990 chunk 612 optimal weight: 0.0470 overall best weight: 2.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS ** D 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 185 HIS ** L 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 124 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.4424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 54576 Z= 0.203 Angle : 0.619 8.006 74028 Z= 0.316 Chirality : 0.042 0.191 8196 Planarity : 0.004 0.042 9804 Dihedral : 5.118 27.158 7464 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer Outliers : 1.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.10), residues: 6816 helix: -0.53 (0.11), residues: 2460 sheet: -2.40 (0.20), residues: 588 loop : -2.69 (0.09), residues: 3768 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13632 Ramachandran restraints generated. 6816 Oldfield, 0 Emsley, 6816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13632 Ramachandran restraints generated. 6816 Oldfield, 0 Emsley, 6816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1272 residues out of total 5712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 1183 time to evaluate : 4.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 89 outliers final: 55 residues processed: 1197 average time/residue: 0.5673 time to fit residues: 1106.5951 Evaluate side-chains 1211 residues out of total 5712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 1156 time to evaluate : 4.783 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 0 residues processed: 55 average time/residue: 0.4124 time to fit residues: 48.3933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 403 optimal weight: 8.9990 chunk 649 optimal weight: 0.7980 chunk 396 optimal weight: 10.0000 chunk 308 optimal weight: 10.0000 chunk 451 optimal weight: 4.9990 chunk 681 optimal weight: 10.0000 chunk 627 optimal weight: 0.8980 chunk 542 optimal weight: 0.0030 chunk 56 optimal weight: 3.9990 chunk 419 optimal weight: 10.0000 chunk 332 optimal weight: 1.9990 overall best weight: 1.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN ** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS ** D 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 217 GLN ** H 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 185 HIS ** L 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.4541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 54576 Z= 0.175 Angle : 0.606 8.007 74028 Z= 0.308 Chirality : 0.041 0.208 8196 Planarity : 0.004 0.076 9804 Dihedral : 4.960 28.672 7464 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.10), residues: 6816 helix: -0.39 (0.11), residues: 2532 sheet: -2.37 (0.20), residues: 588 loop : -2.68 (0.09), residues: 3696 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13632 Ramachandran restraints generated. 6816 Oldfield, 0 Emsley, 6816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13632 Ramachandran restraints generated. 6816 Oldfield, 0 Emsley, 6816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1196 residues out of total 5712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 1176 time to evaluate : 4.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 1180 average time/residue: 0.5618 time to fit residues: 1080.7040 Evaluate side-chains 1147 residues out of total 5712 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 1136 time to evaluate : 4.812 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.3826 time to fit residues: 14.6051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 431 optimal weight: 0.9990 chunk 578 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 chunk 500 optimal weight: 10.0000 chunk 80 optimal weight: 0.3980 chunk 150 optimal weight: 10.0000 chunk 543 optimal weight: 4.9990 chunk 227 optimal weight: 9.9990 chunk 558 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS D 217 GLN ** D 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 GLN F 321 HIS ** H 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 26 ASN ** K 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 185 HIS ** L 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.161977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.136695 restraints weight = 77266.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.140160 restraints weight = 43990.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.142418 restraints weight = 30427.233| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 54576 Z= 0.219 Angle : 0.627 8.363 74028 Z= 0.320 Chirality : 0.043 0.185 8196 Planarity : 0.004 0.043 9804 Dihedral : 5.041 26.635 7464 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.10), residues: 6816 helix: -0.41 (0.11), residues: 2532 sheet: -2.20 (0.21), residues: 564 loop : -2.70 (0.09), residues: 3720 =============================================================================== Job complete usr+sys time: 16476.66 seconds wall clock time: 286 minutes 17.07 seconds (17177.07 seconds total)